Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution.

Science.gov (United States)

Comitani, Federico; Rossi, Kevin; Ceriotti, Michele; Sanz, M Eugenia; Molteni, Carla

2017-04-14

The conformational free energy landscape of aspartic acid, a proteogenic amino acid involved in a wide variety of biological functions, was investigated as an example of the complexity that multiple rotatable bonds produce even in relatively simple molecules. To efficiently explore such a landscape, this molecule was studied in the neutral and zwitterionic forms, in the gas phase and in water solution, by means of molecular dynamics and the enhanced sampling method metadynamics with classical force-fields. Multi-dimensional free energy landscapes were reduced to bi-dimensional maps through the non-linear dimensionality reduction algorithm sketch-map to identify the energetically stable conformers and their interconnection paths. Quantum chemical calculations were then performed on the minimum free energy structures. Our procedure returned the low energy conformations observed experimentally in the gas phase with rotational spectroscopy [M. E. Sanz et al., Phys. Chem. Chem. Phys. 12, 3573 (2010)]. Moreover, it provided information on higher energy conformers not accessible to experiments and on the conformers in water. The comparison between different force-fields and quantum chemical data highlighted the importance of the underlying potential energy surface to accurately capture energy rankings. The combination of force-field based metadynamics, sketch-map analysis, and quantum chemical calculations was able to produce an exhaustive conformational exploration in a range of significant free energies that complements the experimental data. Similar protocols can be applied to larger peptides with complex conformational landscapes and would greatly benefit from the next generation of accurate force-fields.

Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution

Science.gov (United States)

Comitani, Federico; Rossi, Kevin; Ceriotti, Michele; Sanz, M. Eugenia; Molteni, Carla

2017-04-01

The conformational free energy landscape of aspartic acid, a proteogenic amino acid involved in a wide variety of biological functions, was investigated as an example of the complexity that multiple rotatable bonds produce even in relatively simple molecules. To efficiently explore such a landscape, this molecule was studied in the neutral and zwitterionic forms, in the gas phase and in water solution, by means of molecular dynamics and the enhanced sampling method metadynamics with classical force-fields. Multi-dimensional free energy landscapes were reduced to bi-dimensional maps through the non-linear dimensionality reduction algorithm sketch-map to identify the energetically stable conformers and their interconnection paths. Quantum chemical calculations were then performed on the minimum free energy structures. Our procedure returned the low energy conformations observed experimentally in the gas phase with rotational spectroscopy [M. E. Sanz et al., Phys. Chem. Chem. Phys. 12, 3573 (2010)]. Moreover, it provided information on higher energy conformers not accessible to experiments and on the conformers in water. The comparison between different force-fields and quantum chemical data highlighted the importance of the underlying potential energy surface to accurately capture energy rankings. The combination of force-field based metadynamics, sketch-map analysis, and quantum chemical calculations was able to produce an exhaustive conformational exploration in a range of significant free energies that complements the experimental data. Similar protocols can be applied to larger peptides with complex conformational landscapes and would greatly benefit from the next generation of accurate force-fields.

Use of conformal mapping to describe MHD wave propagation

International Nuclear Information System (INIS)

Bulanov, S.V.; Pegoraro, F.

1993-01-01

A method is proposed for finding explicit exact solutions of the magnetohydrodynamic equations describing the propagation of magnetoacoustic waves in a plasma in a magnetic potential that depends on two spatial coordinates. This method is based on the use of conformal mappings to transform the wave equation into an equation describing the propagation of waves in a uniform magnetic field. The basic properties of magnetoacoustic and Alfven waves near the critical points, magnetic separatrices, and in configuration with magnetic islands are discussed. Expressions are found for the dimensionless parameters which determine the relative roles of the plasma pressure, nonlinearity, and dissipation near the critical points. 30 refs

Moduli of families of curves for conformal and quasiconformal mappings

CERN Document Server

Vasil’ev, Alexander

2002-01-01

The monograph is concerned with the modulus of families of curves on Riemann surfaces and its applications to extremal problems for conformal, quasiconformal mappings, and the extension of the modulus onto Teichmüller spaces. The main part of the monograph deals with extremal problems for compact classes of univalent conformal and quasiconformal mappings. Many of them are grouped around two-point distortion theorems. Montel's functions and functions with fixed angular derivatives are also considered. The last portion of problems is directed to the extension of the modulus varying the complex structure of the underlying Riemann surface that sheds some new light on the metric problems of Teichmüller spaces.

Assignment of Side-Chain Conformation Using Adiabatic Energy Mapping, Free Energy Perturbation, and Molecular Dynamic Simulations

DEFF Research Database (Denmark)

Frimurer, Thomas M.; Günther, Peter H.; Sørensen, Morten Dahl

1999-01-01

adiabatic mapping, conformational change, essentialdynamics, free energy simulations, Kunitz type inhibitor *ga3(VI)......adiabatic mapping, conformational change, essentialdynamics, free energy simulations, Kunitz type inhibitor *ga3(VI)...

The hypersurfaces with conformal normal Gauss map in Hn+1 and S1n+1

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Shuguo Shi

2008-03-01

Full Text Available In this paper, we introduce the fourth fundamental forms for hypersurfaces in Hn+1 and space-like hypersurfaces in S1n+1, and discuss the conformality of the normal Gauss map of the hypersurfaces in Hn+1 and S1n+1. Particularly, we discuss the surfaces with conformal normal Gauss map in H³ and S³1, and prove a duality property. We give a Weierstrass representation formula for space-like surfaces in S³1 with conformal normal Gauss map. We also state the similar results for time-like surfaces in S³1. Some examples of surfaces in S³1 with conformal normal Gauss map are given and a fully nonlinear equation of Monge-Ampère type for the graphs in S³1 with conformal normal Gauss map is derived.Neste artigo, introduzimos a quarta forma fundamental de uma hipersuperfície em Hn+1 de uma hipersuperfície tipo-espaço em S1n+1, e discutimos a conformalidade da aplicação normal de Gauss de tais hipersuperfícies. Em particular, investigamos o caso de superfícies com aplicação normal de Gauss conforme em H³ e S³1, e provamos um teorema de dualidade. Apresentamos uma representação de Weierstrass para superfícies tipo-espaço em S³1 com aplicação de Gauss conforme. Enunciamos também resultados semelhantes para superfícies tipo-tempo em S³1. São dados alguns exemplos de superfícies em S³1 com aplicações de Gauss conformes, e é deduzida uma equação totalmente não-linear do tipo Monge-Ampère para gráficos em S³1 com aplicações de Gauss conformes.

Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation.

Science.gov (United States)

Liu, Xiaofeng; Bai, Fang; Ouyang, Sisheng; Wang, Xicheng; Li, Honglin; Jiang, Hualiang

2009-03-31

Conformation generation is a ubiquitous problem in molecule modelling. Many applications require sampling the broad molecular conformational space or perceiving the bioactive conformers to ensure success. Numerous in silico methods have been proposed in an attempt to resolve the problem, ranging from deterministic to non-deterministic and systemic to stochastic ones. In this work, we described an efficient conformation sampling method named Cyndi, which is based on multi-objective evolution algorithm. The conformational perturbation is subjected to evolutionary operation on the genome encoded with dihedral torsions. Various objectives are designated to render the generated Pareto optimal conformers to be energy-favoured as well as evenly scattered across the conformational space. An optional objective concerning the degree of molecular extension is added to achieve geometrically extended or compact conformations which have been observed to impact the molecular bioactivity (J Comput -Aided Mol Des 2002, 16: 105-112). Testing the performance of Cyndi against a test set consisting of 329 small molecules reveals an average minimum RMSD of 0.864 A to corresponding bioactive conformations, indicating Cyndi is highly competitive against other conformation generation methods. Meanwhile, the high-speed performance (0.49 +/- 0.18 seconds per molecule) renders Cyndi to be a practical toolkit for conformational database preparation and facilitates subsequent pharmacophore mapping or rigid docking. The copy of precompiled executable of Cyndi and the test set molecules in mol2 format are accessible in Additional file 1. On the basis of MOEA algorithm, we present a new, highly efficient conformation generation method, Cyndi, and report the results of validation and performance studies comparing with other four methods. The results reveal that Cyndi is capable of generating geometrically diverse conformers and outperforms other four multiple conformer generators in the case of

Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation

Directory of Open Access Journals (Sweden)

Li Honglin

2009-03-01

Full Text Available Abstract Background Conformation generation is a ubiquitous problem in molecule modelling. Many applications require sampling the broad molecular conformational space or perceiving the bioactive conformers to ensure success. Numerous in silico methods have been proposed in an attempt to resolve the problem, ranging from deterministic to non-deterministic and systemic to stochastic ones. In this work, we described an efficient conformation sampling method named Cyndi, which is based on multi-objective evolution algorithm. Results The conformational perturbation is subjected to evolutionary operation on the genome encoded with dihedral torsions. Various objectives are designated to render the generated Pareto optimal conformers to be energy-favoured as well as evenly scattered across the conformational space. An optional objective concerning the degree of molecular extension is added to achieve geometrically extended or compact conformations which have been observed to impact the molecular bioactivity (J Comput -Aided Mol Des 2002, 16: 105–112. Testing the performance of Cyndi against a test set consisting of 329 small molecules reveals an average minimum RMSD of 0.864 Å to corresponding bioactive conformations, indicating Cyndi is highly competitive against other conformation generation methods. Meanwhile, the high-speed performance (0.49 ± 0.18 seconds per molecule renders Cyndi to be a practical toolkit for conformational database preparation and facilitates subsequent pharmacophore mapping or rigid docking. The copy of precompiled executable of Cyndi and the test set molecules in mol2 format are accessible in Additional file 1. Conclusion On the basis of MOEA algorithm, we present a new, highly efficient conformation generation method, Cyndi, and report the results of validation and performance studies comparing with other four methods. The results reveal that Cyndi is capable of generating geometrically diverse conformers and outperforms

Conformable variational iteration method

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Omer Acan

2017-02-01

Full Text Available In this study, we introduce the conformable variational iteration method based on new defined fractional derivative called conformable fractional derivative. This new method is applied two fractional order ordinary differential equations. To see how the solutions of this method, linear homogeneous and non-linear non-homogeneous fractional ordinary differential equations are selected. Obtained results are compared the exact solutions and their graphics are plotted to demonstrate efficiency and accuracy of the method.

Self Organizing Maps to efficiently cluster and functionally interpret protein conformational ensembles

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Fabio Stella

2013-09-01

Full Text Available An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the original ensembles can be summarized by using only the representative conformations of the clusters obtained. In addition the network components analysis allows to discover and interpret the dynamic behavior of the conformations won by each neuron. The results showed the ability of this approach to efficiently derive a functional interpretation of the protein dynamics described by the original conformational ensemble, highlighting its potential as a support for protein engineering.

Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps

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Stella Fabio

2011-05-01

Full Text Available Abstract Background Molecular dynamics (MD simulations are powerful tools to investigate the conformational dynamics of proteins that is often a critical element of their function. Identification of functionally relevant conformations is generally done clustering the large ensemble of structures that are generated. Recently, Self-Organising Maps (SOMs were reported performing more accurately and providing more consistent results than traditional clustering algorithms in various data mining problems. We present a novel strategy to analyse and compare conformational ensembles of protein domains using a two-level approach that combines SOMs and hierarchical clustering. Results The conformational dynamics of the α-spectrin SH3 protein domain and six single mutants were analysed by MD simulations. The Cα's Cartesian coordinates of conformations sampled in the essential space were used as input data vectors for SOM training, then complete linkage clustering was performed on the SOM prototype vectors. A specific protocol to optimize a SOM for structural ensembles was proposed: the optimal SOM was selected by means of a Taguchi experimental design plan applied to different data sets, and the optimal sampling rate of the MD trajectory was selected. The proposed two-level approach was applied to single trajectories of the SH3 domain independently as well as to groups of them at the same time. The results demonstrated the potential of this approach in the analysis of large ensembles of molecular structures: the possibility of producing a topological mapping of the conformational space in a simple 2D visualisation, as well as of effectively highlighting differences in the conformational dynamics directly related to biological functions. Conclusions The use of a two-level approach combining SOMs and hierarchical clustering for conformational analysis of structural ensembles of proteins was proposed. It can easily be extended to other study cases and to

Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps

Science.gov (United States)

2011-01-01

Background Molecular dynamics (MD) simulations are powerful tools to investigate the conformational dynamics of proteins that is often a critical element of their function. Identification of functionally relevant conformations is generally done clustering the large ensemble of structures that are generated. Recently, Self-Organising Maps (SOMs) were reported performing more accurately and providing more consistent results than traditional clustering algorithms in various data mining problems. We present a novel strategy to analyse and compare conformational ensembles of protein domains using a two-level approach that combines SOMs and hierarchical clustering. Results The conformational dynamics of the α-spectrin SH3 protein domain and six single mutants were analysed by MD simulations. The Cα's Cartesian coordinates of conformations sampled in the essential space were used as input data vectors for SOM training, then complete linkage clustering was performed on the SOM prototype vectors. A specific protocol to optimize a SOM for structural ensembles was proposed: the optimal SOM was selected by means of a Taguchi experimental design plan applied to different data sets, and the optimal sampling rate of the MD trajectory was selected. The proposed two-level approach was applied to single trajectories of the SH3 domain independently as well as to groups of them at the same time. The results demonstrated the potential of this approach in the analysis of large ensembles of molecular structures: the possibility of producing a topological mapping of the conformational space in a simple 2D visualisation, as well as of effectively highlighting differences in the conformational dynamics directly related to biological functions. Conclusions The use of a two-level approach combining SOMs and hierarchical clustering for conformational analysis of structural ensembles of proteins was proposed. It can easily be extended to other study cases and to conformational ensembles from

Numerical conformal mapping and its inverse of unbounded multiply connected regions onto logarithmic spiral slit regions and straight slit regions.

Science.gov (United States)

Yunus, A A M; Murid, A H M; Nasser, M M S

2014-02-08

This paper presents a boundary integral equation method with the adjoint generalized Neumann kernel for computing conformal mapping of unbounded multiply connected regions and its inverse onto several classes of canonical regions. For each canonical region, two integral equations are solved before one can approximate the boundary values of the mapping function. Cauchy's-type integrals are used for computing the mapping function and its inverse for interior points. This method also works for regions with piecewise smooth boundaries. Three examples are given to illustrate the effectiveness of the proposed method.

Conformal Nets II: Conformal Blocks

Science.gov (United States)

Bartels, Arthur; Douglas, Christopher L.; Henriques, André

2017-08-01

Conformal nets provide a mathematical formalism for conformal field theory. Associated to a conformal net with finite index, we give a construction of the `bundle of conformal blocks', a representation of the mapping class groupoid of closed topological surfaces into the category of finite-dimensional projective Hilbert spaces. We also construct infinite-dimensional spaces of conformal blocks for topological surfaces with smooth boundary. We prove that the conformal blocks satisfy a factorization formula for gluing surfaces along circles, and an analogous formula for gluing surfaces along intervals. We use this interval factorization property to give a new proof of the modularity of the category of representations of a conformal net.

Determination of alpha(s)(M(tau)(2)): conformal mapping approach

Czech Academy of Sciences Publication Activity Database

Caprini, I.; Fischer, Jan

2011-01-01

Roč. 218, - (2011), s. 128-133 ISSN 0920-5632. [11th International Workshop on Tau Lepton Physics. Manchester, 13.09.2010-17.09.2010] R&D Projects: GA MŠk LC527; GA MŠk LA08015 Institutional research plan: CEZ:AV0Z10100502 Keywords : perturbative QCD expansion * conformal mapping * hadronic decay of the tau lepton Subject RIV: BF - Elementary Particles and High Energy Physics

On an application of conformal maps to inequalities for rational functions

International Nuclear Information System (INIS)

Dubinin, V N

2002-01-01

Using classical properties of conformal maps, we get new exact inequalities for rational functions with prescribed poles. In particular, we prove a new Bernstein-type inequality, an inequality for Blaschke products and a theorem that generalizes the Turan inequality for polynomials. The estimates obtained strengthen some familiar inequalities of Videnskii and Rusak. They are also related to recent results of Borwein, Erdelyi, Li, Mohapatra, Rodriguez, Aziz and others

Conformal methods in general relativity

CERN Document Server

Valiente Kroon, Juan A

2016-01-01

This book offers a systematic exposition of conformal methods and how they can be used to study the global properties of solutions to the equations of Einstein's theory of gravity. It shows that combining these ideas with differential geometry can elucidate the existence and stability of the basic solutions of the theory. Introducing the differential geometric, spinorial and PDE background required to gain a deep understanding of conformal methods, this text provides an accessible account of key results in mathematical relativity over the last thirty years, including the stability of de Sitter and Minkowski spacetimes. For graduate students and researchers, this self-contained account includes useful visual models to help the reader grasp abstract concepts and a list of further reading, making this the perfect reference companion on the topic.

A scalable and accurate method for classifying protein-ligand binding geometries using a MapReduce approach.

Science.gov (United States)

Estrada, T; Zhang, B; Cicotti, P; Armen, R S; Taufer, M

2012-07-01

We present a scalable and accurate method for classifying protein-ligand binding geometries in molecular docking. Our method is a three-step process: the first step encodes the geometry of a three-dimensional (3D) ligand conformation into a single 3D point in the space; the second step builds an octree by assigning an octant identifier to every single point in the space under consideration; and the third step performs an octree-based clustering on the reduced conformation space and identifies the most dense octant. We adapt our method for MapReduce and implement it in Hadoop. The load-balancing, fault-tolerance, and scalability in MapReduce allow screening of very large conformation spaces not approachable with traditional clustering methods. We analyze results for docking trials for 23 protein-ligand complexes for HIV protease, 21 protein-ligand complexes for Trypsin, and 12 protein-ligand complexes for P38alpha kinase. We also analyze cross docking trials for 24 ligands, each docking into 24 protein conformations of the HIV protease, and receptor ensemble docking trials for 24 ligands, each docking in a pool of HIV protease receptors. Our method demonstrates significant improvement over energy-only scoring for the accurate identification of native ligand geometries in all these docking assessments. The advantages of our clustering approach make it attractive for complex applications in real-world drug design efforts. We demonstrate that our method is particularly useful for clustering docking results using a minimal ensemble of representative protein conformational states (receptor ensemble docking), which is now a common strategy to address protein flexibility in molecular docking. Copyright © 2012 Elsevier Ltd. All rights reserved.

Conformational analysis of oligosaccharides and polysaccharides using molecular dynamics simulations.

Science.gov (United States)

Frank, Martin

2015-01-01

Complex carbohydrates usually have a large number of rotatable bonds and consequently a large number of theoretically possible conformations can be generated (combinatorial explosion). The application of systematic search methods for conformational analysis of carbohydrates is therefore limited to disaccharides and trisaccharides in a routine analysis. An alternative approach is to use Monte-Carlo methods or (high-temperature) molecular dynamics (MD) simulations to explore the conformational space of complex carbohydrates. This chapter describes how to use MD simulation data to perform a conformational analysis (conformational maps, hydrogen bonds) of oligosaccharides and how to build realistic 3D structures of large polysaccharides using Conformational Analysis Tools (CAT).

On the use of Schwarz-Christoffel conformal mappings to the grid generation for global ocean models

Science.gov (United States)

Xu, S.; Wang, B.; Liu, J.

2015-10-01

In this article we propose two grid generation methods for global ocean general circulation models. Contrary to conventional dipolar or tripolar grids, the proposed methods are based on Schwarz-Christoffel conformal mappings that map areas with user-prescribed, irregular boundaries to those with regular boundaries (i.e., disks, slits, etc.). The first method aims at improving existing dipolar grids. Compared with existing grids, the sample grid achieves a better trade-off between the enlargement of the latitudinal-longitudinal portion and the overall smooth grid cell size transition. The second method addresses more modern and advanced grid design requirements arising from high-resolution and multi-scale ocean modeling. The generated grids could potentially achieve the alignment of grid lines to the large-scale coastlines, enhanced spatial resolution in coastal regions, and easier computational load balance. Since the grids are orthogonal curvilinear, they can be easily utilized by the majority of ocean general circulation models that are based on finite difference and require grid orthogonality. The proposed grid generation algorithms can also be applied to the grid generation for regional ocean modeling where complex land-sea distribution is present.

Dipole-magnet field models based on a conformal map

Directory of Open Access Journals (Sweden)

P. L. Walstrom

2012-10-01

Full Text Available In general, generation of charged-particle transfer maps for conventional iron-pole-piece dipole magnets to third and higher order requires a model for the midplane field profile and its transverse derivatives (soft-edge model to high order and numerical integration of map coefficients. An exact treatment of the problem for a particular magnet requires use of measured magnetic data. However, in initial design of beam transport systems, users of charged-particle optics codes generally rely on magnet models built into the codes. Indeed, if maps to third order are adequate for the problem, an approximate analytic field model together with numerical map coefficient integration can capture the important features of the transfer map. The model described in this paper is based on the fact that, except at very large distances from the magnet, the magnetic field for parallel pole-face magnets with constant pole gap height and wide pole faces is basically two dimensional (2D. The field for all space outside of the pole pieces is given by a single (complex analytic expression and includes a parameter that controls the rate of falloff of the fringe field. Since the field function is analytic in the complex plane outside of the pole pieces, it satisfies two basic requirements of a field model for higher-order map codes: it is infinitely differentiable at the midplane and also a solution of the Laplace equation. It is apparently the only simple model available that combines an exponential approach to the central field with an inverse cubic falloff of field at large distances from the magnet in a single expression. The model is not intended for detailed fitting of magnetic field data, but for use in numerical map-generating codes for studying the effect of extended fringe fields on higher-order transfer maps. It is based on conformally mapping the area between the pole pieces to the upper half plane, and placing current filaments on the pole faces. An

Uniform stable conformal convolutional perfectly matched layer for enlarged cell technique conformal finite-difference time-domain method

International Nuclear Information System (INIS)

Wang Yue; Wang Jian-Guo; Chen Zai-Gao

2015-01-01

Based on conformal construction of physical model in a three-dimensional Cartesian grid, an integral-based conformal convolutional perfectly matched layer (CPML) is given for solving the truncation problem of the open port when the enlarged cell technique conformal finite-difference time-domain (ECT-CFDTD) method is used to simulate the wave propagation inside a perfect electric conductor (PEC) waveguide. The algorithm has the same numerical stability as the ECT-CFDTD method. For the long-time propagation problems of an evanescent wave in a waveguide, several numerical simulations are performed to analyze the reflection error by sweeping the constitutive parameters of the integral-based conformal CPML. Our numerical results show that the integral-based conformal CPML can be used to efficiently truncate the open port of the waveguide. (paper)

CD2 probe infrared method for determining polymethylene chain conformation

International Nuclear Information System (INIS)

Maroncelli, M.; Strauss, H.L.; Snyder, R.G.

1985-01-01

The rocking mode frequency of a CD 2 group substituted in a polymethylene chain is sensitive to conformation in the immediate vicinity of the CD 2 group. This sensitivity forms the basis of a commonly used infrared method for determining site-specific conformation in polymethylene systems. In the present work, the CD 2 probe method has been extended and quantified with the use of infrared data on model CD 2 -substituted n-alkanes. The frequency of the CD 2 rocking band is determined primarily by the conformation of adjoining CC bonds, i.e., by tt, gt, and gg pairs. However, we have found that there are significant frequency shifts associated with other factors. These include the conformation of the next nearest CC bonds, both with the CD 2 positioned at the end and in the interior of the chain, and chain length. In addition, the ratio of the absorptivities of the tt to gt bands has been established. These results enable the method to provide new details about the conformation of the chains in polymethylene systems and reliable estimates of the concentrations of specific kinds of short conformational sequences. 14 references, 6 figures, 2 tables

Reply to Comment on 'Excited states in the infinite quantum lens potential: conformal mapping and moment quantization methods'

International Nuclear Information System (INIS)

RodrIguez, Arezky H; Handy, Carlos R; Trallero-Giner, C

2004-01-01

The suitability of conformal transformation (CT) analysis, and the eigenvalue moment method (EMM), for determining the eigenenergies and eigenfunctions of a quantum particle confined within a lens geometry, is reviewed and compared to the recent results by Even and Loualiche (2003 J. Phys.: Condens. Matter 15 8465). It is shown that CT and EMM define two accurate and versatile analytical/computational methods relevant to lens shaped regions of varying geometrical aspect ratios. (reply)

Conformal geometry and invariants of 3-strand Brownian braids

International Nuclear Information System (INIS)

Nechaev, Sergei; Voituriez, Raphael

2005-01-01

We propose a simple geometrical construction of topological invariants of 3-strand Brownian braids viewed as world lines of 3 particles performing independent Brownian motions in the complex plane z. Our construction is based on the properties of conformal maps of doubly-punctured plane z to the universal covering surface. The special attention is paid to the case of indistinguishable particles. Our method of conformal maps allows us to investigate the statistical properties of the topological complexity of a bunch of 3-strand Brownian braids and to compute the expectation value of the irreducible braid length in the non-Abelian case

Surface Design Based on Discrete Conformal Transformations

Science.gov (United States)

Duque, Carlos; Santangelo, Christian; Vouga, Etienne

Conformal transformations are angle-preserving maps from one domain to another. Although angles are preserved, the lengths between arbitrary points are not generally conserved. As a consequence there is always a given amount of distortion associated to any conformal map. Different uses of such transformations can be found in various fields, but have been used by us to program non-uniformly swellable gel sheets to buckle into prescribed three dimensional shapes. In this work we apply circle packings as a kind of discrete conformal map in order to find conformal maps from the sphere to the plane that can be used as nearly uniform swelling patterns to program non-Euclidean sheets to buckle into spheres. We explore the possibility of tuning the area distortion to fit the experimental range of minimum and maximum swelling by modifying the boundary of the planar domain through the introduction of different cutting schemes.

Low-Mode Conformational Search Method with Semiempirical Quantum Mechanical Calculations: Application to Enantioselective Organocatalysis.

Science.gov (United States)

Kamachi, Takashi; Yoshizawa, Kazunari

2016-02-22

A conformational search program for finding low-energy conformations of large noncovalent complexes has been developed. A quantitatively reliable semiempirical quantum mechanical PM6-DH+ method, which is able to accurately describe noncovalent interactions at a low computational cost, was employed in contrast to conventional conformational search programs in which molecular mechanical methods are usually adopted. Our approach is based on the low-mode method whereby an initial structure is perturbed along one of its low-mode eigenvectors to generate new conformations. This method was applied to determine the most stable conformation of transition state for enantioselective alkylation by the Maruoka and cinchona alkaloid catalysts and Hantzsch ester hydrogenation of imines by chiral phosphoric acid. Besides successfully reproducing the previously reported most stable DFT conformations, the conformational search with the semiempirical quantum mechanical calculations newly discovered a more stable conformation at a low computational cost.

Comparative characteristic of the methods of protein antigens epitope mapping

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O. Yu. Galkin

2014-08-01

Full Text Available Comparative analysis of experimental methods of epitope mapping of protein antigens has been carried out. The vast majority of known techniques are involved in immunochemical study of the interaction of protein molecules or peptides with antibodies of corresponding specifici­ty. The most effective and widely applicable metho­dological techniques are those that use synthetic and genetically engineered peptides. Over the past 30 years, these groups of methods have travelled a notable evolutionary path up to the maximum automation and the detection of antigenic determinants of various types (linear and conformational epitopes, and mimotopes. Most of epitope searching algorithms were integrated into a computer program, which greatly facilitates the analysis of experimental data and makes it possible to create spatial models. It is possible to use comparative epitope mapping for solving the applied problems; this less time-consuming method is based on the analysis of competition between different antibodies interactions with the same antigen. The physical method of antigenic structure study is X-ray analysis of antigen-antibody complexes, which may be applied only to crystallizing­ proteins, and nuclear magnetic resonance.

Global mapping of DNA conformational flexibility on Saccharomyces cerevisiae.

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Giulia Menconi

2015-04-01

Full Text Available In this study we provide the first comprehensive map of DNA conformational flexibility in Saccharomyces cerevisiae complete genome. Flexibility plays a key role in DNA supercoiling and DNA/protein binding, regulating DNA transcription, replication or repair. Specific interest in flexibility analysis concerns its relationship with human genome instability. Enrichment in flexible sequences has been detected in unstable regions of human genome defined fragile sites, where genes map and carry frequent deletions and rearrangements in cancer. Flexible sequences have been suggested to be the determinants of fragile gene proneness to breakage; however, their actual role and properties remain elusive. Our in silico analysis carried out genome-wide via the StabFlex algorithm, shows the conserved presence of highly flexible regions in budding yeast genome as well as in genomes of other Saccharomyces sensu stricto species. Flexibile peaks in S. cerevisiae identify 175 ORFs mapping on their 3'UTR, a region affecting mRNA translation, localization and stability. (TAn repeats of different extension shape the central structure of peaks and co-localize with polyadenylation efficiency element (EE signals. ORFs with flexible peaks share common features. Transcripts are characterized by decreased half-life: this is considered peculiar of genes involved in regulatory systems with high turnover; consistently, their function affects biological processes such as cell cycle regulation or stress response. Our findings support the functional importance of flexibility peaks, suggesting that the flexible sequence may be derived by an expansion of canonical TAYRTA polyadenylation efficiency element. The flexible (TAn repeat amplification could be the outcome of an evolutionary neofunctionalization leading to a differential 3'-end processing and expression regulation in genes with peculiar function. Our study provides a new support to the functional role of flexibility in

Global mapping of DNA conformational flexibility on Saccharomyces cerevisiae.

Science.gov (United States)

Menconi, Giulia; Bedini, Andrea; Barale, Roberto; Sbrana, Isabella

2015-04-01

In this study we provide the first comprehensive map of DNA conformational flexibility in Saccharomyces cerevisiae complete genome. Flexibility plays a key role in DNA supercoiling and DNA/protein binding, regulating DNA transcription, replication or repair. Specific interest in flexibility analysis concerns its relationship with human genome instability. Enrichment in flexible sequences has been detected in unstable regions of human genome defined fragile sites, where genes map and carry frequent deletions and rearrangements in cancer. Flexible sequences have been suggested to be the determinants of fragile gene proneness to breakage; however, their actual role and properties remain elusive. Our in silico analysis carried out genome-wide via the StabFlex algorithm, shows the conserved presence of highly flexible regions in budding yeast genome as well as in genomes of other Saccharomyces sensu stricto species. Flexibile peaks in S. cerevisiae identify 175 ORFs mapping on their 3'UTR, a region affecting mRNA translation, localization and stability. (TA)n repeats of different extension shape the central structure of peaks and co-localize with polyadenylation efficiency element (EE) signals. ORFs with flexible peaks share common features. Transcripts are characterized by decreased half-life: this is considered peculiar of genes involved in regulatory systems with high turnover; consistently, their function affects biological processes such as cell cycle regulation or stress response. Our findings support the functional importance of flexibility peaks, suggesting that the flexible sequence may be derived by an expansion of canonical TAYRTA polyadenylation efficiency element. The flexible (TA)n repeat amplification could be the outcome of an evolutionary neofunctionalization leading to a differential 3'-end processing and expression regulation in genes with peculiar function. Our study provides a new support to the functional role of flexibility in genomes and a

Conformal Killing horizons and their thermodynamics

Science.gov (United States)

Nielsen, Alex B.; Shoom, Andrey A.

2018-05-01

Certain dynamical black hole solutions can be mapped to static spacetimes by conformal metric transformations. This mapping provides a physical link between the conformal Killing horizon of the dynamical black hole and the Killing horizon of the static spacetime. Using the Vaidya spacetime as an example, we show how this conformal relation can be used to derive thermodynamic properties of such dynamical black holes. Although these horizons are defined quasi-locally and can be located by local experiments, they are distinct from other popular notions of quasi-local horizons such as apparent horizons. Thus in the dynamical Vaidya spacetime describing constant accretion of null dust, the conformal Killing horizon, which is null by construction, is the natural horizon to describe the black hole.

Dual conformal transformations of smooth holographic Wilson loops

Energy Technology Data Exchange (ETDEWEB)

Dekel, Amit [Nordita, KTH Royal Institute of Technology and Stockholm University, Roslagstullsbacken 23, SE-106 91 Stockholm (Sweden)

2017-01-19

We study dual conformal transformations of minimal area surfaces in AdS{sub 5}×S{sup 5} corresponding to holographic smooth Wilson loops and some other related observables. To act with dual conformal transformations we map the string solutions to the dual space by means of T-duality, then we apply a conformal transformation and finally T-dualize back to the original space. The transformation maps between string solutions with different boundary contours. The boundary contours of the minimal surfaces are not mapped back to the AdS boundary, and the regularized area of the surface changes.

Divergence-Conforming Discontinuous Galerkin Methods and $C^0$ Interior Penalty Methods

KAUST Repository

Kanschat, Guido; Sharma, Natasha

2014-01-01

© 2014 Society for Industrial and Applied Mathematics. In this paper, we show that recently developed divergence-conforming methods for the Stokes problem have discrete stream functions. These stream functions in turn solve a continuous interior

Method and apparatus for enhancing vortex pinning by conformal crystal arrays

Science.gov (United States)

Janko, Boldizsar; Reichhardt, Cynthia; Reichhardt, Charles; Ray, Dipanjan

2015-07-14

Disclosed is a method and apparatus for strongly enhancing vortex pinning by conformal crystal arrays. The conformal crystal array is constructed by a conformal transformation of a hexagonal lattice, producing a non-uniform structure with a gradient where the local six-fold coordination of the pinning sites is preserved, and with an arching effect. The conformal pinning arrays produce significantly enhanced vortex pinning over a much wider range of field than that found for other vortex pinning geometries with an equivalent number of vortex pinning sites, such as random, square, and triangular.

Heat transfer analysis in internally-cooled fuel elements by means of a conformal mapping approach

International Nuclear Information System (INIS)

Sarmiento, G.S.; Laura, P.A.A.

1981-01-01

The present paper deals with an approximate solution of the steady-state heat conduction problem in internally cooled fuel elements of fast breeder reactors. Explicit expressions for the dimensionless temperature distribution in terms of the governing physical and geometrical parameters are determined by means of a coupled conformal mapping-variational approach. The results obtained are found to be in very good agreement with those calculated by means of a finite element code. (orig.)

Conformal maps and group contractions in nuclear structure

International Nuclear Information System (INIS)

Bonatsos, D.

2011-01-01

In mathematics, a conformal map is a function which preserves angles. We show how this procedure can be used in the framework of the Bohr Hamiltonian, leading to a Hamiltonian in a curved space, in which the mass depends on the nuclear deformation β, while it remains independent of the collective variable γ and the three Euler angles. This Hamiltonian is proved to be equivalent to that obtained using techniques of Supersymmetric Quantum Mechanics. Group contraction is a procedure in which a symmetry group is reduced into a group of lower symmetry in a certain limiting case. Examples are provided in the large boson number limit of the Interacting Boson Approximation (IBA) model by a) the contraction of the SU(3) algebra into the [R 5 ]SO(3) algebra of the rigid rotator, consisting of the angular momentum operators forming SO(3), plus 5 mutually commuting quantities, the quadrupole operators, b) the contraction of the O(6) algebra into the [R 5 ]SO(5) algebra of the γ-unstable rotator. We show how contractions can be used for constructing symmetry lines in the interior of the symmetry triangle of the IBA model. (author)

Open conformal systems and perturbations of transfer operators

CERN Document Server

Pollicott, Mark

2017-01-01

The focus of this book is on open conformal dynamical systems corresponding to the escape of a point through an open Euclidean ball. The ultimate goal is to understand the asymptotic behavior of the escape rate as the radius of the ball tends to zero. In the case of hyperbolic conformal systems this has been addressed by various authors. The conformal maps considered in this book are far more general, and the analysis correspondingly more involved. The asymptotic existence of escape rates is proved and they are calculated in the context of (finite or infinite) countable alphabets, uniformly contracting conformal graph-directed Markov systems, and in particular, conformal countable alphabet iterated function systems. These results have direct applications to interval maps, meromorphic maps and rational functions. Towards this goal the authors develop, on a purely symbolic level, a theory of singular perturbations of Perron--Frobenius (transfer) operators associated with countable alphabet subshifts of finite t...

Conformal group actions and Segal's cosmology

International Nuclear Information System (INIS)

Werth, J.-E.

1984-01-01

A mathematical description of Segal's cosmological model in the framework of conformal group actions is presented. The relation between conformal and causal group actions on time-orientable Lorentzian manifolds is analysed and several examples are discussed. A criterion for the conformality of a map between Lorentzian manifolds is given. The results are applied to Segal's 'conformal compactification' of Minkowski space. Furthermore, the 'unitary formulation' of Segal's cosmology is regarded. (Author) [pt

The calculations of small molecular conformation energy differences by density functional method

Science.gov (United States)

Topol, I. A.; Burt, S. K.

1993-03-01

The differences in the conformational energies for the gauche (G) and trans(T) conformers of 1,2-difluoroethane and for myo-and scyllo-conformer of inositol have been calculated by local density functional method (LDF approximation) with geometry optimization using different sets of calculation parameters. It is shown that in the contrast to Hartree—Fock methods, density functional calculations reproduce the correct sign and value of the gauche effect for 1,2-difluoroethane and energy difference for both conformers of inositol. The results of normal vibrational analysis for1,2-difluoroethane showed that harmonic frequencies calculated in LDF approximation agree with experimental data with the accuracy typical for scaled large basis set Hartree—Fock calculations.

Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.

Directory of Open Access Journals (Sweden)

Gómez Marcela

2009-12-01

Full Text Available Abstract Background Expressed sequence tags (ESTs are an important source of gene-based markers such as those based on insertion-deletions (Indels or single-nucleotide polymorphisms (SNPs. Several gel based methods have been reported for the detection of sequence variants, however they have not been widely exploited in common bean, an important legume crop of the developing world. The objectives of this project were to develop and map EST based markers using analysis of single strand conformation polymorphisms (SSCPs, to create a transcript map for common bean and to compare synteny of the common bean map with sequenced chromosomes of other legumes. Results A set of 418 EST based amplicons were evaluated for parental polymorphisms using the SSCP technique and 26% of these presented a clear conformational or size polymorphism between Andean and Mesoamerican genotypes. The amplicon based markers were then used for genetic mapping with segregation analysis performed in the DOR364 × G19833 recombinant inbred line (RIL population. A total of 118 new marker loci were placed into an integrated molecular map for common bean consisting of 288 markers. Of these, 218 were used for synteny analysis and 186 presented homology with segments of the soybean genome with an e-value lower than 7 × 10-12. The synteny analysis with soybean showed a mosaic pattern of syntenic blocks with most segments of any one common bean linkage group associated with two soybean chromosomes. The analysis with Medicago truncatula and Lotus japonicus presented fewer syntenic regions consistent with the more distant phylogenetic relationship between the galegoid and phaseoloid legumes. Conclusion The SSCP technique is a useful and inexpensive alternative to other SNP or Indel detection techniques for saturating the common bean genetic map with functional markers that may be useful in marker assisted selection. In addition, the genetic markers based on ESTs allowed the construction

Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.).

Science.gov (United States)

Galeano, Carlos H; Fernández, Andrea C; Gómez, Marcela; Blair, Matthew W

2009-12-23

Expressed sequence tags (ESTs) are an important source of gene-based markers such as those based on insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). Several gel based methods have been reported for the detection of sequence variants, however they have not been widely exploited in common bean, an important legume crop of the developing world. The objectives of this project were to develop and map EST based markers using analysis of single strand conformation polymorphisms (SSCPs), to create a transcript map for common bean and to compare synteny of the common bean map with sequenced chromosomes of other legumes. A set of 418 EST based amplicons were evaluated for parental polymorphisms using the SSCP technique and 26% of these presented a clear conformational or size polymorphism between Andean and Mesoamerican genotypes. The amplicon based markers were then used for genetic mapping with segregation analysis performed in the DOR364 x G19833 recombinant inbred line (RIL) population. A total of 118 new marker loci were placed into an integrated molecular map for common bean consisting of 288 markers. Of these, 218 were used for synteny analysis and 186 presented homology with segments of the soybean genome with an e-value lower than 7 x 10-12. The synteny analysis with soybean showed a mosaic pattern of syntenic blocks with most segments of any one common bean linkage group associated with two soybean chromosomes. The analysis with Medicago truncatula and Lotus japonicus presented fewer syntenic regions consistent with the more distant phylogenetic relationship between the galegoid and phaseoloid legumes. The SSCP technique is a useful and inexpensive alternative to other SNP or Indel detection techniques for saturating the common bean genetic map with functional markers that may be useful in marker assisted selection. In addition, the genetic markers based on ESTs allowed the construction of a transcript map and given their high conservation

Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics

International Nuclear Information System (INIS)

Donnamaira, M.C.; Howard, E.I.; Grigera, J.R.

1992-09-01

Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs

Modeling 3D Dynamic Rupture on Arbitrarily-Shaped faults by Boundary-Conforming Finite Difference Method

Science.gov (United States)

Zhu, D.; Zhu, H.; Luo, Y.; Chen, X.

2008-12-01

We use a new finite difference method (FDM) and the slip-weakening law to model the rupture dynamics of a non-planar fault embedded in a 3-D elastic media with free surface. The new FDM, based on boundary- conforming grid, sets up the mapping equations between the curvilinear coordinate and the Cartesian coordinate and transforms irregular physical space to regular computational space; it also employs a higher- order non-staggered DRP/opt MacCormack scheme which is of low dispersion and low dissipation so that the high accuracy and stability of our rupture modeling are guaranteed. Compared with the previous methods, not only we can compute the spontaneous rupture of an arbitrarily shaped fault, but also can model the influence of the surface topography on the rupture process of earthquake. In order to verify the feasibility of this method, we compared our results and other previous results, and found out they matched perfectly. Thanks to the boundary-conforming FDM, problems such as dynamic rupture with arbitrary dip, strike and rake over an arbitrary curved plane can be handled; and supershear or subshear rupture can be simulated with different parameters such as the initial stresses and the critical slip displacement Dc. Besides, our rupture modeling is economical to be implemented owing to its high efficiency and does not suffer from displacement leakage. With the help of inversion data of rupture by field observations, this method is convenient to model rupture processes and seismograms of natural earthquakes.

Comparative analysis of various methods for modelling permanent magnet machines

NARCIS (Netherlands)

Ramakrishnan, K.; Curti, M.; Zarko, D.; Mastinu, G.; Paulides, J.J.H.; Lomonova, E.A.

2017-01-01

In this paper, six different modelling methods for permanent magnet (PM) electric machines are compared in terms of their computational complexity and accuracy. The methods are based primarily on conformal mapping, mode matching, and harmonic modelling. In the case of conformal mapping, slotted air

Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins

Science.gov (United States)

Harada, Ryuhei; Takano, Yu; Shigeta, Yasuteru

2014-03-01

A powerful conformational sampling method for accelerating structural transitions of proteins, "Fluctuation Flooding Method (FFM)," is proposed. In FFM, cycles of the following steps enhance the transitions: (i) extractions of largely fluctuating snapshots along anisotropic modes obtained from trajectories of multiple independent molecular dynamics (MD) simulations and (ii) conformational re-sampling of the snapshots via re-generations of initial velocities when re-starting MD simulations. In an application to bacteriophage T4 lysozyme, FFM successfully accelerated the open-closed transition with the 6 ns simulation starting solely from the open state, although the 1-μs canonical MD simulation failed to sample such a rare event.

Mapping Mixed Methods Research: Methods, Measures, and Meaning

Science.gov (United States)

Wheeldon, J.

2010-01-01

This article explores how concept maps and mind maps can be used as data collection tools in mixed methods research to combine the clarity of quantitative counts with the nuance of qualitative reflections. Based on more traditional mixed methods approaches, this article details how the use of pre/post concept maps can be used to design qualitative…

Single-molecule diffusion and conformational dynamics by spatial integration of temporal fluctuations

KAUST Repository

Serag, Maged F.

2014-10-06

Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields.

Single-molecule diffusion and conformational dynamics by spatial integration of temporal fluctuations

KAUST Repository

Serag, Maged F.; Abadi, Maram; Habuchi, Satoshi

2014-01-01

Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields.

Killing tensors and conformal Killing tensors from conformal Killing vectors

International Nuclear Information System (INIS)

Rani, Raffaele; Edgar, S Brian; Barnes, Alan

2003-01-01

Koutras has proposed some methods to construct reducible proper conformal Killing tensors and Killing tensors (which are, in general, irreducible) when a pair of orthogonal conformal Killing vectors exist in a given space. We give the completely general result demonstrating that this severe restriction of orthogonality is unnecessary. In addition, we correct and extend some results concerning Killing tensors constructed from a single conformal Killing vector. A number of examples demonstrate that it is possible to construct a much larger class of reducible proper conformal Killing tensors and Killing tensors than permitted by the Koutras algorithms. In particular, by showing that all conformal Killing tensors are reducible in conformally flat spaces, we have a method of constructing all conformal Killing tensors, and hence all the Killing tensors (which will in general be irreducible) of conformally flat spaces using their conformal Killing vectors

Colon flattening by landmark-driven optimal quasiconformal mapping.

Science.gov (United States)

Zeng, Wei; Yang, Yi-Jun

2014-01-01

In virtual colonoscopy, colon conformal flattening plays an important role, which unfolds the colon wall surface to a rectangle planar image and preserves local shapes by conformal mapping, so that the cancerous polyps and other abnormalities can be easily and thoroughly recognized and visualized without missing hidden areas. In such maps, the anatomical landmarks (taeniae coli, flexures, and haustral folds) are naturally mapped to convoluted curves on 2D domain, which poses difficulty for comparing shapes from geometric feature details. Understanding the nature of landmark curves to the whole surface structure is meaningful but it remains challenging and open. In this work, we present a novel and effective colon flattening method based on quasiconformal mapping, which straightens the main anatomical landmark curves with least conformality (angle) distortion. It provides a canonical and straightforward view of the long, convoluted and folded tubular colon surface. The computation is based on the holomorphic 1-form method with landmark straightening constraints and quasiconformal optimization, and has linear time complexity due to the linearity of 1-forms in each iteration. Experiments on various colon data demonstrate the efficiency and efficacy of our algorithm and its practicability for polyp detection and findings visualization; furthermore, the result reveals the geometric characteristics of anatomical landmarks on colon surfaces.

Superintegrability of d-dimensional conformal blocks

International Nuclear Information System (INIS)

Isachenkov, Mikhail

2016-02-01

We observe that conformal blocks of scalar 4-point functions in a d-dimensional conformal field theory can mapped to eigenfunctions of a 2-particle hyperbolic Calogero-Sutherland Hamiltonian. The latter describes two coupled Poeschl-Teller particles. Their interaction, whose strength depends smoothly on the dimension d, is known to be superintegrable. Our observation enables us to exploit the rich mathematical literature on Calogero-Sutherland models in deriving various results for conformal field theory. These include an explicit construction of conformal blocks in terms of Heckman-Opdam hypergeometric functions and a remarkable duality that relates the blocks of theories in different dimensions.

Superintegrability of d-dimensional conformal blocks

Energy Technology Data Exchange (ETDEWEB)

Isachenkov, Mikhail [Weizmann Institute of Science, Rehovot (Israel). Dept. of Particle Physics and Astronomy; Schomerus, Volker [DESY Theory Group, Hamburg (Germany)

2016-02-15

We observe that conformal blocks of scalar 4-point functions in a d-dimensional conformal field theory can mapped to eigenfunctions of a 2-particle hyperbolic Calogero-Sutherland Hamiltonian. The latter describes two coupled Poeschl-Teller particles. Their interaction, whose strength depends smoothly on the dimension d, is known to be superintegrable. Our observation enables us to exploit the rich mathematical literature on Calogero-Sutherland models in deriving various results for conformal field theory. These include an explicit construction of conformal blocks in terms of Heckman-Opdam hypergeometric functions and a remarkable duality that relates the blocks of theories in different dimensions.

Bioactive conformational generation of small molecules: A comparative analysis between force-field and multiple empirical criteria based methods

Directory of Open Access Journals (Sweden)

Jiang Hualiang

2010-11-01

Full Text Available Abstract Background Conformational sampling for small molecules plays an essential role in drug discovery research pipeline. Based on multi-objective evolution algorithm (MOEA, we have developed a conformational generation method called Cyndi in the previous study. In this work, in addition to Tripos force field in the previous version, Cyndi was updated by incorporation of MMFF94 force field to assess the conformational energy more rationally. With two force fields against a larger dataset of 742 bioactive conformations of small ligands extracted from PDB, a comparative analysis was performed between pure force field based method (FFBM and multiple empirical criteria based method (MECBM hybrided with different force fields. Results Our analysis reveals that incorporating multiple empirical rules can significantly improve the accuracy of conformational generation. MECBM, which takes both empirical and force field criteria as the objective functions, can reproduce about 54% (within 1Å RMSD of the bioactive conformations in the 742-molecule testset, much higher than that of pure force field method (FFBM, about 37%. On the other hand, MECBM achieved a more complete and efficient sampling of the conformational space because the average size of unique conformations ensemble per molecule is about 6 times larger than that of FFBM, while the time scale for conformational generation is nearly the same as FFBM. Furthermore, as a complementary comparison study between the methods with and without empirical biases, we also tested the performance of the three conformational generation methods in MacroModel in combination with different force fields. Compared with the methods in MacroModel, MECBM is more competitive in retrieving the bioactive conformations in light of accuracy but has much lower computational cost. Conclusions By incorporating different energy terms with several empirical criteria, the MECBM method can produce more reasonable conformational

Derivation and application of an analytical rock displacement solution on rectangular cavern wall using the inverse mapping method.

Directory of Open Access Journals (Sweden)

Mingzhong Gao

Full Text Available Rectangular caverns are increasingly used in underground engineering projects, the failure mechanism of rectangular cavern wall rock is significantly different as a result of the cross-sectional shape and variations in wall stress distributions. However, the conventional computational method always results in a long-winded computational process and multiple displacement solutions of internal rectangular wall rock. This paper uses a Laurent series complex method to obtain a mapping function expression based on complex variable function theory and conformal transformation. This method is combined with the Schwarz-Christoffel method to calculate the mapping function coefficient and to determine the rectangular cavern wall rock deformation. With regard to the inverse mapping concept, the mapping relation between the polar coordinate system within plane ς and a corresponding unique plane coordinate point inside the cavern wall rock is discussed. The disadvantage of multiple solutions when mapping from the plane to the polar coordinate system is addressed. This theoretical formula is used to calculate wall rock boundary deformation and displacement field nephograms inside the wall rock for a given cavern height and width. A comparison with ANSYS numerical software results suggests that the theoretical solution and numerical solution exhibit identical trends, thereby demonstrating the method's validity. This method greatly improves the computing accuracy and reduces the difficulty in solving for cavern boundary and internal wall rock displacements. The proposed method provides a theoretical guide for controlling cavern wall rock deformation failure.

Robust fluence map optimization via alternating direction method of multipliers with empirical parameter optimization

International Nuclear Information System (INIS)

Gao, Hao

2016-01-01

For the treatment planning during intensity modulated radiation therapy (IMRT) or volumetric modulated arc therapy (VMAT), beam fluence maps can be first optimized via fluence map optimization (FMO) under the given dose prescriptions and constraints to conformally deliver the radiation dose to the targets while sparing the organs-at-risk, and then segmented into deliverable MLC apertures via leaf or arc sequencing algorithms. This work is to develop an efficient algorithm for FMO based on alternating direction method of multipliers (ADMM). Here we consider FMO with the least-square cost function and non-negative fluence constraints, and its solution algorithm is based on ADMM, which is efficient and simple-to-implement. In addition, an empirical method for optimizing the ADMM parameter is developed to improve the robustness of the ADMM algorithm. The ADMM based FMO solver was benchmarked with the quadratic programming method based on the interior-point (IP) method using the CORT dataset. The comparison results suggested the ADMM solver had a similar plan quality with slightly smaller total objective function value than IP. A simple-to-implement ADMM based FMO solver with empirical parameter optimization is proposed for IMRT or VMAT. (paper)

Conformal Killing vectors in Robertson-Walker spacetimes

International Nuclear Information System (INIS)

Maartens, R.; Maharaj, S.d.

1986-01-01

It is well known that Robertson-Walker spacetimes admit a conformal Killingl vector normal to the spacelike homogeneous hypersurfaces. Because these spacetimes are conformally flat, there are a further eight conformal Killing vectors, which are neither normal nor tangent to the homogeneous hypersurfaces. The authors find these further conformal Killing vectors and the Lie algebra of the full G 15 of conformal motions. Conditions on the metric scale factor are determined which reduce some of the conformal Killing vectors to homothetic Killing vectors or Killing vectors, allowing one to regain in a unified way the known special geometries. The non-normal conformal Killing vectors provide a counter-example to show that conformal motions do not, in general, map a fluid flow conformally. These non-normal vectors are also used to find the general solution of the null geodesic equation and photon Liouville equation. (author)

Conformational analysis and vibrational studies of ethylenediamine-d4, using DFT method

International Nuclear Information System (INIS)

Catikkas, B.

2010-01-01

In this work, conformational analysis and quantum chemical calculations of ethylenediamine-d4 were carried out. The geometry optimization and the geometric parameters (bond length, bond angle and tortion angle) were calculated. The Infrared and Raman frequencies of fundamental modes of the most stable conformer were determined. Calculations were carried out by using the MPW1PW91/6-311+G(d,p) method and Gaussian03 and GaussView3.0 programs. Populations of the conformers was calculated. Vibrational assignments of the title molecule were calculated by using Scaled Quantum Mechanical (SQM) analysis. Calculated values were compared with the experimental ones.

Identification of potential small molecule allosteric modulator sites on IL-1R1 ectodomain using accelerated conformational sampling method.

Directory of Open Access Journals (Sweden)

Chao-Yie Yang

Full Text Available The interleukin-1 receptor (IL-1R is the founding member of the interleukin 1 receptor family which activates innate immune response by its binding to cytokines. Reports showed dysregulation of cytokine production leads to aberrant immune cells activation which contributes to auto-inflammatory disorders and diseases. Current therapeutic strategies focus on utilizing antibodies or chimeric cytokine biologics. The large protein-protein interaction interface between cytokine receptor and cytokine poses a challenge in identifying binding sites for small molecule inhibitor development. Based on the significant conformational change of IL-1R type 1 (IL-1R1 ectodomain upon binding to different ligands observed in crystal structures, we hypothesized that transient small molecule binding sites may exist when IL-1R1 undergoes conformational transition and thus suitable for inhibitor development. Here, we employed accelerated molecular dynamics (MD simulation to efficiently sample conformational space of IL-1R1 ectodomain. Representative IL-1R1 ectodomain conformations determined from the hierarchy cluster analysis were analyzed by the SiteMap program which leads to identify small molecule binding sites at the protein-protein interaction interface and allosteric modulator locations. The cosolvent mapping analysis using phenol as the probe molecule further confirms the allosteric modulator site as a binding hotspot. Eight highest ranked fragment molecules identified from in silico screening at the modulator site were evaluated by MD simulations. Four of them restricted the IL-1R1 dynamical motion to inactive conformational space. The strategy from this study, subject to in vitro experimental validation, can be useful to identify small molecule compounds targeting the allosteric modulator sites of IL-1R and prevent IL-1R from binding to cytokine by trapping IL-1R in inactive conformations.

Schwarz-Christoffel Conformal Mapping based Grid Generation for Global Oceanic Circulation Models

Science.gov (United States)

Xu, Shiming

2015-04-01

We propose new grid generation algorithms for global ocean general circulation models (OGCMs). Contrary to conventional, analytical forms based dipolar or tripolar grids, the new algorithm are based on Schwarz-Christoffel (SC) conformal mapping with prescribed boundary information. While dealing with the conventional grid design problem of pole relocation, it also addresses more advanced issues of computational efficiency and the new requirements on OGCM grids arisen from the recent trend of high-resolution and multi-scale modeling. The proposed grid generation algorithm could potentially achieve the alignment of grid lines to coastlines, enhanced spatial resolution in coastal regions, and easier computational load balance. Since the generated grids are still orthogonal curvilinear, they can be readily 10 utilized in existing Bryan-Cox-Semtner type ocean models. The proposed methodology can also be applied to the grid generation task for regional ocean modeling when complex land-ocean distribution is present.

Stochastic geometry of critical curves, Schramm-Loewner evolutions and conformal field theory

International Nuclear Information System (INIS)

Gruzberg, Ilya A

2006-01-01

Conformally invariant curves that appear at critical points in two-dimensional statistical mechanics systems and their fractal geometry have received a lot of attention in recent years. On the one hand, Schramm (2000 Israel J. Math. 118 221 (Preprint math.PR/9904022)) has invented a new rigorous as well as practical calculational approach to critical curves, based on a beautiful unification of conformal maps and stochastic processes, and by now known as Schramm-Loewner evolution (SLE). On the other hand, Duplantier (2000 Phys. Rev. Lett. 84 1363; Fractal Geometry and Applications: A Jubilee of Benot Mandelbrot: Part 2 (Proc. Symp. Pure Math. vol 72) (Providence, RI: American Mathematical Society) p 365 (Preprint math-ph/0303034)) has applied boundary quantum gravity methods to calculate exact multifractal exponents associated with critical curves. In the first part of this paper, I provide a pedagogical introduction to SLE. I present mathematical facts from the theory of conformal maps and stochastic processes related to SLE. Then I review basic properties of SLE and provide practical derivation of various interesting quantities related to critical curves, including fractal dimensions and crossing probabilities. The second part of the paper is devoted to a way of describing critical curves using boundary conformal field theory (CFT) in the so-called Coulomb gas formalism. This description provides an alternative (to quantum gravity) way of obtaining the multifractal spectrum of critical curves using only traditional methods of CFT based on free bosonic fields

Calculation of pole profiles for the design of particle accelerators magnets. Equivalent current and conformal representation methods; Calcul de profils polaires destines a des aimants d'accelerateurs de particules. Methode des courants et methode des transformations conformes

Energy Technology Data Exchange (ETDEWEB)

Jaidane, S [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1968-04-01

These two methods allow the determination of the shape of the poles in magnets, for a given field distribution in the air-gap. First method: The principle of the method consists to create the desired law of field by means of current sheets in which one can adjust the density given in a polynomial form. For the right distribution of these currents, the equipotential corresponding to the magnetic potential of the excitation coils is calculated. The pole profile of the H or C magnet identified with this equipotential line will finally take the place of the distribution of the current sheets used in the calculation. Steel permeability is assumed to be infinite and Foucault current effects are neglected in the case of variable fields. Second method: It consists to find a conformal representation that maps the pole profile plane upon the upper half of another plane where the equipotentials are two half straight lines, and where the field problems are easier to solve. Steel permeability is also considered to be infinite and the coils far from the pole faces. This known method has been applied to be compared with the first one. (author) [French] Ces deux methodes consistent a determiner la forme des pieces polaires d'aimants pour une distribution de champ determinee a l'avance dans l'entrefer. Premiere methode: Le principe de la methode consiste a creer la loi de champ desiree par l'intermediaire de nappes de courant dont on peut ajuster la densite exprimee sous une forme polynominale. Pour une distribution convenable de ces courants, on calcule l'equipotentielle correspondant au potentiel magnetique des bobines d'excitation. Le profil polaire d'un aimant en H ou C identifie a l'equipotentielle se substitue finalement a la repartition des nappes de courant utilisee dans la methode de calcul. La permeabilite de l'acier est supposee infinie et les courants de Foucault sont negliges dans le cas des champs variables. Seconde methode: Elle consiste a trouver une transformation

On the conformal equivalence of harmonic maps and exponentially harmonic maps

International Nuclear Information System (INIS)

Hong Minchun.

1991-06-01

Suppose that (M,g) and (N,h) are compact smooth Riemannian manifolds without boundaries. For m = dim M ≥3, and Φ: (M,g) → (N,h) is exponentially harmonic, there exists a smooth metric g-tilde conformally equivalent to g such that Φ: (M,g-tilde) → (N,h) is harmonic. (author). 7 refs

Divergence-Conforming Discontinuous Galerkin Methods and $C^0$ Interior Penalty Methods

KAUST Repository

Kanschat, Guido

2014-01-01

© 2014 Society for Industrial and Applied Mathematics. In this paper, we show that recently developed divergence-conforming methods for the Stokes problem have discrete stream functions. These stream functions in turn solve a continuous interior penalty problem for biharmonic equations. The equivalence is established for the most common methods in two dimensions based on interior penalty terms. Then, extensions of the concept to discontinuous Galerkin methods defined through lifting operators, for different weak formulations of the Stokes problem, and to three dimensions are discussed. Application of the equivalence result yields an optimal error estimate for the Stokes velocity without involving the pressure. Conversely, combined with a recent multigrid method for Stokes flow, we obtain a simple and uniform preconditioner for harmonic problems with simply supported and clamped boundary.

Analysis of a flip-chip bonded tunable high-temperature superconducting coplanar waveguide resonator using the conformal mapping technique

CERN Document Server

Misra, M; Murakami, H; Tonouchi, M

2003-01-01

We have studied the tuning properties of a high-temperature superconducting (HTS) half-wavelength coplanar waveguide (CPW) resonator operating at 5 GHz. The tuning schemes are based on flip-chip bonding of an electrically tunable ferroelectric (FE) thin film and a mechanically movable low-loss single crystal on top of the resonator. Using the conformal mapping method, closed-form analytical expressions have been derived for a flip-chip bonded conductor-backed and top-shielded CPW transmission line. The obtained expressions are used to analyse the volume effect of the FE thin film and the gap between the flip-chip and the CPW resonator on the tuning properties of the device. It has been found that large frequency modulation of the resonator produces impedance mismatch, which can considerably enhance the insertion loss of high-performance HTS microwave devices. Analysis also suggests that, for electrically tunable devices, flip-chip bonded FE thin films on HTS CPW devices provide a relatively higher performance...

Relating c 0 conformal field theories

International Nuclear Information System (INIS)

Guruswamy, S.; Ludwig, A.W.W.

1998-03-01

A 'canonical mapping' is established between the c = -1 system of bosonic ghosts at the c = 2 complex scalar theory and, a similar mapping between the c = -2 system of fermionic ghosts and the c = 1 Dirac theory. The existence of this mapping is suggested by the identity of the characters of the respective theories. The respective c 0 theories share the same space of states, whereas the spaces of conformal fields are different. Upon this mapping from their c 0) complex scalar and the Dirac theories inherit hidden nonlocal sl(2) symmetries. (author)

More on the conformal mapping of quasi-local masses: the Hawking–Hayward case

International Nuclear Information System (INIS)

Hammad, Fayçal

2016-01-01

The conformal transformation of the Hawking–Hayward quasi-local mass is re-examined. It has been found recently that the conformal transformation of the latter exhibits the ‘wrong’ conformal factor compared to the way usual masses transform under conformal transformations of spacetime. We show, in analogy with what was found recently for the Misner–Sharp mass, that unlike the purely geometric definition of the Hawking–Hayward mass, the latter exhibits the ‘right’ conformal factor whenever expressed in terms of its material content via the field equations. The case of conformally invariant scalar–tensor theories of gravity is also examined. The equivalence between the Misner–Sharp mass and the Hawking–Hayward mass for spherically symmetric spacetimes manifests itself by giving identical peculiar behaviors under conformal transformations. (paper)

Entanglement evolution across a conformal interface

Science.gov (United States)

Wen, Xueda; Wang, Yuxuan; Ryu, Shinsei

2018-05-01

For two-dimensional conformal field theories (CFTs) in the ground state, it is known that a conformal interface along the entanglement cut can suppress the entanglement entropy from to , where L is the length of the subsystem A, and is the effective central charge which depends on the transmission property of the conformal interface. In this work, by making use of conformal mappings, we show that a conformal interface has the same effect on entanglement evolution in non-equilibrium cases, including global, local and certain inhomogeneous quantum quenches. I.e. a conformal interface suppresses the time evolution of entanglement entropy by effectively replacing the central charge c with , where is exactly the same as that in the ground state case. We confirm this conclusion by a numerical study on a critical fermion chain. Furthermore, based on the quasi-particle picture, we conjecture that this conclusion holds for an arbitrary quantum quench in CFTs, as long as the initial state can be described by a regularized conformal boundary state.

Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors.

Science.gov (United States)

Esquivel-Rodríguez, Juan; Kihara, Daisuke

2012-06-14

A novel computational method for fitting high-resolution structures of multiple proteins into a cryoelectron microscopy map is presented. The method named EMLZerD generates a pool of candidate multiple protein docking conformations of component proteins, which are later compared with a provided electron microscopy (EM) density map to select the ones that fit well into the EM map. The comparison of docking conformations and the EM map is performed using the 3D Zernike descriptor (3DZD), a mathematical series expansion of three-dimensional functions. The 3DZD provides a unified representation of the surface shape of multimeric protein complex models and EM maps, which allows a convenient, fast quantitative comparison of the three-dimensional structural data. Out of 19 multimeric complexes tested, near native complex structures with a root-mean-square deviation of less than 2.5 Å were obtained for 14 cases while medium range resolution structures with correct topology were computed for the additional 5 cases.

Scattering of electromagnetic waves from a cone with conformal mapping: Application to scanning near-field optical microscope

Science.gov (United States)

Chui, S. T.; Chen, Xinzhong; Liu, Mengkun; Lin, Zhifang; Zi, Jian

2018-02-01

We study the response of a conical metallic surface to an external electromagnetic (em) field by representing the fields in basis functions containing the integrable singularity at the tip of the cone. A fast analytical solution is obtained by the conformal mapping between the cone and a round disk. We apply our calculation to the scattering-type scanning near-field optical microscope (s-SNOM) and successfully quantify the elastic light scattering from a vibrating metallic tip over a uniform sample. We find that the field-induced charge distribution consists of localized terms at the tip and the base and an extended bulk term along the body of the cone far away from the tip. In recent s-SNOM experiments at the visible and infrared range (600 nm to 1 μ m ) the fundamental of the demodulated near-field signal is found to be much larger than the higher harmonics whereas at THz range (100 μ m to 3 mm) the fundamental becomes comparable to the higher harmonics. We find that the localized tip charge dominates the contribution to the higher harmonics and becomes larger for the THz experiments, thus providing an intuitive understanding of the origin of the near-field signals. We demonstrate the application of our method by extracting a two-dimensional effective dielectric constant map from the s-SNOM image of a finite metallic disk, where the variation comes from the charge density induced by the em field.

A Continuation Method for Weakly Kannan Maps

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Ariza-Ruiz David

2010-01-01

Full Text Available The first continuation method for contractive maps in the setting of a metric space was given by Granas. Later, Frigon extended Granas theorem to the class of weakly contractive maps, and recently Agarwal and O'Regan have given the corresponding result for a certain type of quasicontractions which includes maps of Kannan type. In this note we introduce the concept of weakly Kannan maps and give a fixed point theorem, and then a continuation method, for this class of maps.

Mapped Chebyshev Pseudo-Spectral Method for Dynamic Aero-Elastic Problem of Limit Cycle Oscillation

Science.gov (United States)

Im, Dong Kyun; Kim, Hyun Soon; Choi, Seongim

2018-05-01

A mapped Chebyshev pseudo-spectral method is developed as one of the Fourier-spectral approaches and solves nonlinear PDE systems for unsteady flows and dynamic aero-elastic problem in a given time interval, where the flows or elastic motions can be periodic, nonperiodic, or periodic with an unknown frequency. The method uses the Chebyshev polynomials of the first kind for the basis function and redistributes the standard Chebyshev-Gauss-Lobatto collocation points more evenly by a conformal mapping function for improved numerical stability. Contributions of the method are several. It can be an order of magnitude more efficient than the conventional finite difference-based, time-accurate computation, depending on the complexity of solutions and the number of collocation points. The method reformulates the dynamic aero-elastic problem in spectral form for coupled analysis of aerodynamics and structures, which can be effective for design optimization of unsteady and dynamic problems. A limit cycle oscillation (LCO) is chosen for the validation and a new method to determine the LCO frequency is introduced based on the minimization of a second derivative of the aero-elastic formulation. Two examples of the limit cycle oscillation are tested: nonlinear, one degree-of-freedom mass-spring-damper system and two degrees-of-freedom oscillating airfoil under pitch and plunge motions. Results show good agreements with those of the conventional time-accurate simulations and wind tunnel experiments.

A Novel Method Using Abstract Convex Underestimation in Ab-Initio Protein Structure Prediction for Guiding Search in Conformational Feature Space.

Science.gov (United States)

Hao, Xiao-Hu; Zhang, Gui-Jun; Zhou, Xiao-Gen; Yu, Xu-Feng

2016-01-01

To address the searching problem of protein conformational space in ab-initio protein structure prediction, a novel method using abstract convex underestimation (ACUE) based on the framework of evolutionary algorithm was proposed. Computing such conformations, essential to associate structural and functional information with gene sequences, is challenging due to the high-dimensionality and rugged energy surface of the protein conformational space. As a consequence, the dimension of protein conformational space should be reduced to a proper level. In this paper, the high-dimensionality original conformational space was converted into feature space whose dimension is considerably reduced by feature extraction technique. And, the underestimate space could be constructed according to abstract convex theory. Thus, the entropy effect caused by searching in the high-dimensionality conformational space could be avoided through such conversion. The tight lower bound estimate information was obtained to guide the searching direction, and the invalid searching area in which the global optimal solution is not located could be eliminated in advance. Moreover, instead of expensively calculating the energy of conformations in the original conformational space, the estimate value is employed to judge if the conformation is worth exploring to reduce the evaluation time, thereby making computational cost lower and the searching process more efficient. Additionally, fragment assembly and the Monte Carlo method are combined to generate a series of metastable conformations by sampling in the conformational space. The proposed method provides a novel technique to solve the searching problem of protein conformational space. Twenty small-to-medium structurally diverse proteins were tested, and the proposed ACUE method was compared with It Fix, HEA, Rosetta and the developed method LEDE without underestimate information. Test results show that the ACUE method can more rapidly and more

The DosiMap, a new 2D scintillating dosimeter for IMRT quality assurance: Characterization of two Cerenkov discrimination methods

International Nuclear Information System (INIS)

Frelin, A-M.; Fontbonne, J-M.; Ban, G.; Colin, J.; Labalme, M.; Batalla, A.; Vela, A.; Boher, P.; Braud, M.; Leroux, T.

2008-01-01

New radiation therapy techniques such as IMRT present significant efficiency due to their highly conformal dose distributions. A consequence of the complexity of their dose distributions (high gradients, small irradiation fields, low dose distribution, ...) is the requirement for better precision quality assurance than in classical radiotherapy in order to compare the conformation of the delivered dose with the planned dose distribution and to guarantee the quality of the treatment. Currently this control is mostly performed by matrices of ionization chambers, diode detectors, dosimetric films, portal imaging, or dosimetric gels. Another approach is scintillation dosimetry, which has been developed in the last 15 years mainly through scintillating fiber devices. Despite having many advantages over other methods it is still at an experimental level for routine dosimetry because the Cerenkov radiation produced under irradiation represents an important stem effect. A new 2D water equivalent scintillating dosimeter, the DosiMap, and two different Cerenkov discrimination methods were developed with the collaboration of the Laboratoire de Physique Corpusculaire of Caen, the Comprehensive Cancer Center Francois Baclesse, and the ELDIM Co., in the frame of the MAESTRO European project. The DosiMap consists of a plastic scintillating sheet placed inside a transparent polystyrene phantom. The light distribution produced under irradiation is recorded by a CCD camera. Our first Cerenkov discrimination technique is subtractive. It uses a chessboard pattern placed in front of the scintillator, which provides a background signal containing only Cerenkov light. Our second discrimination technique is colorimetric. It performs a spectral analysis of the light signal, which allows the unfolding of the Cerenkov radiation and the scintillation. Tests were carried out with our DosiMap prototype and the performances of the two discrimination methods were assessed. The comparison of the

The DosiMap, a new 2D scintillating dosimeter for IMRT quality assurance: characterization of two Cerenkov discrimination methods.

Science.gov (United States)

Frelin, A M; Fontbonne, J M; Ban, G; Colin, J; Labalme, M; Batalla, A; Vela, A; Boher, P; Braud, M; Leroux, T

2008-05-01

New radiation therapy techniques such as IMRT present significant efficiency due to their highly conformal dose distributions. A consequence of the complexity of their dose distributions (high gradients, small irradiation fields, low dose distribution, ...) is the requirement for better precision quality assurance than in classical radiotherapy in order to compare the conformation of the delivered dose with the planned dose distribution and to guarantee the quality of the treatment. Currently this control is mostly performed by matrices of ionization chambers, diode detectors, dosimetric films, portal imaging, or dosimetric gels. Another approach is scintillation dosimetry, which has been developed in the last 15 years mainly through scintillating fiber devices. Despite having many advantages over other methods it is still at an experimental level for routine dosimetry because the Cerenkov radiation produced under irradiation represents an important stem effect. A new 2D water equivalent scintillating dosimeter, the DosiMap, and two different Cerenkov discrimination methods were developed with the collaboration of the Laboratoire de Physique Corpusculaire of Caen, the Comprehensive Cancer Center François Baclesse, and the ELDIM Co., in the frame of the MAESTRO European project. The DosiMap consists of a plastic scintillating sheet placed inside a transparent polystyrene phantom. The light distribution produced under irradiation is recorded by a CCD camera. Our first Cerenkov discrimination technique is subtractive. It uses a chessboard pattern placed in front of the scintillator, which provides a background signal containing only Cerenkov light. Our second discrimination technique is colorimetric. It performs a spectral analysis of the light signal, which allows the unfolding of the Cerenkov radiation and the scintillation. Tests were carried out with our DosiMap prototype and the performances of the two discrimination methods were assessed. The comparison of the

Optimal Conformal Polynomial Projections for Croatia According to the Airy/Jordan Criterion

Directory of Open Access Journals (Sweden)

Dražen Tutić

2009-05-01

Full Text Available The paper describes optimal conformal polynomial projections for Croatia according to the Airy/Jordan criterion. A brief introduction of history and theory of conformal mapping is followed by descriptions of conformal polynomial projections and their current application. The paper considers polynomials of degrees 1 to 10. Since there are conditions in which the 1st degree polynomial becomes the famous Mercator projection, it was not considered specifically for Croatian territory. The area of Croatia was defined as a union of national territory and the continental shelf. Area definition data were taken from the Euro Global Map 1:1 000 000 for Croatia, as well as from two maritime delimitation treaties. Such an irregular area was approximated with a regular grid consisting of 11 934 ellipsoidal trapezoids 2' large. The Airy/Jordan criterion for the optimal projection is defined as minimum of weighted mean of Airy/Jordan measure of distortion in points. The value of the Airy/Jordan criterion is calculated from all 11 934 centres of ellipsoidal trapezoids, while the weights are equal to areas of corresponding ellipsoidal trapezoids. The minimum is obtained by Nelder and Mead’s method, as implemented in the fminsearch function of the MATLAB package. Maps of Croatia representing the distribution of distortions are given for polynomial degrees 2 to 6 and 10. Increasing the polynomial degree results in better projections considering the criterion, and the 6th degree polynomial provides a good ratio of formula complexity and criterion value.

Bootstrapping conformal field theories with the extremal functional method.

Science.gov (United States)

El-Showk, Sheer; Paulos, Miguel F

2013-12-13

The existence of a positive linear functional acting on the space of (differences between) conformal blocks has been shown to rule out regions in the parameter space of conformal field theories (CFTs). We argue that at the boundary of the allowed region the extremal functional contains, in principle, enough information to determine the dimensions and operator product expansion (OPE) coefficients of an infinite number of operators appearing in the correlator under analysis. Based on this idea we develop the extremal functional method (EFM), a numerical procedure for deriving the spectrum and OPE coefficients of CFTs lying on the boundary (of solution space). We test the EFM by using it to rederive the low lying spectrum and OPE coefficients of the two-dimensional Ising model based solely on the dimension of a single scalar quasiprimary--no Virasoro algebra required. Our work serves as a benchmark for applications to more interesting, less known CFTs in the near future.

The "Set Map" Method of Navigation.

Science.gov (United States)

Tippett, Julian

1998-01-01

Explains the "set map" method of using the baseplate compass to solve walkers' navigational needs as opposed to the 1-2-3 method for taking a bearing. The map, with the compass permanently clipped to it, is rotated to the position in which its features have the same orientation as their counterparts on the ground. Includes directions and…

Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation.

Science.gov (United States)

Belaghzal, Houda; Dekker, Job; Gibcus, Johan H

2017-07-01

Chromosome conformation capture-based methods such as Hi-C have become mainstream techniques for the study of the 3D organization of genomes. These methods convert chromatin interactions reflecting topological chromatin structures into digital information (counts of pair-wise interactions). Here, we describe an updated protocol for Hi-C (Hi-C 2.0) that integrates recent improvements into a single protocol for efficient and high-resolution capture of chromatin interactions. This protocol combines chromatin digestion and frequently cutting enzymes to obtain kilobase (kb) resolution. It also includes steps to reduce random ligation and the generation of uninformative molecules, such as unligated ends, to improve the amount of valid intra-chromosomal read pairs. This protocol allows for obtaining information on conformational structures such as compartment and topologically associating domains, as well as high-resolution conformational features such as DNA loops. Copyright © 2017 Elsevier Inc. All rights reserved.

An automated and efficient conformation search of L-cysteine and L,L-cystine using the scaled hypersphere search method

Science.gov (United States)

Kishimoto, Naoki; Waizumi, Hiroki

2017-10-01

Stable conformers of L-cysteine and L,L-cystine were explored using an automated and efficient conformational searching method. The Gibbs energies of the stable conformers of L-cysteine and L,L-cystine were calculated with G4 and MP2 methods, respectively, at 450, 298.15, and 150 K. By assuming thermodynamic equilibrium and the barrier energies for the conformational isomerization pathways, the estimated ratios of the stable conformers of L-cysteine were compared with those determined by microwave spectroscopy in a previous study. Equilibrium structures of 1:1 and 2:1 cystine-Fe complexes were also calculated, and the energy of insertion of Fe into the disulfide bond was obtained.

Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics.

Directory of Open Access Journals (Sweden)

Barry J Grant

2009-03-01

Full Text Available Ras mediates signaling pathways controlling cell proliferation and development by cycling between GTP- and GDP-bound active and inactive conformational states. Understanding the complete reaction path of this conformational change and its intermediary structures is critical to understanding Ras signaling. We characterize nucleotide-dependent conformational transition using multiple-barrier-crossing accelerated molecular dynamics (aMD simulations. These transitions, achieved for the first time for wild-type Ras, are impossible to observe with classical molecular dynamics (cMD simulations due to the large energetic barrier between end states. Mapping the reaction path onto a conformer plot describing the distribution of the crystallographic structures enabled identification of highly populated intermediate structures. These structures have unique switch orientations (residues 25-40 and 57-75 intermediate between GTP and GDP states, or distinct loop3 (46-49, loop7 (105-110, and alpha5 C-terminus (159-166 conformations distal from the nucleotide-binding site. In addition, these barrier-crossing trajectories predict novel nucleotide-dependent correlated motions, including correlations of alpha2 (residues 66-74 with alpha3-loop7 (93-110, loop2 (26-37 with loop10 (145-151, and loop3 (46-49 with alpha5 (152-167. The interconversion between newly identified Ras conformations revealed by this study advances our mechanistic understanding of Ras function. In addition, the pattern of correlated motions provides new evidence for a dynamic linkage between the nucleotide-binding site and the membrane interacting C-terminus critical for the signaling function of Ras. Furthermore, normal mode analysis indicates that the dominant collective motion that occurs during nucleotide-dependent conformational exchange, and captured in aMD (but absent in cMD simulations, is a low-frequency motion intrinsic to the structure.

Arbitrary spin conformal fields in (A)dS

International Nuclear Information System (INIS)

Metsaev, R.R.

2014-01-01

Totally symmetric arbitrary spin conformal fields in (A)dS space of even dimension greater than or equal to four are studied. Ordinary-derivative and gauge invariant Lagrangian formulation for such fields is obtained. Gauge symmetries are realized by using auxiliary fields and Stueckelberg fields. We demonstrate that Lagrangian of conformal field is decomposed into a sum of gauge invariant Lagrangians for massless, partial-massless, and massive fields. We obtain a mass spectrum of the partial-massless and massive fields and confirm the conjecture about the mass spectrum made in the earlier literature. In contrast to conformal fields in flat space, the kinetic terms of conformal fields in (A)dS space turn out to be diagonal with respect to fields entering the Lagrangian. Explicit form of conformal transformation which maps conformal field in flat space to conformal field in (A)dS space is obtained. Covariant Lorentz-like and de-Donder like gauge conditions leading to simple gauge-fixed Lagrangian of conformal fields are proposed. Using such gauge-fixed Lagrangian, which is invariant under global BRST transformations, we explain how the partition function of conformal field is obtained in the framework of our approach

A method to correct coordinate distortion in EBSD maps

International Nuclear Information System (INIS)

Zhang, Y.B.; Elbrønd, A.; Lin, F.X.

2014-01-01

Drift during electron backscatter diffraction mapping leads to coordinate distortions in resulting orientation maps, which affects, in some cases significantly, the accuracy of analysis. A method, thin plate spline, is introduced and tested to correct such coordinate distortions in the maps after the electron backscatter diffraction measurements. The accuracy of the correction as well as theoretical and practical aspects of using the thin plate spline method is discussed in detail. By comparing with other correction methods, it is shown that the thin plate spline method is most efficient to correct different local distortions in the electron backscatter diffraction maps. - Highlights: • A new method is suggested to correct nonlinear spatial distortion in EBSD maps. • The method corrects EBSD maps more precisely than presently available methods. • Errors less than 1–2 pixels are typically obtained. • Direct quantitative analysis of dynamic data are available after this correction

CrowdMapping: A Crowdsourcing-Based Terminology Mapping Method for Medical Data Standardization.

Science.gov (United States)

Mao, Huajian; Chi, Chenyang; Huang, Boyu; Meng, Haibin; Yu, Jinghui; Zhao, Dongsheng

2017-01-01

Standardized terminology is the prerequisite of data exchange in analysis of clinical processes. However, data from different electronic health record systems are based on idiosyncratic terminology systems, especially when the data is from different hospitals and healthcare organizations. Terminology standardization is necessary for the medical data analysis. We propose a crowdsourcing-based terminology mapping method, CrowdMapping, to standardize the terminology in medical data. CrowdMapping uses a confidential model to determine how terminologies are mapped to a standard system, like ICD-10. The model uses mappings from different health care organizations and evaluates the diversity of the mapping to determine a more sophisticated mapping rule. Further, the CrowdMapping model enables users to rate the mapping result and interact with the model evaluation. CrowdMapping is a work-in-progress system, we present initial results mapping terminologies.

Complex analysis conformal inequalities and the Bieberbach conjecture

CERN Document Server

Kythe, Prem K

2015-01-01

Complex Analysis: Conformal Inequalities and the Bieberbach Conjecture discusses the mathematical analysis created around the Bieberbach conjecture, which is responsible for the development of many beautiful aspects of complex analysis, especially in the geometric-function theory of univalent functions. Assuming basic knowledge of complex analysis and differential equations, the book is suitable for graduate students engaged in analytical research on the topics and researchers working on related areas of complex analysis in one or more complex variables. The author first reviews the theory of analytic functions, univalent functions, and conformal mapping before covering various theorems related to the area principle and discussing Löwner theory. He then presents Schiffer’s variation method, the bounds for the fourth and higher-order coefficients, various subclasses of univalent functions, generalized convexity and the class of a-convex functions, and numerical estimates of the coefficient problem. The boo...

Conformational study of glyoxal bis(amidinohydrazone) by ab initio methods

Science.gov (United States)

Mannfors, B.; Koskinen, J. T.; Pietilä, L.-O.

1997-08-01

We report the first ab initio molecular orbital study on the ground state of the endiamine tautomer of glyoxal bis(amidinohydrazone) (or glyoxal bis(guanylhydrazone), GBG) free base. The calculations were performed at the following levels of theory: Hartree-Fock, second-order Møller-Plesset perturbation theory and density functional theory (B-LYP and B3-LYP) as implemented in the Gaussian 94 software. The standard basis set 6-31G(d) was found to be sufficient. The default fine grid of Gaussian 94 was used in the density functional calculations. Molecular properties, such as optimized structures, total energies and the electrostatic potential derived (CHELPG) atomic charges, were studied as functions of C-C and N-N conformations. The lowest energy conformation was found to be all- trans, in agreement with the experimental solid-state structure. The second conformer with respect to rotation around the central C-C bond was found to be the cis conformer with an MP2//HF energy of 4.67 kcal mol -1. For rotation around the N-N bond the energy increased monotonically from the trans conformation to the cis conformation, the cis energy being very high, 22.01 kcal mol -1 (MP2//HF). The atomic charges were shown to be conformation dependent, and the bond charge increments and especially the conformational changes of the bond charge increments were found to be easily transferable between structurally related systems.

A map of the universe

Energy Technology Data Exchange (ETDEWEB)

Gott III, J. Richard; Juric, Mario; Schlegel, David; Hoyle, Fiona; Vogeley, Michael; Tegmark, Max; Bahcall, Neta; Brinkmann, Jon

2003-10-20

We have produced a new conformal map of the universe illustrating recent discoveries, ranging from Kuiper belt objects in the Solar system, to the galaxies and quasars from the Sloan Digital Sky Survey. This map projection, based on the logarithm map of the complex plane, preserves shapes locally, and yet is able to display the entire range of astronomical scales from the Earth s neighborhood to the cosmic microwave background. The conformal nature of the projection, preserving shapes locally, may be of particular use for analyzing large scale structure. Prominent in the map is a Sloan Great Wall of galaxies 1.37 billion light years long, 80 percent longer than the Great Wall discovered by Geller and Huchra and therefore the largest observed structure in the universe.

Method of making large area conformable shape structures for detector/sensor applications using glass drawing technique and postprocessing

Science.gov (United States)

Ivanov, Ilia N [Knoxville, TN; Simpson, John T [Clinton, IN

2012-01-24

A method of making a large area conformable shape structure comprises drawing a plurality of tubes to form a plurality of drawn tubes, and cutting the plurality of drawn tubes into cut drawn tubes of a predetermined shape. The cut drawn tubes have a first end and a second end along the longitudinal direction of the cut drawn tubes. The method further comprises conforming the first end of the cut drawn tubes into a predetermined curve to form the large area conformable shape structure, wherein the cut drawn tubes contain a material.

Possibilities and methods for mapping air pollution

Energy Technology Data Exchange (ETDEWEB)

LeBlanc, F

1971-01-01

For various reasons lichens seem to be much more sensitive to air pollution than flowering plants. Various methods to map the long-range effect of phytotoxicants on epiphytic lichens and mosses have been proposed. This paper outlines a few of these and proposes a new method. In Sudbury, Ontario, vegetation has been greatly affected by sulfur dioxide emanating from three huge smelters. The author shows that his map based on the response of lichens matches quite well with another map from the same area based on continuous SO/sub 2/ monitoring. The advantage of the biological map is that it took two weeks to accumulate the data required while the other one took ten years.

Dimension of non-conformal repellers: a survey

International Nuclear Information System (INIS)

Chen, Jianyu; Pesin, Yakov

2010-01-01

This paper is a survey of recent results on the dimension of repellers for expanding maps and limit sets for iterated function systems. While the case of conformal repellers is well understood, the study of non-conformal repellers is in its early stages though a number of interesting phenomena have been discovered, some remarkable results obtained and several interesting examples constructed. We will describe contemporary state of the art in the area with emphasis on some new emerging ideas and open problems. (invited article)

Mapcurves: a quantitative method for comparing categorical maps.

Science.gov (United States)

William W. Hargrove; M. Hoffman Forrest; Paul F. Hessburg

2006-01-01

We present Mapcurves, a quantitative goodness-of-fit (GOF) method that unambiguously shows the degree of spatial concordance between two or more categorical maps. Mapcurves graphically and quantitatively evaluate the degree of fit among any number of maps and quantify a GOF for each polygon, as well as the entire map. The Mapcurve method indicates a perfect fit even if...

Conformal invariance in supergravity

International Nuclear Information System (INIS)

Bergshoeff, E.A.

1983-01-01

In this thesis the author explains the role of conformal invariance in supergravity. He presents the complete structure of extended conformal supergravity for N <= 4. The outline of this work is as follows. In chapter 2 he briefly summarizes the essential properties of supersymmetry and supergravity and indicates the use of conformal invariance in supergravity. The idea that the introduction of additional symmetry transformations can make clear the structure of a field theory is not reserved to supergravity only. By means of some simple examples it is shown in chapter 3 how one can always introduce additional gauge transformations in a theory of massive vector fields. Moreover it is shown how the gauge invariant formulation sometimes explains the quantum mechanical properties of the theory. In chapter 4 the author defines the conformal transformations and summarizes their main properties. He explains how these conformal transformations can be used to analyse the structure of gravity. The supersymmetric extension of these results is discussed in chapter 5. Here he describes as an example how N=1 supergravity can be reformulated in a conformally-invariant way. He also shows that beyond N=1 the gauge fields of the superconformal symmetries do not constitute an off-shell field representation of extended conformal supergravity. Therefore, in chapter 6, a systematic method to construct the off-shell formulation of all extended conformal supergravity theories with N <= 4 is developed. As an example he uses this method to construct N=1 conformal supergravity. Finally, in chapter 7 N=4 conformal supergravity is discussed. (Auth.)

Defects in conformal field theory

International Nuclear Information System (INIS)

Billò, Marco; Gonçalves, Vasco; Lauria, Edoardo; Meineri, Marco

2016-01-01

We discuss consequences of the breaking of conformal symmetry by a flat or spherical extended operator. We adapt the embedding formalism to the study of correlation functions of symmetric traceless tensors in the presence of the defect. Two-point functions of a bulk and a defect primary are fixed by conformal invariance up to a set of OPE coefficients, and we identify the allowed tensor structures. A correlator of two bulk primaries depends on two cross-ratios, and we study its conformal block decomposition in the case of external scalars. The Casimir equation in the defect channel reduces to a hypergeometric equation, while the bulk channel blocks are recursively determined in the light-cone limit. In the special case of a defect of codimension two, we map the Casimir equation in the bulk channel to the one of a four-point function without defect. Finally, we analyze the contact terms of the stress-tensor with the extended operator, and we deduce constraints on the CFT data. In two dimensions, we relate the displacement operator, which appears among the contact terms, to the reflection coefficient of a conformal interface, and we find unitarity bounds for the latter.

Defects in conformal field theory

Energy Technology Data Exchange (ETDEWEB)

Billò, Marco [Dipartimento di Fisica, Università di Torino, and Istituto Nazionale di Fisica Nucleare - sezione di Torino,Via P. Giuria 1 I-10125 Torino (Italy); Gonçalves, Vasco [Centro de Física do Porto,Departamento de Física e Astronomia Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto (Portugal); ICTP South American Institute for Fundamental Research Instituto de Física Teórica,UNESP - University Estadual Paulista,Rua Dr. Bento T. Ferraz 271, 01140-070, São Paulo, SP (Brazil); Lauria, Edoardo [Institute for Theoretical Physics, KU Leuven, Celestijnenlaan 200D, B-3001 Leuven (Belgium); Meineri, Marco [Perimeter Institute for Theoretical Physics,Waterloo, Ontario, N2L 2Y5 (Canada); Scuola Normale Superiore, and Istituto Nazionale di Fisica Nucleare - sezione di Pisa,Piazza dei Cavalieri 7 I-56126 Pisa (Italy)

2016-04-15

We discuss consequences of the breaking of conformal symmetry by a flat or spherical extended operator. We adapt the embedding formalism to the study of correlation functions of symmetric traceless tensors in the presence of the defect. Two-point functions of a bulk and a defect primary are fixed by conformal invariance up to a set of OPE coefficients, and we identify the allowed tensor structures. A correlator of two bulk primaries depends on two cross-ratios, and we study its conformal block decomposition in the case of external scalars. The Casimir equation in the defect channel reduces to a hypergeometric equation, while the bulk channel blocks are recursively determined in the light-cone limit. In the special case of a defect of codimension two, we map the Casimir equation in the bulk channel to the one of a four-point function without defect. Finally, we analyze the contact terms of the stress-tensor with the extended operator, and we deduce constraints on the CFT data. In two dimensions, we relate the displacement operator, which appears among the contact terms, to the reflection coefficient of a conformal interface, and we find unitarity bounds for the latter.

Conformal dimension theory and application

CERN Document Server

Mackay, John M

2010-01-01

Conformal dimension measures the extent to which the Hausdorff dimension of a metric space can be lowered by quasisymmetric deformations. Introduced by Pansu in 1989, this concept has proved extremely fruitful in a diverse range of areas, including geometric function theory, conformal dynamics, and geometric group theory. This survey leads the reader from the definitions and basic theory through to active research applications in geometric function theory, Gromov hyperbolic geometry, and the dynamics of rational maps, amongst other areas. It reviews the theory of dimension in metric spaces and of deformations of metric spaces. It summarizes the basic tools for estimating conformal dimension and illustrates their application to concrete problems of independent interest. Numerous examples and proofs are provided. Working from basic definitions through to current research areas, this book can be used as a guide for graduate students interested in this field, or as a helpful survey for experts. Background needed ...

An Entropy Stable h/p Non-Conforming Discontinuous Galerkin Method with the Summation-by-Parts Property

KAUST Repository

Friedrich, Lucas

2017-12-29

This work presents an entropy stable discontinuous Galerkin (DG) spectral element approximation for systems of non-linear conservation laws with general geometric (h) and polynomial order (p) non-conforming rectangular meshes. The crux of the proofs presented is that the nodal DG method is constructed with the collocated Legendre-Gauss-Lobatto nodes. This choice ensures that the derivative/mass matrix pair is a summation-by-parts (SBP) operator such that entropy stability proofs from the continuous analysis are discretely mimicked. Special attention is given to the coupling between nonconforming elements as we demonstrate that the standard mortar approach for DG methods does not guarantee entropy stability for non-linear problems, which can lead to instabilities. As such, we describe a precise procedure and modify the mortar method to guarantee entropy stability for general non-linear hyperbolic systems on h/p non-conforming meshes. We verify the high-order accuracy and the entropy conservation/stability of fully non-conforming approximation with numerical examples.

Accelerated convergence of perturbative QCD by conformal mappings in the Borel plane

International Nuclear Information System (INIS)

Caprini, I.; Fischer, J.

1998-01-01

The behaviour of the large order terms in perturbative QCD received much attention in recent years. The presence of instantons and certain classes of Feynman diagrams lead to increasing coefficients of the perturbative expansion of the QCD Green functions, making this series divergent and even Borel non-summable. In the present paper we adopt a definite prescription for the Borel summation and investigate the improvement of the low order expansion by using some information about the behaviour of the large order coefficients. We use the technique of conformal mappings to extend the convergence region of the Borel series, and exploit the behaviour of the Borel transform near the first renormalons. Our approach improves previous work where only the ultraviolet renormalons were considered. The polarization function, relevant for the hadronic τ decay, which allows the determinations of the strong coupling constant a s (m τ 2 ) is used. We consider the Adler function D(s), i.e. the logarithmic derivative of the vacuum polarization for massless quarks, and its QCD perturbative expansion (D(a s )) in terms of the running coupling a s (-s). The first 3 coefficients D n of Adler function D(s) are known from explicit calculations, while for large n they are expected to have a factorial growth. By applying the Borel method with the Principal Value (PV) prescription to avoid the infrared renormalons, we write D(a s ) in terms of its Borel transform B(u). The Borel integral is given as a function of a s for a model function resembling the Borel transform of the Adler function in the large β 0 limit. The data obtained by truncating the expansion at N=3 which corresponds to the physical situation are presented. Even at such low values of N our method gives very good results (the improvement increases with N, since the optimality is an asymptotic feature). Using this technique we calculated also the running coupling constant a s (m τ 2 ), for which we obtained the value 0

Conformal Infinity

Directory of Open Access Journals (Sweden)

Frauendiener Jörg

2000-08-01

Full Text Available The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, ``conformal infinity'' is related with almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved out of physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation and how it lends itself very naturally to solve radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

Conformal Infinity.

Science.gov (United States)

Frauendiener, Jörg

2004-01-01

The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, "conformal infinity" is related to almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved from physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation, and how it lends itself very naturally to the solution of radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

A time-delayed method for controlling chaotic maps

International Nuclear Information System (INIS)

Chen Maoyin; Zhou Donghua; Shang Yun

2005-01-01

Combining the repetitive learning strategy and the optimality principle, this Letter proposes a time-delayed method to control chaotic maps. This method can effectively stabilize unstable periodic orbits within chaotic attractors in the sense of least mean square. Numerical simulations of some chaotic maps verify the effectiveness of this method

Modelling of bow-tie microstrip antennas using modified locally conformal FDTD method

NARCIS (Netherlands)

George, J.

2000-01-01

An analysis of bow-tie microstrip antennas is presented based on the use of the modified locally conformal finite-difference time-domain (FDTD) method. This approach enables the number of cells along the antenna length and width to be chosen independently of the antenna central width, which helps to

Energy Landscape of Pentapeptides in a Higher-Order (ϕ,ψ Conformational Subspace

Directory of Open Access Journals (Sweden)

Karim M. ElSawy

2016-01-01

Full Text Available The potential energy landscape of pentapeptides was mapped in a collective coordinate principal conformational subspace derived from principal component analysis of a nonredundant representative set of protein structures from the PDB. Three pentapeptide sequences that are known to be distinct in terms of their secondary structure characteristics, (Ala5, (Gly5, and Val.Asn.Thr.Phe.Val, were considered. Partitioning the landscapes into different energy valleys allowed for calculation of the relative propensities of the peptide secondary structures in a statistical mechanical framework. The distribution of the observed conformations of pentapeptide data showed good correspondence to the topology of the energy landscape of the (Ala5 sequence where, in accord with reported trends, the α-helix showed a predominant propensity at 298 K. The topography of the landscapes indicates that the stabilization of the α-helix in the (Ala5 sequence is enthalpic in nature while entropic factors are important for stabilization of the β-sheet in the Val.Asn.Thr.Phe.Val sequence. The results indicate that local interactions within small pentapeptide segments can lead to conformational preference of one secondary structure over the other where account of conformational entropy is important in order to reveal such preference. The method, therefore, can provide critical structural information for ab initio protein folding methods.

Method and system for a network mapping service

Science.gov (United States)

Bynum, Leo

2017-10-17

A method and system of publishing a map includes providing access to a plurality of map data files or mapping services between at least one publisher and at least one subscriber; defining a map in a map context comprising parameters and descriptors to substantially duplicate a map by reference to mutually accessible data or mapping services, publishing a map to a channel in a table file on server; accessing the channel by at least one subscriber, transmitting the mapping context from the server to the at least one subscriber, executing the map context by the at least one subscriber, and generating the map on a display software associated with the at least one subscriber by reconstituting the map from the references and other data in the mapping context.

Conformal Infinity

Directory of Open Access Journals (Sweden)

Frauendiener Jörg

2004-01-01

Full Text Available The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, 'conformal infinity' is related to almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved from physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation, and how it lends itself very naturally to the solution of radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

A conformal mapping based fractional order approach for sub-optimal tuning of PID controllers with guaranteed dominant pole placement

Science.gov (United States)

Saha, Suman; Das, Saptarshi; Das, Shantanu; Gupta, Amitava

2012-09-01

A novel conformal mapping based fractional order (FO) methodology is developed in this paper for tuning existing classical (Integer Order) Proportional Integral Derivative (PID) controllers especially for sluggish and oscillatory second order systems. The conventional pole placement tuning via Linear Quadratic Regulator (LQR) method is extended for open loop oscillatory systems as well. The locations of the open loop zeros of a fractional order PID (FOPID or PIλDμ) controller have been approximated in this paper vis-à-vis a LQR tuned conventional integer order PID controller, to achieve equivalent integer order PID control system. This approach eases the implementation of analog/digital realization of a FOPID controller with its integer order counterpart along with the advantages of fractional order controller preserved. It is shown here in the paper that decrease in the integro-differential operators of the FOPID/PIλDμ controller pushes the open loop zeros of the equivalent PID controller towards greater damping regions which gives a trajectory of the controller zeros and dominant closed loop poles. This trajectory is termed as "M-curve". This phenomena is used to design a two-stage tuning algorithm which reduces the existing PID controller's effort in a significant manner compared to that with a single stage LQR based pole placement method at a desired closed loop damping and frequency.

Moment methods for nonlinear maps

International Nuclear Information System (INIS)

Pusch, G.D.; Atomic Energy of Canada Ltd., Chalk River, ON

1993-01-01

It is shown that Differential Algebra (DA) may be used to push moments of distributions through a map, at a computational cost per moment comparable to pushing a single particle. The algorithm is independent of order, and whether or not the map is symplectic. Starting from the known result that moment-vectors transform linearly - like a tensor - even under a nonlinear map, I suggest that the form of the moment transformation rule indicates that the moment-vectors are elements of the dual to DA-vector space. I propose several methods of manipulating moments and constructing invariants using DA. I close with speculations on how DA might be used to ''close the circle'' to solve the inverse moment problem, yielding an entirely DA-and-moment-based space-charge code. (Author)

Radiation Source Mapping with Bayesian Inverse Methods

Science.gov (United States)

Hykes, Joshua Michael

We present a method to map the spectral and spatial distributions of radioactive sources using a small number of detectors. Locating and identifying radioactive materials is important for border monitoring, accounting for special nuclear material in processing facilities, and in clean-up operations. Most methods to analyze these problems make restrictive assumptions about the distribution of the source. In contrast, the source-mapping method presented here allows an arbitrary three-dimensional distribution in space and a flexible group and gamma peak distribution in energy. To apply the method, the system's geometry and materials must be known. A probabilistic Bayesian approach is used to solve the resulting inverse problem (IP) since the system of equations is ill-posed. The probabilistic approach also provides estimates of the confidence in the final source map prediction. A set of adjoint flux, discrete ordinates solutions, obtained in this work by the Denovo code, are required to efficiently compute detector responses from a candidate source distribution. These adjoint fluxes are then used to form the linear model to map the state space to the response space. The test for the method is simultaneously locating a set of 137Cs and 60Co gamma sources in an empty room. This test problem is solved using synthetic measurements generated by a Monte Carlo (MCNP) model and using experimental measurements that we collected for this purpose. With the synthetic data, the predicted source distributions identified the locations of the sources to within tens of centimeters, in a room with an approximately four-by-four meter floor plan. Most of the predicted source intensities were within a factor of ten of their true value. The chi-square value of the predicted source was within a factor of five from the expected value based on the number of measurements employed. With a favorable uniform initial guess, the predicted source map was nearly identical to the true distribution

Revealing time bunching effect in single-molecule enzyme conformational dynamics.

Science.gov (United States)

Lu, H Peter

2011-04-21

In this perspective, we focus our discussion on how the single-molecule spectroscopy and statistical analysis are able to reveal enzyme hidden properties, taking the study of T4 lysozyme as an example. Protein conformational fluctuations and dynamics play a crucial role in biomolecular functions, such as in enzymatic reactions. Single-molecule spectroscopy is a powerful approach to analyze protein conformational dynamics under physiological conditions, providing dynamic perspectives on a molecular-level understanding of protein structure-function mechanisms. Using single-molecule fluorescence spectroscopy, we have probed T4 lysozyme conformational motions under the hydrolysis reaction of a polysaccharide of E. coli B cell walls by monitoring the fluorescence resonant energy transfer (FRET) between a donor-acceptor probe pair tethered to T4 lysozyme domains involving open-close hinge-bending motions. Based on the single-molecule spectroscopic results, molecular dynamics simulation, a random walk model analysis, and a novel 2D statistical correlation analysis, we have revealed a time bunching effect in protein conformational motion dynamics that is critical to enzymatic functions. Bunching effect implies that conformational motion times tend to bunch in a finite and narrow time window. We show that convoluted multiple Poisson rate processes give rise to the bunching effect in the enzymatic reaction dynamics. Evidently, the bunching effect is likely common in protein conformational dynamics involving in conformation-gated protein functions. In this perspective, we will also discuss a new approach of 2D regional correlation analysis capable of analyzing fluctuation dynamics of complex multiple correlated and anti-correlated fluctuations under a non-correlated noise background. Using this new method, we are able to map out any defined segments along the fluctuation trajectories and determine whether they are correlated, anti-correlated, or non-correlated; after which, a

Linear Algebraic Method for Non-Linear Map Analysis

International Nuclear Information System (INIS)

Yu, L.; Nash, B.

2009-01-01

We present a newly developed method to analyze some non-linear dynamics problems such as the Henon map using a matrix analysis method from linear algebra. Choosing the Henon map as an example, we analyze the spectral structure, the tune-amplitude dependence, the variation of tune and amplitude during the particle motion, etc., using the method of Jordan decomposition which is widely used in conventional linear algebra.

A method to correct coordinate distortion in EBSD maps

DEFF Research Database (Denmark)

Zhang, Yubin; Elbrønd, Andreas Benjamin; Lin, Fengxiang

2014-01-01

Drift during electron backscatter diffraction mapping leads to coordinate distortions in resulting orientation maps, which affects, in some cases significantly, the accuracy of analysis. A method, thin plate spline, is introduced and tested to correct such coordinate distortions in the maps after...... the electron backscatter diffraction measurements. The accuracy of the correction as well as theoretical and practical aspects of using the thin plate spline method is discussed in detail. By comparing with other correction methods, it is shown that the thin plate spline method is most efficient to correct...

Conformation Generation: The State of the Art.

Science.gov (United States)

Hawkins, Paul C D

2017-08-28

The generation of conformations for small molecules is a problem of continuing interest in cheminformatics and computational drug discovery. This review will present an overview of methods used to sample conformational space, focusing on those methods designed for organic molecules commonly of interest in drug discovery. Different approaches to both the sampling of conformational space and the scoring of conformational stability will be compared and contrasted, with an emphasis on those methods suitable for conformer sampling of large numbers of drug-like molecules. Particular attention will be devoted to the appropriate utilization of information from experimental solid-state structures in validating and evaluating the performance of these tools. The review will conclude with some areas worthy of further investigation.

From spinning conformal blocks to matrix Calogero-Sutherland models

Science.gov (United States)

Schomerus, Volker; Sobko, Evgeny

2018-04-01

In this paper we develop further the relation between conformal four-point blocks involving external spinning fields and Calogero-Sutherland quantum mechanics with matrix-valued potentials. To this end, the analysis of [1] is extended to arbitrary dimensions and to the case of boundary two-point functions. In particular, we construct the potential for any set of external tensor fields. Some of the resulting Schrödinger equations are mapped explicitly to the known Casimir equations for 4-dimensional seed conformal blocks. Our approach furnishes solutions of Casimir equations for external fields of arbitrary spin and dimension in terms of functions on the conformal group. This allows us to reinterpret standard operations on conformal blocks in terms of group-theoretic objects. In particular, we shall discuss the relation between the construction of spinning blocks in any dimension through differential operators acting on seed blocks and the action of left/right invariant vector fields on the conformal group.

Airfoils and method for designing airfoils

DEFF Research Database (Denmark)

2010-01-01

The present invention relates to airfoils and design and design optimization of airfoils, in particular airfoils of rotor blades for wind turbines. One aspect of the invention relates to an airfoil with an external shape provided by an airfoil profile defined by a limited number of parameters......, such as a set of parameters. Another aspect of the invention relates to a method for designing an airfoil by means of an analytical airfoil profile, said method comprising the step of applying a conformal mapping to a near circle in a near circle plane, wherein the near circle is at least partly expressed...... by means of an analytical function, said conformal mapping transforming the near circle in the near circle plane to the airfoil profile in an airfoil plane. L...

Coadjoint orbits and conformal field theory

International Nuclear Information System (INIS)

Taylor, W. IV.

1993-08-01

This thesis is primarily a study of certain aspects of the geometric and algebraic structure of coadjoint orbit representations of infinite-dimensional Lie groups. The goal of this work is to use coadjoint orbit representations to construct conformal field theories, in a fashion analogous to the free-field constructions of conformal field theories. The new results which are presented in this thesis are as follows: First, an explicit set of formulae are derived giving an algebraic realization of coadjoint orbit representations in terms of differential operators acting on a polynomial Fock space. These representations are equivalent to dual Verma module representations. Next, intertwiners are explicitly constructed which allow the construction of resolutions for irreducible representations using these Fock space realizations. Finally, vertex operators between these irreducible representations are explicitly constructed as chain maps between the resolutions; these vertex operators allow the construction of rational conformal field theories according to an algebraic prescription

Predictive Sampling of Rare Conformational Events in Aqueous Solution: Designing a Generalized Orthogonal Space Tempering Method.

Science.gov (United States)

Lu, Chao; Li, Xubin; Wu, Dongsheng; Zheng, Lianqing; Yang, Wei

2016-01-12

In aqueous solution, solute conformational transitions are governed by intimate interplays of the fluctuations of solute-solute, solute-water, and water-water interactions. To promote molecular fluctuations to enhance sampling of essential conformational changes, a common strategy is to construct an expanded Hamiltonian through a series of Hamiltonian perturbations and thereby broaden the distribution of certain interactions of focus. Due to a lack of active sampling of configuration response to Hamiltonian transitions, it is challenging for common expanded Hamiltonian methods to robustly explore solvent mediated rare conformational events. The orthogonal space sampling (OSS) scheme, as exemplified by the orthogonal space random walk and orthogonal space tempering methods, provides a general framework for synchronous acceleration of slow configuration responses. To more effectively sample conformational transitions in aqueous solution, in this work, we devised a generalized orthogonal space tempering (gOST) algorithm. Specifically, in the Hamiltonian perturbation part, a solvent-accessible-surface-area-dependent term is introduced to implicitly perturb near-solute water-water fluctuations; more importantly in the orthogonal space response part, the generalized force order parameter is generalized as a two-dimension order parameter set, in which essential solute-solvent and solute-solute components are separately treated. The gOST algorithm is evaluated through a molecular dynamics simulation study on the explicitly solvated deca-alanine (Ala10) peptide. On the basis of a fully automated sampling protocol, the gOST simulation enabled repetitive folding and unfolding of the solvated peptide within a single continuous trajectory and allowed for detailed constructions of Ala10 folding/unfolding free energy surfaces. The gOST result reveals that solvent cooperative fluctuations play a pivotal role in Ala10 folding/unfolding transitions. In addition, our assessment

[Analysis of Conformational Features of Watson-Crick Duplex Fragments by Molecular Mechanics and Quantum Mechanics Methods].

Science.gov (United States)

Poltev, V I; Anisimov, V M; Sanchez, C; Deriabina, A; Gonzalez, E; Garcia, D; Rivas, F; Polteva, N A

2016-01-01

It is generally accepted that the important characteristic features of the Watson-Crick duplex originate from the molecular structure of its subunits. However, it still remains to elucidate what properties of each subunit are responsible for the significant characteristic features of the DNA structure. The computations of desoxydinucleoside monophosphates complexes with Na-ions using density functional theory revealed a pivotal role of DNA conformational properties of single-chain minimal fragments in the development of unique features of the Watson-Crick duplex. We found that directionality of the sugar-phosphate backbone and the preferable ranges of its torsion angles, combined with the difference between purines and pyrimidines. in ring bases, define the dependence of three-dimensional structure of the Watson-Crick duplex on nucleotide base sequence. In this work, we extended these density functional theory computations to the minimal' fragments of DNA duplex, complementary desoxydinucleoside monophosphates complexes with Na-ions. Using several computational methods and various functionals, we performed a search for energy minima of BI-conformation for complementary desoxydinucleoside monophosphates complexes with different nucleoside sequences. Two sequences are optimized using ab initio method at the MP2/6-31++G** level of theory. The analysis of torsion angles, sugar ring puckering and mutual base positions of optimized structures demonstrates that the conformational characteristic features of complementary desoxydinucleoside monophosphates complexes with Na-ions remain within BI ranges and become closer to the corresponding characteristic features of the Watson-Crick duplex crystals. Qualitatively, the main characteristic features of each studied complementary desoxydinucleoside monophosphates complex remain invariant when different computational methods are used, although the quantitative values of some conformational parameters could vary lying within the

Conformational analysis by intersection: CONAN.

Science.gov (United States)

Smellie, Andrew; Stanton, Robert; Henne, Randy; Teig, Steve

2003-01-15

As high throughput techniques in chemical synthesis and screening improve, more demands are placed on computer assisted design and virtual screening. Many of these computational methods require one or more three-dimensional conformations for molecules, creating a demand for a conformational analysis tool that can rapidly and robustly cover the low-energy conformational spaces of small molecules. A new algorithm of intersection is presented here, which quickly generates (on average heuristics are applied after intersection to generate a small representative collection of conformations that span the conformational space. In a study of approximately 97,000 randomly selected molecules from the MDDR, results are presented that explore these conformations and their ability to cover low-energy conformational space. Copyright 2002 Wiley Periodicals, Inc. J Comput Chem 24: 10-20, 2003

Full three-dimensional isotropic carpet cloak designed by quasi-conformal transformation optics.

Science.gov (United States)

Silva, Daniely G; Teixeira, Poliane A; Gabrielli, Lucas H; Junqueira, Mateus A F C; Spadoti, Danilo H

2017-09-18

A fully three-dimensional carpet cloak presenting invisibility in all viewing angles is theoretically demonstrated. The design is developed using transformation optics and three-dimensional quasi-conformal mapping. Parametrization strategy and numerical optimization of the coordinate transformation deploying a quasi-Newton method is applied. A discussion about the minimum achievable anisotropy in the 3D transformation optics is presented. The method allows to reduce the anisotropy in the cloak and an isotropic medium could be considered. Numerical simulations confirm the strategy employed enabling the design of an isotropic reflectionless broadband carpet cloak independently of the incident light direction and polarization.

High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure

NARCIS (Netherlands)

M. Rosa-Garrido (Manuel); Chapski, D.J. (Douglas J.); Schmitt, A.D. (Anthony D.); Kimball, T.H. (Todd H.); Karbassi, E. (Elaheh); Monte, E. (Emma); Balderas, E. (Enrique); Pellegrini, M. (Matteo); Shih, T.-T. (Tsai-Ting); Soehalim, E. (Elizabeth); D.A. Liem (David); Ping, P. (Peipei); N.J. Galjart (Niels); Ren, S. (Shuxun); Wang, Y. (Yibin); Ren, B. (Bing); Vondriska, T.M. (Thomas M.)

2017-01-01

textabstractBACKGROUND: Cardiovascular disease is associated with epigenomic changes in the heart; however, the endogenous structure of cardiac myocyte chromatin has never been determined.METHODS: To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation

A multi-scale method of mapping urban influence

Science.gov (United States)

Timothy G. Wade; James D. Wickham; Nicola Zacarelli; Kurt H. Riitters

2009-01-01

Urban development can impact environmental quality and ecosystem services well beyond urban extent. Many methods to map urban areas have been developed and used in the past, but most have simply tried to map existing extent of urban development, and all have been single-scale techniques. The method presented here uses a clustering approach to look beyond the extant...

Further results for crack-edge mappings by ray methods

International Nuclear Information System (INIS)

Norris, A.N.; Achenbach, J.D.; Ahlberg, L.; Tittman, B.R.

1984-01-01

This chapter discusses further extensions of the local edge mapping method to the pulse-echo case and to configurations of water-immersed specimens and transducers. Crack edges are mapped by the use of arrival times of edge-diffracted signals. Topics considered include local edge mapping in a homogeneous medium, local edge mapping algorithms, local edge mapping through an interface, and edge mapping through an interface using synthetic data. Local edge mapping is iterative, with two or three iterations required for convergence

Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm.

Directory of Open Access Journals (Sweden)

Rudy Clausen

2015-09-01

Full Text Available An important goal in molecular biology is to understand functional changes upon single-point mutations in proteins. Doing so through a detailed characterization of structure spaces and underlying energy landscapes is desirable but continues to challenge methods based on Molecular Dynamics. In this paper we propose a novel algorithm, SIfTER, which is based instead on stochastic optimization to circumvent the computational challenge of exploring the breadth of a protein's structure space. SIfTER is a data-driven evolutionary algorithm, leveraging experimentally-available structures of wildtype and variant sequences of a protein to define a reduced search space from where to efficiently draw samples corresponding to novel structures not directly observed in the wet laboratory. The main advantage of SIfTER is its ability to rapidly generate conformational ensembles, thus allowing mapping and juxtaposing landscapes of variant sequences and relating observed differences to functional changes. We apply SIfTER to variant sequences of the H-Ras catalytic domain, due to the prominent role of the Ras protein in signaling pathways that control cell proliferation, its well-studied conformational switching, and abundance of documented mutations in several human tumors. Many Ras mutations are oncogenic, but detailed energy landscapes have not been reported until now. Analysis of SIfTER-computed energy landscapes for the wildtype and two oncogenic variants, G12V and Q61L, suggests that these mutations cause constitutive activation through two different mechanisms. G12V directly affects binding specificity while leaving the energy landscape largely unchanged, whereas Q61L has pronounced, starker effects on the landscape. An implementation of SIfTER is made available at http://www.cs.gmu.edu/~ashehu/?q=OurTools. We believe SIfTER is useful to the community to answer the question of how sequence mutations affect the function of a protein, when there is an

Conformally connected universes

International Nuclear Information System (INIS)

Cantor, M.; Piran, T.

1983-01-01

A well-known difficulty associated with the conformal method for the solution of the general relativistic Hamiltonian constraint is the appearance of an aphysical ''bag of gold'' singularity at the nodal surface of the conformal factor. This happens whenever the background Ricci scalar is too large. Using a simple model, it is demonstrated that some of these singular solutions do have a physical meaning, and that these can be considered as initial data for Universe containing black holes, which are connected, in a conformally nonsingular way with each other. The relation between the ADM mass and the horizon area in this solution supports the cosmic censorship conjecture. (author)

Quantitative trait loci mapping of calving and conformation traits on Bos taurus autosome 18 in the German Holstein population.

Science.gov (United States)

Brand, B; Baes, C; Mayer, M; Reinsch, N; Seidenspinner, T; Thaller, G; Kühn, Ch

2010-03-01

Linkage, linkage disequilibrium, and combined linkage and linkage disequilibrium analyses were performed to map quantitative trait loci (QTL) affecting calving and conformation traits on Bos taurus autosome 18 (BTA18) in the German Holstein population. Six paternal half-sib families consisting of a total of 1,054 animals were genotyped on 28 genetic markers in the telomeric region on BTA18 spanning approximately 30 Mb. Calving traits, body type traits, and udder type traits were investigated. Using univariately estimated breeding values, maternal and direct effects on calving ease and stillbirth were analyzed separately for first- and further-parity calvings. The QTL initially identified by separate linkage and linkage disequilibrium analyses could be confirmed by a combined linkage and linkage disequilibrium analysis for udder composite index, udder depth, fore udder attachment, front teat placement, body depth, rump angle, and direct effects on calving ease and stillbirth. Concurrence of QTL peaks and a similar shape of restricted log-likelihood ratio profiles were observed between udder type traits and for body depth and calving traits, respectively. Association analyses were performed for markers flanking the most likely QTL positions by applying a mixed model including a fixed allele effect of the maternally inherited allele and a random polygenic effect. Results indicated that microsatellite marker DIK4234 (located at 53.3 Mb) is associated with maternal effects on stillbirth, direct effects on calving ease, and body depth. A comparison of effects for maternally inherited DIK4234 alleles indicated a favorable, positive correlation of maternal and direct effects on calving. Additionally, the association of maternally inherited DIK4234 marker alleles with body depth implied that conformation traits might provide the functional background of the QTL for calving traits. For udder type traits, the strong coincidence of QTL peaks and the position of the QTL in a

Operator algebras and conformal field theory

International Nuclear Information System (INIS)

Gabbiani, F.; Froehlich, J.

1993-01-01

We define and study two-dimensional, chiral conformal field theory by the methods of algebraic field theory. We start by characterizing the vacuum sectors of such theories and show that, under very general hypotheses, their algebras of local observables are isomorphic to the unique hyperfinite type III 1 factor. The conformal net determined by the algebras of local observables is proven to satisfy Haag duality. The representation of the Moebius group (and presumably of the entire Virasoro algebra) on the vacuum sector of a conformal field theory is uniquely determined by the Tomita-Takesaki modular operators associated with its vacuum state and its conformal net. We then develop the theory of Mebius covariant representations of a conformal net, using methods of Doplicher, Haag and Roberts. We apply our results to the representation theory of loop groups. Our analysis is motivated by the desire to find a 'background-independent' formulation of conformal field theories. (orig.)

Conformational Analysis of Contrast Media for X-Ray Diagnostic Radiology

International Nuclear Information System (INIS)

Solieman, A.H.M.

2010-01-01

The conformational analysis of iodinated non-ionic contrast agent, Iobitridol, was carried out using theoretical calculations to explore its conformational space, and to study different aspects connected with application of different search techniques. Monte Carlo (MC), random search (RS) and molecular dynamics (MD) based conformational search techniques were used to extract a reasonable-size sample that adequately represents and has an average behavior of the entire conformational ensemble.While MC is good for quick search for lowest energy conformer, RS is better in obtaining conformational sample that cover the whole conformational space and MD is the best for investigation of isomeric preferences inside the conformational ensemble at thermal equilibrium. Conformational analysis of the produced gas phase samples reveals that RS and MD methods could sufficiently present the 18 distinct isomeric classes that constitute the total conformational space of the Iobitridol. S samples of conformational space of Iobitridol are extensively studied, as it hypothetically cover the total conformational space. They are used to test the suitability of different methods (charge distribution methods, energy calculation methods) for Iobitridol molecular computations and internal structure forces (steric hindrance, resonance interaction), as well as dependences among the internal coordinates (dihedral angles correlations and coincidences). The atomic partial charge distribution is found to greatly affect the energy calculation for the molecular mechanics based conformational energy distributions. Further energy minimization of conformational sample by the quantum molecular orbital methods is crucial to obtain charge independent as well as energy balanced conformational sample.

A Progressive Buffering Method for Road Map Update Using OpenStreetMap Data

Directory of Open Access Journals (Sweden)

Changyong Liu

2015-07-01

Full Text Available Web 2.0 enables a two-way interaction between servers and clients. GPS receivers become available to more citizens and are commonly found in vehicles and smart phones, enabling individuals to record and share their trajectory data on the Internet and edit them online. OpenStreetMap (OSM makes it possible for citizens to contribute to the acquisition of geographic information. This paper studies the use of OSM data to find newly mapped or built roads that do not exist in a reference road map and create its updated version. For this purpose, we propose a progressive buffering method for determining an optimal buffer radius to detect the new roads in the OSM data. In the next step, the detected new roads are merged into the reference road maps geometrically, topologically, and semantically. Experiments with OSM data and reference road maps over an area of 8494 km2 in the city of Wuhan, China and five of its 5 km × 5 km areas are conducted to demonstrate the feasibility and effectiveness of the method. It is shown that the OSM data can add 11.96% or a total of 2008.6 km of new roads to the reference road maps with an average precision of 96.49% and an average recall of 97.63%.

Conformal expansions and renormalons

Energy Technology Data Exchange (ETDEWEB)

Rathsman, J.

2000-02-07

The coefficients in perturbative expansions in gauge theories are factorially increasing, predominantly due to renormalons. This type of factorial increase is not expected in conformal theories. In QCD conformal relations between observables can be defined in the presence of a perturbative infrared fixed-point. Using the Banks-Zaks expansion the authors study the effect of the large-order behavior of the perturbative series on the conformal coefficients. The authors find that in general these coefficients become factorially increasing. However, when the factorial behavior genuinely originates in a renormalon integral, as implied by a postulated skeleton expansion, it does not affect the conformal coefficients. As a consequence, the conformal coefficients will indeed be free of renormalon divergence, in accordance with previous observations concerning the smallness of these coefficients for specific observables. The authors further show that the correspondence of the BLM method with the skeleton expansion implies a unique scale-setting procedure. The BLM coefficients can be interpreted as the conformal coefficients in the series relating the fixed-point value of the observable with that of the skeleton effective charge. Through the skeleton expansion the relevance of renormalon-free conformal coefficients extends to real-world QCD.

What is an evidence map? A systematic review of published evidence maps and their definitions, methods, and products.

Science.gov (United States)

Miake-Lye, Isomi M; Hempel, Susanne; Shanman, Roberta; Shekelle, Paul G

2016-02-10

The need for systematic methods for reviewing evidence is continuously increasing. Evidence mapping is one emerging method. There are no authoritative recommendations for what constitutes an evidence map or what methods should be used, and anecdotal evidence suggests heterogeneity in both. Our objectives are to identify published evidence maps and to compare and contrast the presented definitions of evidence mapping, the domains used to classify data in evidence maps, and the form the evidence map takes. We conducted a systematic review of publications that presented results with a process termed "evidence mapping" or included a figure called an "evidence map." We identified publications from searches of ten databases through 8/21/2015, reference mining, and consulting topic experts. We abstracted the research question, the unit of analysis, the search methods and search period covered, and the country of origin. Data were narratively synthesized. Thirty-nine publications met inclusion criteria. Published evidence maps varied in their definition and the form of the evidence map. Of the 31 definitions provided, 67 % described the purpose as identification of gaps and 58 % referenced a stakeholder engagement process or user-friendly product. All evidence maps explicitly used a systematic approach to evidence synthesis. Twenty-six publications referred to a figure or table explicitly called an "evidence map," eight referred to an online database as the evidence map, and five stated they used a mapping methodology but did not present a visual depiction of the evidence. The principal conclusion of our evaluation of studies that call themselves "evidence maps" is that the implied definition of what constitutes an evidence map is a systematic search of a broad field to identify gaps in knowledge and/or future research needs that presents results in a user-friendly format, often a visual figure or graph, or a searchable database. Foundational work is needed to better

Testing statistical isotropy in cosmic microwave background polarization maps

Science.gov (United States)

Rath, Pranati K.; Samal, Pramoda Kumar; Panda, Srikanta; Mishra, Debesh D.; Aluri, Pavan K.

2018-04-01

We apply our symmetry based Power tensor technique to test conformity of PLANCK Polarization maps with statistical isotropy. On a wide range of angular scales (l = 40 - 150), our preliminary analysis detects many statistically anisotropic multipoles in foreground cleaned full sky PLANCK polarization maps viz., COMMANDER and NILC. We also study the effect of residual foregrounds that may still be present in the Galactic plane using both common UPB77 polarization mask, as well as the individual component separation method specific polarization masks. However, some of the statistically anisotropic modes still persist, albeit significantly in NILC map. We further probed the data for any coherent alignments across multipoles in several bins from the chosen multipole range.

Introducing a method for mapping recreational experience

DEFF Research Database (Denmark)

Lindholst, Andrej Christian; Dempsey, Nicola; Burton, Mel

2013-01-01

spaces provide and support a range of recreational experiences. The exploration reported here is based on a short review of the methods background and an application in two test sites in Sheffield, South Yorkshire in early summer 2010. This paper critically appraises the application of rec......-mapping’, an innovative method of analysing and mapping positive recreational experiences in urban green spaces is explored and piloted within the UK planning context. Originating in the Nordic countries, this on-site method can provide urban planners and designers with data about the extent to which specific green......-mapping at smaller spatial scales and recommends further explorations within the UK planning context, as the method adds to existing open space assessment by providing a unique layer of information to analyse more fully the recreational qualities of urban green spaces....

Acoustic methods for cavitation mapping in biomedical applications

Science.gov (United States)

Wan, M.; Xu, S.; Ding, T.; Hu, H.; Liu, R.; Bai, C.; Lu, S.

2015-12-01

In recent years, cavitation is increasingly utilized in a wide range of applications in biomedical field. Monitoring the spatial-temporal evolution of cavitation bubbles is of great significance for efficiency and safety in biomedical applications. In this paper, several acoustic methods for cavitation mapping proposed or modified on the basis of existing work will be presented. The proposed novel ultrasound line-by-line/plane-by-plane method can depict cavitation bubbles distribution with high spatial and temporal resolution and may be developed as a potential standard 2D/3D cavitation field mapping method. The modified ultrafast active cavitation mapping based upon plane wave transmission and reception as well as bubble wavelet and pulse inversion technique can apparently enhance the cavitation to tissue ratio in tissue and further assist in monitoring the cavitation mediated therapy with good spatial and temporal resolution. The methods presented in this paper will be a foundation to promote the research and development of cavitation imaging in non-transparent medium.

Approximate quantum chemical methods for modelling carbohydrate conformation and aromatic interactions: β-cyclodextrin and its adsorption on a single-layer graphene sheet.

Science.gov (United States)

Jaiyong, Panichakorn; Bryce, Richard A

2017-06-14

Noncovalent functionalization of graphene by carbohydrates such as β-cyclodextrin (βCD) has the potential to improve graphene dispersibility and its use in biomedical applications. Here we explore the ability of approximate quantum chemical methods to accurately model βCD conformation and its interaction with graphene. We find that DFTB3, SCC-DFTB and PM3CARB-1 methods provide the best agreement with density functional theory (DFT) in calculation of relative energetics of gas-phase βCD conformers; however, the remaining NDDO-based approaches we considered underestimate the stability of the trans,gauche vicinal diol conformation. This diol orientation, corresponding to a clockwise hydrogen bonding arrangement in the glucosyl residue of βCD, is present in the lowest energy βCD conformer. Consequently, for adsorption on graphene of clockwise or counterclockwise hydrogen bonded forms of βCD, calculated with respect to this unbound conformer, the DFTB3 method provides closer agreement with DFT values than PM7 and PM6-DH2 approaches. These findings suggest approximate quantum chemical methods as potentially useful tools to guide the design of carbohydrate-graphene interactions, but also highlights the specific challenge to NDDO-based methods in capturing the relative energetics of carbohydrate hydrogen bond networks.

Mapped Fourier Methods for stiff problems in toroidal geometry

OpenAIRE

Guillard , Herve

2014-01-01

Fourier spectral or pseudo-spectral methods are usually extremely efficient for periodic problems. However this efficiency is lost if the solutions have zones of rapid variations or internal layers. For these cases, a large number of Fourier modes are required and this makes the Fourier method unpractical in many cases. This work investigates the use of mapped Fourier method as a way to circumvent this problem. Mapped Fourier method uses instead of the usual Fourier interpolant the compositio...

Fabrication challenges associated with conformal optics

Science.gov (United States)

Schaefer, John; Eichholtz, Richard A.; Sulzbach, Frank C.

2001-09-01

A conformal optic is typically an optical window that conforms smoothly to the external shape of a system platform to improve aerodynamics. Conformal optics can be on-axis, such as an ogive missile dome, or off-axis, such as in a free form airplane wing. A common example of conformal optics is the automotive head light window that conforms to the body of the car aerodynamics and aesthetics. The unusual shape of conformal optics creates tremendous challenges for design, manufacturing, and testing. This paper will discuss fabrication methods that have been successfully demonstrated to produce conformal missile domes and associated wavefront corrector elements. It will identify challenges foreseen with more complex free-form configurations. Work presented in this paper was directed by the Precision Conformal Optics Consortium (PCOT). PCOT is comprised of both industrial and academic members who teamed to develop and demonstrate conformal optical systems suitable for insertion into future military programs. The consortium was funded under DARPA agreement number MDA972-96-9-08000.

Santos Basin Geological Structures Mapped by Cross-gradient Method

Science.gov (United States)

Jilinski, P.; Fontes, S. L.

2011-12-01

Introduction We mapped regional-scale geological structures localized in offshore zone Santos Basin, South-East Brazilian Coast. The region is dominated by transition zone from oceanic to continental crust. Our objective was to determine the imprint of deeper crustal structures from correlation between bathymetric, gravity and magnetic anomaly maps. The region is extensively studied for oil and gas deposits including large tectonic sub-salt traps. Our method is based on gradient directions and their magnitudes product. We calculate angular differences and cross-product and access correlation between properties and map structures. Theory and Method We used angular differences and cross-product to determine correlated region between bathymetric, free-air gravity and magnetic anomaly maps. This gradient based method focuses on borders of anomalies and uses its morphological properties to access correlation between their sources. We generated maps of angles and cross-product distribution to locate correlated regions. Regional scale potential fields maps of FA and MA are a reflection of the overlaying and overlapping effects of the adjacent structures. Our interest was in quantifying and characterizing the relation between shapes of magnetic anomalies and gravity anomalies. Results Resulting maps show strong correlation between bathymetry and gravity anomaly and bathymetry and magnetic anomaly for large strictures including Serra do Mar, shelf, continental slope and rise. All maps display the regional dominance of NE-SW geological structures alignment parallel to the shore. Special interest is presented by structures transgressing this tendency. Magnetic, gravity anomaly and bathymetry angles map show large correlated region over the shelf zone and smaller scale NE-SW banded structures over abyssal plane. From our interpretation the large band of inverse correlation adjacent to the shore is generated by the gravity effect of Serra do Mar. Disrupting structures including

A scalable hybrid multi-robot SLAM method for highly detailed maps

NARCIS (Netherlands)

Pfingsthorn, M.; Slamet, B.; Visser, A.

2008-01-01

Recent successful SLAM methods employ hybrid map representations combining the strengths of topological maps and occupancy grids. Such representations often facilitate multi-agent mapping. In this paper, a successful SLAM method is presented, which is inspired by the manifold data structure by

Complex mapping of aerofoils - a different perspective

Science.gov (United States)

Matthews, Miccal T.

2012-01-01

In this article an application of conformal mapping to aerofoil theory is studied from a geometric and calculus point of view. The problem is suitable for undergraduate teaching in terms of a project or extended piece of work, and brings together the concepts of geometric mapping, parametric equations, complex numbers and calculus. The Joukowski and Karman-Trefftz aerofoils are studied, and it is shown that the Karman-Trefftz aerofoil is an improvement over the Joukowski aerofoil from a practical point of view. For the most part only a spreadsheet program and pen and paper is required, only for the last portion of the study of the Karman-Trefftz aerofoils a symbolic computer package is employed. Ignoring the concept of a conformal mapping and instead viewing the problem from a parametric point of view, some interesting mappings are obtained. By considering the derivative of the mapped mapping via the chain rule, some new and interesting analytical results are obtained for the Joukowski aerofoil, and numerical results for the Karman-Trefftz aerofoil.

Functional methods and mappings of dissipative quantum systems

International Nuclear Information System (INIS)

Baur, H.

2006-01-01

In the first part of this work we extract the algebraic structure behind the method of the influence functional in the context of dissipative quantum mechanics. Special emphasis was put on the transition from a quantum mechanical description to a classical one, since it allows a deeper understanding of the measurement-process. This is tightly connected with the transition from a microscopic to a macroscopic world where the former one is described by the rules of quantum mechanics whereas the latter follows the rules of classical mechanics. In addition we show how the results of the influence functional method can be interpreted as a stochastical process, which in turn allows an easy comparison with the well known time development of a quantum mechanical system by use of the Schroedinger equation. In the following we examine the tight-binding approximation of models of which their hamiltionian shows discrete eigenstates in position space and where transitions between those states are suppressed so that propagation either is described by tunneling or by thermal activation. In the framework of dissipative quantum mechanics this leads to a tremendous simplification of the effective description of the system since instead of looking at the full history of all paths in the path integral description, we only have to look at all possible jump times and the possible corresponding set of weights for the jump direction, which is much easier to handle both analytically and numerically. In addition we deal with the mapping and the connection of dissipative quantum mechanical models with ones in quantum field theory and in particular models in statistical field theory. As an example we mention conformal invariance in two dimensions which always becomes relevant if a statistical system only has local interaction and is invariant under scaling. (orig.)

Quantum critical phenomena and conformal invariance

International Nuclear Information System (INIS)

Zhe Chang.

1995-05-01

We show that the Abelian bosonization of continuum limit of the 1D Hubbard model corresponds to the 2D explicitly conformal invariant Gaussian model at weak coupling limit. A universality argument is used to extend the equivalence to an entire segment of the critical line of the strongly correlated electron system. An integral equation satisfied by the mapping function between critical lines of the 1D Hubbard model and 2D Gaussian model is obtained and then solved in some limiting cases. By making use of the fact that the free Hubbard system reduces to four fermions and each of them is related to a c = 1/2 conformal field theory, we present exactly the partition function of the Hubbard model on a finite 1D lattice. (author). 16 refs

Conformal field theory in conformal space

International Nuclear Information System (INIS)

Preitschopf, C.R.; Vasiliev, M.A.

1999-01-01

We present a new framework for a Lagrangian description of conformal field theories in various dimensions based on a local version of d + 2-dimensional conformal space. The results include a true gauge theory of conformal gravity in d = (1, 3) and any standard matter coupled to it. An important feature is the automatic derivation of the conformal gravity constraints, which are necessary for the analysis of the matter systems

Backtracking Method of Coloring Administrative Maps Considering Visual Perception Rules

Directory of Open Access Journals (Sweden)

WEI Zhiwei

2018-03-01

Full Text Available Color design in administrative maps should incorporate and balance area configuration, color harmony, and users' purposes. Based on visual perceptual rules, this paper quantifies color harmony, color contrast and perceptual balance in coloring administrative maps, and a model is suggested to evaluate the coloring quality after color template is selected. Then a backtracking method based on area balance is proposed to compute colored areas. Experiments show that this method can well meet visual perceptual rules while coloring administrative maps, and can be used for later map design.

Conformational analysis of lignin models

International Nuclear Information System (INIS)

Santos, Helio F. dos

2001-01-01

The conformational equilibrium for two 5,5' biphenyl lignin models have been analyzed using a quantum mechanical semiempirical method. The gas phase and solution structures are discussed based on the NMR and X-ray experimental data. The results obtained showed that the observed conformations are solvent-dependent, being the geometries and the thermodynamic properties correlated with the experimental information. This study shows how a systematic theoretical conformational analysis can help to understand chemical processes at a molecular level. (author)

A Body of Work Standard-Setting Method with Construct Maps

Science.gov (United States)

Wyse, Adam E.; Bunch, Michael B.; Deville, Craig; Viger, Steven G.

2014-01-01

This article describes a novel variation of the Body of Work method that uses construct maps to overcome problems of transparency, rater inconsistency, and scores gaps commonly occurring with the Body of Work method. The Body of Work method with construct maps was implemented to set cut-scores for two separate K-12 assessment programs in a large…

Landau-Ginsburg models with N=2 supersymmetry as conventional conformal theories

International Nuclear Information System (INIS)

Marshakov, A.

1990-01-01

The conformal Landau-Ginsburg (LG) models are identified with the Toda-like two-dimensional field theories. At least in the N=2 supersymmetric case they possess a simple free-field representation, related to the Nicolai map. (orig.)

Hypotrochoids in conformal restriction systems and Virasoro descendants

International Nuclear Information System (INIS)

Doyon, Benjamin

2013-01-01

A conformal restriction system is a commutative, associative, unital algebra equipped with a representation of the groupoid of univalent conformal maps on connected open sets of the Riemann sphere, along with a family of linear functionals on subalgebras, satisfying a set of properties including conformal invariance and a type of restriction. This embodies some expected properties of expectation values in conformal loop ensembles CLE κ (at least for 8/3 iθ and w. We find that it has an expansion in positive powers of u and u-bar , and that the coefficients of pure u ( u-bar ) powers are holomorphic in w ( w-bar ). We identify these coefficients (the ‘hypotrochoid fields’) with certain Virasoro descendants of the identity field in conformal field theory, thereby showing that they form part of a vertex operator algebraic structure. This largely generalizes works by the author (in CLE), and the author with his collaborators Riva and Cardy (in SLE 8/3 and other restriction measures), where the case of the ellipse, at the order u 2 , led to the stress–energy tensor of CFT. The derivation uses in an essential way the Virasoro vertex operator algebra structure of conformal derivatives established recently by the author. The results suggest in particular the exact evaluation of CLE expectations of products of hypotrochoid fields as well as nontrivial relations amongst them through the vertex operator algebra, and further shed light onto the relationship between CLE and CFT. (paper)

Fast mapping of global protein folding states by multivariate NMR:

DEFF Research Database (Denmark)

Malmendal, Anders; Underhaug, Jarl; Otzen, Daniel

2010-01-01

To obtain insight into the functions of proteins and their specific roles, it is important to establish efficient procedures for exploring the states that encapsulate their conformational space. Global Protein folding State mapping by multivariate NMR (GPS NMR) is a powerful high-throughput method......-lactalbumin in the presence of the anionic surfactant sodium dodecyl sulfate, SDS, and compare these with other surfactants, acid, denaturants and heat....

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

International Nuclear Information System (INIS)

Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G.; Hummer, Gerhard

2014-01-01

Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

Energy Technology Data Exchange (ETDEWEB)

Nedialkova, Lilia V.; Amat, Miguel A. [Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544 (United States); Kevrekidis, Ioannis G., E-mail: yannis@princeton.edu, E-mail: gerhard.hummer@biophys.mpg.de [Department of Chemical and Biological Engineering and Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544 (United States); Hummer, Gerhard, E-mail: yannis@princeton.edu, E-mail: gerhard.hummer@biophys.mpg.de [Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main (Germany)

2014-09-21

Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.

18 CFR 4.39 - Specifications for maps and drawings.

Science.gov (United States)

2010-04-01

... and drawings. 4.39 Section 4.39 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY....39 Specifications for maps and drawings. All required maps and drawings must conform to the following specifications, except as otherwise prescribed in this chapter: (a) Each original map or drawing must consist of...

SU-E-T-279: Realization of Three-Dimensional Conformal Dose Planning in Prostate Brachytherapy

Energy Technology Data Exchange (ETDEWEB)

Li, Z; Jiang, S; Yang, Z [Tianjin University, Tianjin (China); Bai, H; Zhang, X [Seeds biological Pharmacy Ltd, Tianjin (China)

2014-06-01

Purpose: Successful clinical treatment in prostate brachytherapy is largely dependent on the effectiveness of pre-surgery dose planning. Conventional dose planning method could hardly arrive at a satisfy result. In this abstract, a three-dimensional conformal localized dose planning method is put forward to ensure the accuracy and effectiveness of pre-implantation dose planning. Methods: Using Monte Carlo method, the pre-calculated 3-D dose map for single source is obtained. As for multiple seeds dose distribution, the maps are combined linearly to acquire the 3-D distribution. The 3-D dose distribution is exhibited in the form of isodose surface together with reconstructed 3-D organs group real-timely. Then it is possible to observe the dose exposure to target volume and normal tissues intuitively, thus achieving maximum dose irradiation to treatment target and minimum healthy tissues damage. In addition, the exfoliation display of different isodose surfaces can be realized applying multi-values contour extraction algorithm based on voxels. The needles could be displayed in the system by tracking the position of the implanted seeds in real time to conduct block research in optimizing insertion trajectory. Results: This study extends dose planning from two-dimensional to three-dimensional, realizing the three-dimensional conformal irradiation, which could eliminate the limitations of 2-D images and two-dimensional dose planning. A software platform is developed using VC++ and Visualization Toolkit (VTK) to perform dose planning. The 3-D model reconstruction time is within three seconds (on a Intel Core i5 PC). Block research could be conducted to avoid inaccurate insertion into sensitive organs or internal obstructions. Experiments on eight prostate cancer cases prove that this study could make the dose planning results more reasonable. Conclusion: The three-dimensional conformal dose planning method could improve the rationality of dose planning by safely reducing

a Mapping Method of Slam Based on Look up Table

Science.gov (United States)

Wang, Z.; Li, J.; Wang, A.; Wang, J.

2017-09-01

In the last years several V-SLAM(Visual Simultaneous Localization and Mapping) approaches have appeared showing impressive reconstructions of the world. However these maps are built with far more than the required information. This limitation comes from the whole process of each key-frame. In this paper we present for the first time a mapping method based on the LOOK UP TABLE(LUT) for visual SLAM that can improve the mapping effectively. As this method relies on extracting features in each cell divided from image, it can get the pose of camera that is more representative of the whole key-frame. The tracking direction of key-frames is obtained by counting the number of parallax directions of feature points. LUT stored all mapping needs the number of cell corresponding to the tracking direction which can reduce the redundant information in the key-frame, and is more efficient to mapping. The result shows that a better map with less noise is build using less than one-third of the time. We believe that the capacity of LUT efficiently building maps makes it a good choice for the community to investigate in the scene reconstruction problems.

METHODS OF SIMULATION ON THE MAP OF ETHNOGEOGRAPHICAL KNOWLEDGE

Directory of Open Access Journals (Sweden)

A. M. Saraeva

2017-01-01

Full Text Available The article deals with the features of the spatial representation of the location of objects and phenomena on the Earth. One of the types of “cartographic representation” is modeling on the contour map. The advantages of the method are revealed. The application of modeling techniques that allows one to include ethnogeographic data in the content of the characteristics of the territory and reflect them on the contour map. The basis of ethnogeographic modeling is the identification and creation of elements of the material and spiritual culture of peoples by means of conventional signs. Comparison of these elements, their superimposition with respect to each other, as well as their comparison with geographic maps allow us to determine the interrelations and the dependence of the phenomenon. Modeling on contour maps is the basic method of learning in geography. On the one hand, it creates a cartographic image of the studied territory, and on the other hand it facilitates the creation of “visual supports” on the map.Modeling on contour maps, at the beginning students put the basic geographical names, which will serve as the basic knowledge. Then, by purposefully analyzing and comparing the thematic maps of the atlas or textbook, the students reflect specific ethno-geographical knowledge on contour maps. As a result, contour maps acquire “their own face”, and do not become a simple copy of maps of an atlas or textbook.Also, the features of the effect of this technique on the formation of spatial representations about the studied object have been analyzed. Thanks to the cartographic model, one can maintain a constant cognitive interest in the material studied. Modeling on the contour map will allow one to present the structure of the links between the elements of the ethnogeographical material. The basis of ethnogeographic modeling on the contour map is the identification and mapping of elements of the material and spiritual culture of

Progress in Geo-Electrical Methods for Hydrogeological Mapping?

DEFF Research Database (Denmark)

Schrøder, Niels

2014-01-01

In most of the 20th century the geo-electrical methods were primarily used for groundwater exploration and the application of the methods were normally followed by a borehole, and a moment of truth. In this process the use of DC (direct current) soundings have been developed to a high grade...... of excellence. In the last 25 years the geo-electrical methods are more used in connection with groundwater protection and planning, and new methods, as transient electromagnetic (TEM) soundings, have been developed that provide more measurements per hour. In Denmark this change is very explicit, and a paper....... The test area was earlier mapped by DC-soundings, so it is possible to test the methods against each other. It is concluded that well performed DC-soundings with a Schlumberger configuration still provide the best base for hydrogeological mapping...

Multiresolution Computation of Conformal Structures of Surfaces

Directory of Open Access Journals (Sweden)

Xianfeng Gu

2003-10-01

Full Text Available An efficient multiresolution method to compute global conformal structures of nonzero genus triangle meshes is introduced. The homology, cohomology groups of meshes are computed explicitly, then a basis of harmonic one forms and a basis of holomorphic one forms are constructed. A progressive mesh is generated to represent the original surface at different resolutions. The conformal structure is computed for the coarse level first, then used as the estimation for that of the finer level, by using conjugate gradient method it can be refined to the conformal structure of the finer level.

Conformal mapping calculation of railgun skin inductance

International Nuclear Information System (INIS)

Huerta, M.A.; Nearing, J.C.

1991-01-01

This paper considers the common rail arrangement consisting of two long, parallel, rectangular rails. The authors calculate the inductance per unit length L' in the short flight time limit where the skin depth is much smaller than any rail dimensions, the current is all on the rail surface, and the magnetic field does not penetrate the rails. The authors give the solution based on the Schwartz-Christoffel transformation that maps the boundaries of the problem into a simpler shape

Applying Clustering Methods in Drawing Maps of Science: Case Study of the Map For Urban Management Science

Directory of Open Access Journals (Sweden)

Mohammad Abuei Ardakan

2010-04-01

Full Text Available The present paper offers a basic introduction to data clustering and demonstrates the application of clustering methods in drawing maps of science. All approaches towards classification and clustering of information are briefly discussed. Their application to the process of visualization of conceptual information and drawing of science maps are illustrated by reviewing similar researches in this field. By implementing aggregated hierarchical clustering algorithm, which is an algorithm based on complete-link method, the map for urban management science as an emerging, interdisciplinary scientific field is analyzed and reviewed.

The butane condensed matter conformational problem

NARCIS (Netherlands)

Weber, A.C.J.; de Lange, C.A.; Meerts, W.L.; Burnell, E.E.

2010-01-01

From the dipolar couplings of orientationally ordered n-butane obtained by NMR spectroscopy we have calculated conformer probabilities using the modified Chord (Cd) and Size-and-Shape (CI) models to estimate the conformational dependence of the order matrix. All calculation methods make use of

Second-Order Conformally Equivariant Quantization in Dimension 1|2

Directory of Open Access Journals (Sweden)

Najla Mellouli

2009-12-01

Full Text Available This paper is the next step of an ambitious program to develop conformally equivariant quantization on supermanifolds. This problem was considered so far in (superdimensions 1 and 1|1. We will show that the case of several odd variables is much more difficult. We consider the supercircle S^{1|2} equipped with the standard contact structure. The conformal Lie superalgebra K(2 of contact vector fields on S^{1|2} contains the Lie superalgebra osp(2|2. We study the spaces of linear differential operators on the spaces of weighted densities as modules over osp(2|2. We prove that, in the non-resonant case, the spaces of second order differential operators are isomorphic to the corresponding spaces of symbols as osp(2|2-modules. We also prove that the conformal equivariant quantization map is unique and calculate its explicit formula.

An Efficient Null Model for Conformational Fluctuations in Proteins

DEFF Research Database (Denmark)

Harder, Tim Philipp; Borg, Mikael; Bottaro, Sandro

2012-01-01

Protein dynamics play a crucial role in function, catalytic activity, and pathogenesis. Consequently, there is great interest in computational methods that probe the conformational fluctuations of a protein. However, molecular dynamics simulations are computationally costly and therefore are often...... limited to comparatively short timescales. TYPHON is a probabilistic method to explore the conformational space of proteins under the guidance of a sophisticated probabilistic model of local structure and a given set of restraints that represent nonlocal interactions, such as hydrogen bonds or disulfide...... on conformational fluctuations that is in correspondence with experimental measurements. TYPHON provides a flexible, yet computationally efficient, method to explore possible conformational fluctuations in proteins....

Can a combination of the conformal thin-sandwich and puncture methods yield binary black hole solutions in quasiequilibrium?

International Nuclear Information System (INIS)

Hannam, Mark D.; Evans, Charles R.; Cook, Gregory B.; Baumgarte, Thomas W.

2003-01-01

We consider combining two important methods for constructing quasiequilibrium initial data for binary black holes: the conformal thin-sandwich formalism and the puncture method. The former seeks to enforce stationarity in the conformal three-metric and the latter attempts to avoid internal boundaries, like minimal surfaces or apparent horizons. We show that these two methods make partially conflicting requirements on the boundary conditions that determine the time slices. In particular, it does not seem possible to construct slices that are quasistationary and that avoid physical singularities while simultaneously are connected by an everywhere positive lapse function, a condition which must be obtained if internal boundaries are to be avoided. Some relaxation of these conflicting requirements may yield a soluble system, but some of the advantages that were sought in combining these approaches will be lost

Quantifying polypeptide conformational space: sensitivity to conformation and ensemble definition.

Science.gov (United States)

Sullivan, David C; Lim, Carmay

2006-08-24

Quantifying the density of conformations over phase space (the conformational distribution) is needed to model important macromolecular processes such as protein folding. In this work, we quantify the conformational distribution for a simple polypeptide (N-mer polyalanine) using the cumulative distribution function (CDF), which gives the probability that two randomly selected conformations are separated by less than a "conformational" distance and whose inverse gives conformation counts as a function of conformational radius. An important finding is that the conformation counts obtained by the CDF inverse depend critically on the assignment of a conformation's distance span and the ensemble (e.g., unfolded state model): varying ensemble and conformation definition (1 --> 2 A) varies the CDF-based conformation counts for Ala(50) from 10(11) to 10(69). In particular, relatively short molecular dynamics (MD) relaxation of Ala(50)'s random-walk ensemble reduces the number of conformers from 10(55) to 10(14) (using a 1 A root-mean-square-deviation radius conformation definition) pointing to potential disconnections in comparing the results from simplified models of unfolded proteins with those from all-atom MD simulations. Explicit waters are found to roughen the landscape considerably. Under some common conformation definitions, the results herein provide (i) an upper limit to the number of accessible conformations that compose unfolded states of proteins, (ii) the optimal clustering radius/conformation radius for counting conformations for a given energy and solvent model, (iii) a means of comparing various studies, and (iv) an assessment of the applicability of random search in protein folding.

A new method for mapping perceptual biases across visual space.

Science.gov (United States)

Finlayson, Nonie J; Papageorgiou, Andriani; Schwarzkopf, D Samuel

2017-08-01

How we perceive the environment is not stable and seamless. Recent studies found that how a person qualitatively experiences even simple visual stimuli varies dramatically across different locations in the visual field. Here we use a method we developed recently that we call multiple alternatives perceptual search (MAPS) for efficiently mapping such perceptual biases across several locations. This procedure reliably quantifies the spatial pattern of perceptual biases and also of uncertainty and choice. We show that these measurements are strongly correlated with those from traditional psychophysical methods and that exogenous attention can skew biases without affecting overall task performance. Taken together, MAPS is an efficient method to measure how an individual's perceptual experience varies across space.

Boundary states in c=-2 logarithmic conformal field theory

International Nuclear Information System (INIS)

Bredthauer, Andreas; Flohr, Michael

2002-01-01

Starting from first principles, a constructive method is presented to obtain boundary states in conformal field theory. It is demonstrated that this method is well suited to compute the boundary states of logarithmic conformal field theories. By studying the logarithmic conformal field theory with central charge c=-2 in detail, we show that our method leads to consistent results. In particular, it allows to define boundary states corresponding to both, indecomposable representations as well as their irreducible subrepresentations

Experimental conformational energy maps of proteins and peptides.

Science.gov (United States)

Balaji, Govardhan A; Nagendra, H G; Balaji, Vitukudi N; Rao, Shashidhar N

2017-06-01

We have presented an extensive analysis of the peptide backbone dihedral angles in the PDB structures and computed experimental Ramachandran plots for their distributions seen under a various constraints on X-ray resolution, representativeness at different sequence identity percentages, and hydrogen bonding distances. These experimental distributions have been converted into isoenergy contour plots using the approach employed previously by F. M. Pohl. This has led to the identification of energetically favored minima in the Ramachandran (ϕ, ψ) plots in which global minima are predominantly observed either in the right-handed α-helical or the polyproline II regions. Further, we have identified low energy pathways for transitions between various minima in the (ϕ,ψ) plots. We have compared and presented the experimental plots with published theoretical plots obtained from both molecular mechanics and quantum mechanical approaches. In addition, we have developed and employed a root mean square deviation (RMSD) metric for isoenergy contours in various ranges, as a measure (in kcal.mol -1 ) to compare any two plots and determine the extent of correlation and similarity between their isoenergy contours. In general, we observe a greater degree of compatibility with experimental plots for energy maps obtained from molecular mechanics methods compared to most quantum mechanical methods. The experimental energy plots we have investigated could be helpful in refining protein structures obtained from X-ray, NMR, and electron microscopy and in refining force field parameters to enable simulations of peptide and protein structures that have higher degree of consistency with experiments. Proteins 2017; 85:979-1001. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

System and method for image mapping and visual attention

Science.gov (United States)

Peters, II, Richard A. (Inventor)

2011-01-01

A method is described for mapping dense sensory data to a Sensory Ego Sphere (SES). Methods are also described for finding and ranking areas of interest in the images that form a complete visual scene on an SES. Further, attentional processing of image data is best done by performing attentional processing on individual full-size images from the image sequence, mapping each attentional location to the nearest node, and then summing all attentional locations at each node.

Conformal deformation of Riemann space and torsion

International Nuclear Information System (INIS)

Pyzh, V.M.

1981-01-01

Method for investigating conformal deformations of Riemann spaces using torsion tensor, which permits to reduce the second ' order equations for Killing vectors to the system of the first order equations, is presented. The method is illustrated using conformal deformations of dimer sphere as an example. A possibility of its use when studying more complex deformations is discussed [ru

Study of polymer molecules and conformations with a nanopore

Science.gov (United States)

Golovchenko, Jene A.; Li, Jiali; Stein, Derek; Gershow, Marc H.

2010-12-07

The invention features methods for evaluating the conformation of a polymer, for example, for determining the conformational distribution of a plurality of polymers and to detect binding or denaturation events. The methods employ a nanopore which the polymer, e.g., a nucleic acid, traverses. As the polymer traverses the nanopore, measurements of transport properties of the nanopore yield data on the conformation of the polymer.

Workers’ Conformism

Directory of Open Access Journals (Sweden)

Nikolay Ivantchev

2013-10-01

Full Text Available Conformism was studied among 46 workers with different kinds of occupations by means of two modified scales measuring conformity by Santor, Messervey, and Kusumakar (2000 – scale for perceived peer pressure and scale for conformism in antisocial situations. The hypothesis of the study that workers’ conformism is expressed in a medium degree was confirmed partly. More than a half of the workers conform in a medium degree for taking risk, and for the use of alcohol and drugs, and for sexual relationships. More than a half of the respondents conform in a small degree for anti-social activities (like a theft. The workers were more inclined to conform for risk taking (10.9%, then – for the use of alcohol, drugs and for sexual relationships (8.7%, and in the lowest degree – for anti-social activities (6.5%. The workers who were inclined for the use of alcohol and drugs tended also to conform for anti-social activities.

Method II : The energy-momentum map

NARCIS (Netherlands)

Broer, H.; Hoveijn, I.; Lunter, G.; Vegter, G.

2003-01-01

In this chapter we apply the energy–momentum map reduction method to the same class of systems as in Chap. 2, namely two degree-of-freedom systems with optional symmetry, near equilibrium and close to resonance. We calculate the tangent space and nondegeneracy conditions for the 1:2, 1:3 and 1:4

Method for Pre-Conditioning a Measured Surface Height Map for Model Validation

Science.gov (United States)

Sidick, Erkin

2012-01-01

This software allows one to up-sample or down-sample a measured surface map for model validation, not only without introducing any re-sampling errors, but also eliminating the existing measurement noise and measurement errors. Because the re-sampling of a surface map is accomplished based on the analytical expressions of Zernike-polynomials and a power spectral density model, such re-sampling does not introduce any aliasing and interpolation errors as is done by the conventional interpolation and FFT-based (fast-Fourier-transform-based) spatial-filtering method. Also, this new method automatically eliminates the measurement noise and other measurement errors such as artificial discontinuity. The developmental cycle of an optical system, such as a space telescope, includes, but is not limited to, the following two steps: (1) deriving requirements or specs on the optical quality of individual optics before they are fabricated through optical modeling and simulations, and (2) validating the optical model using the measured surface height maps after all optics are fabricated. There are a number of computational issues related to model validation, one of which is the "pre-conditioning" or pre-processing of the measured surface maps before using them in a model validation software tool. This software addresses the following issues: (1) up- or down-sampling a measured surface map to match it with the gridded data format of a model validation tool, and (2) eliminating the surface measurement noise or measurement errors such that the resulted surface height map is continuous or smoothly-varying. So far, the preferred method used for re-sampling a surface map is two-dimensional interpolation. The main problem of this method is that the same pixel can take different values when the method of interpolation is changed among the different methods such as the "nearest," "linear," "cubic," and "spline" fitting in Matlab. The conventional, FFT-based spatial filtering method used to

Computational methods for constructing protein structure models from 3D electron microscopy maps.

Science.gov (United States)

Esquivel-Rodríguez, Juan; Kihara, Daisuke

2013-10-01

Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided. Copyright © 2013 Elsevier Inc. All rights reserved.

A Karnaugh-Map based fingerprint minutiae extraction method

Directory of Open Access Journals (Sweden)

Sunil Kumar Singla

2010-07-01

Full Text Available Fingerprint is one of the most promising method among all the biometric techniques and has been used for thepersonal authentication for a long time because of its wide acceptance and reliability. Features (Minutiae are extracted fromthe fingerprint in question and are compared with the features already stored in the database for authentication. Crossingnumber (CN is the most commonly used minutiae extraction method for fingerprints. In this paper, a new Karnaugh-Mapbased fingerprint minutiae extraction method has been proposed and discussed. In the proposed algorithm the 8 neighborsof a pixel in a 33 window are arranged as 8 bits of a byte and corresponding hexadecimal (hex value is calculated. Thesehex values are simplified using standard Karnaugh-Map (K-map technique to obtain the minimized logical expression.Experiments conducted on the FVC2002/Db1_a database reveals that the developed method is better than the crossingnumber (CN method.

Selective stimulation of conformational conversions in free molecules

International Nuclear Information System (INIS)

Ismailzade, G.I.; Movsumov, I.Z.; Menzeleev, M.R.; Kazymova, S.B.

2014-01-01

Application of double-resonance (RF-MW, IR-MW, MW-MW) methods to enhance studies of unstable isomeric structures was discussed. The use of infrared pump radiation to excite conformational energy levels in order to stimulate selectively conformational conversions and to correct spectral line intensities of separate conformations was substantiated. (authors)

Computational Prediction of Atomic Structures of Helical Membrane Proteins Aided by EM Maps

Science.gov (United States)

Kovacs, Julio A.; Yeager, Mark; Abagyan, Ruben

2007-01-01

Integral membrane proteins pose a major challenge for protein-structure prediction because only ≈100 high-resolution structures are available currently, thereby impeding the development of rules or empirical potentials to predict the packing of transmembrane α-helices. However, when an intermediate-resolution electron microscopy (EM) map is available, it can be used to provide restraints which, in combination with a suitable computational protocol, make structure prediction feasible. In this work we present such a protocol, which proceeds in three stages: 1), generation of an ensemble of α-helices by flexible fitting into each of the density rods in the low-resolution EM map, spanning a range of rotational angles around the main helical axes and translational shifts along the density rods; 2), fast optimization of side chains and scoring of the resulting conformations; and 3), refinement of the lowest-scoring conformations with internal coordinate mechanics, by optimizing the van der Waals, electrostatics, hydrogen bonding, torsional, and solvation energy contributions. In addition, our method implements a penalty term through a so-called tethering map, derived from the EM map, which restrains the positions of the α-helices. The protocol was validated on three test cases: GpA, KcsA, and MscL. PMID:17496035

Conformation radiotherapy and conformal radiotherapy

International Nuclear Information System (INIS)

Morita, Kozo

1999-01-01

In order to coincide the high dose region to the target volume, the 'Conformation Radiotherapy Technique' using the multileaf collimator and the device for 'hollow-out technique' was developed by Prof. S. Takahashi in 1960. This technique can be classified a type of 2D-dynamic conformal RT techniques. By the clinical application of this technique, the late complications of the lens, the intestine and the urinary bladder after radiotherapy for the maxillary cancer and the cervical cancer decreased. Since 1980's the exact position and shape of the tumor and the surrounding normal tissues can be easily obtained by the tremendous development of the CT/MRI imaging technique. As a result, various kinds of new conformal techniques such as the 3D-CRT, the dose intensity modulation, the tomotherapy have been developed since the beginning of 1990'. Several 'dose escalation study with 2D-/3D conformal RT' is now under way to improve the treatment results. (author)

Ramachandran and his Map

Indian Academy of Sciences (India)

Ramachandran map, detailed in this article. His current interests are peptide, cyclic peptide and protein conforma- tions, energetics, data analysis, computer modeling as well as development of new algorithms useful for the conformational studies. C Ramakrishnan. Introduction. Professor G N Ramachandran was one of the ...

Method to map individual electromagnetic field components inside a photonic crystal

NARCIS (Netherlands)

Denis, T.; Reijnders, B.; Lee, J.H.H.; van der Slot, Petrus J.M.; Vos, Willem L.; Boller, Klaus J.

2012-01-01

We present a method to map the absolute electromagnetic field strength inside photonic crystals. We apply the method to map the dominant electric field component Ez of a two-dimensional photonic crystal slab at microwave frequencies. The slab is placed between two mirrors to select Bloch standing

Enhancing Architecture-Implementation Conformance with Change Management and Support for Behavioral Mapping

Science.gov (United States)

Zheng, Yongjie

2012-01-01

Software architecture plays an increasingly important role in complex software development. Its further application, however, is challenged by the fact that software architecture, over time, is often found not conformant to its implementation. This is usually caused by frequent development changes made to both artifacts. Against this background,…

Statistical methods in physical mapping

International Nuclear Information System (INIS)

Nelson, D.O.

1995-05-01

One of the great success stories of modern molecular genetics has been the ability of biologists to isolate and characterize the genes responsible for serious inherited diseases like fragile X syndrome, cystic fibrosis and myotonic muscular dystrophy. This dissertation concentrates on constructing high-resolution physical maps. It demonstrates how probabilistic modeling and statistical analysis can aid molecular geneticists in the tasks of planning, execution, and evaluation of physical maps of chromosomes and large chromosomal regions. The dissertation is divided into six chapters. Chapter 1 provides an introduction to the field of physical mapping, describing the role of physical mapping in gene isolation and ill past efforts at mapping chromosomal regions. The next two chapters review and extend known results on predicting progress in large mapping projects. Such predictions help project planners decide between various approaches and tactics for mapping large regions of the human genome. Chapter 2 shows how probability models have been used in the past to predict progress in mapping projects. Chapter 3 presents new results, based on stationary point process theory, for progress measures for mapping projects based on directed mapping strategies. Chapter 4 describes in detail the construction of all initial high-resolution physical map for human chromosome 19. This chapter introduces the probability and statistical models involved in map construction in the context of a large, ongoing physical mapping project. Chapter 5 concentrates on one such model, the trinomial model. This chapter contains new results on the large-sample behavior of this model, including distributional results, asymptotic moments, and detection error rates. In addition, it contains an optimality result concerning experimental procedures based on the trinomial model. The last chapter explores unsolved problems and describes future work

Statistical methods in physical mapping

Energy Technology Data Exchange (ETDEWEB)

Nelson, David O. [Univ. of California, Berkeley, CA (United States)

1995-05-01

One of the great success stories of modern molecular genetics has been the ability of biologists to isolate and characterize the genes responsible for serious inherited diseases like fragile X syndrome, cystic fibrosis and myotonic muscular dystrophy. This dissertation concentrates on constructing high-resolution physical maps. It demonstrates how probabilistic modeling and statistical analysis can aid molecular geneticists in the tasks of planning, execution, and evaluation of physical maps of chromosomes and large chromosomal regions. The dissertation is divided into six chapters. Chapter 1 provides an introduction to the field of physical mapping, describing the role of physical mapping in gene isolation and ill past efforts at mapping chromosomal regions. The next two chapters review and extend known results on predicting progress in large mapping projects. Such predictions help project planners decide between various approaches and tactics for mapping large regions of the human genome. Chapter 2 shows how probability models have been used in the past to predict progress in mapping projects. Chapter 3 presents new results, based on stationary point process theory, for progress measures for mapping projects based on directed mapping strategies. Chapter 4 describes in detail the construction of all initial high-resolution physical map for human chromosome 19. This chapter introduces the probability and statistical models involved in map construction in the context of a large, ongoing physical mapping project. Chapter 5 concentrates on one such model, the trinomial model. This chapter contains new results on the large-sample behavior of this model, including distributional results, asymptotic moments, and detection error rates. In addition, it contains an optimality result concerning experimental procedures based on the trinomial model. The last chapter explores unsolved problems and describes future work.

A novel method of S-box design based on chaotic map and composition method

International Nuclear Information System (INIS)

Lambić, Dragan

2014-01-01

Highlights: • Novel chaotic S-box generation method is presented. • Presented S-box has better cryptographic properties than other examples of chaotic S-boxes. • The advantages of the proposed method are the low complexity and large key space. -- Abstract: An efficient algorithm for obtaining random bijective S-boxes based on chaotic maps and composition method is presented. The proposed method is based on compositions of S-boxes from a fixed starting set. The sequence of the indices of starting S-boxes used is obtained by using chaotic maps. The results of performance test show that the S-box presented in this paper has good cryptographic properties. The advantages of the proposed method are the low complexity and the possibility to achieve large key space

Methodical Aspects of Applying Strategy Map in an Organization

Directory of Open Access Journals (Sweden)

Piotr Markiewicz

2013-06-01

Full Text Available One of important aspects of strategic management is the instrumental aspect included in a rich set of methods and techniques used at particular stages of strategic management process. The object of interest in this study is the development of views and the implementation of strategy as an element of strategic management and instruments in the form of methods and techniques. The commonly used method in strategy implementation and measuring progress is Balanced Scorecard (BSC. The method was created as a result of implementing the project “Measuring performance in the Organization of the future” of 1990, completed by a team under the supervision of David Norton (Kaplan, Norton 2002. The developed method was used first of all to evaluate performance by decomposition of a strategy into four perspectives and identification of measures of achievement. In the middle of 1990s the method was improved by enriching it, first of all, with a strategy map, in which the process of transition of intangible assets into tangible financial effects is reflected (Kaplan, Norton 2001. Strategy map enables illustration of cause and effect relationship between processes in all four perspectives and performance indicators at the level of organization. The purpose of the study being prepared is to present methodical conditions of using strategy maps in the strategy implementation process in organizations of different nature.

Adaptive Multilevel Methods with Local Smoothing for $H^1$- and $H^{\\mathrm{curl}}$-Conforming High Order Finite Element Methods

KAUST Repository

Janssen, Bärbel

2011-01-01

A multilevel method on adaptive meshes with hanging nodes is presented, and the additional matrices appearing in the implementation are derived. Smoothers of overlapping Schwarz type are discussed; smoothing is restricted to the interior of the subdomains refined to the current level; thus it has optimal computational complexity. When applied to conforming finite element discretizations of elliptic problems and Maxwell equations, the method\\'s convergence rates are very close to those for the nonadaptive version. Furthermore, the smoothers remain efficient for high order finite elements. We discuss the implementation in a general finite element code using the example of the deal.II library. © 2011 Societ y for Industrial and Applied Mathematics.

Orbital tomography: Molecular band maps, momentum maps and the imaging of real space orbitals of adsorbed molecules

Energy Technology Data Exchange (ETDEWEB)

Offenbacher, Hannes; Lüftner, Daniel; Ules, Thomas; Reinisch, Eva Maria; Koller, Georg, E-mail: georg.koller@uni-graz.at; Puschnig, Peter; Ramsey, Michael G., E-mail: michael.ramsey@uni-graz.at

2015-10-01

Highlights: • Orbital tomography within the plane wave final state approximation. • One electron orbital predictions versus angle resolved photoemission experiment. • Geometric and electronic structure of organic thin films elucidated by ARUPS. • Influence of molecular conformation and orientation on ARUPS. • Retrieval of sexiphenyl and pentacene orbitals in real space. - Abstract: The frontier orbitals of molecules are the prime determinants of their chemical, optical and electronic properties. Arguably, the most direct method of addressing the (filled) frontier orbitals is ultra-violet photoemission spectroscopy (UPS). Although UPS is a mature technique from the early 1970s on, the angular distribution of the photoemitted electrons was thought to be too complex to be analysed quantitatively. Recently angle resolved UPS (ARUPS) work on conjugated molecules both, in ordered thick films and chemisorbed monolayers, has shown that the angular (momentum) distribution of the photocurrent from orbital emissions can be simply understood. The approach, based on the assumption of a plane wave final state is becoming known as orbital tomography. Here we will demonstrate, with selected examples of pentacene (5A) and sexiphenyl (6P), the potential of orbital tomography. First it will be shown how the full angular distribution of the photocurrent (momentum map) from a specific orbital is related to the real space orbital by a Fourier transform. Examples of the reconstruction of 5A orbitals will be given and the procedure for recovering the lost phase information will be outlined. We then move to examples of sexiphenyl where we interrogate the original band maps of thick sexiphenyl in the light of our understanding of orbital tomography that has developed since then. With comparison to theoretical simulations of the molecular band maps, the molecular conformation and orientation will be concluded. New results for the sexiphenyl monolayer on Al(1 1 0) will then be

Improvements to robotics-inspired conformational sampling in rosetta.

Directory of Open Access Journals (Sweden)

Amelie Stein

Full Text Available To accurately predict protein conformations in atomic detail, a computational method must be capable of sampling models sufficiently close to the native structure. All-atom sampling is difficult because of the vast number of possible conformations and extremely rugged energy landscapes. Here, we test three sampling strategies to address these difficulties: conformational diversification, intensification of torsion and omega-angle sampling and parameter annealing. We evaluate these strategies in the context of the robotics-based kinematic closure (KIC method for local conformational sampling in Rosetta on an established benchmark set of 45 12-residue protein segments without regular secondary structure. We quantify performance as the fraction of sub-Angstrom models generated. While improvements with individual strategies are only modest, the combination of intensification and annealing strategies into a new "next-generation KIC" method yields a four-fold increase over standard KIC in the median percentage of sub-Angstrom models across the dataset. Such improvements enable progress on more difficult problems, as demonstrated on longer segments, several of which could not be accurately remodeled with previous methods. Given its improved sampling capability, next-generation KIC should allow advances in other applications such as local conformational remodeling of multiple segments simultaneously, flexible backbone sequence design, and development of more accurate energy functions.

Wada-test, functional magnetic resonance imaging and direct electrical stimulation - brain mapping methods

International Nuclear Information System (INIS)

Minkin, K.; Tanova, R.; Busarski, A.; Penkov, M.; Penev, L.; Hadjidekov, V.

2009-01-01

Modern neurosurgery requires accurate preoperative and intraoperative localization of brain pathologies but also of brain functions. The presence of individual variations in healthy subjects and the shift of brain functions in brain diseases provoke the introduction of various methods for brain mapping. The aim of this paper was to analyze the most widespread methods for brain mapping: Wada-test, functional magnetic resonance imaging (fMRI) and intraoperative direct electrical stimulation (DES). This study included 4 patients with preoperative brain mapping using Wada-test and fMRI. Intraoperative mapping with DES during awake craniotomy was performed in one case. The histopathological diagnosis was low-grade glioma in 2 cases, cortical dysplasia (1 patient) and arteriovenous malformation (1 patient). The brain mapping permits total lesion resection in three of four patients. There was no new postoperative deficit despite surgery near or within functional brain areas. Brain plasticity provoking shift of eloquent areas from their usual locations was observed in two cases. The brain mapping methods allow surgery in eloquent brain areas recognized in the past as 'forbidden areas'. Each method has advantages and disadvantages. The precise location of brain functions and pathologies frequently requires combination of different brain mapping methods. (authors)

Comparing 511 keV Attenuation Maps Obtained from Different Energy Mapping Methods for CT Based Attenuation Correction of PET Data

Directory of Open Access Journals (Sweden)

Maryam Shirmohammad

2008-06-01

Full Text Available Introduction:  The  advent  of  dual-modality  PET/CT  scanners  has  revolutionized  clinical  oncology  by  improving lesion localization and facilitating treatment planning for radiotherapy. In addition, the use of  CT images for CT-based attenuation correction (CTAC decreases the overall scanning time and creates  a noise-free  attenuation  map  (6map.  CTAC  methods  include  scaling,  segmentation,  hybrid  scaling/segmentation, bilinear and dual energy methods. All CTAC methods require the transformation  of CT Hounsfield units (HU to linear attenuation coefficients (LAC at 511 keV. The aim of this study is  to compare the results of implementing different methods of energy mapping in PET/CT scanners.   Materials and Methods: This study was conducted in 2 phases, the first phase in a phantom and the  second  one  on  patient  data.  To  perform  the  first  phase,  a  cylindrical  phantom  with  different  concentrations of K2HPO4 inserts was CT scanned and energy mapping methods were implemented on  it. For performing the second phase, different energy  mapping  methods  were implemented on several  clinical studies and compared to the transmission (TX image derived using Ga-68 radionuclide source  acquired on the GE Discovery LS PET/CT scanner.   Results: An ROI analysis was performed on different positions of the resultant 6maps and the average  6value of each ROI was compared to the reference value. The results of the 6maps obtained for 511 keV  compared to the theoretical  values showed that in the phantom for low  concentrations  of K 2 HPO 4 all  these  methods  produce  511  keV  attenuation  maps  with  small  relative  difference  compared  to  gold  standard. The relative difference for scaling, segmentation, hybrid, bilinear and dual energy methods was  4.92,  3.21,  4.43,  2.24  and  2.29%,  respectively.  Although  for  high  concentration �

Conformal three dimensional radiotherapy treatment planning in Lund

International Nuclear Information System (INIS)

Knoos, T.; Nilsson, P.; Anders, A.

1995-01-01

The use of conformal therapy is based on 3-dimensional treatment planning as well as on methods and routines for 3-dimensional patient mapping, 3-dimensional virtual simulation and others. The management of patients at the Radiotherapy Department at the University Hospital in Lund (Sweden) is discussed. About 2100 new patients are annually treated with external radiotherapy using seven linear accelerators. Three of the accelerators have dual photon energies and electron treatment facilities. A multi-leaf collimator as well as an electronic portal imaging device are available on one machine. Two simulators and an in-house CT-scanner are used for treatment planning. From 1988 to 1992 Scandiplan (Umplan) was used. Since 1992, the treatment planning system is TMS (HELAX AB, Sweden), which is based on the pencil beam algorithm of Ahnesjo. The calculations use patient modulated accelerator specific energy fluence spectra which are compiled with pencil beams from Monte Carlo generated energy absorption kernels. Heterogeneity corrections are performed with results close to conventional algorithms. Irregular fields, either from standard or individual blocks and from multi-leaf collimators are handled by the treatment planning system. The field shape is determined conveniently using the beam's eye view. The final field shape is exported electronically to either the block cutting machine or the multileaf collimator control computer. All patient fields are checked against the beam's eye view during simulation using manual methods. Treatment verification is performed by portal films and in vivo dosimetry with silicon diodes or TL-dosimetry. Up to now, approximately 4400 patients have received a highly individualized 3-dimensional conformal treatment

Conformational analysis of cellobiose by electronic structure theories.

Science.gov (United States)

French, Alfred D; Johnson, Glenn P; Cramer, Christopher J; Csonka, Gábor I

2012-03-01

Adiabatic Φ/ψ maps for cellobiose were prepared with B3LYP density functional theory. A mixed basis set was used for minimization, followed with 6-31+G(d) single-point calculations, with and without SMD continuum solvation. Different arrangements of the exocyclic groups (38 starting geometries) were considered for each Φ/ψ point. The vacuum calculations agreed with earlier computational and experimental results on the preferred gas phase conformation (anti-Φ(H), syn-ψ(H)), and the results from the solvated calculations were consistent with the (syn Φ(H)/ψ(H) conformations from condensed phases (crystals or solutions). Results from related studies were compared, and there is substantial dependence on the solvation model as well as arrangements of exocyclic groups. New stabilizing interactions were revealed by Atoms-In-Molecules theory. Published by Elsevier Ltd.

Replacement between conformity and counter-conformity in consumption decisions.

Science.gov (United States)

Chou, Ting-Jui; Chang, En-Chung; Dai, Qi; Wong, Veronica

2013-02-01

This study assessed, in a Chinese context, how self-esteem interacts with perceived similarity and uniqueness to yield cognitive dissonance, and whether the dissonance leads to self-reported conformity or counter-conformity behavior. Participants were 408 respondents from 4 major Chinese cities (M age = 33.0 yr., SD = 4.3; 48% men). Self-perceptions of uniqueness, similarity, cognitive dissonance, self-esteem and need to behave in conformity or counter-conformity were measured. A theoretical model was assessed in four situations, relating the ratings of self-esteem and perceived similarity/uniqueness to the way other people at a wedding were dressed, and the resultant cognitive dissonance and conformity/ counter-conformity behavior. Regardless of high or low self-esteem, all participants reported cognitive dissonance when they were told that they were dressed extremely similarly to or extremely differently from the other people attending the wedding. However, the conforming/counter-conforming strategies used by participants to resolve the cognitive dissonance differed. When encountering dissonance induced by the perceived extreme uniqueness of dress, participants with low self-esteem tended to say they would dress next time so as to conform with the way others were dressed, while those with high self-esteem indicated they would continue their counter-conformity in attire. When encountering dissonance induced by the perceived extreme similarity to others, both those with high and low self-esteem tended to say they would dress in an unorthodox manner to surprise other people in the future.

Conformity of LINAC-Based Stereotactic Radiosurgery Using Dynamic Conformal Arcs and Micro-Multileaf Collimator

International Nuclear Information System (INIS)

Hazard, Lisa J.; Wang, Brian; Skidmore, Thomas B.; Chern, Shyh-Shi; Salter, Bill J.; Jensen, Randy L.; Shrieve, Dennis C.

2009-01-01

Purpose: To assess the conformity of dynamic conformal arc linear accelerator-based stereotactic radiosurgery and to describe a standardized method of isodose surface (IDS) selection. Methods and Materials: In 174 targets, the conformity index (CI) at the prescription IDS used for treatment was calculated as CI = (PIV/PVTV)/(PVTV/TV), where TV is the target volume, PIV (prescription isodose volume) is the total volume encompassed by the prescription IDS, and PVTV is the TV encompassed by the IDS. In addition, a 'standardized' prescription IDS (sIDS) was chosen according to the following criteria: 95% of the TV was encompassed by the PIV and 99% of TV was covered by 95% of the prescription dose. The CIs at the sIDS were also calculated. Results: The median CI at the prescription IDS and sIDS was 1.63 and 1.47, respectively (p < 0.001). In 132 of 174 cases, the volume of normal tissue in the PIV was reduced by the prescription to the sIDS compared with the prescription IDS, in 20 cases it remained unchanged, and in 22 cases it was increased. Conclusion: The CIs obtained with linear accelerator-based stereotactic radiosurgery are comparable to those previously reported for gamma knife stereotactic radiosurgery. Using a uniform method to select the sIDS, adequate target coverage was usually achievable with prescription to an IDS greater than that chosen by the treating physician (prescription IDS), providing sparing of normal tissue. Thus, the sIDS might aid physicians in identifying a prescription IDS that balances coverage and conformity

Hybrid inverse design method for nonlifting bodies in incompressible flow

CSIR Research Space (South Africa)

Broughton, BA

2006-11-01

Full Text Available A methodology for the inverse design of non-lifting axisymmetric bodies in compressible flow is presented. In this method, an inverse design approach based on conformal mapping is used to design a set of airfoils in isolation. These airfoils...

Synthesis of conformationally restricted beta-turn mimics

NARCIS (Netherlands)

IJsselstijn, M.

2006-01-01

This thesis aims at developing methods for introducing conformational restriction in Beta-turns, the turn elements present in Beta-sheets. A conformationally restricted peptide might either be formed via incorporation of a bridging diamino acids in a growing peptide chain, or via covalent bond

Peer influence: neural mechanisms underlying in-group conformity.

Science.gov (United States)

Stallen, Mirre; Smidts, Ale; Sanfey, Alan G

2013-01-01

People often conform to the behavior of others with whom they identify. However, it is unclear what fundamental mechanisms underlie this type of conformity. Here, we investigate the processes mediating in-group conformity by using functional magnetic resonance imaging (fMRI). Participants completed a perceptual decision-making task while undergoing fMRI, during which they were exposed to the judgments of both in-group and out-group members. Our data suggest that conformity to the in-group is mediated by both positive affect as well as the cognitive capacity of perspective taking. Examining the processes that drive in-group conformity by utilizing a basic decision-making paradigm combined with neuroimaging methods provides important insights into the potential mechanisms of conformity. These results may provide an integral step in developing more effective campaigns using group conformity as a tool for behavioral change.

Nearly auto-parallel maps and conservation laws on curved spaces

International Nuclear Information System (INIS)

Vacaru, S.

1994-01-01

The theory of nearly auto-parallel maps (na-maps, generalization of conformal transforms) of Einstein-Cartan spaces is formulated. The transformation laws of geometrical objects and gravitational and matter field equations under superpositions of na-maps are considered. A special attention is paid to the very important problem of definition of conservation laws for gravitational fields. (Author)

Conformational changes in glycine tri- and hexapeptide

DEFF Research Database (Denmark)

Yakubovich, Alexander V.; Solov'yov, Ilia; Solov'yov, Andrey V.

2006-01-01

conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of the characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods...... also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids....

Flood Hazard Mapping by Applying Fuzzy TOPSIS Method

Science.gov (United States)

Han, K. Y.; Lee, J. Y.; Keum, H.; Kim, B. J.; Kim, T. H.

2017-12-01

There are lots of technical methods to integrate various factors for flood hazard mapping. The purpose of this study is to suggest the methodology of integrated flood hazard mapping using MCDM(Multi Criteria Decision Making). MCDM problems involve a set of alternatives that are evaluated on the basis of conflicting and incommensurate criteria. In this study, to apply MCDM to assessing flood risk, maximum flood depth, maximum velocity, and maximum travel time are considered as criterion, and each applied elements are considered as alternatives. The scheme to find the efficient alternative closest to a ideal value is appropriate way to assess flood risk of a lot of element units(alternatives) based on various flood indices. Therefore, TOPSIS which is most commonly used MCDM scheme is adopted to create flood hazard map. The indices for flood hazard mapping(maximum flood depth, maximum velocity, and maximum travel time) have uncertainty concerning simulation results due to various values according to flood scenario and topographical condition. These kind of ambiguity of indices can cause uncertainty of flood hazard map. To consider ambiguity and uncertainty of criterion, fuzzy logic is introduced which is able to handle ambiguous expression. In this paper, we made Flood Hazard Map according to levee breach overflow using the Fuzzy TOPSIS Technique. We confirmed the areas where the highest grade of hazard was recorded through the drawn-up integrated flood hazard map, and then produced flood hazard map can be compared them with those indicated in the existing flood risk maps. Also, we expect that if we can apply the flood hazard map methodology suggested in this paper even to manufacturing the current flood risk maps, we will be able to make a new flood hazard map to even consider the priorities for hazard areas, including more varied and important information than ever before. Keywords : Flood hazard map; levee break analysis; 2D analysis; MCDM; Fuzzy TOPSIS

A Hybrid Vision-Map Method for Urban Road Detection

Directory of Open Access Journals (Sweden)

Carlos Fernández

2017-01-01

Full Text Available A hybrid vision-map system is presented to solve the road detection problem in urban scenarios. The standardized use of machine learning techniques in classification problems has been merged with digital navigation map information to increase system robustness. The objective of this paper is to create a new environment perception method to detect the road in urban environments, fusing stereo vision with digital maps by detecting road appearance and road limits such as lane markings or curbs. Deep learning approaches make the system hard-coupled to the training set. Even though our approach is based on machine learning techniques, the features are calculated from different sources (GPS, map, curbs, etc., making our system less dependent on the training set.

A Method of Generating Indoor Map Spatial Data Automatically from Architectural Plans

Directory of Open Access Journals (Sweden)

SUN Weixin

2016-06-01

Full Text Available Taking architectural plans as data source, we proposed a method which can automatically generate indoor map spatial data. Firstly, referring to the spatial data demands of indoor map, we analyzed the basic characteristics of architectural plans, and introduced concepts of wall segment, adjoining node and adjoining wall segment, based on which basic flow of indoor map spatial data automatic generation was further established. Then, according to the adjoining relation between wall lines at the intersection with column, we constructed a repair method for wall connectivity in relation to the column. Utilizing the method of gradual expansibility and graphic reasoning to judge wall symbol local feature type at both sides of door or window, through update the enclosing rectangle of door or window, we developed a repair method for wall connectivity in relation to the door or window and a method for transform door or window into indoor map point feature. Finally, on the basis of geometric relation between adjoining wall segment median lines, a wall center-line extraction algorithm was presented. Taking one exhibition hall's architectural plan as example, we performed experiment and results show that the proposed methods have preferable applicability to deal with various complex situations, and realized indoor map spatial data automatic extraction effectively.

Concept mapping as a promising method to bring practice into science

NARCIS (Netherlands)

van Bon, M.J.H.; van de Goor, L.A.M.; Holsappel, J.C.; Kuunders, T.J.M.; Jacobs-van der Bruggen, M.A.M.; te Brake, J.H.M.; van Oers, J.A.M.

2014-01-01

Objective Concept mapping is a method for developing a conceptual framework of a complex topic for use as a guide to evaluation or planning. In concept mapping, thoughts and ideas are represented in the form of a picture or map, the content of which is determined by a group of stakeholders. This

QCD-instantons and conformal space-time inversion symmetry

International Nuclear Information System (INIS)

Klammer, D.

2008-04-01

In this paper, we explore the appealing possibility that the strong suppression of large-size QCD instantons - as evident from lattice data - is due to a surviving conformal space-time inversion symmetry. This symmetry is both suggested from the striking invariance of highquality lattice data for the instanton size distribution under inversion of the instanton size ρ→(left angle ρ right angle 2 )/(ρ) and from the known validity of space-time inversion symmetry in the classical instanton sector. We project the instanton calculus onto the four-dimensional surface of a five-dimensional sphere via conformal stereographic mapping, before investigating conformal inversion. This projection to a compact, curved geometry is both to avoid the occurence of divergences and to introduce the average instanton size left angle ρ right angle from the lattice data as a new length scale. The average instanton size is identified with the radius b of this 5d-sphere and acts as the conformal inversion radius. For b= left angle ρ right angle, our corresponding results are almost perfectly symmetric under space-time inversion and in good qualitative agreement with the lattice data. For (ρ)/(b)→0 we recover the familiar results of instanton perturbation theory in flat 4d-space. Moreover, we illustrate that a (weakly broken) conformal inversion symmetry would have significant consequences for QCD beyond instantons. As a further successful test for inversion symmetry, we present striking implications for another instanton dominated lattice observable, the chirality-flip ratio in the QCD vacuum. (orig.)

Adaptive Multilevel Methods with Local Smoothing for $H^1$- and $H^{\\mathrm{curl}}$-Conforming High Order Finite Element Methods

KAUST Repository

Janssen, Bä rbel; Kanschat, Guido

2011-01-01

A multilevel method on adaptive meshes with hanging nodes is presented, and the additional matrices appearing in the implementation are derived. Smoothers of overlapping Schwarz type are discussed; smoothing is restricted to the interior of the subdomains refined to the current level; thus it has optimal computational complexity. When applied to conforming finite element discretizations of elliptic problems and Maxwell equations, the method's convergence rates are very close to those for the nonadaptive version. Furthermore, the smoothers remain efficient for high order finite elements. We discuss the implementation in a general finite element code using the example of the deal.II library. © 2011 Societ y for Industrial and Applied Mathematics.

Structural alphabets derived from attractors in conformational space

Directory of Open Access Journals (Sweden)

Kleinjung Jens

2010-02-01

Full Text Available Abstract Background The hierarchical and partially redundant nature of protein structures justifies the definition of frequently occurring conformations of short fragments as 'states'. Collections of selected representatives for these states define Structural Alphabets, describing the most typical local conformations within protein structures. These alphabets form a bridge between the string-oriented methods of sequence analysis and the coordinate-oriented methods of protein structure analysis. Results A Structural Alphabet has been derived by clustering all four-residue fragments of a high-resolution subset of the protein data bank and extracting the high-density states as representative conformational states. Each fragment is uniquely defined by a set of three independent angles corresponding to its degrees of freedom, capturing in simple and intuitive terms the properties of the conformational space. The fragments of the Structural Alphabet are equivalent to the conformational attractors and therefore yield a most informative encoding of proteins. Proteins can be reconstructed within the experimental uncertainty in structure determination and ensembles of structures can be encoded with accuracy and robustness. Conclusions The density-based Structural Alphabet provides a novel tool to describe local conformations and it is specifically suitable for application in studies of protein dynamics.

Matching methods to produce maps for pest risk analysis to resources

Directory of Open Access Journals (Sweden)

Richard Baker

2013-09-01

Full Text Available Decision support systems (DSSs for pest risk mapping are invaluable for guiding pest risk analysts seeking to add maps to pest risk analyses (PRAs. Maps can help identify the area of potential establishment, the area at highest risk and the endangered area for alien plant pests. However, the production of detailed pest risk maps may require considerable time and resources and it is important to match the methods employed to the priority, time and detail required. In this paper, we apply PRATIQUE DSSs to Phytophthora austrocedrae, a pathogen of the Cupressaceae, Thaumetopoea pityocampa, the pine processionary moth, Drosophila suzukii, spotted wing Drosophila, and Thaumatotibia leucotreta, the false codling moth. We demonstrate that complex pest risk maps are not always a high priority and suggest that simple methods may be used to determine the geographic variation in relative risks posed by invasive alien species within an area of concern.

Inverse bootstrapping conformal field theories

Science.gov (United States)

Li, Wenliang

2018-01-01

We propose a novel approach to study conformal field theories (CFTs) in general dimensions. In the conformal bootstrap program, one usually searches for consistent CFT data that satisfy crossing symmetry. In the new method, we reverse the logic and interpret manifestly crossing-symmetric functions as generating functions of conformal data. Physical CFTs can be obtained by scanning the space of crossing-symmetric functions. By truncating the fusion rules, we are able to concentrate on the low-lying operators and derive some approximate relations for their conformal data. It turns out that the free scalar theory, the 2d minimal model CFTs, the ϕ 4 Wilson-Fisher CFT, the Lee-Yang CFTs and the Ising CFTs are consistent with the universal relations from the minimal fusion rule ϕ 1 × ϕ 1 = I + ϕ 2 + T , where ϕ 1 , ϕ 2 are scalar operators, I is the identity operator and T is the stress tensor.

Method to planarize three-dimensional structures to enable conformal electrodes

Science.gov (United States)

Nikolic, Rebecca J; Conway, Adam M; Graff, Robert T; Reinhardt, Catherine; Voss, Lars F; Shao, Qinghui

2012-11-20

Methods for fabricating three-dimensional PIN structures having conformal electrodes are provided, as well as the structures themselves. The structures include a first layer and an array of pillars with cavity regions between the pillars. A first end of each pillar is in contact with the first layer. A segment is formed on the second end of each pillar. The cavity regions are filled with a fill material, which may be a functional material such as a neutron sensitive material. The fill material covers each segment. A portion of the fill material is etched back to produce an exposed portion of the segment. A first electrode is deposited onto the fill material and each exposed segment, thereby forming a conductive layer that provides a common contact to each the exposed segment. A second electrode is deposited onto the first layer.

Conformal house

DEFF Research Database (Denmark)

Ryttov, Thomas Aaby; Sannino, Francesco

2010-01-01

fixed point. As a consistency check we recover the previously investigated bounds of the conformal windows when restricting to a single matter representation. The earlier conformal windows can be imagined to be part now of the new conformal house. We predict the nonperturbative anomalous dimensions...... at the infrared fixed points. We further investigate the effects of adding mass terms to the condensates on the conformal house chiral dynamics and construct the simplest instanton induced effective Lagrangian terms...

Nonperturbative results for two-index conformal windows

Energy Technology Data Exchange (ETDEWEB)

Bergner, Georg [Albert Einstein Center for Fundamental Physics,Institute for Theoretical Physics, University of Bern,Sidlerstrasse 5, CH-3012 Bern (Switzerland); Ryttov, Thomas A.; Sannino, Francesco [CP-Origins and the Danish IAS, University of Southern Denmark,5230 Odense M (Denmark)

2015-12-10

Via large and small N{sub c} relations we derive nonperturbative results about the conformal window of two-index theories. Using Schwinger-Dyson methods as well as four-loops results we estimate subleading corrections and show that naive large number of colors extrapolations are unreliable when N{sub c} is less than about six. Nevertheless useful nonperturbative inequalities for the size of the conformal windows, for any number of colors, can be derived. By further observing that the adjoint conformal window is independent of the number of colors we argue, among other things, that: the large N{sub c} two-index conformal window is twice the conformal window of the adjoint representation (which can be determined at small N{sub c}) expressed in terms of Dirac fermions; lattice results for adjoint matter can be used to provide independent information on the conformal dynamics of two-index theories such as SU(N{sub c}) with two and four symmetric Dirac flavors.

Nonperturbative results for two-index conformal windows

International Nuclear Information System (INIS)

Bergner, Georg; Ryttov, Thomas A.; Sannino, Francesco

2015-01-01

Via large and small N c relations we derive nonperturbative results about the conformal window of two-index theories. Using Schwinger-Dyson methods as well as four-loops results we estimate subleading corrections and show that naive large number of colors extrapolations are unreliable when N c is less than about six. Nevertheless useful nonperturbative inequalities for the size of the conformal windows, for any number of colors, can be derived. By further observing that the adjoint conformal window is independent of the number of colors we argue, among other things, that: the large N c two-index conformal window is twice the conformal window of the adjoint representation (which can be determined at small N c ) expressed in terms of Dirac fermions; lattice results for adjoint matter can be used to provide independent information on the conformal dynamics of two-index theories such as SU(N c ) with two and four symmetric Dirac flavors.

A Bayesian-probability-based method for assigning protein backbone dihedral angles based on chemical shifts and local sequences

Energy Technology Data Exchange (ETDEWEB)

Wang Jun; Liu Haiyan [University of Science and Technology of China, Hefei National Laboratory for Physical Sciences at the Microscale, and Key Laboratory of Structural Biology, School of Life Sciences (China)], E-mail: hyliu@ustc.edu.cn

2007-01-15

Chemical shifts contain substantial information about protein local conformations. We present a method to assign individual protein backbone dihedral angles into specific regions on the Ramachandran map based on the amino acid sequences and the chemical shifts of backbone atoms of tripeptide segments. The method uses a scoring function derived from the Bayesian probability for the central residue of a query tripeptide segment to have a particular conformation. The Ramachandran map is partitioned into representative regions at two levels of resolution. The lower resolution partitioning is equivalent to the conventional definitions of different secondary structure regions on the map. At the higher resolution level, the {alpha} and {beta} regions are further divided into subregions. Predictions are attempted at both levels of resolution. We compared our method with TALOS using the original TALOS database, and obtained comparable results. Although TALOS may produce the best results with currently available databases which are much enlarged, the Bayesian-probability-based approach can provide a quantitative measure for the reliability of predictions.

Non-linear realizations of conformal symmetry and effective field theory for the pseudo-conformal universe

International Nuclear Information System (INIS)

Hinterbichler, Kurt; Joyce, Austin; Khoury, Justin

2012-01-01

The pseudo-conformal scenario is an alternative to inflation in which the early universe is described by an approximate conformal field theory on flat, Minkowski space. Some fields acquire a time-dependent expectation value, which breaks the flat space so(4,2) conformal algebra to its so(4,1) de Sitter subalgebra. As a result, weight-0 fields acquire a scale invariant spectrum of perturbations. The scenario is very general, and its essential features are determined by the symmetry breaking pattern, irrespective of the details of the underlying microphysics. In this paper, we apply the well-known coset technique to derive the most general effective lagrangian describing the Goldstone field and matter fields, consistent with the assumed symmetries. The resulting action captures the low energy dynamics of any pseudo-conformal realization, including the U(1)-invariant quartic model and the Galilean Genesis scenario. We also derive this lagrangian using an alternative method of curvature invariants, consisting of writing down geometric scalars in terms of the conformal mode. Using this general effective action, we compute the two-point function for the Goldstone and a fiducial weight-0 field, as well as some sample three-point functions involving these fields

Modelling Multi Hazard Mapping in Semarang City Using GIS-Fuzzy Method

Science.gov (United States)

Nugraha, A. L.; Awaluddin, M.; Sasmito, B.

2018-02-01

One important aspect of disaster mitigation planning is hazard mapping. Hazard mapping can provide spatial information on the distribution of locations that are threatened by disaster. Semarang City as the capital of Central Java Province is one of the cities with high natural disaster intensity. Frequent natural disasters Semarang city is tidal flood, floods, landslides, and droughts. Therefore, Semarang City needs spatial information by doing multi hazard mapping to support disaster mitigation planning in Semarang City. Multi Hazards map modelling can be derived from parameters such as slope maps, rainfall, land use, and soil types. This modelling is done by using GIS method with scoring and overlay technique. However, the accuracy of modelling would be better if the GIS method is combined with Fuzzy Logic techniques to provide a good classification in determining disaster threats. The Fuzzy-GIS method will build a multi hazards map of Semarang city can deliver results with good accuracy and with appropriate threat class spread so as to provide disaster information for disaster mitigation planning of Semarang city. from the multi-hazard modelling using GIS-Fuzzy can be known type of membership that has a good accuracy is the type of membership Gauss with RMSE of 0.404 the smallest of the other membership and VAF value of 72.909% of the largest of the other membership.

Adaptive multiresolution method for MAP reconstruction in electron tomography

Energy Technology Data Exchange (ETDEWEB)

Acar, Erman, E-mail: erman.acar@tut.fi [Department of Signal Processing, Tampere University of Technology, P.O. Box 553, FI-33101 Tampere (Finland); BioMediTech, Tampere University of Technology, Biokatu 10, 33520 Tampere (Finland); Peltonen, Sari; Ruotsalainen, Ulla [Department of Signal Processing, Tampere University of Technology, P.O. Box 553, FI-33101 Tampere (Finland); BioMediTech, Tampere University of Technology, Biokatu 10, 33520 Tampere (Finland)

2016-11-15

3D image reconstruction with electron tomography holds problems due to the severely limited range of projection angles and low signal to noise ratio of the acquired projection images. The maximum a posteriori (MAP) reconstruction methods have been successful in compensating for the missing information and suppressing noise with their intrinsic regularization techniques. There are two major problems in MAP reconstruction methods: (1) selection of the regularization parameter that controls the balance between the data fidelity and the prior information, and (2) long computation time. One aim of this study is to provide an adaptive solution to the regularization parameter selection problem without having additional knowledge about the imaging environment and the sample. The other aim is to realize the reconstruction using sequences of resolution levels to shorten the computation time. The reconstructions were analyzed in terms of accuracy and computational efficiency using a simulated biological phantom and publically available experimental datasets of electron tomography. The numerical and visual evaluations of the experiments show that the adaptive multiresolution method can provide more accurate results than the weighted back projection (WBP), simultaneous iterative reconstruction technique (SIRT), and sequential MAP expectation maximization (sMAPEM) method. The method is superior to sMAPEM also in terms of computation time and usability since it can reconstruct 3D images significantly faster without requiring any parameter to be set by the user. - Highlights: • An adaptive multiresolution reconstruction method is introduced for electron tomography. • The method provides more accurate results than the conventional reconstruction methods. • The missing wedge and noise problems can be compensated by the method efficiently.

Conformation analysis - ConfC | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us ConfC Conformation analysis Data detail Data name Conformation analysis DOI 10.18908/lsdba.n...bdc00400-005 Description of data contents Results of conformation analysis for PDB files (raw data) Each res...ile size: 63.9 MB Simple search URL - Data acquisition method - Data analysis method - Number of data entrie...s 352 entries - About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Conformation analysis - ConfC | LSDB Archive ...

Pro region engineering of nerve growth factor by deep mutational scanning enables a yeast platform for conformational epitope mapping of anti-NGF monoclonal antibodies.

Science.gov (United States)

Medina-Cucurella, Angélica V; Zhu, Yaqi; Bowen, Scott J; Bergeron, Lisa M; Whitehead, Timothy A

2018-04-12

Nerve growth factor (NGF) plays a central role in multiple chronic pain conditions. As such, anti-NGF monoclonal antibodies (mAbs) that function by antagonizing NGF downstream signaling are leading drug candidates for non-opioid pain relief. To evaluate anti-canine NGF (cNGF) mAbs we sought a yeast surface display platform of cNGF. Both mature cNGF and pro-cNGF displayed on the yeast surface but bound conformationally sensitive mAbs at most 2.5-fold in mean fluorescence intensity above background, suggesting that cNGF was mostly misfolded. To improve the amount of folded, displayed cNGF, we used comprehensive mutagenesis, FACS, and deep sequencing to identify point mutants in the pro-region of canine NGF that properly enhance the folded protein displayed on the yeast surface. Out of 1,737 tested single point mutants in the pro region, 49 increased the amount of NGF recognized by conformationally sensitive mAbs. These gain-of-function mutations cluster around residues A-61-P-26. Gain-of-function mutants were additive, and a construct containing three mutations increased amount of folded cNGF to 23- fold above background. Using this new cNGF construct, fine conformational epitopes for tanezumab and three anti-cNGF mAbs were evaluated. The epitope revealed by the yeast experiments largely overlapped with the tanezumab epitope previously determined by X-ray crystallography. The other mAbs showed site-specific differences with tanezumab. As the number of binding epitopes of functionally neutralizing anti-NGF mAbs on NGF are limited, subtle differences in the individual interacting residues on NGF that bind each mAb contribute to the understanding of each antibody and variations in its neutralizing activity. These results demonstrate the potential of deep sequencing-guided protein engineering to improve the production of folded surface-displayed protein, and the resulting cNGF construct provides a platform to map conformational epitopes for other anti-neurotrophin m

Conformal and Nearly Conformal Theories at Large N

Science.gov (United States)

Tarnoplskiy, Grigory M.

In this thesis we present new results in conformal and nearly conformal field theories in various dimensions. In chapter two, we study different properties of the conformal Quantum Electrodynamics (QED) in continuous dimension d. At first we study conformal QED using large Nf methods, where Nf is the number of massless fermions. We compute its sphere free energy as a function of d, ignoring the terms of order 1/Nf and higher. For finite Nf we use the epsilon-expansion. Next we use a large Nf diagrammatic approach to calculate the leading corrections to CT, the coefficient of the two-point function of the stress-energy tensor, and CJ, the coefficient of the two-point function of the global symmetry current. We present explicit formulae as a function of d and check them versus the expectations in 2 and 4 - epsilon dimensions. In chapter three, we discuss vacuum stability in 1 + 1 dimensional conformal field theories with external background fields. We show that the vacuum decay rate is given by a non-local two-form. This two-form is a boundary term that must be added to the effective in/out Lagrangian. The two-form is expressed in terms of a Riemann-Hilbert decomposition for background gauge fields, and is given by its novel "functional'' version in the gravitational case. In chapter four, we explore Tensor models. Such models possess the large N limit dominated by the melon diagrams. The quantum mechanics of a real anti-commuting rank-3 tensor has a large N limit similar to the Sachdev-Ye-Kitaev (SYK) model. We also discuss the quantum mechanics of a complex 3-index anti-commuting tensor and argue that it is equivalent in the large N limit to a version of SYK model with complex fermions. Finally, we discuss models of a commuting tensor in dimension d. We study the spectrum of the large N quantum field theory of bosonic rank-3 tensors using the Schwinger-Dyson equations. We compare some of these results with the 4 - epsilon expansion, finding perfect agreement. We

Empirical evaluation of a practical indoor mobile robot navigation method using hybrid maps

DEFF Research Database (Denmark)

Özkil, Ali Gürcan; Fan, Zhun; Xiao, Jizhong

2010-01-01

This video presents a practical navigation scheme for indoor mobile robots using hybrid maps. The method makes use of metric maps for local navigation and a topological map for global path planning. Metric maps are generated as occupancy grids by a laser range finder to represent local information...... about partial areas. The global topological map is used to indicate the connectivity of the ‘places-of-interests’ in the environment and the interconnectivity of the local maps. Visual tags on the ceiling to be detected by the robot provide valuable information and contribute to reliable localization...... that the method is implemented successfully on physical robot in a hospital environment, which provides a practical solution for indoor navigation....

Radiation hybrid mapping as one of the main methods of the creation of high resolution maps of human and animal genomes

International Nuclear Information System (INIS)

Sulimova, G.E.; Kompanijtsev, A.A.; Mojsyak, E.V.; Rakhmanaliev, Eh.R.; Klimov, E.A.; Udina, I.G.; Zakharov, I.A.

2000-01-01

Radiation hybrid mapping (RH mapping) is considered as one of the main method of constructing physical maps of mammalian genomes. In introduction, theoretical prerequisites of developing of the RH mapping and statistical methods of data analysis are discussed. Comparative characteristics of universal commercial panels of the radiation hybrid somatic cells (RH panels) are shown. In experimental part of the work, RH mapping is used to localize nucleotide sequences adjacent to Not I sites of human chromosome 3 with the aim to integrate contig map of Nor I clones to comprehensive maps of human genome. Five nucleotide sequences adjacent to the sites of integration of papilloma virus in human genome and expressed in the cells of cervical cancer involved localized. It is demonstrated that the region 13q14.3-q21.1 was enriched with nucleotide sequences involved in the processes of carcinogenesis. RH mapping can be considered as one of the most perspective applications of modern radiation biology in the field of molecular genetics, that is, in constructing physical maps of mammalian genomes with high resolution level [ru

Case studies: Soil mapping using multiple methods

Science.gov (United States)

Petersen, Hauke; Wunderlich, Tina; Hagrey, Said A. Al; Rabbel, Wolfgang; Stümpel, Harald

2010-05-01

Soil is a non-renewable resource with fundamental functions like filtering (e.g. water), storing (e.g. carbon), transforming (e.g. nutrients) and buffering (e.g. contamination). Degradation of soils is meanwhile not only to scientists a well known fact, also decision makers in politics have accepted this as a serious problem for several environmental aspects. National and international authorities have already worked out preservation and restoration strategies for soil degradation, though it is still work of active research how to put these strategies into real practice. But common to all strategies the description of soil state and dynamics is required as a base step. This includes collecting information from soils with methods ranging from direct soil sampling to remote applications. In an intermediate scale mobile geophysical methods are applied with the advantage of fast working progress but disadvantage of site specific calibration and interpretation issues. In the framework of the iSOIL project we present here some case studies for soil mapping performed using multiple geophysical methods. We will present examples of combined field measurements with EMI-, GPR-, magnetic and gammaspectrometric techniques carried out with the mobile multi-sensor-system of Kiel University (GER). Depending on soil type and actual environmental conditions, different methods show a different quality of information. With application of diverse methods we want to figure out, which methods or combination of methods will give the most reliable information concerning soil state and properties. To investigate the influence of varying material we performed mapping campaigns on field sites with sandy, loamy and loessy soils. Classification of measured or derived attributes show not only the lateral variability but also gives hints to a variation in the vertical distribution of soil material. For all soils of course soil water content can be a critical factor concerning a succesful

From conformal Haag-Kastler nets to Wightman functions

International Nuclear Information System (INIS)

Joerss, M.

1996-08-01

Starting from a chiral conformal Haag-Kastler net on 2 dimensional Minkowski space we present a canonical construction that leads to a complete set of conformally covariant N-point-functions fulfilling the Wightman axioms. Our method consists of an explicit use of the representation theory of the universal covering group of SL(2,R) combined with a generalization of the conformal cluster theorem to N-point-functions. (orig.)

Methods for enhancing mapping of thermal fronts in oil recovery

Science.gov (United States)

Lee, D.O.; Montoya, P.C.; Wayland, J.R. Jr.

1984-03-30

A method for enhancing the resistivity contrasts of a thermal front in an oil recovery production field as measured by the controlled source audio frequency magnetotelluric (CSAMT) technique is disclosed. This method includes the steps of: (1) preparing a CSAMT-determined topological resistivity map of the production field; (2) introducing a solution of a dopant material into the production field at a concentration effective to alter the resistivity associated with the thermal front; said dopant material having a high cation exchange capacity which might be selected from the group consisting of montmorillonite, illite, and chlorite clays; said material being soluble in the conate water of the production field; (3) preparing a CSAMT-determined topological resistivity map of the production field while said dopant material is moving therethrough; and (4) mathematically comparing the maps from step (1) and step (3) to determine the location of the thermal front. This method is effective with the steam flood, fire flood and water flood techniques.

A new fundamental type of conformational isomerism

Science.gov (United States)

Canfield, Peter J.; Blake, Iain M.; Cai, Zheng-Li; Luck, Ian J.; Krausz, Elmars; Kobayashi, Rika; Reimers, Jeffrey R.; Crossley, Maxwell J.

2018-06-01

Isomerism is a fundamental chemical concept, reflecting the fact that the arrangement of atoms in a molecular entity has a profound influence on its chemical and physical properties. Here we describe a previously unclassified fundamental form of conformational isomerism through four resolved stereoisomers of a transoid (BF)O(BF)-quinoxalinoporphyrin. These comprise two pairs of enantiomers that manifest structural relationships not describable within existing IUPAC nomenclature and terminology. They undergo thermal diastereomeric interconversion over a barrier of 104 ± 2 kJ mol-1, which we term `akamptisomerization'. Feasible interconversion processes between conceivable synthesis products and reaction intermediates were mapped out by density functional theory calculations, identifying bond-angle inversion (BAI) at a singly bonded atom as the reaction mechanism. We also introduce the necessary BAI stereodescriptors parvo and amplo. Based on an extended polytope formalism of molecular structure and stereoisomerization, BAI-driven akamptisomerization is shown to be the final fundamental type of conformational isomerization.

Molecular modeling of the conformational dynamics of the cellular prion protein

Science.gov (United States)

Nguyen, Charles; Colling, Ian; Bartz, Jason; Soto, Patricia

2014-03-01

Prions are infectious agents responsible for transmissible spongiform encephalopathies (TSEs), a type of fatal neurodegenerative disease in mammals. Prions propagate biological information by conversion of the non-pathological version of the prion protein to the infectious conformation, PrPSc. A wealth of knowledge has shed light on the nature and mechanism of prion protein conversion. In spite of the significance of this problem, we are far from fully understanding the conformational dynamics of the cellular isoform. To remedy this situation we employ multiple biomolecular modeling techniques such as docking and molecular dynamics simulations to map the free energy landscape and determine what specific regions of the prion protein are most conductive to binding. The overall goal is to characterize the conformational dynamics of the cell form of the prion protein, PrPc, to gain insight into inhibition pathways against misfolding. NE EPSCoR FIRST Award to Patricia Soto.

Comparison of model reference and map based control method for vehicle stability enhancement

NARCIS (Netherlands)

Baek, S.; Son, M.; Song, J.; Boo, K.; Kim, H.

2012-01-01

A map based controller method to improve a vehicle lateral stability is proposed in this study and compared with the conventional method, a model referenced controller. A model referenced controller to determine compensated yaw moment uses the sliding mode method, but the proposed map based

Contribution mapping: a method for mapping the contribution of research to enhance its impact

Science.gov (United States)

2012-01-01

Background At a time of growing emphasis on both the use of research and accountability, it is important for research funders, researchers and other stakeholders to monitor and evaluate the extent to which research contributes to better action for health, and find ways to enhance the likelihood that beneficial contributions are realized. Past attempts to assess research 'impact' struggle with operationalizing 'impact', identifying the users of research and attributing impact to research projects as source. In this article we describe Contribution Mapping, a novel approach to research monitoring and evaluation that aims to assess contributions instead of impacts. The approach focuses on processes and actors and systematically assesses anticipatory efforts that aim to enhance contributions, so-called alignment efforts. The approach is designed to be useful for both accountability purposes and for assisting in better employing research to contribute to better action for health. Methods Contribution Mapping is inspired by a perspective from social studies of science on how research and knowledge utilization processes evolve. For each research project that is assessed, a three-phase process map is developed that includes the main actors, activities and alignment efforts during research formulation, production and knowledge extension (e.g. dissemination and utilization). The approach focuses on the actors involved in, or interacting with, a research project (the linked actors) and the most likely influential users, who are referred to as potential key users. In the first stage, the investigators of the assessed project are interviewed to develop a preliminary version of the process map and first estimation of research-related contributions. In the second stage, potential key-users and other informants are interviewed to trace, explore and triangulate possible contributions. In the third stage, the presence and role of alignment efforts is analyzed and the preliminary

Conformal three dimensional radiotherapy treatment planning in Lund

Energy Technology Data Exchange (ETDEWEB)

Knoos, T; Nilsson, P [Lund Univ. (Sweden). Dept. of Radiation Physics; Anders, A [Lund Univ. (Sweden). Dept. of Oncology

1995-12-01

The use of conformal therapy is based on 3-dimensional treatment planning as well as on methods and routines for 3-dimensional patient mapping, 3-dimensional virtual simulation and others. The management of patients at the Radiotherapy Department at the University Hospital in Lund (Sweden) is discussed. About 2100 new patients are annually treated with external radiotherapy using seven linear accelerators. Three of the accelerators have dual photon energies and electron treatment facilities. A multi-leaf collimator as well as an electronic portal imaging device are available on one machine. Two simulators and an in-house CT-scanner are used for treatment planning. From 1988 to 1992 Scandiplan (Umplan) was used. Since 1992, the treatment planning system is TMS (HELAX AB, Sweden), which is based on the pencil beam algorithm of Ahnesjo. The calculations use patient modulated accelerator specific energy fluence spectra which are compiled with pencil beams from Monte Carlo generated energy absorption kernels. Heterogeneity corrections are performed with results close to conventional algorithms. Irregular fields, either from standard or individual blocks and from multi-leaf collimators are handled by the treatment planning system. The field shape is determined conveniently using the beam`s eye view. The final field shape is exported electronically to either the block cutting machine or the multileaf collimator control computer. All patient fields are checked against the beam`s eye view during simulation using manual methods. Treatment verification is performed by portal films and in vivo dosimetry with silicon diodes or TL-dosimetry. Up to now, approximately 4400 patients have received a highly individualized 3-dimensional conformal treatment.

A Study on Remote Probing Method for Drawing Ecology/Nature Map and the Application (III) - Drawing the Swamp Classification Map around River

Energy Technology Data Exchange (ETDEWEB)

Jeon, Seong Woo; Cho, Jeong Keon; Jeong, Hwi Chol [Korea Environment Institute, Seoul (Korea)

2000-12-01

The map of ecology/nature in the amended Natural Environment Conservation Act is the necessary data, which is drawn through assessing the national land with ecological factors, to execute the Korea's environmental policy. Such important ecology/nature map should be continuously revised and improved the reliability with adding several new factors. In this point of view, this study has the significance in presenting the improvement scheme of ecology/nature map. 'A Study on Remote Probing Method for Drawing Ecology/Nature Map and the Application' that has been performed for 3 years since 1998 has researched the drawing method of subject maps that could be built in a short time - a land-covering classification map, a vegetation classification map, and a swamp classification map around river - and the promoting principles hereafter. This study also presented the possibility and limit of classification by several satellite image data, so it would be a big help to build the subject map in the Government level. The land-covering classification map, a result of the first year, has been already being built by Ministry of Environment as a national project, and the improvement scheme of the vegetation map that was presented as a result of second year has been used in building the basic ecology/nature map. We hope that the results from this study will be applied as basic data to draw an ecology/nature map and contribute to expanding the understanding on the usefulness of the several ecosystem analysis methods with applying an ecology/nature map and a remote probe. 55 refs., 38 figs., 24 tabs.

A method for statistically comparing spatial distribution maps

Directory of Open Access Journals (Sweden)

Reynolds Mary G

2009-01-01

Full Text Available Abstract Background Ecological niche modeling is a method for estimation of species distributions based on certain ecological parameters. Thus far, empirical determination of significant differences between independently generated distribution maps for a single species (maps which are created through equivalent processes, but with different ecological input parameters, has been challenging. Results We describe a method for comparing model outcomes, which allows a statistical evaluation of whether the strength of prediction and breadth of predicted areas is measurably different between projected distributions. To create ecological niche models for statistical comparison, we utilized GARP (Genetic Algorithm for Rule-Set Production software to generate ecological niche models of human monkeypox in Africa. We created several models, keeping constant the case location input records for each model but varying the ecological input data. In order to assess the relative importance of each ecological parameter included in the development of the individual predicted distributions, we performed pixel-to-pixel comparisons between model outcomes and calculated the mean difference in pixel scores. We used a two sample Student's t-test, (assuming as null hypothesis that both maps were identical to each other regardless of which input parameters were used to examine whether the mean difference in corresponding pixel scores from one map to another was greater than would be expected by chance alone. We also utilized weighted kappa statistics, frequency distributions, and percent difference to look at the disparities in pixel scores. Multiple independent statistical tests indicated precipitation as the single most important independent ecological parameter in the niche model for human monkeypox disease. Conclusion In addition to improving our understanding of the natural factors influencing the distribution of human monkeypox disease, such pixel-to-pixel comparison

Sampling Realistic Protein Conformations Using Local Structural Bias

DEFF Research Database (Denmark)

Hamelryck, Thomas Wim; Kent, John T.; Krogh, A.

2006-01-01

The prediction of protein structure from sequence remains a major unsolved problem in biology. The most successful protein structure prediction methods make use of a divide-and-conquer strategy to attack the problem: a conformational sampling method generates plausible candidate structures, which...... are subsequently accepted or rejected using an energy function. Conceptually, this often corresponds to separating local structural bias from the long-range interactions that stabilize the compact, native state. However, sampling protein conformations that are compatible with the local structural bias encoded...... in a given protein sequence is a long-standing open problem, especially in continuous space. We describe an elegant and mathematically rigorous method to do this, and show that it readily generates native-like protein conformations simply by enforcing compactness. Our results have far-reaching implications...

A recognition method research based on the heart sound texture map

Directory of Open Access Journals (Sweden)

Huizhong Cheng

2016-06-01

Full Text Available In order to improve the Heart Sound recognition rate and reduce the recognition time, in this paper, we introduces a new method for Heart Sound pattern recognition by using Heart Sound Texture Map. Based on the Heart Sound model, we give the Heart Sound time-frequency diagram and the Heart Sound Texture Map definition, we study the structure of the Heart Sound Window Function principle and realization method, and then discusses how to use the Heart Sound Window Function and the Short-time Fourier Transform to obtain two-dimensional Heart Sound time-frequency diagram, propose corner correlation recognition algorithm based on the Heart Sound Texture Map according to the characteristics of Heart Sound. The simulation results show that the Heart Sound Window Function compared with the traditional window function makes the first (S1 and the second (S2 Heart Sound texture clearer. And the corner correlation recognition algorithm based on the Heart Sound Texture Map can significantly improve the recognition rate and reduce the expense, which is an effective Heart Sound recognition method.

Optimal contact definition for reconstruction of Contact Maps

Directory of Open Access Journals (Sweden)

Stehr Henning

2010-05-01

Full Text Available Abstract Background Contact maps have been extensively used as a simplified representation of protein structures. They capture most important features of a protein's fold, being preferred by a number of researchers for the description and study of protein structures. Inspired by the model's simplicity many groups have dedicated a considerable amount of effort towards contact prediction as a proxy for protein structure prediction. However a contact map's biological interest is subject to the availability of reliable methods for the 3-dimensional reconstruction of the structure. Results We use an implementation of the well-known distance geometry protocol to build realistic protein 3-dimensional models from contact maps, performing an extensive exploration of many of the parameters involved in the reconstruction process. We try to address the questions: a to what accuracy does a contact map represent its corresponding 3D structure, b what is the best contact map representation with regard to reconstructability and c what is the effect of partial or inaccurate contact information on the 3D structure recovery. Our results suggest that contact maps derived from the application of a distance cutoff of 9 to 11Å around the Cβ atoms constitute the most accurate representation of the 3D structure. The reconstruction process does not provide a single solution to the problem but rather an ensemble of conformations that are within 2Å RMSD of the crystal structure and with lower values for the pairwise average ensemble RMSD. Interestingly it is still possible to recover a structure with partial contact information, although wrong contacts can lead to dramatic loss in reconstruction fidelity. Conclusions Thus contact maps represent a valid approximation to the structures with an accuracy comparable to that of experimental methods. The optimal contact definitions constitute key guidelines for methods based on contact maps such as structure prediction through

Structural characteristics and harmonic vibrational analysis of the stable conformer of 2,3-epoxypropanol by quantum chemical methods.

Science.gov (United States)

Arjunan, V; Rani, T; Santhanam, R; Mohan, S

2012-10-01

The FT-IR and FT-Raman spectra of H bond inner conformer of 2,3-epoxypropanol have been recorded in the regions 3700-400 and 3700-100 cm(-1), respectively. The spectra were interpreted in terms of fundamentals modes, combination and overtone bands. The normal coordinate analysis was carried out to confirm the precision of the assignments. The structure of the conformers H bond inner and H bond outer1 were optimised and the structural characteristics were determined by density functional theory (DFT) using B3LYP and MP2 methods with 6-31G** and 6-311++G** basis sets. The vibrational frequencies were calculated in all these methods and were compared with the experimental frequencies which yield good agreement between observed and calculated frequencies. The electronic properties HOMO and LUMO energies were measured by time-dependent TD-DFT approach. Copyright © 2012 Elsevier B.V. All rights reserved.

Mapping Norway - a Method to Register and Survey the Status of Accessibility

Science.gov (United States)

Michaelis, Sven; Bögelsack, Kathrin

2018-05-01

The Norwegian mapping authority has developed a standard method for mapping accessibility mostly for people with limited or no walking abilities in urban and recreational areas. We choose an object-orientated approach where points, lines and polygons represents objects in the environment. All data are stored in a geospatial database, so they can be presented as web map and analyzed using GIS software. By the end of 2016 more than 160 municipalities are mapped using that method. The aim of this project is to establish a national standard for mapping and to provide a geodatabase that shows the status of accessibility throughout Norway. The data provide a useful tool for national statistics, local planning authorities and private users. First results show that accessibility is low and Norway still faces many challenges to meet the government's goals for Universal Design.

β-Glucans: Relationships between Modification, Conformation and Functional Activities

Directory of Open Access Journals (Sweden)

Qiang Wang

2017-02-01

Full Text Available β-glucan is a type of polysaccharide which widely exists in bacteria, fungi, algae, and plants, and has been well known for its biological activities such as enhancing immunity, antitumor, antibacterial, antiviral, and wound healing activities. The conformation of β-glucan plays a crucial role on its biological activities. Therefore, β-glucans obtained from different sources, while sharing the same basic structures, often show different bioactivities. The basic structure and inter-molecular forces of polysaccharides can be changed by modification, which leads to the conformational transformation in solution that can directly affect bioactivity. In this review, we will first determine different ways to modify β-glucan molecules including physical methods, chemical methods, and biological methods, and then reveal the relationship of the flexible helix form of the molecule chain and the helix conformation to their bioactivities. Last, we summarize the scientific challenges to modifying β-glucan’s conformation and functional activity, and discuss its potential future development.

Keyframes Global Map Establishing Method for Robot Localization through Content-Based Image Matching

Directory of Open Access Journals (Sweden)

Tianyang Cao

2017-01-01

Full Text Available Self-localization and mapping are important for indoor mobile robot. We report a robust algorithm for map building and subsequent localization especially suited for indoor floor-cleaning robots. Common methods, for example, SLAM, can easily be kidnapped by colliding or disturbed by similar objects. Therefore, keyframes global map establishing method for robot localization in multiple rooms and corridors is needed. Content-based image matching is the core of this method. It is designed for the situation, by establishing keyframes containing both floor and distorted wall images. Image distortion, caused by robot view angle and movement, is analyzed and deduced. And an image matching solution is presented, consisting of extraction of overlap regions of keyframes extraction and overlap region rebuild through subblocks matching. For improving accuracy, ceiling points detecting and mismatching subblocks checking methods are incorporated. This matching method can process environment video effectively. In experiments, less than 5% frames are extracted as keyframes to build global map, which have large space distance and overlap each other. Through this method, robot can localize itself by matching its real-time vision frames with our keyframes map. Even with many similar objects/background in the environment or kidnapping robot, robot localization is achieved with position RMSE <0.5 m.

The method of images and Green's function for spherical domains

International Nuclear Information System (INIS)

Gutkin, Eugene; Newton, Paul K

2004-01-01

Motivated by problems in electrostatics and vortex dynamics, we develop two general methods for constructing Green's function for simply connected domains on the surface of the unit sphere. We prove a Riemann mapping theorem showing that such domains can be conformally mapped to the upper hemisphere. We then categorize all domains on the sphere for which Green's function can be constructed by an extension of the classical method of images. We illustrate our methods by several examples, such as the upper hemisphere, geodesic triangles, and latitudinal rectangles. We describe the point vortex motion in these domains, which is governed by a Hamiltonian determined by the Dirichlet Green's function

Experimental demonstration of conformal phased array antenna via transformation optics.

Science.gov (United States)

Lei, Juan; Yang, Juxing; Chen, Xi; Zhang, Zhiya; Fu, Guang; Hao, Yang

2018-02-28

Transformation Optics has been proven a versatile technique for designing novel electromagnetic devices and it has much wider applicability in many subject areas related to general wave equations. Among them, quasi-conformal transformation optics (QCTO) can be applied to minimize anisotropy of transformed media and has opened up the possibility to the design of broadband antennas with arbitrary geometries. In this work, a wide-angle scanning conformal phased array based on all-dielectric QCTO lens is designed and experimentally demonstrated. Excited by the same current distribution as such in a conventional planar array, the conformal system in presence of QCTO lens can preserve the same radiation characteristics of a planar array with wide-angle beam-scanning and low side lobe level (SLL). Laplace's equation subject to Dirichlet-Neumann boundary conditions is adopted to construct the mapping between the virtual and physical spaces. The isotropic lens with graded refractive index is realized by all-dielectric holey structure after an effective parameter approximation. The measurements of the fabricated system agree well with the simulated results, which demonstrate its excellent wide-angle beam scanning performance. Such demonstration paves the way to a robust but efficient array synthesis, as well as multi-beam and beam forming realization of conformal arrays via transformation optics.

Combining Semantic and Lexical Methods for Mapping MedDRA to VCM Icons.

Science.gov (United States)

Lamy, Jean-Baptiste; Tsopra, Rosy

2018-01-01

VCM (Visualization of Concept in Medicine) is an iconic language that represents medical concepts, such as disorders, by icons. VCM has a formal semantics described by an ontology. The icons can be used in medical software for providing a visual summary or enriching texts. However, the use of VCM icons in user interfaces requires to map standard medical terminologies to VCM. Here, we present a method combining semantic and lexical approaches for mapping MedDRA to VCM. The method takes advantage of the hierarchical relations in MedDRA. It also analyzes the groups of lemmas in the term's labels, and relies on a manual mapping of these groups to the concepts in the VCM ontology. We evaluate the method on 50 terms. Finally, we discuss the method and suggest perspectives.

Quantum Conformal Algebras and Closed Conformal Field Theory

CERN Document Server

Anselmi, D

1999-01-01

We investigate the quantum conformal algebras of N=2 and N=1 supersymmetric gauge theories. Phenomena occurring at strong coupling are analysed using the Nachtmann theorem and very general, model-independent, arguments. The results lead us to introduce a novel class of conformal field theories, identified by a closed quantum conformal algebra. We conjecture that they are the exact solution to the strongly coupled large-N_c limit of the open conformal field theories. We study the basic properties of closed conformal field theory and work out the operator product expansion of the conserved current multiplet T. The OPE structure is uniquely determined by two central charges, c and a. The multiplet T does not contain just the stress-tensor, but also R-currents and finite mass operators. For this reason, the ratio c/a is different from 1. On the other hand, an open algebra contains an infinite tower of non-conserved currents, organized in pairs and singlets with respect to renormalization mixing. T mixes with a se...

C-metric solution for conformal gravity with a conformally coupled scalar field

Energy Technology Data Exchange (ETDEWEB)

Meng, Kun, E-mail: mengkun@tjpu.edu.cn [School of Science, Tianjin Polytechnic University, Tianjin 300387 (China); Zhao, Liu, E-mail: lzhao@nankai.edu.cn [School of Physics, Nankai University, Tianjin 300071 (China)

2017-02-15

The C-metric solution of conformal gravity with a conformally coupled scalar field is presented. The solution belongs to the class of Petrov type D spacetimes and is conformal to the standard AdS C-metric appeared in vacuum Einstein gravity. For all parameter ranges, we identify some of the physically interesting static regions and the corresponding coordinate ranges. The solution may contain a black hole event horizon, an acceleration horizon, either of which may be cut by the conformal infinity or be hidden behind the conformal infinity. Since the model is conformally invariant, we also discussed the possible effects of the conformal gauge choices on the structure of the spacetime.

Non-conformable, partial and conformable transposition

DEFF Research Database (Denmark)

König, Thomas; Mäder, Lars Kai

2013-01-01

and the Commission regarding a directive’s outcome, play a much more strategic role than has to date acknowledged in the transposition literature. Whereas disagreement of a member state delays conformable transposition, it speeds up non-conformable transposition. Disagreement of the Commission only prolongs...... the transposition process. We therefore conclude that a stronger focus on an effective sanctioning mechanism is warranted for safeguarding compliance with directives....

How to Map Theory: Reliable Methods Are Fruitless Without Rigorous Theory.

Science.gov (United States)

Gray, Kurt

2017-09-01

Good science requires both reliable methods and rigorous theory. Theory allows us to build a unified structure of knowledge, to connect the dots of individual studies and reveal the bigger picture. Some have criticized the proliferation of pet "Theories," but generic "theory" is essential to healthy science, because questions of theory are ultimately those of validity. Although reliable methods and rigorous theory are synergistic, Action Identification suggests psychological tension between them: The more we focus on methodological details, the less we notice the broader connections. Therefore, psychology needs to supplement training in methods (how to design studies and analyze data) with training in theory (how to connect studies and synthesize ideas). This article provides a technique for visually outlining theory: theory mapping. Theory mapping contains five elements, which are illustrated with moral judgment and with cars. Also included are 15 additional theory maps provided by experts in emotion, culture, priming, power, stress, ideology, morality, marketing, decision-making, and more (see all at theorymaps.org ). Theory mapping provides both precision and synthesis, which helps to resolve arguments, prevent redundancies, assess the theoretical contribution of papers, and evaluate the likelihood of surprising effects.

Conformal Einstein spaces

International Nuclear Information System (INIS)

Kozameh, C.N.; Newman, E.T.; Tod, K.P.

1985-01-01

Conformal transformations in four-dimensional. In particular, a new set of two necessary and sufficient conditions for a space to be conformal to an Einstein space is presented. The first condition defines the class of spaces conformal to C spaces, whereas the last one (the vanishing of the Bach tensor) gives the particular subclass of C spaces which are conformally related to Einstein spaces. (author)

Conformal Gravity

International Nuclear Information System (INIS)

Hooft, G.

2012-01-01

The dynamical degree of freedom for the gravitational force is the metric tensor, having 10 locally independent degrees of freedom (of which 4 can be used to fix the coordinate choice). In conformal gravity, we split this field into an overall scalar factor and a nine-component remainder. All unrenormalizable infinities are in this remainder, while the scalar component can be handled like any other scalar field such as the Higgs field. In this formalism, conformal symmetry is spontaneously broken. An imperative demand on any healthy quantum gravity theory is that black holes should be described as quantum systems with micro-states as dictated by the Hawking-Bekenstein theory. This requires conformal symmetry that may be broken spontaneously but not explicitly, and this means that all conformal anomalies must cancel out. Cancellation of conformal anomalies yields constraints on the matter sector as described by some universal field theory. Thus black hole physics may eventually be of help in the construction of unified field theories. (author)

Optical and Physical Methods for Mapping Flooding with Satellite Imagery

Science.gov (United States)

Fayne, Jessica Fayne; Bolten, John; Lakshmi, Venkat; Ahamed, Aakash

2016-01-01

Flood and surface water mapping is becoming increasingly necessary, as extreme flooding events worldwide can damage crop yields and contribute to billions of dollars economic damages as well as social effects including fatalities and destroyed communities (Xaio et al. 2004; Kwak et al. 2015; Mueller et al. 2016).Utilizing earth observing satellite data to map standing water from space is indispensable to flood mapping for disaster response, mitigation, prevention, and warning (McFeeters 1996; Brakenridge and Anderson 2006). Since the early 1970s(Landsat, USGS 2013), researchers have been able to remotely sense surface processes such as extreme flood events to help offset some of these problems. Researchers have demonstrated countless methods and modifications of those methods to help increase knowledge of areas at risk and areas that are flooded using remote sensing data from optical and radar systems, as well as free publically available and costly commercial datasets.

Conformational analysis of six- and twelve-membered ring compounds by molecular dynamics

DEFF Research Database (Denmark)

Christensen, I T; Jørgensen, Flemming Steen

1997-01-01

. A series of methyl-substituted 1,3-dioxanes were investigated at 1000 K, and the number of chair-chair interconversions could be quantitatively correlated to the experimentally determined ring inversion barrier. Similarly, the distribution of sampled minimum-energy conformations correlated with the energy......-derived Boltzmann distribution. The macrocyclic ring system cyclododecane was subjected to an MD simulation at 1000 K and 71 different conformations could be sampled. These conformations were compared with the results of previously reported conformational analyses using stochastic search methods, and the MD method...

Moyal noncommutative integrability and the Burgers-KdV mapping

International Nuclear Information System (INIS)

Sedra, M.B.

2005-12-01

The Moyal momentum algebra, is once again used to discuss some important aspects of NC integrable models and 2d conformal field theories. Among the results presented, we set up algebraic structures and makes useful convention notations leading to extract non trivial properties of the Moyal momentum algebra. We study also the Lax pair building mechanism for particular examples namely, the noncommutative KdV and Burgers systems. We show in a crucial step that these two systems are mapped to each other through the following crucial mapping ∂ t 2 → ∂ t 3 ≡ ∂ t 2 ∂ x + α∂ x 3 . This makes a strong constraint on the NC Burgers system which corresponds to linearizing its associated differential equation. From the CFT's point of view, this constraint equation is nothing but the analogue of the conservation law of the conformal current. We believe that the considered mapping might help to bring new insights towards understanding the integrability of noncommutative 2d-systems. (author)

Suitability aero-geophysical methods for generating conceptual soil maps and their use in the modeling of process-related susceptibility maps

Science.gov (United States)

Tilch, Nils; Römer, Alexander; Jochum, Birgit; Schattauer, Ingrid

2014-05-01

In the past years, several times large-scale disasters occurred in Austria, which were characterized not only by flooding, but also by numerous shallow landslides and debris flows. Therefore, for the purpose of risk prevention, national and regional authorities also require more objective and realistic maps with information about spatially variable susceptibility of the geosphere for hazard-relevant gravitational mass movements. There are many and various proven methods and models (e.g. neural networks, logistic regression, heuristic methods) available to create such process-related (e.g. flat gravitational mass movements in soil) suszeptibility maps. But numerous national and international studies show a dependence of the suitability of a method on the quality of process data and parameter maps (f.e. Tilch & Schwarz 2011, Schwarz & Tilch 2011). In this case, it is important that also maps with detailed and process-oriented information on the process-relevant geosphere will be considered. One major disadvantage is that only occasionally area-wide process-relevant information exists. Similarly, in Austria often only soil maps for treeless areas are available. However, in almost all previous studies, randomly existing geological and geotechnical maps were used, which often have been specially adapted to the issues and objectives. This is one reason why very often conceptual soil maps must be derived from geological maps with only hard rock information, which often have a rather low quality. Based on these maps, for example, adjacent areas of different geological composition and process-relevant physical properties are razor sharp delineated, which in nature appears quite rarly. In order to obtain more realistic information about the spatial variability of the process-relevant geosphere (soil cover) and its physical properties, aerogeophysical measurements (electromagnetic, radiometric), carried out by helicopter, from different regions of Austria were interpreted

GIS-Based Integration of Subjective and Objective Weighting Methods for Regional Landslides Susceptibility Mapping

Directory of Open Access Journals (Sweden)

Suhua Zhou

2016-04-01

Full Text Available The development of landslide susceptibility maps is of great importance due to rapid urbanization. The purpose of this study is to present a method to integrate the subjective weight with objective weight for regional landslide susceptibility mapping on the geographical information system (GIS platform. The analytical hierarchy process (AHP, which is subjective, was employed to weight predictive factors’ contribution to landslide occurrence. The frequency ratio (FR method, which is objective, was used to derive subclasses’ frequency ratio with respect to landslides that indicate the relative importance of a subclass within each predictive factor. A case study was carried out at Tsushima Island, Japan, using a historical inventory of 534 landslides and seven predictive factors: elevation, slope, aspect, terrain roughness index (TRI, lithology, land cover and mean annual precipitation (MAP. The landslide susceptibility index (LSI was calculated using the weighted linear combination of factors’ weights and subclasses’ weights. The study area was classified into five susceptibility zones according to the LSI. In addition, the produced susceptibility map was compared with maps generated using the conventional FR and AHP method and validated using the relative landslide index (RLI. The validation result showed that the proposed method performed better than the conventional application of the FR method and AHP method. The obtained landslide susceptibility maps could serve as a scientific basis for urban planning and landslide hazard management.

A novel multispectral glacier mapping method and its performance in Greenland

Science.gov (United States)

Citterio, M.; Fausto, R. S.; Ahlstrom, A. P.; Andersen, S. B.

2014-12-01

Multispectral land surface classification methods are widely used for mapping glacier outlines. Significant post-classification manual editing is typically required, and mapping glacier outlines over larger regions remains a rather labour intensive task. In this contribution we introduce a novel method for mapping glacier outlines from multispectral satellite imagery, requiring only minor manual editing.Over the last decade GLIMS (Global Land Ice Measurements from Space) improved the availability of glacier outlines, and in 2012 the Randolph Glacier Inventory (RGI) attained global coverage by compiling existing and new data sources in the wake of the Fifth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC AR5). With the launch of Landsat 8 in 2013 and the upcoming ESA (European Space Agency) Sentinel 2 missions, the availability of multispectral imagery may grow faster than our ability to process it into timely and reliable glacier outline products. Improved automatic classification methods would enable a full exploitation of these new data sources.We outline the theoretical basis of the proposed classification algorithm, provide a step by step walk-through from raw imagery to finished ice cover grids and vector glacier outlines, and evaluate the performance of the new method in mapping the outlines of glaciers, ice caps and the Greenland Ice Sheet from Landsat 8 OLI imagery. The classification output is compared against manually digitized ice margin positions, the RGI vectors, and the PROMICE (Programme for Monitoring of the Greenland Ice Sheet) aerophotogrammetric map of Greenland ice masses over a sector of the Disko Island surge cluster in West Greenland, the Qassimiut ice sheet lobe in South Greenland, and the A.P. Olsen ice cap in NE Greenland.

Mapping the universe of RNA tetraloop folds

DEFF Research Database (Denmark)

Bottaro, Sandro; Lindorff-Larsen, Kresten

2017-01-01

We report a map of RNA tetraloop conformations constructed by calculating pairwise distances among all experimentally determined four-nucleotide hairpin loops. Tetraloops with similar structures are clustered together and, as expected, the two largest clusters are the canonical GNRA and UNCG fold...

Mixed dual finite element methods for the numerical treatment of the diffusion equation in hexagonal geometry

International Nuclear Information System (INIS)

Schneider, D.

2001-01-01

The nodal method Minos has been developed to offer a powerful method for the calculation of nuclear reactor cores in rectangular geometry. This method solves the mixed dual form of the diffusion equation and, also of the simplified P N approximation. The discretization is based on Raviart-Thomas' mixed dual finite elements and the iterative algorithm is an alternating direction method, which uses the current as unknown. The subject of this work is to adapt this method to hexagonal geometry. The guiding idea is to construct and test different methods based on the division of a hexagon into trapeze or rhombi with appropriate mapping of these quadrilaterals onto squares in order to take into advantage what is already available in the Minos solver. The document begins with a review of the neutron diffusion equation. Then we discuss its mixed dual variational formulation from a functional as well as from a numerical point of view. We study conformal and bilinear mappings for the two possible meshing of the hexagon. Thus, four different methods are proposed and are completely described in this work. Because of theoretical and numerical difficulties, a particular treatment has been necessary for methods based on the conformal mapping. Finally, numerical results are presented for a hexagonal benchmark to validate and compare the four methods with respect to pre-defined criteria. (authors)

Quantum-chemical calculation of energies and spectral characteristics of conformers in derivatives of phenylphosphine

International Nuclear Information System (INIS)

Chuvashev, D.D.; Ratovskii, G.V.; Zakzhevskii, V.G.

1987-01-01

The phenylphosphines PhPX 2 calculated by the MNDO method are characterized by two potential minima corresponding to the bisector and gonal conformations. For X = Cl, F, and C=N the bisector conformer predominates considerably, but for X = H and CH 3 the populations of the conformers are approximately the same. The characteristics of the electron transitions of the conformers found, determined by the CNDO/S method, differ substantially, which makes it possible to analyze the conformational compositions of arylphosphines by means of UV spectroscopy. In excited ππ* states the gonal conformation is characterized by a substantial donor effect of the PX 2 group, whereas the bisector conformation gives a certain acceptor effect

Functional brain mapping using H215O positron emission tomography (I): statistical parametric mapping method

International Nuclear Information System (INIS)

Lee, Dong Soo; Lee, Jae Sung; Kim, Kyeong Min; Chung, June Key; Lee, Myung Chul

1998-01-01

We investigated the statistical methods to compose the functional brain map of human working memory and the principal factors that have an effect on the methods for localization. Repeated PET scans with successive four tasks, which consist of one control and three different activation tasks, were performed on six right-handed normal volunteers for 2 minutes after bolus injections of 925 MBq H 2 15 O at the intervals of 30 minutes. Image data were analyzed using SPM96 (Statistical Parametric Mapping) implemented with Matlab (Mathworks Inc., U.S.A.). Images from the same subject were spatially registered and were normalized using linear and nonlinear transformation methods. Significant difference between control and each activation state was estimated at every voxel based on the general linear model. Differences of global counts were removed using analysis of covariance (ANCOVA) with global activity as covariate. Using the mean and variance for each condition which was adjusted using ANCOVA, t-statistics was performed on every voxel. To interpret the results more easily, t-values were transformed to the standard Gaussian distribution (Z-score). All the subjects carried out the activation and control tests successfully. Average rate of correct answers was 95%. The numbers of activated blobs were 4 for verbal memory I, 9 for verbal memory II, 9 for visual memory, and 6 for conjunctive activation of these three tasks. The verbal working memory activates predominantly left-sided structures, and the visual memory activates the right hemisphere. We conclude that rCBF PET imaging and statistical parametric mapping method were useful in the localization of the brain regions for verbal and visual working memory

Conformal FDTD modeling wake fields

Energy Technology Data Exchange (ETDEWEB)

Jurgens, T.; Harfoush, F.

1991-05-01

Many computer codes have been written to model wake fields. Here we describe the use of the Conformal Finite Difference Time Domain (CFDTD) method to model the wake fields generated by a rigid beam traveling through various accelerating structures. The non- cylindrical symmetry of some of the problems considered here requires the use of a three dimensional code. In traditional FDTD codes, curved surfaces are approximated by rectangular steps. The errors introduced in wake field calculations by such an approximation can be reduced by increasing the mesh size, therefore increasing the cost of computing. Another approach, validated here, deforms Ampere and Faraday contours near a media interface so as to conform to the interface. These improvements of the FDTD method result in better accuracy of the fields at asymptotically no computational cost. This method is also capable of modeling thin wires as found in beam profile monitors, and slots and cracks as found in resistive wall motions. 4 refs., 5 figs.

Conformal symmetry in two-dimensional space: recursion representation of conformal block

International Nuclear Information System (INIS)

Zamolodchikov, A.B.

1988-01-01

The four-point conformal block plays an important part in the analysis of the conformally invariant operator algebra in two-dimensional space. The behavior of the conformal block is calculated in the present paper in the limit in which the dimension Δ of the intermediate operator tends to infinity. This makes it possible to construct a recursion relation for this function that connects the conformal block at arbitrary Δ to the blocks corresponding to the dimensions of the zero vectors in the degenerate representations of the Virasoro algebra. The relation is convenient for calculating the expansion of the conformal block in powers of the uniformizing parameters q = i π tau

Theories of inflation and conformal transformations

International Nuclear Information System (INIS)

Kalara, S.; Kaloper, N.; Olive, K.A.

1990-01-01

We show that several different theories of inflation including R 2 , Brans-Dicke, and induced-gravity inflation are all related to generalized or power-law inflation by means of conformal transformations. These theories all involve non-standard gravity, and the use of conformal transformations allows one to obtain standard inflationary predictions such as the expansion time-scale, reheating and density perturbations in each case very simply. We also discuss the possibilities of this method to be applied to string theory. (orig.)

Assessment of Three Flood Hazard Mapping Methods: A Case Study of Perlis

Science.gov (United States)

Azizat, Nazirah; Omar, Wan Mohd Sabki Wan

2018-03-01

Flood is a common natural disaster and also affect the all state in Malaysia. Regarding to Drainage and Irrigation Department (DID) in 2007, about 29, 270 km2 or 9 percent of region of the country is prone to flooding. Flood can be such devastating catastrophic which can effected to people, economy and environment. Flood hazard mapping can be used is an important part in flood assessment to define those high risk area prone to flooding. The purposes of this study are to prepare a flood hazard mapping in Perlis and to evaluate flood hazard using frequency ratio, statistical index and Poisson method. The six factors affecting the occurrence of flood including elevation, distance from the drainage network, rainfall, soil texture, geology and erosion were created using ArcGIS 10.1 software. Flood location map in this study has been generated based on flooded area in year 2010 from DID. These parameters and flood location map were analysed to prepare flood hazard mapping in representing the probability of flood area. The results of the analysis were verified using flood location data in year 2013, 2014, 2015. The comparison result showed statistical index method is better in prediction of flood area rather than frequency ratio and Poisson method.

Conformal symmetry breaking operators for differential forms on spheres

CERN Document Server

Kobayashi, Toshiyuki; Pevzner, Michael

2016-01-01

This work is the first systematic study of all possible conformally covariant differential operators transforming differential forms on a Riemannian manifold X into those on a submanifold Y with focus on the model space (X, Y) = (Sn, Sn-1). The authors give a complete classification of all such conformally covariant differential operators, and find their explicit formulæ in the flat coordinates in terms of basic operators in differential geometry and classical hypergeometric polynomials. Resulting families of operators are natural generalizations of the Rankin–Cohen brackets for modular forms and Juhl's operators from conformal holography. The matrix-valued factorization identities among all possible combinations of conformally covariant differential operators are also established. The main machinery of the proof relies on the "F-method" recently introduced and developed by the authors. It is a general method to construct intertwining operators between C∞-induced representations or to find singular vecto...

Preference of small molecules for local minimum conformations when binding to proteins.

Directory of Open Access Journals (Sweden)

Qi Wang

2007-09-01

Full Text Available It is well known that small molecules (ligands do not necessarily adopt their lowest potential energy conformations when binding to proteins. Analyses of protein-bound ligand crystal structures have reportedly shown that many of them do not even adopt the conformations at local minima of their potential energy surfaces (local minimum conformations. The results of these analyses raise a concern regarding the validity of virtual screening methods that use ligands in local minimum conformations. Here we report a normal-mode-analysis (NMA study of 100 crystal structures of protein-bound ligands. Our data show that the energy minimization of a ligand alone does not automatically stop at a local minimum conformation if the minimum of the potential energy surface is shallow, thus leading to the folding of the ligand. Furthermore, our data show that all 100 ligand conformations in their protein-bound ligand crystal structures are nearly identical to their local minimum conformations obtained from NMA-monitored energy minimization, suggesting that ligands prefer to adopt local minimum conformations when binding to proteins. These results both support virtual screening methods that use ligands in local minimum conformations and caution about possible adverse effect of excessive energy minimization when generating a database of ligand conformations for virtual screening.

Methods to Measure Map Readability

OpenAIRE

Harrie, Lars

2009-01-01

Creation of maps in real-time web services introduces challenges concerning map readability. Therefore we must introduce analytical measures controlling the readability. The aim of this study is to develop and evaluate analytical readability measures with the help of user tests.

Cylinder renormalization for Siegel disks and a constructive Measurable Riemann Mapping Theorem

CERN Document Server

Gaydashev, D G

2006-01-01

The boundary of the Siegel disk of a quadratic polynomial with an irrationally indifferent fixed point with the golden mean rotation number has been observed to be self-similar. The geometry of this self-similarity is universal for a large class of holomorphic maps. A renormalization explanation of this universality has been proposed in the literature. However, one of the ingredients of this explanation, the hyperbolicity of renormalization, has not been proved yet. The present work considers a cylinder renormalization - a novel type of renormalization for holomorphic maps with a Siegel disk which is better suited for a hyperbolicity proof. A key element of a cylinder renormalization of a holomorphic map is a conformal isomorphism of a dynamical quotient of a subset of $\\field{C}$ to a bi-infinite cylinder $\\field{C} / \\field{Z}$. A construction of this conformal isomorphism is an implicit procedure which can be performed using the Measurable Riemann Mapping Theorem. We present a constructive proof of the Mea...

Conformal FDTD modeling of 3-D wake fields

International Nuclear Information System (INIS)

Jurgens, T.G.; Harfoush, F.A.

1991-01-01

Many computer codes have been written to model wake fields. Here the authors describe the use of the Conformal Finite Difference Time Domain (CFDTD) method to model the wake fields generated by a rigid beam traveling through various accelerating structures. The non-cylindrical symmetry of some of the problems considered here requires the use of a three dimensional code. In traditional FDTD codes, curved surfaces are approximated by rectangular steps. The errors introduced in wake field calculations by such an approximation can be reduced by increasing the mesh size, therefore increasing the cost of computing. Another approach, validated here, deforms Ampere and Faraday contours near a media interface so as to conform to the interface. These improvements so as to conform to the interface. These improvements to the FDTD method result in better accuracy of the fields at asymptotically no computational cost. This method is also capable of modeling thin wires as found in beam profile monitors, and slots and cracks as found in resistive wall monitors

Techniques and methods to guarantee Bologna-conform higher education in GNSS

Science.gov (United States)

Mayer, M.

2012-04-01

The Bologna Declaration is aiming for student-centered, outcome-related, and competence-based teaching. In order to fulfill these demands, deep level learning techniques should be used to meet the needs of adult-compatible and self-determined learning. The presentation will summarize selected case studies carried out in the framework of the lecture course "Introduction into GNSS positioning" of the Geodetic Institute of the Karlsruhe Institute of Technology (Karlsruhe, Germany). The lecture course "Introduction into GNSS positioning" is a compulsory part of the Bachelor study course "Geodesy and Geoinformatics" and also a supplementary module of the Bachelor study course "Geophysics". Within the lecture course, basic knowledge and basic principles of Global Navigation Satellite Systems, like GPS, are imparted. The lecture course was migrated starting from a classically designed geodetic lecture course, which consisted of a well-adapted combination of teacher-centered classroom lectures and practical training (e.g., field exercises). The recent Bologna-conform blended learning concepts supports and motivates students to learn more sustainable using online and classroom learning methods. Therefore, an appropriate combination of - classroom lectures: Students and teacher give lectures - practical training: Students select topics individually - online learning: ILIAS (learning management system) is used as data, result, and communication platform. The framing didactical method is based on the so-called anchored instruction approach. Within this approach, an up-to-date scientific GNSS-related paper dealing with the large-scale geodetic project "Fehmarn Belt Fixed Link" is used as anchor. The students have to read the paper individually in the beginning of the semester. This enables them to realize a lot of not-known GNSS-related facts. Therefore, questions can be formulated. The lecture course deals with these questions, in order to answer them. At the end of the

Mapping stellar content to dark matter haloes - III. Environmental dependence and conformity of galaxy colours

Science.gov (United States)

Zu, Ying; Mandelbaum, Rachel

2018-05-01

Recent studies suggest that the quenching properties of galaxies are correlated over several megaparsecs. The large-scale `galactic conformity' phenomenon around central galaxies has been regarded as a potential signature of `galaxy assembly bias' or `pre-heating', both of which interpret conformity as a result of direct environmental effects acting on galaxy formation. Building on the iHOD halo quenching framework developed in Zu and Mandelbaum, we discover that our fiducial halo mass quenching model, without any galaxy assembly bias, can successfully explain the overall environmental dependence and the conformity of galaxy colours in Sloan Digital Sky Survey, as measured by the mark correlation functions of galaxy colours and the red galaxy fractions around isolated primaries, respectively. Our fiducial iHOD halo quenching mock also correctly predicts the differences in the spatial clustering and galaxy-galaxy lensing signals between the more versus less red galaxy subsamples, split by the red-sequence ridge line at fixed stellar mass. Meanwhile, models that tie galaxy colours fully or partially to halo assembly bias have difficulties in matching all these observables simultaneously. Therefore, we demonstrate that the observed environmental dependence of galaxy colours can be naturally explained by the combination of (1) halo quenching and (2) the variation of halo mass function with environment - an indirect environmental effect mediated by two separate physical processes.

Method for mapping population-based case-control studies: an application using generalized additive models

Directory of Open Access Journals (Sweden)

Aschengrau Ann

2006-06-01

Full Text Available Abstract Background Mapping spatial distributions of disease occurrence and risk can serve as a useful tool for identifying exposures of public health concern. Disease registry data are often mapped by town or county of diagnosis and contain limited data on covariates. These maps often possess poor spatial resolution, the potential for spatial confounding, and the inability to consider latency. Population-based case-control studies can provide detailed information on residential history and covariates. Results Generalized additive models (GAMs provide a useful framework for mapping point-based epidemiologic data. Smoothing on location while controlling for covariates produces adjusted maps. We generate maps of odds ratios using the entire study area as a reference. We smooth using a locally weighted regression smoother (loess, a method that combines the advantages of nearest neighbor and kernel methods. We choose an optimal degree of smoothing by minimizing Akaike's Information Criterion. We use a deviance-based test to assess the overall importance of location in the model and pointwise permutation tests to locate regions of significantly increased or decreased risk. The method is illustrated with synthetic data and data from a population-based case-control study, using S-Plus and ArcView software. Conclusion Our goal is to develop practical methods for mapping population-based case-control and cohort studies. The method described here performs well for our synthetic data, reproducing important features of the data and adequately controlling the covariate. When applied to the population-based case-control data set, the method suggests spatial confounding and identifies statistically significant areas of increased and decreased odds ratios.

A method of analyzing rectal surface area irradiated and rectal complications in prostate conformal radiotherapy

International Nuclear Information System (INIS)

Lu Yong; Song, Paul Y.; Li Shidong; Spelbring, Danny R.; Vijayakumar, Srinivasan; Haraf, Daniel J.; Chen, George T.Y.

1995-01-01

Purpose: To develop a method of analyzing rectal surface area irradiated and rectal complications in prostate conformal radiotherapy. Methods and Materials: Dose-surface histograms of the rectum, which state the rectal surface area irradiated to any given dose, were calculated for a group of 27 patients treated with a four-field box technique to a total (tumor minimum) dose ranging from 68 to 70 Gy. Occurrences of rectal toxicities as defined by the Radiation Therapy Oncology Group (RTOG) were recorded and examined in terms of dose and rectal surface area irradiated. For a specified end point of rectal complication, the complication probability was analyzed as a function of dose irradiated to a fixed rectal area, and as a function of area receiving a fixed dose. Lyman's model of normal tissue complication probability (NTCP) was used to fit the data. Results: The observed occurrences of rectal complications appear to depend on the rectal surface area irradiated to a given dose level. The patient distribution of each toxicity grade exhibits a maximum as a function of percentage surface area irradiated, and the maximum moves to higher values of percentage surface area as the toxicity grade increases. The dependence of the NTCP for the specified end point on dose and percentage surface area irradiated was fitted to Lyman's NTCP model with a set of parameters. The curvature of the NTCP as a function of the surface area suggests that the rectum is a parallel structured organ. Conclusions: The described method of analyzing rectal surface area irradiated yields interesting insight into understanding rectal complications in prostate conformal radiotherapy. Application of the method to a larger patient data set has the potential to facilitate the construction of a full dose-surface-complication relationship, which would be most useful in guiding clinical practice

Crystal structures and conformers of CyMe4-BTBP

Directory of Open Access Journals (Sweden)

Lyczko Krzysztof

2015-12-01

Full Text Available The crystal structure of new conformation of the CyMe4-BTBP ligand (ttc has been presented. The ttt conformer of this compound in a form of THF solvate has been also crystallized. The geometries of six possible conformations (ttt, ttc, tct, tcc, ctc and ccc of the CyMe4-BTBP ligand have been modeled in the gas phase and in solutions (MeOH and H2O by DFT calculations using B3LYP/6-31G(d,p method. According to the calculations, in the three different media the conformers with trans orientation of the N atoms in the bipyridyl moiety are the most stable.

Conformal array design on arbitrary polygon surface with transformation optics

Energy Technology Data Exchange (ETDEWEB)

Deng, Li, E-mail: dengl@bupt.edu.cn; Hong, Weijun, E-mail: hongwj@bupt.edu.cn; Zhu, Jianfeng; Peng, Biao; Li, Shufang [Beijing Key Laboratory of Network System Architecture and Convergence, School of Information and Communication Engineering, Beijing University of Posts and Telecommunications, 100876 Beijing (China); Wu, Yongle, E-mail: wuyongle138@gmail.com [Beijing Key Laboratory of Work Safety Intelligent Monitoring, School of Electronic Engineering, Beijing University of Posts and Telecommunications, 100876 Beijing (China)

2016-06-15

A transformation-optics based method to design a conformal antenna array on an arbitrary polygon surface is proposed and demonstrated in this paper. This conformal antenna array can be adjusted to behave equivalently as a uniformly spaced linear array by applying an appropriate transformation medium. An typical example of general arbitrary polygon conformal arrays, not limited to circular array, is presented, verifying the proposed approach. In summary, the novel arbitrary polygon surface conformal array can be utilized in array synthesis and beam-forming, maintaining all benefits of linear array.

Conformal array design on arbitrary polygon surface with transformation optics

International Nuclear Information System (INIS)

Deng, Li; Hong, Weijun; Zhu, Jianfeng; Peng, Biao; Li, Shufang; Wu, Yongle

2016-01-01

A transformation-optics based method to design a conformal antenna array on an arbitrary polygon surface is proposed and demonstrated in this paper. This conformal antenna array can be adjusted to behave equivalently as a uniformly spaced linear array by applying an appropriate transformation medium. An typical example of general arbitrary polygon conformal arrays, not limited to circular array, is presented, verifying the proposed approach. In summary, the novel arbitrary polygon surface conformal array can be utilized in array synthesis and beam-forming, maintaining all benefits of linear array.

Fine mapping of multiple QTL using combined linkage and linkage disequilibrium mapping – A comparison of single QTL and multi QTL methods

Directory of Open Access Journals (Sweden)

Meuwissen Theo HE

2007-04-01

Full Text Available Abstract Two previously described QTL mapping methods, which combine linkage analysis (LA and linkage disequilibrium analysis (LD, were compared for their ability to detect and map multiple QTL. The methods were tested on five different simulated data sets in which the exact QTL positions were known. Every simulated data set contained two QTL, but the distances between these QTL were varied from 15 to 150 cM. The results show that the single QTL mapping method (LDLA gave good results as long as the distance between the QTL was large (> 90 cM. When the distance between the QTL was reduced, the single QTL method had problems positioning the two QTL and tended to position only one QTL, i.e. a "ghost" QTL, in between the two real QTL positions. The multi QTL mapping method (MP-LDLA gave good results for all evaluated distances between the QTL. For the large distances between the QTL (> 90 cM the single QTL method more often positioned the QTL in the correct marker bracket, but considering the broader likelihood peaks of the single point method it could be argued that the multi QTL method was more precise. Since the distances were reduced the multi QTL method was clearly more accurate than the single QTL method. The two methods combine well, and together provide a good tool to position single or multiple QTL in practical situations, where the number of QTL and their positions are unknown.

Capillary Electrophoresis Single-Strand Conformational Polymorphisms as a Method to Differentiate Algal Species

Directory of Open Access Journals (Sweden)

Alice Jernigan

2015-01-01

Full Text Available Capillary electrophoresis single-strand conformational polymorphism (CE-SSCP was explored as a fast and inexpensive method to differentiate both prokaryotic (blue-green and eukaryotic (green and brown algae. A selection of two blue-green algae (Nostoc muscorum and Anabaena inaequalis, five green algae (Chlorella vulgaris, Oedogonium foveolatum, Mougeotia sp., Scenedesmus quadricauda, and Ulothrix fimbriata, and one brown algae (Ectocarpus sp. were examined and CE-SSCP electropherogram “fingerprints” were compared to each other for two variable regions of either the 16S or 18S rDNA gene. The electropherogram patterns were remarkably stable and consistent for each particular species. The patterns were unique to each species, although some common features were observed between the different types of algae. CE-SSCP could be a useful method for monitoring changes in an algae species over time as potential shifts in species occurred.

Grafting, pruning, and the antipodal map on measured laminations

OpenAIRE

Dumas, David

2006-01-01

Grafting a measured lamination on a hyperbolic surface defines a self-map of Teichmuller space, which is a homeomorphism by a result of Scannell and Wolf. In this paper we study the large-scale behavior of pruning, which is the inverse of grafting. Specifically, for each conformal structure $X \\in \\T(S)$, pruning $X$ gives a map $\\ML(S) \\to \\T(S)$. We show that this map extends to the Thurston compactification of $\\T(S)$, and that its boundary values are the natural antipodal involution relat...

Method of Automatic Ontology Mapping through Machine Learning and Logic Mining

Institute of Scientific and Technical Information of China (English)

王英林

2004-01-01

Ontology mapping is the bottleneck of handling conflicts among heterogeneous ontologies and of implementing reconfiguration or interoperability of legacy systems. We proposed an ontology mapping method by using machine learning, type constraints and logic mining techniques. This method is able to find concept correspondences through instances and the result is optimized by using an error function; it is able to find attribute correspondence between two equivalent concepts and the mapping accuracy is enhanced by combining together instances learning, type constraints and the logic relations that are imbedded in instances; moreover, it solves the most common kind of categorization conflicts. We then proposed a merging algorithm to generate the shared ontology and proposed a reconfigurable architecture for interoperation based on multi agents. The legacy systems are encapsulated as information agents to participate in the integration system. Finally we give a simplified case study.

Massless fields in curved space-time: The conformal formalism

International Nuclear Information System (INIS)

Castagnino, M.A.; Sztrajman, J.B.

1986-01-01

A conformally invariant theory for massless quantum fields in curved space-time is formulated. We analyze the cases of spin-0, - 1/2 , and -1. The theory is developed in the important case of an ''expanding universe,'' generalizing the particle model of ''conformal transplantation'' known for spin-0 to spins- 1/2 and -1. For the spin-1 case two methods introducing new conformally invariant gauge conditions are stated, and a problem of inconsistency that was stated for spin-1 is overcome

Indoor Map Acquisition System Using Global Scan Matching Method and Laser Range Scan Data

Science.gov (United States)

Hisanaga, Satoshi; Kase, Takaaki

Simultaneous localization and mapping (SLAM) is the latest technique for constructing indoor maps. In indoor environment, a localization method using the features of the walls as landmarks has been studied in the past. The past study has a drawback. It cannot localize in spaces surrounded by featureless walls or walls on which similar features are repeated. To overcome this drawback, we developed an accuracy localization method that ignores the features of the walls. We noted the fact that the walls in a building are aligned along only two orthogonal directions. By considering a specific wall to be a reference wall, the location of a robot was expressed by using the distance between the robot and the reference wall. We developed the robot in order to evaluate the mapping accuracy of our method and carried out an experiment to map a corridor (40m long) that contained featureless parts. The map obtained had a margin of error of less than 2%.

On possibility of the conformal infrared asymptotics in nonabelian Yang-Mills theories

International Nuclear Information System (INIS)

Vasil'ev, A.N.; Perekalin, M.M.; Pis'mak, Yu.M.

1983-01-01

A possibility of the conformal-invariant infrared asymptotics in nonabelian Yang-Mills theories is discussed. In the framework of the conformal bootstrap method it is shown that the hypothesis about the exact conformal invariance contradicts the transversality of the polarization operator i.e. the Ward identities. However, it is still possible to use the conformal theory as an approximate solution to the bootstrap equations

Dynamical realizations of l-conformal Newton–Hooke group

International Nuclear Information System (INIS)

Galajinsky, Anton; Masterov, Ivan

2013-01-01

The method of nonlinear realizations and the technique previously developed in [A. Galajinsky, I. Masterov, Nucl. Phys. B 866 (2013) 212, (arXiv:1208.1403)] are used to construct a dynamical system without higher derivative terms, which holds invariant under the l-conformal Newton–Hooke group. A configuration space of the model involves coordinates, which parametrize a particle moving in d spatial dimensions and a conformal mode, which gives rise to an effective external field. The dynamical system describes a generalized multi-dimensional oscillator, which undergoes accelerated/decelerated motion in an ellipse in accord with evolution of the conformal mode. Higher derivative formulations are discussed as well. It is demonstrated that the multi-dimensional Pais–Uhlenbeck oscillator enjoys the l=3/2 -conformal Newton–Hooke symmetry for a particular choice of its frequencies

Contribution to the study of conformal theories and integrable models

International Nuclear Information System (INIS)

Sochen, N.

1992-05-01

The purpose of this thesis is the 2-D physics study. The main tool is the conformal field theory with Kac-Moody and W algebra. This theory describes the 2-D models that have translation, rotation and dilatation symmetries, at their critical point. The expanded conformal theories describe models that have a larger symmetry than conformal symmetry. After a review of conformal theory methods, the author effects a detailed study of singular vector form in sl(2) affine algebra. With this important form, correlation functions can be calculated. The classical W algebra is studied and the relations between classical W algebra and quantum W algebra are specified. Bosonization method is presented and sl(2)/sl(2) topological model, studied. Partition function bosonization of different models is described. A program of rational theory classification is described linking rational conformal theories and spin integrable models, and interesting relations between Boltzmann weights of different models have been found. With these relations, the integrability of models by a direct calculation of their Boltzmann weights is proved

Identification of p38α MAP kinase inhibitors by pharmacophore based virtual screening

DEFF Research Database (Denmark)

Gangwal, Rahul P; Das, Nihar R; Thanki, Kaushik

2014-01-01

The p38α mitogen-activated protein (MAP) kinase plays a vital role in treating many inflammatory diseases. In the present study, a combined ligand and structure based pharmacophore model was developed to identify potential DFG-in selective p38 MAP kinase inhibitors. Conformations of co...

A Method of Spatial Mapping and Reclassification for High-Spatial-Resolution Remote Sensing Image Classification

Directory of Open Access Journals (Sweden)

Guizhou Wang

2013-01-01

Full Text Available This paper presents a new classification method for high-spatial-resolution remote sensing images based on a strategic mechanism of spatial mapping and reclassification. The proposed method includes four steps. First, the multispectral image is classified by a traditional pixel-based classification method (support vector machine. Second, the panchromatic image is subdivided by watershed segmentation. Third, the pixel-based multispectral image classification result is mapped to the panchromatic segmentation result based on a spatial mapping mechanism and the area dominant principle. During the mapping process, an area proportion threshold is set, and the regional property is defined as unclassified if the maximum area proportion does not surpass the threshold. Finally, unclassified regions are reclassified based on spectral information using the minimum distance to mean algorithm. Experimental results show that the classification method for high-spatial-resolution remote sensing images based on the spatial mapping mechanism and reclassification strategy can make use of both panchromatic and multispectral information, integrate the pixel- and object-based classification methods, and improve classification accuracy.

Basin boundaries and focal points in a map coming from Bairstow's method.

Science.gov (United States)

Gardini, Laura; Bischi, Gian-Italo; Fournier-Prunaret, Daniele

1999-06-01

This paper is devoted to the study of the global dynamical properties of a two-dimensional noninvertible map, with a denominator which can vanish, obtained by applying Bairstow's method to a cubic polynomial. It is shown that the complicated structure of the basins of attraction of the fixed points is due to the existence of singularities such as sets of nondefinition, focal points, and prefocal curves, which are specific to maps with a vanishing denominator, and have been recently introduced in the literature. Some global bifurcations that change the qualitative structure of the basin boundaries, are explained in terms of contacts among these singularities. The techniques used in this paper put in evidence some new dynamic behaviors and bifurcations, which are peculiar of maps with denominator; hence they can be applied to the analysis of other classes of maps coming from iterative algorithms (based on Newton's method, or others). (c) 1999 American Institute of Physics.

Methodical bases of perceptual mapping of printing industry companies

Directory of Open Access Journals (Sweden)

Kalinin Pavel

2017-01-01

Full Text Available This is to study the methodological foundations of perceptual mapping in printing industry enterprises. This research has a practice focus which affects the choice of its methodological framework. The authors use such scientific research as analysis of cause-effect relationships, synthesis, problem analysis, expert evaluation and image visualization methods. In this paper, the authors present their assessment of the competitive environment of major printing industry companies in Kirov oblast; their assessment employs perceptual mapping enables by Minitab 14. This technique can be used by experts in the field of marketing and branding to assess the competitive environment in any market. The object of research is printing industry in Kirov oblast. The most important conclusion of this study is that in perceptual mapping, all the parameters are integrated in a single system and provide a more objective view of the company’s market situation.

Selecting Map Projections in Minimizing Area Distortions in GIS Applications

Directory of Open Access Journals (Sweden)

Ahmet Kaya

2008-12-01

Full Text Available Varioussoftware for Geographical Information Systems (GISs have been developed and used in many different engineering projects. In GIS applications, map coverage is important in terms of performing reliable and meaningful queries. Map projections can be conformal, equal-area and equidistant. The goal of an application plays an important role in choosing one of those projections. Choosing the equal-area projection for an application in which area information is used (forestry, agriculture, ecosystem etc reduces the amount of distortion on the area, but many users using GIS ignore this fact and continue to use applications with present map sheets no matter in what map projection it is. For example, extracting area information from data whose country system’s map sheet is in conformal projection is relatively more distorted, compared to an equal-area projection one. The goal of this study is to make the best decision in choosing the most proper equal-area projection among the choices provided by ArcGIS 9.0, which is a popular GIS software package, and making a comparison on area errors when conformal projection is used. In this study, the area of parcels chosen in three different regions and geographic coordinates and whose sizes vary between 0.01 to 1,000,000 ha are calculated according to Transversal Mercator (TM, 3°, Universal Transversal Mercator (UTM, 6° and 14 different equal-area projections existing in the ArcGIS 9.0 GIS software package. The parcel areas calculated with geographical coordinates are accepted as definite. The difference between the sizes calculated according to projection coordinates and real sizes of the parcels are determined. Consequently, the appropriate projections are decided for the areas smaller and equal than 1,000 ha and greater than 1,000 ha in the GIS software package.

4D-Qsar Study of Some Pyrazole Pyridine Carboxylic Acid Derivatives by Electron Conformational-Genetic Algorithm Method.

Science.gov (United States)

Tuzun, Burak; Yavuz, Sevtap Caglar; Sabanci, Nazmiye; Saripinar, Emin

2018-05-13

In the present work, pharmacophore identification and biological activity prediction for 86 pyrazole pyridine carboxylic acid derivatives were made using the electron conformational genetic algorithm approach which was introduced as a 4D-QSAR analysis by us in recent years. In the light of the data obtained from quantum chemical calculations at HF/6-311 G** level, the electron conformational matrices of congruity (ECMC) were constructed by EMRE software. Comparing the matrices, electron conformational submatrix of activity (ECSA, Pha) was revealed that are common for these compounds within a minimum tolerance. A parameter pool was generated considering the obtained pharmacophore. To determine the theoretical biological activity of molecules and identify the best subset of variables affecting bioactivities, we used the nonlinear least square regression method and genetic algorithm. The results obtained in this study are in good agreement with the experimental data presented in the literature. The model for training and test sets attained by the optimum 12 parameters gave highly satisfactory results with R2training= 0.889, q2=0.839 and SEtraining=0.066, q2ext1 = 0.770, q2ext2 = 0.750, q2ext3=0.824, ccctr = 0.941, ccctest = 0.869 and cccall = 0.927. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Optimization of the uniformity of a metal flow during continuous extrusion by the Conform method

Science.gov (United States)

Lyubanova, A. Sh.; Gorokhov, Yu. V.; Solopko, I. V.; Ziborov, A. Yu.

2010-03-01

The scheme of plastic deformation of a billet in a container is considered as part of continuous extrusion by the Conform method. A mathematical model of the motion of a viscoplastic Bingham liquid is used to determine the metal velocity distribution in the plastic-deformation zone. As a result, the optimum angle between the longitudinal axes of the die and container is estimated. This angle is found to be one of the main factors affecting the nonuniformity of deformation when a metal flows into the die. The calculated results are compared to experimental data.

Toward a general mixed quantum/classical method for the calculation of the vibronic ECD of a flexible dye molecule with different stable conformers: Revisiting the case of 2,2,2-trifluoro-anthrylethanol.

Science.gov (United States)

Cerezo, Javier; Aranda, Daniel; Avila Ferrer, Francisco J; Prampolini, Giacomo; Mazzeo, Giuseppe; Longhi, Giovanna; Abbate, Sergio; Santoro, Fabrizio

2018-06-01

We extend a recently proposed mixed quantum/classical method for computing the vibronic electronic circular dichroism (ECD) spectrum of molecules with different conformers, to cases where more than one hindered rotation is present. The method generalizes the standard procedure, based on the simple Boltzmann average of the vibronic spectra of the stable conformers, and includes the contribution of structures that sample all the accessible conformational space. It is applied to the simulation of the ECD spectrum of (S)-2,2,2-trifluoroanthrylethanol, a molecule with easily interconvertible conformers, whose spectrum exhibits a pattern of alternating positive and negative vibronic peaks. Results are in very good agreement with experiment and show that spectra averaged over all the sampled conformational space can deviate significantly from the simple average of the contributions of the stable conformers. The present mixed quantum/classical method is able to capture the effect of the nonlinear dependence of the rotatory strength on the molecular structure and of the anharmonic couplings among the modes responsible for molecular flexibility. Despite its computational cost, the procedure is still affordable and promises to be useful in all cases where the ECD shape arises from a subtle balance between vibronic effects and conformational variety. © 2018 Wiley Periodicals, Inc.

Logarithmic conformal field theory through nilpotent conformal dimensions

International Nuclear Information System (INIS)

Moghimi-Araghi, S.; Rouhani, S.; Saadat, M.

2001-01-01

We study logarithmic conformal field theories (LCFTs) through the introduction of nilpotent conformal weights. Using this device, we derive the properties of LCFTs such as the transformation laws, singular vectors and the structure of correlation functions. We discuss the emergence of an extra energy momentum tensor, which is the logarithmic partner of the energy momentum tensor

Viscous conformal gauge theories

DEFF Research Database (Denmark)

Toniato, Arianna; Sannino, Francesco; Rischke, Dirk H.

2017-01-01

We present the conformal behavior of the shear viscosity-to-entropy density ratio and the fermion-number diffusion coefficient within the perturbative regime of the conformal window for gauge-fermion theories.......We present the conformal behavior of the shear viscosity-to-entropy density ratio and the fermion-number diffusion coefficient within the perturbative regime of the conformal window for gauge-fermion theories....

Recursive representation of the torus 1-point conformal block

Science.gov (United States)

Hadasz, Leszek; Jaskólski, Zbigniew; Suchanek, Paulina

2010-01-01

The recursive relation for the 1-point conformal block on a torus is derived and used to prove the identities between conformal blocks recently conjectured by Poghossian in [1]. As an illustration of the efficiency of the recurrence method the modular invariance of the 1-point Liouville correlation function is numerically analyzed.

Mapping the Conformational Dynamics of E-selectin upon Interaction with its Ligands

KAUST Repository

Aleisa, Fajr A

2013-05-15

Selectins are key adhesion molecules responsible for initiating a multistep process that leads a cell out of the blood circulation and into a tissue or organ. The adhesion of cells (expressing ligands) to the endothelium (expressing the selectin i.e.,E-selectin) occurs through spatio-temporally regulated interactions that are mediated by multiple intra- and inter-cellular components. The mechanism of cell adhesion is investigated primarily using ensemble-based experiments, which provides indirect information about how individual molecules work in such a complex system. Recent developments in single-molecule (SM) fluorescence detection allow for the visualization of individual molecules with a good spatio-temporal resolution nanometer spatial resolution and millisecond time resolution). Furthermore, advanced SM fluorescence techniques such as Förster Resonance Energy Transfer (FRET) and super-resolution microscopy provide unique opportunities to obtain information about nanometer-scale conformational dynamics of proteins as well as nano-scale architectures of biological samples. Therefore, the state-of-the-art SM techniques are powerful tools for investigating complex biological system such as the mechanism of cell adhesion. In this project, several constructs of fluorescently labeled E-selectin will be used to study the conformational dynamics of E-selectin binding to its ligand(s) using SM-FRET and combination of SM-FRET and force microscopy. These studies will be beneficial to fully understand the mechanistic details of cell adhesion and migration of cells using the established model system of hematopoietic stem cells (HSCs) adhesion to the selectin expressing endothelial cells (such as the E-selectin expressing endothelial cells in the bone marrow).

Identification of Serine Conformers by Matrix-Isolation IR Spectroscopy Aided by Near-Infrared Laser-Induced Conformational Change, 2D Correlation Analysis, and Quantum Mechanical Anharmonic Computations.

Science.gov (United States)

Najbauer, Eszter E; Bazsó, Gábor; Apóstolo, Rui; Fausto, Rui; Biczysko, Malgorzata; Barone, Vincenzo; Tarczay, György

2015-08-20

The conformers of α-serine were investigated by matrix-isolation IR spectroscopy combined with NIR laser irradiation. This method, aided by 2D correlation analysis, enabled unambiguously grouping the spectral lines to individual conformers. On the basis of comparison of at least nine experimentally observed vibrational transitions of each conformer with empirically scaled (SQM) and anharmonic (GVPT2) computed IR spectra, six conformers were identified. In addition, the presence of at least one more conformer in Ar matrix was proved, and a short-lived conformer with a half-life of (3.7 ± 0.5) × 10(3) s in N2 matrix was generated by NIR irradiation. The analysis of the NIR laser-induced conversions revealed that the excitation of the stretching overtone of both the side chain and the carboxylic OH groups can effectively promote conformational changes, but remarkably different paths were observed for the two kinds of excitations.

A comparison of multidimensional scaling methods for perceptual mapping

NARCIS (Netherlands)

Bijmolt, T.H.A.; Wedel, M.

Multidimensional scaling has been applied to a wide range of marketing problems, in particular to perceptual mapping based on dissimilarity judgments. The introduction of methods based on the maximum likelihood principle is one of the most important developments. In this article, the authors compare

Integrability of conformal fishnet theory

Science.gov (United States)

Gromov, Nikolay; Kazakov, Vladimir; Korchemsky, Gregory; Negro, Stefano; Sizov, Grigory

2018-01-01

We study integrability of fishnet-type Feynman graphs arising in planar four-dimensional bi-scalar chiral theory recently proposed in arXiv:1512.06704 as a special double scaling limit of gamma-deformed N = 4 SYM theory. We show that the transfer matrix "building" the fishnet graphs emerges from the R-matrix of non-compact conformal SU(2 , 2) Heisenberg spin chain with spins belonging to principal series representations of the four-dimensional conformal group. We demonstrate explicitly a relationship between this integrable spin chain and the Quantum Spectral Curve (QSC) of N = 4 SYM. Using QSC and spin chain methods, we construct Baxter equation for Q-functions of the conformal spin chain needed for computation of the anomalous dimensions of operators of the type tr( ϕ 1 J ) where ϕ 1 is one of the two scalars of the theory. For J = 3 we derive from QSC a quantization condition that fixes the relevant solution of Baxter equation. The scaling dimensions of the operators only receive contributions from wheel-like graphs. We develop integrability techniques to compute the divergent part of these graphs and use it to present the weak coupling expansion of dimensions to very high orders. Then we apply our exact equations to calculate the anomalous dimensions with J = 3 to practically unlimited precision at any coupling. These equations also describe an infinite tower of local conformal operators all carrying the same charge J = 3. The method should be applicable for any J and, in principle, to any local operators of bi-scalar theory. We show that at strong coupling the scaling dimensions can be derived from semiclassical quantization of finite gap solutions describing an integrable system of noncompact SU(2 , 2) spins. This bears similarities with the classical strings arising in the strongly coupled limit of N = 4 SYM.

A system and method for online high-resolution mapping of gastric slow-wave activity.

Science.gov (United States)

Bull, Simon H; O'Grady, Gregory; Du, Peng; Cheng, Leo K

2014-11-01

High-resolution (HR) mapping employs multielectrode arrays to achieve spatially detailed analyses of propagating bioelectrical events. A major current limitation is that spatial analyses must currently be performed "off-line" (after experiments), compromising timely recording feedback and restricting experimental interventions. These problems motivated development of a system and method for "online" HR mapping. HR gastric recordings were acquired and streamed to a novel software client. Algorithms were devised to filter data, identify slow-wave events, eliminate corrupt channels, and cluster activation events. A graphical user interface animated data and plotted electrograms and maps. Results were compared against off-line methods. The online system analyzed 256-channel serosal recordings with no unexpected system terminations with a mean delay 18 s. Activation time marking sensitivity was 0.92; positive predictive value was 0.93. Abnormal slow-wave patterns including conduction blocks, ectopic pacemaking, and colliding wave fronts were reliably identified. Compared to traditional analysis methods, online mapping had comparable results with equivalent coverage of 90% of electrodes, average RMS errors of less than 1 s, and CC of activation maps of 0.99. Accurate slow-wave mapping was achieved in near real-time, enabling monitoring of recording quality and experimental interventions targeted to dysrhythmic onset. This work also advances the translation of HR mapping toward real-time clinical application.

Conformational restrictions in ligand binding to the human intestinal di-/tripeptide transporter

DEFF Research Database (Denmark)

Våbenø, Jon; Nielsen, Carsten Uhd; Steffansen, Bente

2005-01-01

The aim of the present study was to develop a computational method aiding the design of dipeptidomimetic pro-moieties targeting the human intestinal di-/tripeptide transporter hPEPT1. First, the conformation in which substrates bind to hPEPT1 (the bioactive conformation) was identified...... to change the peptide backbone conformation (DeltaE(bbone)) from the global energy minimum conformation to the identified bioactive conformation was calculated for 20 hPEPT1 targeted model prodrugs with known K(i) values. Quantitatively, an inverse linear relationship (r(2)=0.81, q(2)=0.80) was obtained...

Microscopic insights into the NMR relaxation based protein conformational entropy meter

Science.gov (United States)

Kasinath, Vignesh; Sharp, Kim A.; Wand, A. Joshua

2013-01-01

Conformational entropy is a potentially important thermodynamic parameter contributing to protein function. Quantitative measures of conformational entropy are necessary for an understanding of its role but have been difficult to obtain. An empirical method that utilizes changes in conformational dynamics as a proxy for changes in conformational entropy has recently been introduced. Here we probe the microscopic origins of the link between conformational dynamics and conformational entropy using molecular dynamics simulations. Simulation of seven pro! teins gave an excellent correlation with measures of side-chain motion derived from NMR relaxation. The simulations show that the motion of methyl-bearing side-chains are sufficiently coupled to that of other side chains to serve as excellent reporters of the overall side-chain conformational entropy. These results tend to validate the use of experimentally accessible measures of methyl motion - the NMR-derived generalized order parameters - as a proxy from which to derive changes in protein conformational entropy. PMID:24007504

Radial expansion for spinning conformal blocks

CERN Document Server

Costa, Miguel S.; Penedones, João; Trevisani, Emilio

2016-07-12

This paper develops a method to compute any bosonic conformal block as a series expansion in the optimal radial coordinate introduced by Hogervorst and Rychkov. The method reduces to the known result when the external operators are all the same scalar operator, but it allows to compute conformal blocks for external operators with spin. Moreover, we explain how to write closed form recursion relations for the coefficients of the expansions. We study three examples of four point functions in detail: one vector and three scalars; two vectors and two scalars; two spin 2 tensors and two scalars. Finally, for the case of two external vectors, we also provide a more efficient way to generate the series expansion using the analytic structure of the blocks as a function of the scaling dimension of the exchanged operator.

Method of solving conformal models in D-dimensional space I

International Nuclear Information System (INIS)

Fradkin, E.S.; Palchik, M.Y.

1996-01-01

We study the Hilbert space of conformal field theory in D-dimensional space. The latter is shown to have model-independent structure. The states of matter fields and gauge fields form orthogonal subspaces. The dynamical principle fixing the choice of model may be formulated either in each of these subspaces or in their direct sum. In the latter case, gauge interactions are necessarily present in the model. We formulate the conditions specifying the class of models where gauge interactions are being neglected. The anomalous Ward identities are derived. Different values of anomalous parameters (D-dimensional analogs of a central charge, including operator ones) correspond to different models. The structure of these models is analogous to that of 2-dimensional conformal theories. Each model is specified by D-dimensional analog of null vector. The exact solutions of the simplest models of this type are examined. It is shown that these models are equivalent to Lagrangian models of scalar fields with a triple interaction. The values of dimensions of such fields are calculated, and the closed sets of differential equations for higher Green functions are derived. Copyright copyright 1996 Academic Press, Inc

Arctic Basemaps In Google Maps

DEFF Research Database (Denmark)

Muggah, J.; Mioc, Darka

2010-01-01

The Ocean Mapping Group has been collecting data in the Arctic since 2003 and there are approximately 2,000 basemaps. In the current online storage format used by the OMG, it is difficult to view the data and users cannot easily pan and zoom. The purpose of this research is to investigate...... the advantages of the use of Google Maps, to display the OMG's Arctic data. The map should should load the large Artic dataset in a reasonable time. The bathymetric images were created using software in Linux written by the OMG, and a step-by-step process was used to create images from the multibeam data...... collected by the OMG in the Arctic. The website was also created using Linux operating system. The projection needed to be changed from Lambert Conformal Conic (useful at higher Latitudes) to Mercator (used by Google Maps) and the data needed to have a common colour scheme. After creating and testing...

From global to heavy-light: 5-point conformal blocks

International Nuclear Information System (INIS)

Alkalaev, Konstantin; Belavin, Vladimir

2016-01-01

We consider Virasoro conformal blocks in the large central charge limit. There are different regimes depending on the behavior of the conformal dimensions. The most simple regime is reduced to the global sl(2,ℂ) conformal blocks while the most complicated one is known as the classical conformal blocks. Recently, Fitzpatrick, Kaplan, and Walters showed that the two regimes are related through the intermediate stage of the so-called heavy-light semiclassical limit. We study this idea in the particular case of the 5-point conformal block. To find the 5-point global block we use the projector technique and the Casimir operator approach. Furthermore, we discuss the relation between the global and the heavy-light limits and construct the heavy-light block from the global block. In this way we reproduce our previous results for the 5-point perturbative classical block obtained by means of the monodromy method.

Teamwork: improved eQTL mapping using combinations of machine learning methods.

Directory of Open Access Journals (Sweden)

Marit Ackermann

Full Text Available Expression quantitative trait loci (eQTL mapping is a widely used technique to uncover regulatory relationships between genes. A range of methodologies have been developed to map links between expression traits and genotypes. The DREAM (Dialogue on Reverse Engineering Assessments and Methods initiative is a community project to objectively assess the relative performance of different computational approaches for solving specific systems biology problems. The goal of one of the DREAM5 challenges was to reverse-engineer genetic interaction networks from synthetic genetic variation and gene expression data, which simulates the problem of eQTL mapping. In this framework, we proposed an approach whose originality resides in the use of a combination of existing machine learning algorithms (committee. Although it was not the best performer, this method was by far the most precise on average. After the competition, we continued in this direction by evaluating other committees using the DREAM5 data and developed a method that relies on Random Forests and LASSO. It achieved a much higher average precision than the DREAM best performer at the cost of slightly lower average sensitivity.

Magic identities for conformal four-point integrals

International Nuclear Information System (INIS)

Drummond, James M.; Henn, Johannes; Smirnov, Vladimir A.; Sokatchev, Emery

2007-01-01

We propose an iterative procedure for constructing classes of off-shell four-point conformal integrals which are identical. The proof of the identity is based on the conformal properties of a subintegral common for the whole class. The simplest example are the so-called 'triple scalar box' and 'tennis court' integrals. In this case we also give an independent proof using the method of Mellin-Barnes representation which can be applied in a similar way for general off-shell Feynman integrals

Localized conformational interrogation of antibody and antibody-drug conjugates by site-specific carboxyl group footprinting.

Science.gov (United States)

Pan, Lucy Yan; Salas-Solano, Oscar; Valliere-Douglass, John F

Establishing and maintaining conformational integrity of monoclonal antibodies (mAbs) and antibody-drug conjugates (ADCs) during development and manufacturing is critical for ensuring their clinical efficacy. As presented here, we applied site-specific carboxyl group footprinting (CGF) for localized conformational interrogation of mAbs. The approach relies on covalent labeling that introduces glycine ethyl ester tags onto solvent-accessible side chains of protein carboxylates. Peptide mapping is used to monitor the labeling kinetics of carboxyl residues and the labeling kinetics reflects the conformation or solvent-accessibility of side chains. Our results for two case studies are shown here. The first study was aimed at defining the conformational changes of mAbs induced by deglycosylation. We found that two residues in C H 2 domain (D268 and E297) show significantly enhanced side chain accessibility upon deglycosylation. This site-specific result highlighted the advantage of monitoring the labeling kinetics at the amino acid level as opposed to the peptide level, which would result in averaging out of highly localized conformational differences. The second study was designed to assess conformational effects brought on by conjugation of mAbs with drug-linkers. All 59 monitored carboxyl residues displayed similar solvent-accessibility between the ADC and mAb under native conditions, which suggests the ADC and mAb share similar side chain conformation. The findings are well correlated and complementary with results from other assays. This work illustrated that site-specific CGF is capable of pinpointing local conformational changes in mAbs or ADCs that might arise during development and manufacturing. The methodology can be readily implemented within the industry to provide comprehensive conformational assessment of these molecules.

Apparatus and method for mapping an area of interest

Science.gov (United States)

Staab, Torsten A. Cohen, Daniel L.; Feller, Samuel [Fairfax, VA

2009-12-01

An apparatus and method are provided for mapping an area of interest using polar coordinates or Cartesian coordinates. The apparatus includes a range finder, an azimuth angle measuring device to provide a heading and an inclinometer to provide an angle of inclination of the range finder as it relates to primary reference points and points of interest. A computer is provided to receive signals from the range finder, inclinometer and azimuth angle measurer to record location data and calculate relative locations between one or more points of interest and one or more primary reference points. The method includes mapping of an area of interest to locate points of interest relative to one or more primary reference points and to store the information in the desired manner. The device may optionally also include an illuminator which can be utilized to paint the area of interest to indicate both points of interest and primary points of reference during and/or after data acquisition.

Interferometric methods for mapping static electric and magnetic fields

DEFF Research Database (Denmark)

Pozzi, Giulio; Beleggia, Marco; Kasama, Takeshi

2014-01-01

The mapping of static electric and magnetic fields using electron probes with a resolution and sensitivity that are sufficient to reveal nanoscale features in materials requires the use of phase-sensitive methods such as the shadow technique, coherent Foucault imaging and the Transport of Intensi......) the model-independent determination of the locations and magnitudes of field sources (electric charges and magnetic dipoles) directly from electron holographic data.......The mapping of static electric and magnetic fields using electron probes with a resolution and sensitivity that are sufficient to reveal nanoscale features in materials requires the use of phase-sensitive methods such as the shadow technique, coherent Foucault imaging and the Transport of Intensity...... on theoretical models that form the basis of the quantitative interpretation of electron holographic data. We review the application of electron holography to a variety of samples (including electric fields associated with p–n junctions in semiconductors, quantized magnetic flux in superconductors...

Controlling non-conformities propagation in manufacturing. Case study in an electromechanical assembly plant.

OpenAIRE

Fiegenwald , Valérie; Bassetto , Samuel; Tollenaere , Michel

2011-01-01

International audience; The purpose of this paper is to control the propagation of non-conformities. The control methods implemented to ensure the quality performance of a production system present weaknesses, inherent to their constitution, which can let non-conformities propagate along the value stream. This propagation cannot be avoided, but it can be mastered. This paper presents a method to master non-conformities propagation in a production system by building the associated control char...

Generative Models of Conformational Dynamics

Science.gov (United States)

Langmead, Christopher James

2014-01-01

Atomistic simulations of the conformational dynamics of proteins can be performed using either Molecular Dynamics or Monte Carlo procedures. The ensembles of three-dimensional structures produced during simulation can be analyzed in a number of ways to elucidate the thermodynamic and kinetic properties of the system. The goal of this chapter is to review both traditional and emerging methods for learning generative models from atomistic simulation data. Here, the term ‘generative’ refers to a model of the joint probability distribution over the behaviors of the constituent atoms. In the context of molecular modeling, generative models reveal the correlation structure between the atoms, and may be used to predict how the system will respond to structural perturbations. We begin by discussing traditional methods, which produce multivariate Gaussian models. We then discuss GAMELAN (GrAphical Models of Energy LANdscapes), which produces generative models of complex, non-Gaussian conformational dynamics (e.g., allostery, binding, folding, etc) from long timescale simulation data. PMID:24446358

Synthetic Methods for Ester Bond Formation and Conformational Analysis of Ester-Containing Carbohydrates

Science.gov (United States)

Hackbusch, Sven

This dissertation encompasses work related to synthetic methods for the formation of ester linkages in organic compounds, as well as the investigation of the conformational influence of the ester functional group on the flexibility of inter-saccharide linkages, specifically, and the solution phase structure of ester-containing carbohydrate derivatives, in general. Stereoselective reactions are an important part of the field of asymmetric synthesis and an understanding of their underlying mechanistic principles is essential for rational method development. Here, the exploration of a diastereoselective O-acylation reaction on a trans-2-substituted cyclohexanol scaffold is presented, along with possible reasons for the observed reversal of stereoselectivity dependent on the presence or absence of an achiral amine catalyst. In particular, this work establishes a structure-activity relationship with regard to the trans-2-substituent and its role as a chiral auxiliary in the reversal of diastereoselectivity. In the second part, the synthesis of various ester-linked carbohydrate derivatives, and their conformational analysis is presented. Using multidimensional NMR experiments and computational methods, the compounds' solution-phase structures were established and the effect of the ester functional group on the molecules' flexibility and three-dimensional (3D) structure was investigated and compared to ether or glycosidic linkages. To aid in this, a novel Karplus equation for the C(sp2)OCH angle in ester-linked carbohydrates was developed on the basis of a model ester-linked carbohydrate. This equation describes the sinusoidal relationship between the C(sp2)OCH dihedral angle and the corresponding 3JCH coupling constant that can be determined from a J-HMBC NMR experiment. The insights from this research will be useful in describing the 3D structure of naturally occurring and lab-made ester-linked derivatives of carbohydrates, as well as guiding the de novo-design of

Solid state protein monolayers: Morphological, conformational, and functional properties

Science.gov (United States)

Pompa, P. P.; Biasco, A.; Frascerra, V.; Calabi, F.; Cingolani, R.; Rinaldi, R.; Verbeet, M. Ph.; de Waal, E.; Canters, G. W.

2004-12-01

We have studied the morphological, conformational, and electron-transfer (ET) function of the metalloprotein azurin in the solid state, by a combination of physical investigation methods, namely atomic force microscopy, intrinsic fluorescence spectroscopy, and scanning tunneling microscopy. We demonstrate that a "solid state protein film" maintains its nativelike conformation and ET function, even after removal of the aqueous solvent.

A Study on remote sensing method for drawing up and utilizing ecological and natural map - concentrated on drawing up of Land Cover Classification Map

Energy Technology Data Exchange (ETDEWEB)

Jun, Sung Woo; Chung, Sung Moon [Korea Environment Institute, Seoul (Korea)

1998-12-01

The drawing up of ecological and natural map, which is highly efficient using remote exploration method, was promoted in this study. As the first step of drawing up of ecological and natural map, this study is working on the drawing up of Land Cover using as a base map. Through the detailed and sufficient consideration on GAP analysis of USA, CORINE project of EU, and examples in Korea, it studied and proposed the Land Cover Classification system and method suitable for Korea. It will be helpful to draw up ecological and natural map by providing two strategies and principles for land cover classification. 26 refs., 33 figs., 9 tabs.

Identification of Serine Conformers by Matrix-Isolation IR Spectroscopy Aided by Near-Infrared Laser Induced Conformational Change, 2D Correlation Analysis, and Quantum Mechanical Anharmonic Computations

Science.gov (United States)

Najbauer, Eszter E.; Bazsó, Gábor; Apóstolo, Rui; Fausto, Rui; Biczysko, Malgorzata; Barone, Vincenzo; Tarczay, György

2018-01-01

The conformers of α-serine were investigated by matrix-isolation IR spectroscopy combined with NIR laser irradiation. This method, aided by 2D correlation analysis, enabled unambiguously grouping the spectral lines to individual conformers. On the basis of comparison of at least nine experimentally observed vibrational transitions of each conformer with empirically scaled (SQM) and anharmonic (GVPT2) computed IR spectra, 6 conformers were identified. In addition, the presence of at least one more conformer in Ar matrix was proved, and a short-lived conformer with a half-live of (3.7±0.5)·103 s in N2 matrix was generated by NIR irradiation. The analysis of the NIR laser induced conversions revealed that the excitation of the stretching overtone of both the side-chain and the carboxylic OH groups can effectively promote conformational changes, but remarkably different paths were observed for the two kinds of excitations. PMID:26201050

Grid generation method to calculate the flow field in a three-dimensional cascade of blades. Sanjigen yokuretsu nagare keisan no tame no koshi keisei

Energy Technology Data Exchange (ETDEWEB)

Inoue, K [National Aerospace Laboratory, Tokyo (Japan)

1992-05-01

For the purpose of developing a fan for an engine with ultra-high by-pass ratio, the design code of three-dimensional cascade of blades based on the Navier-Stokes equation has already been developed. This paper describes a method created by calculation grids which are part of this design code. This method is to generate boundary fitted grids to calculate the flow field across a cascade of blades placed radially in the axially symmetric space between hub and casing. In this method, one-period domain of the cascade of blades is mapped on a box in computational space by a series of combined streching transformation and conformal mapping. The grid in physical space is then obtained by successive inverse conformal mapping on the grid points in computational space. The grid obtained in this method is H-type and has a periodicity which includes the inclination of grid lines at the periodic boundary. As an example of the grid generated by this method, grids for primary and secondary models of the fan with ultra-high by-pass ratio are shown. 6 refs., 12 figs.

Grid generation method to calculate the flow field in a three-dimensional cascade of blades; Sanjigen yokuretsu nagare keisan no tame no koshi keisei

Energy Technology Data Exchange (ETDEWEB)

Inoue, K [National Aerospace Laboratory, Tokyo (Japan)

1992-05-01

For the purpose of developing a fan for an engine with ultra-high by-pass ratio, the design code of three-dimensional cascade of blades based on the Navier-Stokes equation has already been developed. This paper describes a method created by calculation grids which are part of this design code. This method is to generate boundary fitted grids to calculate the flow field across a cascade of blades placed radially in the axially symmetric space between hub and casing. In this method, one-period domain of the cascade of blades is mapped on a box in computational space by a series of combined streching transformation and conformal mapping. The grid in physical space is then obtained by successive inverse conformal mapping on the grid points in computational space. The grid obtained in this method is H-type and has a periodicity which includes the inclination of grid lines at the periodic boundary. As an example of the grid generated by this method, grids for primary and secondary models of the fan with ultra-high by-pass ratio are shown. 6 refs., 12 figs.

Inverse problems for ODEs using contraction maps and suboptimality of the 'collage method'

Science.gov (United States)

Kunze, H. E.; Hicken, J. E.; Vrscay, E. R.

2004-06-01

Broad classes of inverse problems in differential and integral equations can be cast in the following framework: the optimal approximation of a target x of a suitable metric space X by the fixed point \\bar x of a contraction map T on X. The 'collage method' attempts to solve such inverse problems by finding an operator Tc that maps the target x as close as possible to itself. In the case of ODEs, the appropriate contraction maps are integral Picard operators. In practice, the target solutions possibly arise from an interpolation of experimental data points. In this paper, we investigate the suboptimality of the collage method. A simple inequality that provides upper bounds on the improvement over collage coding is presented and some examples are studied. We conclude that, at worst, the collage method provides an excellent starting point for further optimization, in contrast to more traditional searching methods that must first select a good starting point.

A high-throughput shotgun mutagenesis approach to mapping B-cell antibody epitopes.

Science.gov (United States)

Davidson, Edgar; Doranz, Benjamin J

2014-09-01

Characterizing the binding sites of monoclonal antibodies (mAbs) on protein targets, their 'epitopes', can aid in the discovery and development of new therapeutics, diagnostics and vaccines. However, the speed of epitope mapping techniques has not kept pace with the increasingly large numbers of mAbs being isolated. Obtaining detailed epitope maps for functionally relevant antibodies can be challenging, particularly for conformational epitopes on structurally complex proteins. To enable rapid epitope mapping, we developed a high-throughput strategy, shotgun mutagenesis, that enables the identification of both linear and conformational epitopes in a fraction of the time required by conventional approaches. Shotgun mutagenesis epitope mapping is based on large-scale mutagenesis and rapid cellular testing of natively folded proteins. Hundreds of mutant plasmids are individually cloned, arrayed in 384-well microplates, expressed within human cells, and tested for mAb reactivity. Residues are identified as a component of a mAb epitope if their mutation (e.g. to alanine) does not support candidate mAb binding but does support that of other conformational mAbs or allows full protein function. Shotgun mutagenesis is particularly suited for studying structurally complex proteins because targets are expressed in their native form directly within human cells. Shotgun mutagenesis has been used to delineate hundreds of epitopes on a variety of proteins, including G protein-coupled receptor and viral envelope proteins. The epitopes mapped on dengue virus prM/E represent one of the largest collections of epitope information for any viral protein, and results are being used to design better vaccines and drugs. © 2014 John Wiley & Sons Ltd.

Methodologies for conformational studies of oligo- and poly-glucans: crystallography and molecular mechanics

International Nuclear Information System (INIS)

Tran, Huu Vinh

1983-01-01

After some considerations on the conformational analysis of polysaccharides, this research thesis outlines the interest of molecular mechanics as a method to study these components. Technical aspects are presented. The author reports the prediction of the conformations of some specific cyclic oligomers (glucans, glucore), the use of X-ray diffraction to study glucides (and the limitations of this method). He reports the search for another investigation method: relationships between X rays and molecular mechanics, situation with respect to other crystallographic methods, presentation of principle of the 'Packing' method, and applications. He reports the study of regular conformations of polysaccharides, the study of the statistic configuration of polymer chains and the application to alpha-glucans

Hybrid Map-Based Navigation Method for Unmanned Ground Vehicle in Urban Scenario

Directory of Open Access Journals (Sweden)

Huiyan Chen

2013-07-01

Full Text Available To reduce the data size of metric map and map matching computational cost in unmanned ground vehicle self-driving navigation in urban scenarios, a metric-topological hybrid map navigation system is proposed in this paper. According to the different positioning accuracy requirements, urban areas are divided into strong constraint (SC areas, such as roads with lanes, and loose constraint (LC areas, such as intersections and open areas. As direction of the self-driving vehicle is provided by traffic lanes and global waypoints in the road network, a simple topological map is fit for the navigation in the SC areas. While in the LC areas, the navigation of the self-driving vehicle mainly relies on the positioning information. Simultaneous localization and mapping technology is used to provide a detailed metric map in the LC areas, and a window constraint Markov localization algorithm is introduced to achieve accurate position using laser scanner. Furthermore, the real-time performance of the Markov algorithm is enhanced by using a constraint window to restrict the size of the state space. By registering the metric maps into the road network, a hybrid map of the urban scenario can be constructed. Real unmanned vehicle mapping and navigation tests demonstrated the capabilities of the proposed method.

Asymptotic mass degeneracies in conformal field theories

International Nuclear Information System (INIS)

Kani, I.; Vafa, C.

1990-01-01

By applying a method of Hardy and Ramanujan to characters of rational conformal field theories, we find an asymptotic expansion for degeneracy of states in the limit of large mass which is exact for strings propagating in more than two uncompactified space-time dimensions. Moreover we explore how the rationality of the conformal theory is reflected in the degeneracy of states. We also consider the one loop partition function for strings, restricted to physical states, for arbitrary (irrational) conformal theories, and obtain an asymptotic expansion for it in the limit that the torus degenerates. This expansion depends only on the spectrum of (physical and unphysical) relevant operators in the theory. We see how rationality is consistent with the smoothness of mass degeneracies as a function of moduli. (orig.)

Connection Between Group Conformity and Free Sex Behavior in Adolescence

OpenAIRE

Cynthia, Trida

2007-01-01

The aim of this research is to test empirically the connection between group conformity and free sex in adolescence. The method was using 59 statements of group conformity scale and 60 statements of free sex behavior in adolescence. The score was giving depend on favorable and unfavorable statements. Coefficient validity for group conformity was from 0,2551-0,6274 and 0,8038 for coefficient reliability. Coefficient validity for free sex behavior in adolescence was from 0,3706-0,7953 and 0,956...

A molecular modeling approach to understand the structure and conformation relationship of (GlcpA)Xylan.

Science.gov (United States)

Guo, Qingbin; Kang, Ji; Wu, Yan; Cui, Steve W; Hu, Xinzhong; Yada, Rickey Y

2015-12-10

The structure and conformation relationships of a heteropolysaccharide (GlcpA)Xylan in terms of various molecular weights, Xylp/GlcpA ratio and the distribution of GlcpA along xylan chain were investigated using computer modeling. The adiabatic contour maps of xylobiose, XylpXylp(GlcpA) and (GlcpA)XylpXylp(GlcpA) indicated that the insertion of the side group (GlcpA) influenced the accessible conformational space of xylobiose molecule. RIS-Metropolis Monte Carlo method indicated that insertion of GlcpA side chain induced a lowering effect of the calculated chain extension at low GlcpA:Xylp ratio (GlcpA:Xylp = 1:3). The chain, however, became extended when the ratio of GlcpA:Xylp above 2/3. It was also shown that the spatial extension of the polymer chains was dependent on the distribution of side chain: the random distribution demonstrated the most flexible structure compared to block and alternative distribution. The present studies provide a unique insight into the dependence of both side chain ratio and distribution on the stiffness and flexibility of various (GlcpA)Xylan molecules. Copyright © 2015. Published by Elsevier Ltd.

COMPUTER-BASED PREDICTION OF TOXICITY USING THE ELECTRON-CONFORMATIONAL METHOD. APPLICATION TO FRAGRANCE ALLERGENS AND OTHER ENVIRONMENTAL POLLUTANTS

Directory of Open Access Journals (Sweden)

Natalia N. Gorinchoy

2012-06-01

Full Text Available The electron-conformational (EC method is employed for the toxicophore (Tph identification and quantitative prediction of toxicity using the training set of 24 compounds that are considered as fragrance allergens. The values of a=LD50 in oral exposure of rats were chosen as a measure of toxicity. EC parameters are evaluated on the base of conformational analysis and ab initio electronic structure calculations (including solvent influence. The Tph consists of four sites which in this series of compounds are represented by three carbon and one oxygen atoms, but may be any other atoms that have the same electronic and geometric features within the tolerance limits. The regression model taking into consideration the Tph flexibility, anti-Tph shielding, and influence of out-of-Tph functional groups predicts well the experimental values of toxicity (R2 = 0.93 with a reasonable leaveone- out cross-validation.

Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution.

Science.gov (United States)

Ma, Wenxiu; Ay, Ferhat; Lee, Choli; Gulsoy, Gunhan; Deng, Xinxian; Cook, Savannah; Hesson, Jennifer; Cavanaugh, Christopher; Ware, Carol B; Krumm, Anton; Shendure, Jay; Blau, C Anthony; Disteche, Christine M; Noble, William S; Duan, ZhiJun

2018-06-01

The folding and three-dimensional (3D) organization of chromatin in the nucleus critically impacts genome function. The past decade has witnessed rapid advances in genomic tools for delineating 3D genome architecture. Among them, chromosome conformation capture (3C)-based methods such as Hi-C are the most widely used techniques for mapping chromatin interactions. However, traditional Hi-C protocols rely on restriction enzymes (REs) to fragment chromatin and are therefore limited in resolution. We recently developed DNase Hi-C for mapping 3D genome organization, which uses DNase I for chromatin fragmentation. DNase Hi-C overcomes RE-related limitations associated with traditional Hi-C methods, leading to improved methodological resolution. Furthermore, combining this method with DNA capture technology provides a high-throughput approach (targeted DNase Hi-C) that allows for mapping fine-scale chromatin architecture at exceptionally high resolution. Hence, targeted DNase Hi-C will be valuable for delineating the physical landscapes of cis-regulatory networks that control gene expression and for characterizing phenotype-associated chromatin 3D signatures. Here, we provide a detailed description of method design and step-by-step working protocols for these two methods. Copyright © 2018 Elsevier Inc. All rights reserved.

A New Approximation Method for Solving Variational Inequalities and Fixed Points of Nonexpansive Mappings

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Klin-eam Chakkrid

2009-01-01

Full Text Available Abstract A new approximation method for solving variational inequalities and fixed points of nonexpansive mappings is introduced and studied. We prove strong convergence theorem of the new iterative scheme to a common element of the set of fixed points of nonexpansive mapping and the set of solutions of the variational inequality for the inverse-strongly monotone mapping which solves some variational inequalities. Moreover, we apply our main result to obtain strong convergence to a common fixed point of nonexpansive mapping and strictly pseudocontractive mapping in a Hilbert space.

Integrasi concise learning method dengan mind mapping dalam pembelajaran matematika di perguruan tinggi

Directory of Open Access Journals (Sweden)

Ciptianingsari Ayu Vitantri

2017-11-01

Full Text Available [Bahasa]: Penelitian ini bertujuan untuk mendeskripsikan penerapan, pemahaman konsep, dan respon mahasiswa terhadap pembelajaran CLM  yang diintegrasikan dengan mind mapping pada mata kuliah aljabar linier elementer I. Penelitian ini termasuk dalam penelitian deskriptif kualitatif, dengan subjek penelitian adalah mahasiswa prodi matematika dan pendidikan matematika semester gasal tahun ajaran 2016/2017 yang mengambil mata kuliah aljabar linier elementer I. Instrumen utama dalam penelitian ini adalah peneliti sendiri dengan instrumen pendukung yaitu lembar observasi, tes pemahaman konsep, angket respon, dan pedoman wawancara. Hasil penelitian menunjukkan: 1 Langkah-langkah pembelajaran CLM yang diintegrasikan dengan mind mapping meliputi preview, participate, process (mengolah informasi dalam bentuk mind mapping, practice, dan produce. 2 Pemahaman konsep mahasiswa mengalami peningkatan setelah pembelajaran. Dan 3 Mahasiswa memberikan respon positif terhadap pelaksanaan pembelajaran CLM yang diintegrasikan dengan mind mapping. Kata kunci: Concise Learning Method; Mind Mapping; Pemahaman Konsep; Respon; Aljabar Linier Elementer. [English]: This research aimed to describe the implementation, students’ understanding and their responses on CLM integrated with mind mapping on Linear Elementary Algebra I course,  This research was qualitative descriptive research with the subjects involved were students of mathematics and mathematics education on 2016/2017 academic year who took Linear Elementary Algebra I course. The main instrument in this research was the researcher and the supporting instruments used are observation sheet, test, response questionnaire, and interview guide. The results showed that: 1 The steps of CLM integrated with mind mapping include preview, participate, process (process all information into mind mapping, practice, and produce. 2 The students’ understanding of the mathematics concept of were developed. And 3 the students

Causality Constraints in Conformal Field Theory

CERN Multimedia

CERN. Geneva

2015-01-01

Causality places nontrivial constraints on QFT in Lorentzian signature, for example fixing the signs of certain terms in the low energy Lagrangian. In d-dimensional conformal field theory, we show how such constraints are encoded in crossing symmetry of Euclidean correlators, and derive analogous constraints directly from the conformal bootstrap (analytically). The bootstrap setup is a Lorentzian four-point function corresponding to propagation through a shockwave. Crossing symmetry fixes the signs of certain log terms that appear in the conformal block expansion, which constrains the interactions of low-lying operators. As an application, we use the bootstrap to rederive the well known sign constraint on the (∂φ)4 coupling in effective field theory, from a dual CFT. We also find constraints on theories with higher spin conserved currents. Our analysis is restricted to scalar correlators, but we argue that similar methods should also impose nontrivial constraints on the interactions of spinni...

Causality constraints in conformal field theory

Energy Technology Data Exchange (ETDEWEB)

Hartman, Thomas; Jain, Sachin; Kundu, Sandipan [Department of Physics, Cornell University,Ithaca, New York (United States)

2016-05-17

Causality places nontrivial constraints on QFT in Lorentzian signature, for example fixing the signs of certain terms in the low energy Lagrangian. In d dimensional conformal field theory, we show how such constraints are encoded in crossing symmetry of Euclidean correlators, and derive analogous constraints directly from the conformal bootstrap (analytically). The bootstrap setup is a Lorentzian four-point function corresponding to propagation through a shockwave. Crossing symmetry fixes the signs of certain log terms that appear in the conformal block expansion, which constrains the interactions of low-lying operators. As an application, we use the bootstrap to rederive the well known sign constraint on the (∂ϕ){sup 4} coupling in effective field theory, from a dual CFT. We also find constraints on theories with higher spin conserved currents. Our analysis is restricted to scalar correlators, but we argue that similar methods should also impose nontrivial constraints on the interactions of spinning operators.

Flood maps in Europe - methods, availability and use

Science.gov (United States)

de Moel, H.; van Alphen, J.; Aerts, J. C. J. H.

2009-03-01

To support the transition from traditional flood defence strategies to a flood risk management approach at the basin scale in Europe, the EU has adopted a new Directive (2007/60/EC) at the end of 2007. One of the major tasks which member states must carry out in order to comply with this Directive is to map flood hazards and risks in their territory, which will form the basis of future flood risk management plans. This paper gives an overview of existing flood mapping practices in 29 countries in Europe and shows what maps are already available and how such maps are used. Roughly half of the countries considered have maps covering as good as their entire territory, and another third have maps covering significant parts of their territory. Only five countries have very limited or no flood maps available yet. Of the different flood maps distinguished, it appears that flood extent maps are the most commonly produced floods maps (in 23 countries), but flood depth maps are also regularly created (in seven countries). Very few countries have developed flood risk maps that include information on the consequences of flooding. The available flood maps are mostly developed by governmental organizations and primarily used for emergency planning, spatial planning, and awareness raising. In spatial planning, flood zones delimited on flood maps mainly serve as guidelines and are not binding. Even in the few countries (e.g. France, Poland) where there is a legal basis to regulate floodplain developments using flood zones, practical problems are often faced which reduce the mitigating effect of such binding legislation. Flood maps, also mainly extent maps, are also created by the insurance industry in Europe and used to determine insurability, differentiate premiums, or to assess long-term financial solvency. Finally, flood maps are also produced by international river commissions. With respect to the EU Flood Directive, many countries already have a good starting point to map

Computerized mappings of the cerebral cortex: a multiresolution flattening method and a surface-based coordinate system

Science.gov (United States)

Drury, H. A.; Van Essen, D. C.; Anderson, C. H.; Lee, C. W.; Coogan, T. A.; Lewis, J. W.

1996-01-01

We present a new method for generating two-dimensional maps of the cerebral cortex. Our computerized, two-stage flattening method takes as its input any well-defined representation of a surface within the three-dimensional cortex. The first stage rapidly converts this surface to a topologically correct two-dimensional map, without regard for the amount of distortion introduced. The second stage reduces distortions using a multiresolution strategy that makes gross shape changes on a coarsely sampled map and further shape refinements on progressively finer resolution maps. We demonstrate the utility of this approach by creating flat maps of the entire cerebral cortex in the macaque monkey and by displaying various types of experimental data on such maps. We also introduce a surface-based coordinate system that has advantages over conventional stereotaxic coordinates and is relevant to studies of cortical organization in humans as well as non-human primates. Together, these methods provide an improved basis for quantitative studies of individual variability in cortical organization.

DOA Estimation of Cylindrical Conformal Array Based on Geometric Algebra

Directory of Open Access Journals (Sweden)

Minjie Wu

2016-01-01

Full Text Available Due to the variable curvature of the conformal carrier, the pattern of each element has a different direction. The traditional method of analyzing the conformal array is to use the Euler rotation angle and its matrix representation. However, it is computationally demanding especially for irregular array structures. In this paper, we present a novel algorithm by combining the geometric algebra with Multiple Signal Classification (MUSIC, termed as GA-MUSIC, to solve the direction of arrival (DOA for cylindrical conformal array. And on this basis, we derive the pattern and array manifold. Compared with the existing algorithms, our proposed one avoids the cumbersome matrix transformations and largely decreases the computational complexity. The simulation results verify the effectiveness of the proposed method.

The intercomparison of the dose distributions between conformation techniques with pions and photons

International Nuclear Information System (INIS)

Karasawa, K.; Nakagawa, K.; Akanuma, A.

1990-01-01

To compare conformation radiation treatment with pions vs photons, dose volume histograms (DVH) to the critical organs, including the spinal cord, kidney, and intestine, were examined in a patient with retroperitoneal soft tissue sarcoma. For photon conformation treatment, the following techniques were used: 360 degree rotation conformation technique (photon conformation), 4 fixed field technique (photon 4-field), and 2-axis conformation technique (photon 2-axial conformation). According to the DVH reduction method, complication probability was estimated. The concave portion of the target was conformed by pion conformation treatment, but not by photon conformation treatment. Pion conformation for the intestine showed the best DVH, whereas photon 4-field technique showed the worst DVH. For the kidney, pion conformation showed better DVH as compared with any other photon conformation treatment technique. In the spinal cord, photon 2-axial conformation was far superior, followed by pion conformation and then photon conformation and 4-field technique. A 2-axial technique showed a bigger inhomogeneity inside the target volume which is critical in curative treatment. TD 50 was 72 Gy for pion conformation, 53 Gy for photon conformation, 51 Gy for photon 4-field, and 68 Gy for photon 2-axial conformation. Complication probabilities for these conformation techniques at 60 Gy were 3%, 85%, 97%, and 9%. In view of tumor control probabilities, pion seems to have the biggest therapeutic ratio among these techniques. (N.K.)

Revisiting the origin of the preferential π-π stacking conformation of the (+)-8-phenylmenthyl acrylate

International Nuclear Information System (INIS)

Capim, Saulo L.; Santana, Sidney R.; Oliveira, Boaz G. de; Rocha, Gerd B.; Vasconcellos, Mario L.A.A

2010-01-01

In this paper we report a theoretical study aiming to revisit the origin of the preferential π-π stacking conformation of the (+)-8-phenylmenthyl acrylate (2). For this, we have applied several DFT and ab initio methods to calculate local minimum geometries, vibrational frequencies, thermochemical properties and 1 H NMR chemical shifts for 2 and the model compound 3-phenylpropyl acrylate (3). We have observed that the MPW1B95 functional was the most suitable method to explain 1 H NMR experimental data which show the stacking conformation of 2 (2S) is more stable that trans conformation (2T) and the stacking conformation of 3 (3S) is less stable that trans conformation (3T). After that, geometrical and energetic features of the intermolecular complex benzene...methylacrylate (4) have also been studied using MPW1B95 method. From our results, we have noticed that both steric and dispersion effects play a key role in the conformational equilibrium of 2. (author)

Enhanced conformational sampling using enveloping distribution sampling.

Science.gov (United States)

Lin, Zhixiong; van Gunsteren, Wilfred F

2013-10-14

To lessen the problem of insufficient conformational sampling in biomolecular simulations is still a major challenge in computational biochemistry. In this article, an application of the method of enveloping distribution sampling (EDS) is proposed that addresses this challenge and its sampling efficiency is demonstrated in simulations of a hexa-β-peptide whose conformational equilibrium encompasses two different helical folds, i.e., a right-handed 2.7(10∕12)-helix and a left-handed 3(14)-helix, separated by a high energy barrier. Standard MD simulations of this peptide using the GROMOS 53A6 force field did not reach convergence of the free enthalpy difference between the two helices even after 500 ns of simulation time. The use of soft-core non-bonded interactions in the centre of the peptide did enhance the number of transitions between the helices, but at the same time led to neglect of relevant helical configurations. In the simulations of a two-state EDS reference Hamiltonian that envelops both the physical peptide and the soft-core peptide, sampling of the conformational space of the physical peptide ensures that physically relevant conformations can be visited, and sampling of the conformational space of the soft-core peptide helps to enhance the transitions between the two helices. The EDS simulations sampled many more transitions between the two helices and showed much faster convergence of the relative free enthalpy of the two helices compared with the standard MD simulations with only a slightly larger computational effort to determine optimized EDS parameters. Combined with various methods to smoothen the potential energy surface, the proposed EDS application will be a powerful technique to enhance the sampling efficiency in biomolecular simulations.

Food Mapping: A Psychogeographical Method for Raising Food Consciousness

Science.gov (United States)

Wight, R. Alan; Killham, Jennifer

2014-01-01

Food mapping is a new, participatory, interdisciplinary pedagogical approach to learning about our modern food systems. This method is inspired by the Situationist International's practice of the "dérive" and draws from the discourses of critical geography, the food movement's research on food deserts, and participatory action…

Global Seabed Materials and Habitats Mapped: The Computational Methods

Science.gov (United States)

Jenkins, C. J.

2016-02-01

What the seabed is made of has proven difficult to map on the scale of whole ocean-basins. Direct sampling and observation can be augmented with proxy-parameter methods such as acoustics. Both avenues are essential to obtain enough detail and coverage, and also to validate the mapping methods. We focus on the direct observations such as samplings, photo and video, probes, diver and sub reports, and surveyed features. These are often in word-descriptive form: over 85% of the records for site materials are in this form, whether as sample/view descriptions or classifications, or described parameters such as consolidation, color, odor, structures and components. Descriptions are absolutely necessary for unusual materials and for processes - in other words, for research. This project dbSEABED not only has the largest collection of seafloor materials data worldwide, but it uses advanced computing math to obtain the best possible coverages and detail. Included in those techniques are linguistic text analysis (e.g., Natural Language Processing, NLP), fuzzy set theory (FST), and machine learning (ML, e.g., Random Forest). These techniques allow efficient and accurate import of huge datasets, thereby optimizing the data that exists. They merge quantitative and qualitative types of data for rich parameter sets, and extrapolate where the data are sparse for best map production. The dbSEABED data resources are now very widely used worldwide in oceanographic research, environmental management, the geosciences, engineering and survey.

Conformal field theories near a boundary in general dimensions

International Nuclear Information System (INIS)

McAvity, D.M.

1995-01-01

The implications of restricted conformal invariance under conformal transformations preserving a plane boundary are discussed for general dimensions d. Calculations of the universal function of a conformal invariant ξ which appears in the two-point function of scalar operators in conformally invariant theories with a plane boundary are undertaken to first order in the ε=4-d expansion for the operator φ 2 in φ 4 theory. The form for the associated functions of ξ for the two-point functions for the basic field φ α and the auxiliary field λ in the N→∞ limit of the O(N) non-linear sigma model for any d in the range 2 α φ β and λλ. Using this method the form of the two-point function for the energy-momentum tensor in the conformal O(N) model with a plane boundary is also found. General results for the sum of the contributions of all derivative operators appearing in the operator product expansion, and also in a corresponding boundary operator expansion, to the two-point functions are also derived making essential use of conformal invariance. (orig.)

Comparison of saturated areas mapping methods in the Jizera Mountains, Czech Republic

Czech Academy of Sciences Publication Activity Database

Kulasová, A.; Beven, K. J.; Blažková, Š. D.; Řezáčová, Daniela; Cajthaml, J.

2014-01-01

Roč. 62, č. 2 (2014), s. 160-168 ISSN 0042-790X R&D Projects: GA ČR(CZ) GAP209/11/2045 Institutional support: RVO:68378289 Keywords : mapping variable source areas * boot method * piezometers * vegetation mapping Subject RIV: DG - Athmosphere Sciences, Meteorology Impact factor: 1.486, year: 2014 http://147.213.145.2/vc_articles/2014_62_2_Kulasova_160.pdf

Differential equation for genus-two characters in arbitrary rational conformal field theories

International Nuclear Information System (INIS)

Mathur, S.D.; Sen, A.

1989-01-01

We develop a general method for deriving ordinary differential equations for the genus-two ''characters'' of an arbitrary rational conformal field theory using the hyperelliptic representation of the genus-two moduli space. We illustrate our method by explicitly deriving the character differential equations for k=1 SU(2), G 2 , and F 4 WZW models. Our method provides an intrinsic definition of conformal field theories on higher genus Riemann surfaces. (orig.)

Conformal quantum field theory: From Haag-Kastler nets to Wightman fields

International Nuclear Information System (INIS)

Joerss, M.

1996-07-01

Starting from a chiral conformal Haag-Kastler net of local observables on two-dimensional Minkowski space-time, we construct associated pointlike localizable charged fields which intertwine between the superselection sectors with finite statistics of the theory. This amounts to a proof of the spin-statistics theorem, the PCT theorem, the Bisognano-Wichmann identification of modular operators, Haag duality in the vacuum sector, and the existence of operator product expansions. Our method consists of the explicit use of the representation theory of the universal covering group of SL(2,R). A central role is played by a ''conformal cluster theorem'' for conformal two-point functions in algebraic quantum field theory. Generalizing this ''conformal cluster theorem'' to the n-point functions of Haag-Kastler theories, we can finally construct from a chiral conformal net of algebras a compelte set of conformal n-point functions fulfilling the Wightman axioms. (orig.)

A test of conformal invariance: Correlation functions on a disk

International Nuclear Information System (INIS)

Badke, R.; Rittenberg, V.; Ruegg, H.

1985-06-01

Using conformal invariance one can derive the correlation functions of a disk from those in the half-plane. The correlation function in the half-plane is determined by the 'small' conformal invariance up to an unknown function of one variable. By measuring through the Monte Carlo method the correlation function for two different configurations, the unknown function can be eliminated and one obtains a test of conformal invariance. It is shown that the Ising and the three state Potts model pass the test for very small lattices. (orig.)

Dissolvable films of silk fibroin for ultrathin conformal bio-integrated electronics.

Science.gov (United States)

Kim, Dae-Hyeong; Viventi, Jonathan; Amsden, Jason J; Xiao, Jianliang; Vigeland, Leif; Kim, Yun-Soung; Blanco, Justin A; Panilaitis, Bruce; Frechette, Eric S; Contreras, Diego; Kaplan, David L; Omenetto, Fiorenzo G; Huang, Yonggang; Hwang, Keh-Chih; Zakin, Mitchell R; Litt, Brian; Rogers, John A

2010-06-01

Electronics that are capable of intimate, non-invasive integration with the soft, curvilinear surfaces of biological tissues offer important opportunities for diagnosing and treating disease and for improving brain/machine interfaces. This article describes a material strategy for a type of bio-interfaced system that relies on ultrathin electronics supported by bioresorbable substrates of silk fibroin. Mounting such devices on tissue and then allowing the silk to dissolve and resorb initiates a spontaneous, conformal wrapping process driven by capillary forces at the biotic/abiotic interface. Specialized mesh designs and ultrathin forms for the electronics ensure minimal stresses on the tissue and highly conformal coverage, even for complex curvilinear surfaces, as confirmed by experimental and theoretical studies. In vivo, neural mapping experiments on feline animal models illustrate one mode of use for this class of technology. These concepts provide new capabilities for implantable and surgical devices.

Ultra-thin, conformal, and hydratable color-absorbers using silk protein hydrogel

Science.gov (United States)

Umar, Muhammad; Min, Kyungtaek; Jo, Minsik; Kim, Sunghwan

2018-06-01

Planar and multilayered photonic devices offer unprecedented opportunities in biological and chemical sensing due to strong light-matter interactions. However, uses of rigid substances such as semiconductors and dielectrics confront photonic devices with issues of biocompatibility and a mechanical mismatch for their application on humid, uneven, and soft biological surfaces. Here, we report that favorable material traits of natural silk protein led to the fabrication of an ultra-thin, conformal, and water-permeable (hydratable) metal-insulator-metal (MIM) color absorber that was mapped on soft, curved, and hydrated biological interfaces. Strong absorption was induced in the MIM structure and could be tuned by hydration and tilting of the sample. The transferred MIM color absorbers reached the exhibition of a very strong resonant absorption in the visible and near infra-red ranges. In addition, we demonstrated that the conformal resonator could function as a refractometric glucose sensor applied on a contact lens.

IR-IR Conformation Specific Spectroscopy of Na+(Glucose) Adducts

Science.gov (United States)

Voss, Jonathan M.; Kregel, Steven J.; Fischer, Kaitlyn C.; Garand, Etienne

2018-01-01

We report an IR-IR double resonance study of the structural landscape present in the Na+(glucose) complex. Our experimental approach involves minimal modifications to a typical IR predissociation setup, and can be carried out via ion-dip or isomer-burning methods, providing additional flexibility to suit different experimental needs. In the current study, the single-laser IR predissociation spectrum of Na+(glucose), which clearly indicates contributions from multiple structures, was experimentally disentangled to reveal the presence of three α-conformers and five β-conformers. Comparisons with calculations show that these eight conformations correspond to the lowest energy gas-phase structures with distinctive Na+ coordination. [Figure not available: see fulltext.

Metallic stent and stereotactic conformal radiotherapy for hilar cholangiocarcinoma

International Nuclear Information System (INIS)

Li Yu; Wang Ning; Tian Qihe; Guo Zhanwen; Zhang Haibo; Song Liyan

2005-01-01

Objective: To evaluate the effect of metallic stent combined with stereotactic conformal radiotherapy (SCRT) for hilar cholangiocarcinoma. Methods: Fifty-four patients with hilar cholangiocarcinoma were analyzed, including 31 treated with stent plus stereotactic conformal radiotherapy (combined group) and 23 with metallic stent alone (control group). Results: The mean survival time of combined group was 11.1 ± 4.6 months, compared with 5.1 ± 2.8 months of the control group, giving a significant difference between the two groups (P<0.01). Conclusion: The combination of metallic stent and stereotactic conformal radiotherapy is more effective than metallic stent alone for unresectable hilar cholangiocarcinoma. (authors)

A finite integration method for conformal, structured-grid, electromagnetic simulation

International Nuclear Information System (INIS)

Cooke, S.J.; Shtokhamer, R.; Mondelli, A.A.; Levush, B.

2006-01-01

We describe a numerical scheme for solving Maxwell's equations in the frequency domain on a conformal, structured, non-orthogonal, multi-block mesh. By considering Maxwell's equations in a volume parameterized by dimensionless curvilinear coordinates, we obtain a set of tensor equations that are a continuum analogue of common circuit equations, and that separate the metrical and metric-free parts of Maxwell's equations and the material constitutive relations. We discretize these equations using a new formulation that treats the electric field and magnetic induction using simple basis-function representations to obtain a discrete form of Faraday's law of induction, but that uses finite integral representations for the displacement current and magnetic field to obtain a discrete form of Ampere's law, as in the finite integration technique [T. Weiland, A discretization method for the solution of Maxwell's equations for six-component fields, Electron. Commun. (AE U) 31 (1977) 116; T. Weiland, Time domain electromagnetic field computation with finite difference methods, Int. J. Numer. Model: Electron. Netw. Dev. Field 9 (1996) 295-319]. We thereby derive new projection operators for the discrete tensor material equations and obtain a compact numerical scheme for the discrete differential operators. This scheme is shown to exhibit significantly reduced numerical dispersion when compared to the standard linear finite element method. We take advantage of the mesh structure on a block-by-block basis to implement these numerical operators efficiently, and achieve computational speed with modest memory requirements when compared to explicit sparse matrix storage. Using the Jacobi-Davidson [G.L.G. Sleijpen, H.A. van der Vorst, A Jacobi-Davidson iteration method for linear eigenvalue problems, SIAM J. Matrix Anal. Appl. 17 (2) (1996) 401-425; S.J. Cooke, B. Levush, Eigenmode solution of 2-D and 3-D electromagnetic cavities containing absorbing materials using the Jacobi

Superspace conformal field theory

Energy Technology Data Exchange (ETDEWEB)

Quella, Thomas [Koeln Univ. (Germany). Inst. fuer Theoretische Physik; Schomerus, Volker [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

2013-07-15

Conformal sigma models and WZW models on coset superspaces provide important examples of logarithmic conformal field theories. They possess many applications to problems in string and condensed matter theory. We review recent results and developments, including the general construction of WZW models on type I supergroups, the classification of conformal sigma models and their embedding into string theory.

Superspace conformal field theory

International Nuclear Information System (INIS)

Quella, Thomas

2013-07-01

Conformal sigma models and WZW models on coset superspaces provide important examples of logarithmic conformal field theories. They possess many applications to problems in string and condensed matter theory. We review recent results and developments, including the general construction of WZW models on type I supergroups, the classification of conformal sigma models and their embedding into string theory.

Conformal Infinity

OpenAIRE

Frauendiener, J?rg

2000-01-01

The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, 'conformal infinity' is related to almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved from physical issues, namely the need to understand gravitational radiation and isolated systems within the theory...

The Conformational Behaviour of Glucosamine

Science.gov (United States)

Peña, Isabel; Kolesniková, Lucie; Cabezas, Carlos; Bermúdez, Celina; Berdakin, Matías; Simao, Alcides; Alonso, José L.

2014-06-01

A laser ablation method has been successfully used to vaporize the bioactive amino monosaccharide D-glucosamine. Three cyclic α-4C1 pyranose forms have been identified using a combination of CP-FTMW and LA-MB-FTMW spectroscopy. Stereoelectronic hyperconjugative factors, like those associated with anomeric or gauche effects, as well as the cooperative OH\\cdotsO, OH\\cdotsN and NH\\cdotsO chains, extended along the entire molecule, are the main factors driving the conformational behavior. All observed conformers exhibit a counter-clockwise arrangement (cc) of the network of intramolecular hydrogen bonds. The results are compared with those recently obtained for D-glucose. J. L. Alonso, M. A. Lozoya, I. Peña, J. C. López, C. Cabezas, S. Mata, S. Blanco, Chem. Sci. 2014, 5, 515.

Gel dosimetry for conformal radiotherapy

Energy Technology Data Exchange (ETDEWEB)

Gambarini, G [Department of Physics of the University and INFN, Milan (Italy)

2005-07-01

With the continuum development of conformal radio therapies, aimed at delivering high dose to tumor tissue and low dose to the healthy tissue around, the necessities has appeared of suitable improvement of dosimetry techniques giving the possibility of obtaining dose images to be compared with diagnostic images. Also if wide software has been developed for calculating dose distributions in the fields of various radiotherapy units, experimental verifications are necessary, in particular in the case of complex geometries in conformal radiotherapy. Gel dosimetry is a promising method for imaging the absorbed dose in tissue-equivalent phantoms, with the possibility of 3D reconstruction of the spatial dose distribution, with milli metric resolution. Optical imaging of gel dosimeters, based on visible light absorbance analysis, has shown to be a reliable technique for achieving dose distributions. (Author)

Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery

Science.gov (United States)

Fischer, Marcus; Coleman, Ryan G.; Fraser, James S.; Shoichet, Brian K.

2014-07-01

Proteins fluctuate between alternative conformations, which presents a challenge for ligand discovery because such flexibility is difficult to treat computationally owing to problems with conformational sampling and energy weighting. Here we describe a flexible docking method that samples and weights protein conformations using experimentally derived conformations as a guide. The crystallographically refined occupancies of these conformations, which are observable in an apo receptor structure, define energy penalties for docking. In a large prospective library screen, we identified new ligands that target specific receptor conformations of a cavity in cytochrome c peroxidase, and we confirm both ligand pose and associated receptor conformation predictions by crystallography. The inclusion of receptor flexibility led to ligands with new chemotypes and physical properties. By exploiting experimental measures of loop and side-chain flexibility, this method can be extended to the discovery of new ligands for hundreds of targets in the Protein Data Bank for which similar experimental information is available.

NMR investigation and theoretical calculations of the solvent effect on the conformation of valsartan

Science.gov (United States)

Chashmniam, Saeed; Tafazzoli, Mohsen

2017-11-01

Structure and conformational properties of valsartan were studied by advanced NMR techniques and quantum calculation methods. Potential energy scanning using B3LYP/6-311++g** and B3LYP-D3/6-311++g** methods were performed and four conformers (V1-V4) at minimum points of PES diagram were observed. According to the NMR spectra in acetone-d6, there are two conformers (M and m) with m/M = 0.52 ratio simultaneously and energy barriers of the two conformers were predicted from chemical shifts and multiplicities. While, intramolecular hydrogen bond at tetrazole ring and carboxylic groups prevent the free rotation on N6sbnd C11 bond in M-conformer, this bond rotates freely in m-conformer. On the other hand, intramolecular hydrogen bond at carbonyl and carboxylic acid can be observed at m-conformer. So, different intramolecular hydrogen bond is the reason for the stability of both M and m structures. Quite interestingly, 1H NMR spectra in CDCl3 show two distinct conformers (N and n) with unequal ratio which are differ from M-m conformers. Also, intramolecular hydrogen bond seven-member ring involving five-membered tetrazole ring and carboxylic acid group observed in both N and n-conformers Solvent effect, by using a set of polar and non-polar solvents including DMSO-d6, methanol-d4, benzene-d6, THF-d8, nitromethane-d3, methylene chloride-d2 and acetonitrile-d3 were investigated. NMR parameters include chemical shifts and spin-spin coupling constants were obtained from a set of 2D NMR spectra (H-H COSY, HMQC and HMBC). For this purpose, several DFT functionals from LDA, GGA and hybrid categories were used which the hybrid method showed better agreement with experiment values.

Theoretical and Spectroscopic investigations of conformations, rotational barriers and scaled vibrations of 2,3-dimethyl hexane

Directory of Open Access Journals (Sweden)

Aziz Aboulmouhajir

2017-01-01

Full Text Available The 2,3-dimethyl hexane conformational isomerism has been investigated in detail, based on HF, Post-HF and DFT calculations at different basis set. The effect of size of basis, ZPE, thermal contributions, electronic correlation and optimization methods on the conformational stability was discussed. The rotational barriers from the most stable conformer to the lowest energy secondary conformers and their correspondent inversion barriers at both HF and MP2 methods using 6-31G* basis set have also been approached. A normal mode calculation of the most and less-stable conformers using a scaled ab initio force field in terms of non-redundant local symmetry coordinates have been made to elucidate the conformational dependence of the vibrational spectra.

A Double Perturbation Method for Reducing Dynamical Degradation of the Digital Baker Map

Science.gov (United States)

Liu, Lingfeng; Lin, Jun; Miao, Suoxia; Liu, Bocheng

2017-06-01

The digital Baker map is widely used in different kinds of cryptosystems, especially for image encryption. However, any chaotic map which is realized on the finite precision device (e.g. computer) will suffer from dynamical degradation, which refers to short cycle lengths, low complexity and strong correlations. In this paper, a novel double perturbation method is proposed for reducing the dynamical degradation of the digital Baker map. Both state variables and system parameters are perturbed by the digital logistic map. Numerical experiments show that the perturbed Baker map can achieve good statistical and cryptographic properties. Furthermore, a new image encryption algorithm is provided as a simple application. With a rather simple algorithm, the encrypted image can achieve high security, which is competitive to the recently proposed image encryption algorithms.

Conformal superalgebras via tractor calculus

Science.gov (United States)

Lischewski, Andree

2015-01-01

We use the manifestly conformally invariant description of a Lorentzian conformal structure in terms of a parabolic Cartan geometry in order to introduce a superalgebra structure on the space of twistor spinors and normal conformal vector fields formulated in purely algebraic terms on parallel sections in tractor bundles. Via a fixed metric in the conformal class, one reproduces a conformal superalgebra structure that has been considered in the literature before. The tractor approach, however, makes clear that the failure of this object to be a Lie superalgebra in certain cases is due to purely algebraic identities on the spinor module and to special properties of the conformal holonomy representation. Moreover, it naturally generalizes to higher signatures. This yields new formulas for constructing new twistor spinors and higher order normal conformal Killing forms out of existing ones, generalizing the well-known spinorial Lie derivative. Moreover, we derive restrictions on the possible dimension of the space of twistor spinors in any metric signature.

Characterizing protein conformations by correlation analysis of coarse-grained contact matrices

Science.gov (United States)

Lindsay, Richard J.; Siess, Jan; Lohry, David P.; McGee, Trevor S.; Ritchie, Jordan S.; Johnson, Quentin R.; Shen, Tongye

2018-01-01

We have developed a method to capture the essential conformational dynamics of folded biopolymers using statistical analysis of coarse-grained segment-segment contacts. Previously, the residue-residue contact analysis of simulation trajectories was successfully applied to the detection of conformational switching motions in biomolecular complexes. However, the application to large protein systems (larger than 1000 amino acid residues) is challenging using the description of residue contacts. Also, the residue-based method cannot be used to compare proteins with different sequences. To expand the scope of the method, we have tested several coarse-graining schemes that group a collection of consecutive residues into a segment. The definition of these segments may be derived from structural and sequence information, while the interaction strength of the coarse-grained segment-segment contacts is a function of the residue-residue contacts. We then perform covariance calculations on these coarse-grained contact matrices. We monitored how well the principal components of the contact matrices is preserved using various rendering functions. The new method was demonstrated to assist the reduction of the degrees of freedom for describing the conformation space, and it potentially allows for the analysis of a system that is approximately tenfold larger compared with the corresponding residue contact-based method. This method can also render a family of similar proteins into the same conformational space, and thus can be used to compare the structures of proteins with different sequences.

Conformal geometry computational algorithms and engineering applications

CERN Document Server

Jin, Miao; He, Ying; Wang, Yalin

2018-01-01

This book offers an essential overview of computational conformal geometry applied to fundamental problems in specific engineering fields. It introduces readers to conformal geometry theory and discusses implementation issues from an engineering perspective.  The respective chapters explore fundamental problems in specific fields of application, and detail how computational conformal geometric methods can be used to solve them in a theoretically elegant and computationally efficient way. The fields covered include computer graphics, computer vision, geometric modeling, medical imaging, and wireless sensor networks. Each chapter concludes with a summary of the material covered and suggestions for further reading, and numerous illustrations and computational algorithms complement the text.  The book draws on courses given by the authors at the University of Louisiana at Lafayette, the State University of New York at Stony Brook, and Tsinghua University, and will be of interest to senior undergraduates, gradua...

Calibration of groundwater vulnerability mapping using the generalized reduced gradient method.

Science.gov (United States)

Elçi, Alper

2017-12-01

Groundwater vulnerability assessment studies are essential in water resources management. Overlay-and-index methods such as DRASTIC are widely used for mapping of groundwater vulnerability, however, these methods mainly suffer from a subjective selection of model parameters. The objective of this study is to introduce a calibration procedure that results in a more accurate assessment of groundwater vulnerability. The improvement of the assessment is formulated as a parameter optimization problem using an objective function that is based on the correlation between actual groundwater contamination and vulnerability index values. The non-linear optimization problem is solved with the generalized-reduced-gradient (GRG) method, which is numerical algorithm based optimization method. To demonstrate the applicability of the procedure, a vulnerability map for the Tahtali stream basin is calibrated using nitrate concentration data. The calibration procedure is easy to implement and aims the maximization of correlation between observed pollutant concentrations and groundwater vulnerability index values. The influence of each vulnerability parameter in the calculation of the vulnerability index is assessed by performing a single-parameter sensitivity analysis. Results of the sensitivity analysis show that all factors are effective on the final vulnerability index. Calibration of the vulnerability map improves the correlation between index values and measured nitrate concentrations by 19%. The regression coefficient increases from 0.280 to 0.485. It is evident that the spatial distribution and the proportions of vulnerability class areas are significantly altered with the calibration process. Although the applicability of the calibration method is demonstrated on the DRASTIC model, the applicability of the approach is not specific to a certain model and can also be easily applied to other overlay-and-index methods. Copyright © 2017 Elsevier B.V. All rights reserved.

Conformational analysis of lignin models; Analise conformacional de modelos de lignina

Energy Technology Data Exchange (ETDEWEB)

Santos, Helio F. dos [Juiz de Fora Univ., MG (Brazil). Dept. de Quimica]. E-mail: helius@quimica.ufjf.br

2001-08-01

The conformational equilibrium for two 5,5' biphenyl lignin models have been analyzed using a quantum mechanical semiempirical method. The gas phase and solution structures are discussed based on the NMR and X-ray experimental data. The results obtained showed that the observed conformations are solvent-dependent, being the geometries and the thermodynamic properties correlated with the experimental information. This study shows how a systematic theoretical conformational analysis can help to understand chemical processes at a molecular level. (author)

A General Method for QTL Mapping in Multiple Related Populations Derived from Multiple Parents

Directory of Open Access Journals (Sweden)

Yan AO

2009-03-01

Full Text Available It's well known that incorporating some existing populations derived from multiple parents may improve QTL mapping and QTL-based breeding programs. However, no general maximum likelihood method has been available for this strategy. Based on the QTL mapping in multiple related populations derived from two parents, a maximum likelihood estimation method was proposed, which can incorporate several populations derived from three or more parents and also can be used to handle different mating designs. Taking a circle design as an example, we conducted simulation studies to study the effect of QTL heritability and sample size upon the proposed method. The results showed that under the same heritability, enhanced power of QTL detection and more precise and accurate estimation of parameters could be obtained when three F2 populations were jointly analyzed, compared with the joint analysis of any two F2 populations. Higher heritability, especially with larger sample sizes, would increase the ability of QTL detection and improve the estimation of parameters. Potential advantages of the method are as follows: firstly, the existing results of QTL mapping in single population can be compared and integrated with each other with the proposed method, therefore the ability of QTL detection and precision of QTL mapping can be improved. Secondly, owing to multiple alleles in multiple parents, the method can exploit gene resource more adequately, which will lay an important genetic groundwork for plant improvement.

A privacy-preserving sharing method of electricity usage using self-organizing map

Directory of Open Access Journals (Sweden)

Yuichi Nakamura

2018-03-01

Full Text Available Smart meters for measuring electricity usage are expected in electricity usage management. Although the relevant power supplier stores the measured data, the data are worth sharing among power suppliers because the entire data of a city will be required to control the regional grid stability or demand–supply balance. Even though many techniques and methods of privacy-preserving data mining have been studied to share data while preserving data privacy, a study on sharing electricity usage data is still lacking. In this paper, we propose a sharing method of electricity usage while preserving data privacy using a self-organizing map. Keywords: Privacy preserving, Data sharing, Self-Organizing map

Conformal sequestering simplified

International Nuclear Information System (INIS)

Schmaltz, Martin; Sundrum, Raman

2006-01-01

Sequestering is important for obtaining flavor-universal soft masses in models where supersymmetry breaking is mediated at high scales. We construct a simple and robust class of hidden sector models which sequester themselves from the visible sector due to strong and conformally invariant hidden dynamics. Masses for hidden matter eventually break the conformal symmetry and lead to supersymmetry breaking by the mechanism recently discovered by Intriligator, Seiberg and Shih. We give a unified treatment of subtleties due to global symmetries of the CFT. There is enough review for the paper to constitute a self-contained account of conformal sequestering

Concept mapping as an empowering method to promote learning, thinking, teaching and research

Directory of Open Access Journals (Sweden)

Mauri Kalervo Åhlberg

2013-01-01

Full Text Available Results and underpinning of over twenty years of research and development program of concept mapping is presented. Different graphical knowledge presentation tools, especially concept mapping and mind mapping, are compared. There are two main dimensions that differentiate graphical knowledge presentation methods: The first dimension is conceptual explicitness: from mere concepts to flexibly named links and clear propositions in concept maps. The second dimension in the classification system I am suggesting is whether there are pictures or not. Åhlbergʼs and his research groupʼs applications and developments of Novakian concept maps are compared to traditional Novakian concept maps. The main innovations include always using arrowheads to show direction of reading the concept map. Centrality of each concept is estimated from number of links to other concepts. In our empirical research over two decades, number of relevant concepts, and number of relevant propositions in studentsʼ concept maps, have been found to be the best indicators and predictors of meaningful learning. This is used in assessment of learning. Improved concept mapping is presented as a tool to analyze texts. The main innovation is numbering the links to show order of reading the concept map and to make it possible to transform concept map back to the original prose text as closely as possible. In Åhlberg and his research groupʼs research, concept mapping has been tested in all main phases of research, teaching and learning.

A Method for Extracting the Free Energy Surface and Conformational Dynamics of Fast-Folding Proteins from Single Molecule Photon Trajectories

Science.gov (United States)

2015-01-01

Single molecule fluorescence spectroscopy holds the promise of providing direct measurements of protein folding free energy landscapes and conformational motions. However, fulfilling this promise has been prevented by technical limitations, most notably, the difficulty in analyzing the small packets of photons per millisecond that are typically recorded from individual biomolecules. Such limitation impairs the ability to accurately determine conformational distributions and resolve sub-millisecond processes. Here we develop an analytical procedure for extracting the conformational distribution and dynamics of fast-folding proteins directly from time-stamped photon arrival trajectories produced by single molecule FRET experiments. Our procedure combines the maximum likelihood analysis originally developed by Gopich and Szabo with a statistical mechanical model that describes protein folding as diffusion on a one-dimensional free energy surface. Using stochastic kinetic simulations, we thoroughly tested the performance of the method in identifying diverse fast-folding scenarios, ranging from two-state to one-state downhill folding, as a function of relevant experimental variables such as photon count rate, amount of input data, and background noise. The tests demonstrate that the analysis can accurately retrieve the original one-dimensional free energy surface and microsecond folding dynamics in spite of the sub-megahertz photon count rates and significant background noise levels of current single molecule fluorescence experiments. Therefore, our approach provides a powerful tool for the quantitative analysis of single molecule FRET experiments of fast protein folding that is also potentially extensible to the analysis of any other biomolecular process governed by sub-millisecond conformational dynamics. PMID:25988351

Conformity index: A review

International Nuclear Information System (INIS)

Feuvret, Loic; Noel, Georges; Mazeron, Jean-Jacques; Bey, Pierre

2006-01-01

We present a critical analysis of the conformity indices described in the literature and an evaluation of their field of application. Three-dimensional conformal radiotherapy, with or without intensity modulation, is based on medical imaging techniques, three-dimensional dosimetry software, compression accessories, and verification procedures. It consists of delineating target volumes and critical healthy tissues to select the best combination of beams. This approach allows better adaptation of the isodose to the tumor volume, while limiting irradiation of healthy tissues. Tools must be developed to evaluate the quality of proposed treatment plans. Dosimetry software provides the dose distribution in each CT section and dose-volume histograms without really indicating the degree of conformity. The conformity index is a complementary tool that attributes a score to a treatment plan or that can compare several treatment plans for the same patient. The future of conformal index in everyday practice therefore remains unclear

Non-Commutative Geometrical Aspects and Topological Invariants of a Conformally Regular Pentagonal Tiling of the Plane

DEFF Research Database (Denmark)

Ramirez-Solano, Maria

automatically has finite local complexity. In this thesis we give a construction of the continuous and discrete hull just from the combinatorial data. For the discrete hull we construct a C-algebra and a measure. Since this tiling possesses no natural R2 action by translation, there is no a priori reason......The article ”A regular pentagonal tiling of the plane” by Philip L. Bowers and Kenneth Stephenson defines a conformal pentagonal tiling. This is a tiling of the plane with remarkable combinatorial and geometric properties.However, it doesn’t have finite local complexity in any usual sense......, and therefore we cannot study it with the usual tiling theory. The appeal of the tiling is that all the tiles are conformally regular pentagons. But conformal maps are not allowable under finite local complexity. On the other hand, the tiling can be described completely by its combinatorial data, which rather...

Building maps to search the web: the method Sewcom

Directory of Open Access Journals (Sweden)

Corrado Petrucco

2002-01-01

Full Text Available Seeking information on the Internet is becoming a necessity 'at school, at work and in every social sphere. Unfortunately the difficulties' inherent in the use of search engines and the use of unconscious cognitive approaches inefficient limit their effectiveness. It is in this respect presented a method, called SEWCOM that lets you create conceptual maps through interaction with search engines.

Calculation of exit dose for conformal and dynamically‐wedged fields, based on water‐equivalent path length measured with an amorphous silicon electronic portal imaging device

Science.gov (United States)

Glegg, Martin; Metwaly, Mohamed; Currie, Garry; Elliott, Alex

2011-01-01

In this study, we use the quadratic calibration method (QCM), in which an EPID image is converted into a matrix of equivalent path lengths (EPLs) and, therefore, exit doses, so as to model doses in conformal and enhanced dynamic wedge (EDW) fields. The QCM involves acquiring series of EPID images at a reference field size for different thicknesses of homogeneous solid water blocks. From these, a set of coefficients is established that is used to compute the EPL of any other irradiated material. To determine the EPL, the irradiated area must be known in order to establish the appropriate scatter correction. A method was devised for the automatic calculation of areas from the EPID image that facilitated the calculation of EPL for any field and exit dose. For EDW fields, the fitting coefficients were modified by utilizing the linac manufacturer's golden segmented treatment tables (GSTT) methodology and MU fraction model. The nonlinear response of the EPL with lower monitor units (MUs) was investigated and slight modification of the algorithm performed to account for this. The method permits 2D dose distributions at the exit of phantom or patient to be generated by relating the EPL with an appropriate depth dose table. The results indicate that the inclusion of MU correction improved the EPL determination. The irradiated field areas can be accurately determined from EPID images to within ± 1% uncertainty. Cross‐plane profiles and 2D dose distributions of EPID predicted doses were compared with those calculated with the Eclipse treatment planning system (TPS) and those measured directly with MapCHECK 2 device. Comparison of the 2D EPID dose maps to those from TPS and MapCHECK shows that more than 90% of all points passed the gamma index acceptance criteria of 3% dose difference and 3 mm distance to agreement (DTA), for both conformal and EDW study cases. We conclude that the EPID QCM is an accurate and convenient method for in vivo dosimetry and may, therefore

Fermion-scalar conformal blocks

Energy Technology Data Exchange (ETDEWEB)

Iliesiu, Luca [Joseph Henry Laboratories, Princeton University,Washington Road, Princeton, NJ 08544 (United States); Kos, Filip [Department of Physics, Yale University,217 Prospect Street, New Haven, CT 06520 (United States); Poland, David [Department of Physics, Yale University,217 Prospect Street, New Haven, CT 06520 (United States); School of Natural Sciences, Institute for Advanced Study,1 Einstein Dr, Princeton, New Jersey 08540 (United States); Pufu, Silviu S. [Joseph Henry Laboratories, Princeton University,Washington Road, Princeton, NJ 08544 (United States); Simmons-Duffin, David [School of Natural Sciences, Institute for Advanced Study,1 Einstein Dr, Princeton, New Jersey 08540 (United States); Yacoby, Ran [Joseph Henry Laboratories, Princeton University,Washington Road, Princeton, NJ 08544 (United States)

2016-04-13

We compute the conformal blocks associated with scalar-scalar-fermion-fermion 4-point functions in 3D CFTs. Together with the known scalar conformal blocks, our result completes the task of determining the so-called ‘seed blocks’ in three dimensions. Conformal blocks associated with 4-point functions of operators with arbitrary spins can now be determined from these seed blocks by using known differential operators.

A superlinear convergence estimate for an iterative method for the biharmonic equation

Energy Technology Data Exchange (ETDEWEB)

Horn, M.A. [Wichita State Univ., Wichita, KS (United States)

1996-12-31

In [CDH] a method for the solution of boundary value problems for the biharmonic equation using conformal mapping was investigated. The method is an implementation of the classical method of Muskhelishvili. In [CDH] it was shown, using the Hankel structure, that the linear system in [Musk] is the discretization of the identify plus a compact operator, and therefore the conjugate gradient method will converge superlinearly. The purpose of this paper is to give an estimate of the superlinear convergence in the case when the boundary curve is in a Hoelder class.

Functional brain mapping using H{sub 2}{sup 15}O positron emission tomography (I): statistical parametric mapping method

Energy Technology Data Exchange (ETDEWEB)

Lee, Dong Soo; Lee, Jae Sung; Kim, Kyeong Min; Chung, June Key; Lee, Myung Chul [College of Medicine, Seoul National Univ., Seoul (Korea, Republic of)

1998-08-01

We investigated the statistical methods to compose the functional brain map of human working memory and the principal factors that have an effect on the methods for localization. Repeated PET scans with successive four tasks, which consist of one control and three different activation tasks, were performed on six right-handed normal volunteers for 2 minutes after bolus injections of 925 MBq H{sub 2}{sup 15}O at the intervals of 30 minutes. Image data were analyzed using SPM96 (Statistical Parametric Mapping) implemented with Matlab (Mathworks Inc., U.S.A.). Images from the same subject were spatially registered and were normalized using linear and nonlinear transformation methods. Significant difference between control and each activation state was estimated at every voxel based on the general linear model. Differences of global counts were removed using analysis of covariance (ANCOVA) with global activity as covariate. Using the mean and variance for each condition which was adjusted using ANCOVA, t-statistics was performed on every voxel. To interpret the results more easily, t-values were transformed to the standard Gaussian distribution (Z-score). All the subjects carried out the activation and control tests successfully. Average rate of correct answers was 95%. The numbers of activated blobs were 4 for verbal memory I, 9 for verbal memory II, 9 for visual memory, and 6 for conjunctive activation of these three tasks. The verbal working memory activates predominantly left-sided structures, and the visual memory activates the right hemisphere. We conclude that rCBF PET imaging and statistical parametric mapping method were useful in the localization of the brain regions for verbal and visual working memory.

Conformation-independent structural comparison of macromolecules with ProSMART

International Nuclear Information System (INIS)

Nicholls, Robert A.; Fischer, Marcus; McNicholas, Stuart; Murshudov, Garib N.

2014-01-01

The Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed to allow local comparative structural analyses independent of the global conformations and sequence homology of the compared macromolecules. This allows quick and intuitive visualization of the conservation of backbone and side-chain conformations, providing complementary information to existing methods. The identification and exploration of (dis)similarities between macromolecular structures can help to gain biological insight, for instance when visualizing or quantifying the response of a protein to ligand binding. Obtaining a residue alignment between compared structures is often a prerequisite for such comparative analysis. If the conformational change of the protein is dramatic, conventional alignment methods may struggle to provide an intuitive solution for straightforward analysis. To make such analyses more accessible, the Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed, which achieves a conformation-independent structural alignment, as well as providing such additional functionalities as the generation of restraints for use in the refinement of macromolecular models. Sensible comparison of protein (or DNA/RNA) structures in the presence of conformational changes is achieved by enforcing neither chain nor domain rigidity. The visualization of results is facilitated by popular molecular-graphics software such as CCP4mg and PyMOL, providing intuitive feedback regarding structural conservation and subtle dissimilarities between close homologues that can otherwise be hard to identify. Automatically generated colour schemes corresponding to various residue-based scores are provided, which allow the assessment of the conservation of backbone and side-chain conformations relative to the local coordinate frame. Structural comparison tools such as ProSMART can help to break the complexity that accompanies the constantly growing

Conformation-independent structural comparison of macromolecules with ProSMART

Energy Technology Data Exchange (ETDEWEB)

Nicholls, Robert A., E-mail: nicholls@mrc-lmb.cam.ac.uk [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (United Kingdom); Fischer, Marcus [University of California San Francisco, San Francisco, CA 94158 (United States); McNicholas, Stuart [University of York, Heslington, York YO10 5DD (United Kingdom); Murshudov, Garib N. [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (United Kingdom)

2014-09-01

The Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed to allow local comparative structural analyses independent of the global conformations and sequence homology of the compared macromolecules. This allows quick and intuitive visualization of the conservation of backbone and side-chain conformations, providing complementary information to existing methods. The identification and exploration of (dis)similarities between macromolecular structures can help to gain biological insight, for instance when visualizing or quantifying the response of a protein to ligand binding. Obtaining a residue alignment between compared structures is often a prerequisite for such comparative analysis. If the conformational change of the protein is dramatic, conventional alignment methods may struggle to provide an intuitive solution for straightforward analysis. To make such analyses more accessible, the Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed, which achieves a conformation-independent structural alignment, as well as providing such additional functionalities as the generation of restraints for use in the refinement of macromolecular models. Sensible comparison of protein (or DNA/RNA) structures in the presence of conformational changes is achieved by enforcing neither chain nor domain rigidity. The visualization of results is facilitated by popular molecular-graphics software such as CCP4mg and PyMOL, providing intuitive feedback regarding structural conservation and subtle dissimilarities between close homologues that can otherwise be hard to identify. Automatically generated colour schemes corresponding to various residue-based scores are provided, which allow the assessment of the conservation of backbone and side-chain conformations relative to the local coordinate frame. Structural comparison tools such as ProSMART can help to break the complexity that accompanies the constantly growing

Topology Optimization of Passive Micromixers Based on Lagrangian Mapping Method

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Yuchen Guo

2018-03-01

Full Text Available This paper presents an optimization-based design method of passive micromixers for immiscible fluids, which means that the Peclet number infinitely large. Based on topology optimization method, an optimization model is constructed to find the optimal layout of the passive micromixers. Being different from the topology optimization methods with Eulerian description of the convection-diffusion dynamics, this proposed method considers the extreme case, where the mixing is dominated completely by the convection with negligible diffusion. In this method, the mixing dynamics is modeled by the mapping method, a Lagrangian description that can deal with the case with convection-dominance. Several numerical examples have been presented to demonstrate the validity of the proposed method.

An information hiding method based on LSB and tent chaotic map

Science.gov (United States)

Song, Jianhua; Ding, Qun

2011-06-01

In order to protect information security more effectively, a novel information hiding method based on LSB and Tent chaotic map was proposed, first the secret message is Tent chaotic encrypted, and then LSB steganography is executed for the encrypted message in the cover-image. Compared to the traditional image information hiding method, the simulation results indicate that the method greatly improved in imperceptibility and security, and acquired good results.

Identification of key residues for protein conformational transition using elastic network model.

Science.gov (United States)

Su, Ji Guo; Xu, Xian Jin; Li, Chun Hua; Chen, Wei Zu; Wang, Cun Xin

2011-11-07

Proteins usually undergo conformational transitions between structurally disparate states to fulfill their functions. The large-scale allosteric conformational transitions are believed to involve some key residues that mediate the conformational movements between different regions of the protein. In the present work, a thermodynamic method based on the elastic network model is proposed to predict the key residues involved in protein conformational transitions. In our method, the key functional sites are identified as the residues whose perturbations largely influence the free energy difference between the protein states before and after transition. Two proteins, nucleotide binding domain of the heat shock protein 70 and human/rat DNA polymerase β, are used as case studies to identify the critical residues responsible for their open-closed conformational transitions. The results show that the functionally important residues mainly locate at the following regions for these two proteins: (1) the bridging point at the interface between the subdomains that control the opening and closure of the binding cleft; (2) the hinge region between different subdomains, which mediates the cooperative motions between the corresponding subdomains; and (3) the substrate binding sites. The similarity in the positions of the key residues for these two proteins may indicate a common mechanism in their conformational transitions.

Solving variational problems and partial differential equations that map between manifolds via the closest point method

Science.gov (United States)

King, Nathan D.; Ruuth, Steven J.

2017-05-01

Maps from a source manifold M to a target manifold N appear in liquid crystals, color image enhancement, texture mapping, brain mapping, and many other areas. A numerical framework to solve variational problems and partial differential equations (PDEs) that map between manifolds is introduced within this paper. Our approach, the closest point method for manifold mapping, reduces the problem of solving a constrained PDE between manifolds M and N to the simpler problems of solving a PDE on M and projecting to the closest points on N. In our approach, an embedding PDE is formulated in the embedding space using closest point representations of M and N. This enables the use of standard Cartesian numerics for general manifolds that are open or closed, with or without orientation, and of any codimension. An algorithm is presented for the important example of harmonic maps and generalized to a broader class of PDEs, which includes p-harmonic maps. Improved efficiency and robustness are observed in convergence studies relative to the level set embedding methods. Harmonic and p-harmonic maps are computed for a variety of numerical examples. In these examples, we denoise texture maps, diffuse random maps between general manifolds, and enhance color images.

Concept Map Technique as a New Method for Whole Text Translation

Science.gov (United States)

Krishan, Tamara Mohd Altabieri

2017-01-01

This study discusses the use of concept map tool as a new method for teaching translation (from English language to Arabic language). This study comprised 80 students divided into two groups. The first group was taught the new vocabulary by using the concept tool method, whereas the second group was taught the new vocabulary by the traditional…

Monitoring conformational dynamics with solid-state R1ρ experiments

International Nuclear Information System (INIS)

Quinn, Caitlin M.; McDermott, Ann E.

2009-01-01

A new application of solid-state rotating frame (R 1ρ ) relaxation experiments to observe conformational dynamics is presented. Studies on a model compound, dimethyl sulfone (DMS), show that R 1ρ relaxation due to reorientation of a chemical shift anisotropy (CSA) tensor undergoing chemical exchange can be used to monitor slow-to-intermediate timescale conformational exchange processes. Control experiments used d 6 -DMS and alanine to confirm that the technique is monitoring reorientation of the CSA tensor rather than dipolar interactions or methyl group rotation. The application of this method to proteins could represent a new site-specific probe of conformational dynamics

Selection of candidate wells and optimization of conformance treatment design in the Barrancas Field using a 3D conformance simulator

Energy Technology Data Exchange (ETDEWEB)

Crosta, Dante; Elitseche, Luis [Repsol YPF (Argentina); Gutierrez, Mauricio; Ansah, Joe; Everett, Don [Halliburton Argentina S.A., Buenos Aires (Argentina)

2004-07-01

Minimizing the amount of unwanted water production is an important goal at the Barrancas field. This paper describes a selection process for candidate injection wells that is part of a pilot conformance project aimed at improving vertical injection profiles, reducing water cut in producing wells, and improving ultimate oil recovery from this field. The well selection process is based on a review of limited reservoir information available for this field to determine inter-well communications. The methodology focuses on the best use of available information, such as production and injection history, well intervention files, open hole logs and injectivity surveys. After the candidate wells were selected and potential water injection channels were identified, conformance treatment design and future performance of wells in the selected pilot area were evaluated using a new 3 -D conformance simulator, developed specifically for optimization of the design and placement of unwanted fluid shut-off treatments. Thus, when acceptable history match ing of the pilot area production was obtained, the 3 -D simulator was used to: evaluate the required volume of selected conformance treatment fluid; review expected pressures and rates during placement;. model temperature behavior; evaluate placement techniques, and forecast water cut reduction and incremental oil recovery from the producers in this simulated section of the pilot area. This paper outlines a methodology for selecting candidate wells for conformance treatments. The method involves application of several engineering tools, an integral component of which is a user-friendly conformance simulator. The use of the simulator has minimized data preparation time and allows the running of sensitivity cases quickly to explore different possible scenarios that best represent the reservoir. The proposed methodology provides an efficient means of identifying conformance problems and designing optimized solutions for these individual

Reactions driving conformational movements (molecular motors) in gels: conformational and structural chemical kinetics.

Science.gov (United States)

Otero, Toribio F

2017-01-18

In this perspective the empirical kinetics of conducting polymers exchanging anions and solvent during electrochemical reactions to get dense reactive gels is reviewed. The reaction drives conformational movements of the chains (molecular motors), exchange of ions and solvent with the electrolyte and structural (relaxation, swelling, shrinking and compaction) gel changes. Reaction-driven structural changes are identified and quantified from electrochemical responses. The empirical reaction activation energy (E a ), the reaction coefficient (k) and the reaction orders (α and β) change as a function of the conformational energy variation during the reaction. This conformational energy becomes an empirical magnitude. E a , k, α and β include and provide quantitative conformational and structural information. The chemical kinetics becomes structural chemical kinetics (SCK) for reactions driving conformational movements of the reactants. The electrochemically stimulated conformational relaxation model describes empirical results and some results from the literature for biochemical reactions. In parallel the development of an emerging technological world of soft, wet, multifunctional and biomimetic tools and anthropomorphic robots driven by reactions of the constitutive material, as in biological organs, can be now envisaged being theoretically supported by the kinetic model.

Hadron spectroscopy and dynamics from light-front holography and conformal symmetry

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de Téramond Guy F.

2014-06-01

Full Text Available To a first semiclassical approximation one can reduce the multi-parton light-front problem in QCD to an effective one-dimensional quantum field theory, which encodes the fundamental conformal symmetry of the classical QCD Lagrangian. This procedure leads to a relativistic light-front wave equation for arbitrary spin which incorporates essential spectroscopic and non-perturbative dynamical features of hadron physics. The mass scale for confinement and higher dimensional holographic mapping to AdS space are also emergent properties of this framework.

A simple method for combining genetic mapping data from multiple crosses and experimental designs.

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Jeremy L Peirce

Full Text Available BACKGROUND: Over the past decade many linkage studies have defined chromosomal intervals containing polymorphisms that modulate a variety of traits. Many phenotypes are now associated with enough mapping data that meta-analysis could help refine locations of known QTLs and detect many novel QTLs. METHODOLOGY/PRINCIPAL FINDINGS: We describe a simple approach to combining QTL mapping results for multiple studies and demonstrate its utility using two hippocampus weight loci. Using data taken from two populations, a recombinant inbred strain set and an advanced intercross population we demonstrate considerable improvements in significance and resolution for both loci. 1-LOD support intervals were improved 51% for Hipp1a and 37% for Hipp9a. We first generate locus-wise permuted P-values for association with the phenotype from multiple maps, which can be done using a permutation method appropriate to each population. These results are then assigned to defined physical positions by interpolation between markers with known physical and genetic positions. We then use Fisher's combination test to combine position-by-position probabilities among experiments. Finally, we calculate genome-wide combined P-values by generating locus-specific P-values for each permuted map for each experiment. These permuted maps are then sampled with replacement and combined. The distribution of best locus-specific P-values for each combined map is the null distribution of genome-wide adjusted P-values. CONCLUSIONS/SIGNIFICANCE: Our approach is applicable to a wide variety of segregating and non-segregating mapping populations, facilitates rapid refinement of physical QTL position, is complementary to other QTL fine mapping methods, and provides an appropriate genome-wide criterion of significance for combined mapping results.

Improved method for drawing of a glycan map, and the first page of glycan atlas, which is a compilation of glycan maps for a whole organism.

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Shunji Natsuka

Full Text Available Glycan Atlas is a set of glycan maps over the whole body of an organism. The glycan map that includes data of glycan structure and quantity displays micro-heterogeneity of the glycans in a tissue, an organ, or cells. The two-dimensional glycan mapping is widely used for structure analysis of N-linked oligosaccharides on glycoproteins. In this study we developed a comprehensive method for the mapping of both N- and O-glycans with and without sialic acid. The mapping data of 150 standard pyridylaminated glycans were collected. The empirical additivity rule which was proposed in former reports was able to adapt for this extended glycan map. The adapted rule is that the elution time of pyridylamino glycans on high performance liquid chromatography (HPLC is expected to be the simple sum of the partial elution times assigned to each monosaccharide residue. The comprehensive mapping method developed in this study is a powerful tool for describing the micro-heterogeneity of the glycans. Furthermore, we prepared 42 pyridylamino (PA- glycans from human serum and were able to draw the map of human serum N- and O-glycans as an initial step of Glycan Atlas editing.

Axiomatic conformal field theory

International Nuclear Information System (INIS)

Gaberdiel, M.R.; Goddard, P.

2000-01-01

A new rigourous approach to conformal field theory is presented. The basic objects are families of complex-valued amplitudes, which define a meromorphic conformal field theory (or chiral algebra) and which lead naturally to the definition of topological vector spaces, between which vertex operators act as continuous operators. In fact, in order to develop the theory, Moebius invariance rather than full conformal invariance is required but it is shown that every Moebius theory can be extended to a conformal theory by the construction of a Virasoro field. In this approach, a representation of a conformal field theory is naturally defined in terms of a family of amplitudes with appropriate analytic properties. It is shown that these amplitudes can also be derived from a suitable collection of states in the meromorphic theory. Zhu's algebra then appears naturally as the algebra of conditions which states defining highest weight representations must satisfy. The relationship of the representations of Zhu's algebra to the classification of highest weight representations is explained. (orig.)

Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis

DEFF Research Database (Denmark)

Villa, Elizabeth; Sengupta, Jayati; Trabuco, Leonard G.

2009-01-01

In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced conformational changes of the factor that play a pivotal role in the selection of the cognate aminoacyl-tRNAs. We present a 6.......7-A cryo-electron microscopy map of the aminoacyl-tRNA x EF-Tu x GDP x kirromycin-bound Escherichia coli ribosome, together with an atomic model of the complex obtained through molecular dynamics flexible fitting. The model reveals the conformational changes in the conserved GTPase switch regions...... of EF-Tu that trigger hydrolysis of GTP, along with key interactions, including those between the sarcin-ricin loop and the P loop of EF-Tu, and between the effector loop of EF-Tu and a conserved region of the 16S rRNA. Our data suggest that GTP hydrolysis on EF-Tu is controlled through a hydrophobic...

Conformal description of spinning particles

International Nuclear Information System (INIS)

Todorov, I.T.

1986-01-01

This book is an introduction to the application of the conformal group to quantum field theory of particles with spin. After an introduction to the twistor representations of the conformal group of a conformally flat space-time and twistor flag manifolds with Su(2,2) orbits the classical phase space of conformal spinning particles is described. Thereafter the twistor description of classical zero mass fields is considered together with the quantization. (HSI)

Conformal boundaries of warped products

DEFF Research Database (Denmark)

Kokkendorff, Simon Lyngby

2006-01-01

In this note we prove a result on how to determine the conformal boundary of a type of warped product of two length spaces in terms of the individual conformal boundaries. In the situation, that we treat, the warping and conformal distortion functions are functions of distance to a base point....... The result is applied to produce examples of CAT(0)-spaces, where the conformal and ideal boundaries differ in interesting ways....

DFT study of conformational and vibrational characteristics of 2-(2-hydroxyphenyl)benzothiazole molecule.

Science.gov (United States)

Pandey, Urmila; Srivastava, Mayuri; Singh, R P; Yadav, R A

2014-08-14

The conformational and IR and Raman spectral studies of 2-(2-hydroxyphenyl)benzothiazole have been carried out by using the DFT method at the B3LYP/6-311++G(**) level. The detailed vibrational assignments have been done on the basis of calculated potential energy distributions. Comparative studies of molecular geometries, atomic charges and vibrational fundamentals of all the conformers have been made. There are four possible conformers for this molecule. The optimized geometrical parameters obtained by B3LYP/6-311++G(**) method showed good agreement with the experimental X-ray data. The atomic polar tensor (APT) charges, Mulliken atomic charges, natural bond orbital (NBO) analysis and HOMO-LUMO energy gap of HBT and its conformers were also computed. Copyright © 2014 Elsevier B.V. All rights reserved.

A New General Iterative Method for a Finite Family of Nonexpansive Mappings in Hilbert Spaces

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Singthong Urailuk

2010-01-01

Full Text Available We introduce a new general iterative method by using the -mapping for finding a common fixed point of a finite family of nonexpansive mappings in the framework of Hilbert spaces. A strong convergence theorem of the purposed iterative method is established under some certain control conditions. Our results improve and extend the results announced by many others.

A probabilistic model of RNA conformational space

DEFF Research Database (Denmark)

Frellsen, Jes; Moltke, Ida; Thiim, Martin

2009-01-01

, the discrete nature of the fragments necessitates the use of carefully tuned, unphysical energy functions, and their non-probabilistic nature impairs unbiased sampling. We offer a solution to the sampling problem that removes these important limitations: a probabilistic model of RNA structure that allows...... conformations for 9 out of 10 test structures, solely using coarse-grained base-pairing information. In conclusion, the method provides a theoretical and practical solution for a major bottleneck on the way to routine prediction and simulation of RNA structure and dynamics in atomic detail.......The increasing importance of non-coding RNA in biology and medicine has led to a growing interest in the problem of RNA 3-D structure prediction. As is the case for proteins, RNA 3-D structure prediction methods require two key ingredients: an accurate energy function and a conformational sampling...

A theoretical and spectroscopic study of conformational structures of piroxicam

Science.gov (United States)

Souza, Kely Ferreira de; Martins, José A.; Pessine, Francisco B. T.; Custodio, Rogério

2010-02-01

Piroxicam (PRX) has been widely studied in an attempt to elucidate the causes and mechanisms of its side effects, mainly the photo-toxicity. In this paper fluorescence spectra in non-protic solvents and different polarities were carried out along with theoretical calculations. Preliminary potential surfaces of the keto and enol forms were obtained at AM1 level of theory providing the most stable conformers, which had their structure re-optimized through the B3LYP/CEP-31G(d,p) method. From the optimized structures, the electronic spectra were calculated using the TD-DFT method in vacuum and including the solvent effect through the PCM method and a single water molecule near PRX. A new potential surface was constructed to the enol tautomer at DFT level and the most stable conformers were submitted to the QST2 calculations. The experimental data showed that in apolar media, the solution fluorescence is raised. Based on conformational analysis for the two tautomers, keto and enol, the results indicated that the PRX-enol is the main tautomer related to the drug fluorescence, which is reinforced by the spectra results, as well as the interconvertion barrier obtained from the QST2 calculations. The results suggest that the PRX one of the enol conformers presents great possibility of involvement in the photo-toxicity mechanisms.

Braiding and fusion properties of the Neveu-Schwarz super-conformal blocks

OpenAIRE

Chorazkiewicz, Damian; Hadasz, Leszek

2008-01-01

We construct, generalizing appropriately the method applied by J. Teschner in the case of the Virasoro conformal blocks, the braiding and fusion matrices of the Neveu-Schwarz super-conformal blocks. Their properties allow for an explicit verification of the bootstrap equation in the NS sector of the N=1 supersymmetric Liouville field theory.

Braiding and fusion properties of the Neveu-Schwarz super-conformal blocks

International Nuclear Information System (INIS)

Chorazkiewicz, Damian; Hadasz, Leszek

2009-01-01

We construct, generalizing appropriately the method applied by J. Teschner in the case of the Virasoro conformal blocks, the braiding and fusion matrices of the Neveu-Schwarz super-conformal blocks. Their properties allow for an explicit verification of the bootstrap equation in the NS sector of the N = 1 supersymmetric Liouville field theory.

Three-dimensional conformal pancreas treatment: comparison of four- to six-field techniques

International Nuclear Information System (INIS)

Higgins, Patrick D.; Sohn, Jason W.; Fine, Robert M.; Schell, Michael C.

1995-01-01

Purpose: We compare practical conformal treatment approaches to pancreatic cancer using 6 and 18 MV photons and contrast those approaches against standard techniques. Methods and Materials: A four-field conformal technique for treating pancreas cancer has been developed using nonopposed 18 MV photons. This approach has been extended to 6 MV photon application by the addition of one to two fields. These techniques have been optimized to increase sparing of normal liver and bowel, compared with opposed-field methods, to improve patient tolerance of high doses. In this study we compare these techniques in a simulated tumor model in a cylindrical phantom. Dose-volume analysis is used to quantify differences between the conformal, nonopposed techniques with conformal, opposed field methods. This model is also used to evaluate the effect of 1-2 cm setup errors on dose-volume coverage. Results: Dose-volume analysis demonstrates that five-to-six field conformal treatments using 6 MV photons provides similar or better dose coverage and normal tissue sparing characteristics as an optimized 18 MV, four-field approach when 1-2 cm margins are included for setup uncertainty. All approaches using nonopposed beam geometry provide significant reduction in the volume of tissue encompassed by the 30-50% isodose surfaces, as compared with four-field box techniques. Conclusions: Three-dimensional (3D) conformal treatments can be designed that significantly improve dose-volume characteristics over conventional treatment designs without costing unacceptable amounts of machine time. Further, deep intraabdominal sites can be adequately accessed and treated on intermediate energy machines with a relatively moderate increase in machine time

The Salient Map Analysis for Research and Teaching (SMART) method: Powerful potential as a formative assessment in the biomedical sciences

Science.gov (United States)

Cathcart, Laura Anne

This dissertation consists of two studies: 1) development and characterization of the Salient Map Analysis for Research and Teaching (SMART) method as a formative assessment tool and 2) a case study exploring how a paramedic instructor's beliefs about learners affect her utilization of the SMART method and vice versa. The first study explored: How can a novel concept map analysis method be designed as an effective formative assessment tool? The SMART method improves upon existing concept map analysis methods because it does not require hierarchically structured concept maps and it preserves the rich content of the maps instead of reducing each map down to a numerical score. The SMART method is performed by comparing a set of students' maps to each other and to an instructor's map. The resulting composite map depicts, in percentages and highlighted colors, the similarities and differences between all of the maps. Some advantages of the SMART method as a formative assessment tool include its ability to highlight changes across time, problematic or alternative conceptions, and patterns of student responses at a glance. Study two explored: How do a paramedic instructor's beliefs about students and learning affect---and become affected by---her use of the SMART method as a formative assessment tool? This case study of Angel, an expert paramedic instructor, begins to address a gap in the emergency medical services (EMS) education literature, which contains almost no research on teachers or pedagogy. Angel and I worked together as participant co-researchers (Heron & Reason, 1997) exploring the affordances of the SMART method. This study, based on those interactions with Angel, involved using open coding to identify themes (Strauss & Corbin, 1998) from Angel's views of students and use of the SMART method. Angel views learning as a sense-making process. She has a multi-faceted view of her students as novices and invests substantial time trying to understand their concept

Conformational analysis of the deoxyribofuranose ring in DNA by means of sums of proton-proton coupling constants: A graphical method

International Nuclear Information System (INIS)

Rinkel, L.J.; Altona, C.

1987-01-01

A graphical method is presented for the conformational analysis of the sugar ring in DNA fragments by means of proton-proton couplings. The coupling data required for this analysis consist of sums of couplings, which are referred to as sigma 1' (= J1'2' + J1'2''), sigma 2' (= J1'2' + J2'3' + J2'2''), sigma 2'' (= J1'2'' + J2''3' + J2'2'') and sigma 3' (= J2'3' + J2''3' + J3'4'). These sums of couplings correspond to the distance between the outer peaks of the H1', H2', H2'' and H3' [31P] resonances, respectively, (except for sigma 2' and sigma 2'' in the case of a small chemical shift difference between the H2' and H2'' resonances) and can often be obtained from 1H-NMR spectra via first-order measurement, obviating the necessity of a computer-assisted simulation of the fine structure of these resonances. Two different types of graphs for the interpretation of the coupling data are discussed: the first type of graph serves to probe as to whether or not the sugar ring occurs as a single conformer, and if so to analyze the coupling data in terms of the geometry of this sugar ring. In cases where the sugar ring does not occur as a single conformer, but as a blend of N- and S-type sugar puckers, the second type of graph is used to analyze the coupling data in terms of the geometry and population of the most abundant form. It is shown that the latter type of analysis can be carried out on the basis of experimental values for merely sigma 1',sigma 2' and sigma 2'', without any assumptions or restrictions concerning a relation between the geometry of the N- and S-type conformer. In addition, the question is discussed as to how insight can be gained into the conformational purity of the sugar ring from the observed fine structure of the H1' resonance

Integrating Multi-omic features exploiting Chromosome Conformation Capture data