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Sample records for spectrometry conformation space

  1. Characterizing ion mobility-mass spectrometry conformation space for the analysis of complex biological samples

    Science.gov (United States)

    Fenn, Larissa S.; Kliman, Michal; Mahsut, Ablatt; Zhao, Sophie R.

    2009-01-01

    The conformation space occupied by different classes of biomolecules measured by ion mobility-mass spectrometry (IM-MS) is described for utility in the characterization of complex biological samples. Although the qualitative separation of different classes of biomolecules on the basis of structure or collision cross section is known, there is relatively little quantitative cross-section information available for species apart from peptides. In this report, collision cross sections are measured for a large suite of biologically salient species, including oligonucleotides (n=96), carbohydrates (n=192), and lipids (n=53), which are compared to reported values for peptides (n= 610). In general, signals for each class are highly correlated, and at a given mass, these correlations result in predicted collision cross sections that increase in the order oligonucleotidescarbohydratescarbohydrates. The utility of conformation space analysis in the direct analysis of complex biological samples is described, both in the context of qualitative molecular class identification and in fine structure examination within a class. The latter is demonstrated in IM-MS separations of isobaric oligonucleotides, which are interpreted by molecular dynamics simulations. PMID:19247641

  2. Twistor space, Minkowski space and the conformal group

    NARCIS (Netherlands)

    van den Broek, P.M.

    1983-01-01

    It is shown that the conformal group of compactified Minkowski space is isomorphic to a group of rays of semilinear transformations of twistor space. The action of the conformal group on twistor space is given by an explicit realisation of this isomorphism. In this way we determine the

  3. Conformal basis for flat space amplitudes

    Science.gov (United States)

    Pasterski, Sabrina; Shao, Shu-Heng

    2017-09-01

    We study solutions of the Klein-Gordon, Maxwell, and linearized Einstein equations in R1 ,d +1 that transform as d -dimensional conformal primaries under the Lorentz group S O (1 ,d +1 ). Such solutions, called conformal primary wavefunctions, are labeled by a conformal dimension Δ and a point in Rd, rather than an on-shell (d +2 )-dimensional momentum. We show that the continuum of scalar conformal primary wavefunctions on the principal continuous series Δ ∈d/2 +i R of S O (1 ,d +1 ) spans a complete set of normalizable solutions to the wave equation. In the massless case, with or without spin, the transition from momentum space to conformal primary wavefunctions is implemented by a Mellin transform. As a consequence of this construction, scattering amplitudes in this basis transform covariantly under S O (1 ,d +1 ) as d -dimensional conformal correlators.

  4. Conformal Bootstrap in Mellin Space

    Science.gov (United States)

    Gopakumar, Rajesh; Kaviraj, Apratim; Sen, Kallol; Sinha, Aninda

    2017-02-01

    We propose a new approach towards analytically solving for the dynamical content of conformal field theories (CFTs) using the bootstrap philosophy. This combines the original bootstrap idea of Polyakov with the modern technology of the Mellin representation of CFT amplitudes. We employ exchange Witten diagrams with built-in crossing symmetry as our basic building blocks rather than the conventional conformal blocks in a particular channel. Demanding consistency with the operator product expansion (OPE) implies an infinite set of constraints on operator dimensions and OPE coefficients. We illustrate the power of this method in the ɛ expansion of the Wilson-Fisher fixed point by reproducing anomalous dimensions and, strikingly, obtaining OPE coefficients to higher orders in ɛ than currently available using other analytic techniques (including Feynman diagram calculations). Our results enable us to get a somewhat better agreement between certain observables in the 3D Ising model and the precise numerical values that have been recently obtained.

  5. A probabilistic model of RNA conformational space

    DEFF Research Database (Denmark)

    Frellsen, Jes; Moltke, Ida; Thiim, Martin

    2009-01-01

    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...... procedure. Both are only partly solved problems. Here, we focus on the problem of conformational sampling. The current state of the art solution is based on fragment assembly methods, which construct plausible conformations by stringing together short fragments obtained from experimental structures. However...... efficient sampling of RNA conformations in continuous space, and with associated probabilities. We show that the model captures several key features of RNA structure, such as its rotameric nature and the distribution of the helix lengths. Furthermore, the model readily generates native-like 3-D...

  6. The solutions of time and space conformable fractional heat equations with conformable Fourier transform

    Directory of Open Access Journals (Sweden)

    Çenesiz Yücel

    2015-12-01

    Full Text Available In this paper our aim is to find the solutions of time and space fractional heat differential equations by using new definition of fractional derivative called conformable fractional derivative. Also based on conformable fractional derivative definition conformable Fourier Transform is defined. Fourier sine and Fourier cosine transform definitions are given and space fractional heat equation is solved by conformable Fourier transform.

  7. Application of Conformational Space Search in Drug Action | Adikwu ...

    African Journals Online (AJOL)

    The role of conformational space in drug action is presented. Two examples of molecules in different therapeutic groups are presented. Conformational space search will lead to isolating the exact conformation with the desired medicinal properties. Many conformations of a plant isolate may exist which are active, weakly ...

  8. Implications of conformal invariance in momentum space

    Science.gov (United States)

    Bzowski, Adam; McFadden, Paul; Skenderis, Kostas

    2014-03-01

    We present a comprehensive analysis of the implications of conformal invariance for 3-point functions of the stress-energy tensor, conserved currents and scalar operators in general dimension and in momentum space. Our starting point is a novel and very effective decomposition of tensor correlators which reduces their computation to that of a number of scalar form factors. For example, the most general 3-point function of a conserved and traceless stress-energy tensor is determined by only five form factors. Dilatations and special conformal Ward identities then impose additional conditions on these form factors. The special conformal Ward identities become a set of first and second order differential equations, whose general solution is given in terms of integrals involving a product of three Bessel functions (`triple- K integrals'). All in all, the correlators are completely determined up to a number of constants, in agreement with well-known position space results. In odd dimensions 3-point functions are finite without renormalisation while in even dimensions non-trivial renormalisation in required. In this paper we restrict ourselves to odd dimensions. A comprehensive analysis of renormalisation will be discussed elsewhere. This paper contains two parts that can be read independently of each other. In the first part, we explain the method that leads to the solution for the correlators in terms of triple- K integrals while the second part contains a self-contained presentation of all results. Readers interested only in results may directly consult the second part of the paper.

  9. Boundary conformal anomalies on hyperbolic spaces and Euclidean balls

    Science.gov (United States)

    Rodriguez-Gomez, Diego; Russo, Jorge G.

    2017-12-01

    We compute conformal anomalies for conformal field theories with free conformal scalars and massless spin 1/2 fields in hyperbolic space ℍ d and in the ball B^d , for 2≤d≤7. These spaces are related by a conformal transformation. In even dimensional spaces, the conformal anomalies on ℍ2 n and B^{2n} are shown to be identical. In odd dimensional spaces, the conformal anomaly on B^{2n+1} comes from a boundary contribution, which exactly coincides with that of ℍ2 n + 1 provided one identifies the UV short-distance cutoff on B^{2n+1} with the inverse large distance IR cutoff on ℍ2 n + 1, just as prescribed by the conformal map. As an application, we determine, for the first time, the conformal anomaly coefficients multiplying the Euler characteristic of the boundary for scalars and half-spin fields with various boundary conditions in d = 5 and d = 7.

  10. Double conformal space-time algebra

    Science.gov (United States)

    Easter, Robert Benjamin; Hitzer, Eckhard

    2017-01-01

    The Double Conformal Space-Time Algebra (DCSTA) is a high-dimensional 12D Geometric Algebra G 4,8that extends the concepts introduced with the Double Conformal / Darboux Cyclide Geometric Algebra (DCGA) G 8,2 with entities for Darboux cyclides (incl. parabolic and Dupin cyclides, general quadrics, and ring torus) in spacetime with a new boost operator. The base algebra in which spacetime geometry is modeled is the Space-Time Algebra (STA) G 1,3. Two Conformal Space-Time subalgebras (CSTA) G 2,4 provide spacetime entities for points, flats (incl. worldlines), and hyperbolics, and a complete set of versors for their spacetime transformations that includes rotation, translation, isotropic dilation, hyperbolic rotation (boost), planar reflection, and (pseudo)spherical inversion in rounds or hyperbolics. The DCSTA G 4,8 is a doubling product of two G 2,4 CSTA subalgebras that inherits doubled CSTA entities and versors from CSTA and adds new bivector entities for (pseudo)quadrics and Darboux (pseudo)cyclides in spacetime that are also transformed by the doubled versors. The "pseudo" surface entities are spacetime hyperbolics or other surface entities using the time axis as a pseudospatial dimension. The (pseudo)cyclides are the inversions of (pseudo)quadrics in rounds or hyperbolics. An operation for the directed non-uniform scaling (anisotropic dilation) of the bivector general quadric entities is defined using the boost operator and a spatial projection. DCSTA allows general quadric surfaces to be transformed in spacetime by the same complete set of doubled CSTA versor (i.e., DCSTA versor) operations that are also valid on the doubled CSTA point entity (i.e., DCSTA point) and the other doubled CSTA entities. The new DCSTA bivector entities are formed by extracting values from the DCSTA point entity using specifically defined inner product extraction operators. Quadric surface entities can be boosted into moving surfaces with constant velocities that display the length

  11. Probing conformational changes in rhodopsin using hydrogen-deuterium exchange coupled to mass spectrometry.

    Science.gov (United States)

    Orban, Tivadar; Tsybovsky, Yaroslav

    2015-01-01

    Hydrogen-deuterium exchange coupled to mass spectrometry is a powerful tool to evaluate changes in protein conformation between two or more states. Here, we describe a complete methodology that can be used to assess conformational changes in rhodopsin accompanying its transition from the inactive to activated state upon light exposure. This approach may be employed to investigate the structure and conformational changes of various membrane proteins.

  12. On the local non-conforming virtual element spaces

    Energy Technology Data Exchange (ETDEWEB)

    Manzini, Gianmarco [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Gyrya, Vitaliy [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2014-11-13

    The construction of the local non-conforming virtual element spaces is discussed and the isomorphism between their functions and the polynomial moments of such functions is established by a formal argument and two different constructive proofs.

  13. Conformal higher spin scattering amplitudes from twistor space

    Energy Technology Data Exchange (ETDEWEB)

    Adamo, Tim [Blackett Laboratory, Imperial College, London, SW7 2AZ (United Kingdom); Hähnel, Philipp; McLoughlin, Tristan [School of Mathematics, Trinity College Dublin, College Green, Dublin 2 (Ireland)

    2017-04-04

    We use the formulation of conformal higher spin (CHS) theories in twistor space to study their tree-level scattering amplitudes, finding expressions for all three-point (MHV)-bar amplitudes and all MHV amplitudes involving positive helicity conformal gravity particles and two negative helicity higher spins. This provides the on-shell analogue for the covariant coupling of CHS fields to a conformal gravity background. We discuss the restriction of the theory to a ghost-free unitary subsector, analogous to restricting conformal gravity to general relativity with a cosmological constant. We study the flat-space limit and show that the restricted amplitudes vanish, supporting the conjecture that in the unitary sector the S-matrix of CHS theories is trivial. However, by appropriately rescaling the amplitudes we find non-vanishing results which we compare with chiral flat-space higher spin theories.

  14. Conformal higher spin scattering amplitudes from twistor space

    Science.gov (United States)

    Adamo, Tim; Hähnel, Philipp; McLoughlin, Tristan

    2017-04-01

    We use the formulation of conformal higher spin (CHS) theories in twistor space to study their tree-level scattering amplitudes, finding expressions for all three-point \\overline{MHV} amplitudes and all MHV amplitudes involving positive helicity conformal gravity particles and two negative helicity higher spins. This provides the on-shell analogue for the covariant coupling of CHS fields to a conformal gravity background. We discuss the restriction of the theory to a ghost-free unitary subsector, analogous to restricting conformal gravity to general relativity with a cosmological constant. We study the flat-space limit and show that the restricted amplitudes vanish, supporting the conjecture that in the unitary sector the S-matrix of CHS theories is trivial. However, by appropriately rescaling the amplitudes we find non-vanishing results which we compare with chiral flat-space higher spin theories.

  15. Space Applications of Mass Spectrometry. Chapter 31

    Science.gov (United States)

    Hoffman, John H.; Griffin, Timothy P.; Limero, Thomas; Arkin, C. Richard

    2010-01-01

    Mass spectrometers have been involved in essentially all aspects of space exploration. This chapter outlines some of these many uses. Mass spectrometers have not only helped to expand our knowledge and understanding of the world and solar system around us, they have helped to put man safely in space and expand our frontier. Mass spectrometry continues to prove to be a very reliable, robust, and flexible analytical instrument, ensuring that its use will continue to help aid our investigation of the universe and this small planet that we call home.

  16. Entanglement entropy from the truncated conformal space

    Energy Technology Data Exchange (ETDEWEB)

    Palmai, T., E-mail: palmai@phy.bme.hu

    2016-08-10

    A new numerical approach to entanglement entropies of the Rényi type is proposed for one-dimensional quantum field theories. The method extends the truncated conformal spectrum approach and we will demonstrate that it is especially suited to study the crossover from massless to massive behavior when the subsystem size is comparable to the correlation length. We apply it to different deformations of massless free fermions, corresponding to the scaling limit of the Ising model in transverse and longitudinal fields. For massive free fermions the exactly known crossover function is reproduced already in very small system sizes. The new method treats ground states and excited states on the same footing, and the applicability for excited states is illustrated by reproducing Rényi entropies of low-lying states in the transverse field Ising model.

  17. Entanglement entropy from the truncated conformal space

    Directory of Open Access Journals (Sweden)

    T. Palmai

    2016-08-01

    Full Text Available A new numerical approach to entanglement entropies of the Rényi type is proposed for one-dimensional quantum field theories. The method extends the truncated conformal spectrum approach and we will demonstrate that it is especially suited to study the crossover from massless to massive behavior when the subsystem size is comparable to the correlation length. We apply it to different deformations of massless free fermions, corresponding to the scaling limit of the Ising model in transverse and longitudinal fields. For massive free fermions the exactly known crossover function is reproduced already in very small system sizes. The new method treats ground states and excited states on the same footing, and the applicability for excited states is illustrated by reproducing Rényi entropies of low-lying states in the transverse field Ising model.

  18. Distance Geometry Protocol to Generate Conformations of Natural Products to Structurally Interpret Ion Mobility-Mass Spectrometry Collision Cross Sections

    Science.gov (United States)

    2015-01-01

    Ion mobility-mass spectrometry (IM-MS) allows the separation of ionized molecules based on their charge-to-surface area (IM) and mass-to-charge ratio (MS), respectively. The IM drift time data that is obtained is used to calculate the ion-neutral collision cross section (CCS) of the ionized molecule with the neutral drift gas, which is directly related to the ion conformation and hence molecular size and shape. Studying the conformational landscape of these ionized molecules computationally provides interpretation to delineate the potential structures that these CCS values could represent, or conversely, structural motifs not consistent with the IM data. A challenge in the IM-MS community is the ability to rapidly compute conformations to interpret natural product data, a class of molecules exhibiting a broad range of biological activity. The diversity of biological activity is, in part, related to the unique structural characteristics often observed for natural products. Contemporary approaches to structurally interpret IM-MS data for peptides and proteins typically utilize molecular dynamics (MD) simulations to sample conformational space. However, MD calculations are computationally expensive, they require a force field that accurately describes the molecule of interest, and there is no simple metric that indicates when sufficient conformational sampling has been achieved. Distance geometry is a computationally inexpensive approach that creates conformations based on sampling different pairwise distances between the atoms within the molecule and therefore does not require a force field. Progressively larger distance bounds can be used in distance geometry calculations, providing in principle a strategy to assess when all plausible conformations have been sampled. Our results suggest that distance geometry is a computationally efficient and potentially superior strategy for conformational analysis of natural products to interpret gas-phase CCS data. PMID:25360896

  19. CR-submanifolds of a locally conformal Kaehler space form

    Directory of Open Access Journals (Sweden)

    M. Hasan Shahid

    1994-01-01

    Full Text Available (Bejancu [1,2] The purpose of this paper is to continue the study of CR-submanifolds, and in particular of those of a locally conformal Kaehler space form (Matsumoto [3]. Some results on the holomorphic sectional curvature, D-totally geodesic, D1-totally geodesic and D1-minimal CR-submanifolds of locally conformal Kaehler (1.c.k.-space from M¯(c are obtained. We have also discussed Ricci curvature as well as scalar curvature of CR-submanifolds of M¯(c.

  20. Structural alphabets derived from attractors in conformational space

    Science.gov (United States)

    2010-01-01

    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. PMID:20170534

  1. Structural alphabets derived from attractors in conformational space.

    Science.gov (United States)

    Pandini, Alessandro; Fornili, Arianna; Kleinjung, Jens

    2010-02-20

    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. 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. 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.

  2. 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.

  3. Mapping the conformational space accessible to catechol-O-methyltransferase.

    Science.gov (United States)

    Ehler, Andreas; Benz, Jörg; Schlatter, Daniel; Rudolph, Markus G

    2014-08-01

    Methylation catalysed by catechol-O-methyltransferase (COMT) is the main pathway of catechol neurotransmitter deactivation in the prefrontal cortex. Low levels of this class of neurotransmitters are held to be causative of diseases such as schizophrenia, depression and Parkinson's disease. Inhibition of COMT may increase neurotransmitter levels, thus offering a route for treatment. Structure-based drug design hitherto seems to be based on the closed enzyme conformation. Here, a set of apo, semi-holo, holo and Michaelis form crystal structures are described that define the conformational space available to COMT and that include likely intermediates along the catalytic pathway. Domain swaps and sizeable loop movements around the active site testify to the flexibility of this enzyme, rendering COMT a difficult drug target. The low affinity of the co-substrate S-adenosylmethionine and the large conformational changes involved during catalysis highlight significant energetic investment to achieve the closed conformation. Since each conformation of COMT is a bona fide target for inhibitors, other states than the closed conformation may be promising to address. Crystallographic data for an alternative avenue of COMT inhibition, i.e. locking of the apo state by an inhibitor, are presented. The set of COMT structures may prove to be useful for the development of novel classes of inhibitors.

  4. Conformal higher spin theory and twistor space actions

    Science.gov (United States)

    Hähnel, Philipp; McLoughlin, Tristan

    2017-12-01

    We consider the twistor description of conformal higher spin theories and give twistor space actions for the self-dual sector of theories with spin greater than two that produce the correct flat space-time spectrum. We identify a ghost-free subsector, analogous to the embedding of Einstein gravity with cosmological constant in Weyl gravity, which generates the unique spin-s three-point anti-MHV amplitude consistent with Poincaré invariance and helicity constraints. By including interactions between the infinite tower of higher-spin fields we give a geometric interpretation to the twistor equations of motion as the integrability condition for a holomorphic structure on an infinite jet bundle. Finally, we conjecture anti-self-dual interaction terms which give an implicit definition of a twistor action for the full conformal higher spin theory.

  5. Einstein equations and conformal structure: Existence of Anti-de Sitter-type space-times

    Science.gov (United States)

    Friedrich, Helmut

    1995-10-01

    We discuss Einstein's equations in the context of normal conformal Cartan connections, derive a new conformal representation of the equations, and express the equations in a conformally invariant gauge. The resulting formulation of the equations is used to show the existence of asymptotically simple solutions to Einstein's equations with a positive cosmological constant. The solutions are characterized by Cauchy data on a space-like slice and by the intrinsic conformal structure on the conformal boundary at space-like and null infinity.

  6. Monitoring Conformational Landscape of Ovine Prion Protein Monomer Using Ion Mobility Coupled to Mass Spectrometry

    Science.gov (United States)

    Van der Rest, Guillaume; Rezaei, Human; Halgand, Frédéric

    2017-02-01

    Prion protein is involved in deadly neurodegenerative diseases. Its pathogenicity is linked to its structural conversion (α-helix to β-strand transition). However, recent studies suggest that prion protein can follow a plurality of conversion pathways, which hints towards different conformers that might coexist in solution. To gain insights on the plasticity of the ovine prion protein (PrP) monomer, wild type (A136, R154, Q171), mutants and deletions of ARQ were studied by traveling wave ion mobility experiments coupled to mass spectrometry. In order to perform the analysis of a large body of data sets, we designed and evaluated the performance of a processing pipeline based on Driftscope peak detection and a homemade script for automated peak assignment, annotation, and quantification on specific multiply charged protein data. Using this approach, we showed that in the gas phase, PrPs are represented by at least three conformer families differing in both charge state distribution and collisional cross-section, in agreement with the work of Hilton et al. (2010). We also showed that this plasticity is borne both by the N- and C-terminal domains. Effect of protein concentration, pH and temperature were also assessed, showing that (1) pH does not affect conformer distributions, (2) protein concentration modifies the conformational landscape of one mutant (I208M) only, and (3) heating leads to other unfolded species and to a modification of the conformer intensity ratios.

  7. Chemical Crosslinking Mass Spectrometry Analysis of Protein Conformations and Supercomplexes in Heart Tissue.

    Science.gov (United States)

    Chavez, Juan D; Lee, Chi Fung; Caudal, Arianne; Keller, Andrew; Tian, Rong; Bruce, James E

    2017-11-24

    While modern structural biology technologies have greatly expanded the size and type of protein complexes that can now be studied, the ability to derive large-scale structural information on proteins and complexes as they exist within tissues is practically nonexistent. Here, we demonstrate the application of crosslinking mass spectrometry to identify protein structural features and interactions in tissue samples, providing systems structural biology insight into protein complexes as they exist in the mouse heart. This includes insights into multiple conformational states of sarcomere proteins, as well as interactions among OXPHOS complexes indicative of supercomplex assembly. The extension of crosslinking mass spectrometry analysis into the realm of tissues opens the door to increasing our understanding of protein structures and interactions within the context of the greater biological system. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Probing Conformational Changes of Human DNA Polymerase λ Using Mass Spectrometry-Based Protein Footprinting

    Science.gov (United States)

    Fowler, Jason D.; Brown, Jessica A.; Kvaratskhelia, Mamuka; Suo, Zucai

    2009-01-01

    SUMMARY Crystallographic studies of the C-terminal, DNA polymerase β-like domain of human DNA polymerase lambda (fPolλ) suggested that the catalytic cycle might not involve a large protein domain rearrangement as observed with several replicative DNA polymerases and DNA polymerase β. To examine solution-phase protein conformation changes in fPolλ, which also contains a breast cancer susceptibility gene 1 C-terminal domain and a Proline-rich domain at its N-terminus, we used a mass spectrometry - based protein footprinting approach. In parallel experiments, surface accessibility maps for Arg residues were compared for the free fPolλ versus the binary complex of enzyme•gapped DNA and the ternary complex of enzyme•gapped DNA•dNTP. These experiments suggested that fPolλ does not undergo major conformational changes during the catalysis in the solution phase. Furthermore, the mass spectrometry-based protein footprinting experiments revealed that active site residue R386 was shielded from the surface only in the presence of both a gapped DNA substrate and an incoming nucleotide dNTP. Site-directed mutagenesis and pre-steady state kinetic studies confirmed the importance of R386 for the enzyme activity, and indicated the key role for its guanidino group in stabilizing the negative charges of an incoming nucleotide and the leaving pyrophosphate product. We suggest that such interactions could be shared by and important for catalytic functions of other DNA polymerases. PMID:19467241

  9. Probing conformational changes of human DNA polymerase lambda using mass spectrometry-based protein footprinting.

    Science.gov (United States)

    Fowler, Jason D; Brown, Jessica A; Kvaratskhelia, Mamuka; Suo, Zucai

    2009-07-17

    Crystallographic studies of the C-terminal DNA polymerase-beta-like domain of full-length human DNA polymerase lambda (fPollambda) suggested that the catalytic cycle might not involve a large protein domain rearrangement as observed with several replicative DNA polymerases and DNA polymerase beta. To examine solution-phase protein conformational changes in fPollambda, which also contains a breast cancer susceptibility gene 1 C-terminal domain and a proline-rich domain at its N-terminus, we used a mass spectrometry-based protein footprinting approach. In parallel experiments, surface accessibility maps for Arg residues were compared for the free fPollambda versus the binary complex of enzyme*gapped DNA and the ternary complex of enzyme*gapped DNA*dNTP (2'-deoxynucleotide triphosphate). These experiments suggested that fPollambda does not undergo major conformational changes during the catalysis in the solution phase. Furthermore, the mass spectrometry-based protein footprinting experiments revealed that active site residue R386 was shielded from the surface only in the presence of both a gapped DNA substrate and an incoming nucleotide. Site-directed mutagenesis and pre-steady-state kinetic studies confirmed the importance of R386 for the enzyme activity and indicated the key role for its guanidino group in stabilizing the negative charges of an incoming nucleotide and the leaving pyrophosphate product. We suggest that such interactions could be shared by and important for catalytic functions of other DNA polymerases.

  10. Effects of Select Anions from the Hofmeister Series on the Gas-Phase Conformations of Protein Ions Measured with Traveling-Wave Ion Mobility Spectrometry/Mass Spectrometry

    Science.gov (United States)

    Merenbloom, Samuel I.; Flick, Tawnya G.; Daly, Michael P.; Williams, Evan R.

    2011-11-01

    The gas-phase conformations of ubiquitin, cytochrome c, lysozyme, and α-lactalbumin ions, formed by electrospray ionization (ESI) from aqueous solutions containing 5 mM ammonium perchlorate, ammonium iodide, ammonium sulfate, ammonium chloride, ammonium thiocyanate, or guanidinium chloride, are examined using traveling-wave ion mobility spectrometry (TWIMS) coupled to time-of-flight (TOF) mass spectrometry (MS). For ubiquitin, cytochrome c, and α-lactalbumin, adduction of multiple acid molecules results in no significant conformational changes to the highest and lowest charge states formed from aqueous solutions, whereas the intermediate charge states become more compact. The transition to more compact conformers for the intermediate charge states occurs with fewer bound H2SO4 molecules than HClO4 or HI molecules, suggesting ion-ion or salt-bridge interactions are stabilizing more compact forms of the gaseous protein. However, the drift time distributions for protein ions of the same net charge with the highest levels of adduction of each acid are comparable, indicating that these protein ions all adopt similarly compact conformations or families of conformers. No significant change in conformation is observed upon the adduction of multiple acid molecules to charge states of lysozyme. These results show that the attachment of HClO4, HI, or H2SO4 to multiply protonated proteins can induce compact conformations in the resulting gas-phase protein ions. In contrast, differing Hofmeister effects are observed for the corresponding anions in solution at higher concentrations.

  11. Probing Conformational Dynamics of Tau Protein by Hydrogen/Deuterium Exchange Mass Spectrometry

    Science.gov (United States)

    Huang, Richard Y.-C.; Iacob, Roxana E.; Sankaranarayanan, Sethu; Yang, Ling; Ahlijanian, Michael; Tao, Li; Tymiak, Adrienne A.; Chen, Guodong

    2017-10-01

    Fibrillization of the microtubule-associated protein tau has been recognized as one of the signature pathologies of the nervous system in Alzheimer's disease, progressive supranuclear palsy, and other tauopathies. The conformational transition of tau in the fibrillization process, tau monomer to soluble aggregates to fibrils in particular, remains unclear. Here we report on the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) in combination with other biochemical approaches, including Thioflavin S fluorescence measurements, enzyme-linked immunosorbent assay (ELISA), and Western blotting to understand the heparin-induced tau's fibrillization. HDX-MS studies including anti-tau antibody epitope mapping experiments provided molecular level details of the full-length tau's conformational dynamics and its regional solvent accessibility upon soluble aggregates formation. The results demonstrate that R3 region in the full-length tau's microtubule binding repeat region (MTBR) is stabilized in the aggregation process, leaving both N and C terminal regions to be solvent exposed in the soluble aggregates and fibrils. The findings also illustrate the practical utility of orthogonal analytical methodologies for the characterization of protein higher order structure. [Figure not available: see fulltext.

  12. Micropolar Fluids Using B-spline Divergence Conforming Spaces

    KAUST Repository

    Sarmiento, Adel

    2014-06-06

    We discretized the two-dimensional linear momentum, microrotation, energy and mass conservation equations from micropolar fluids theory, with the finite element method, creating divergence conforming spaces based on B-spline basis functions to obtain pointwise divergence free solutions [8]. Weak boundary conditions were imposed using Nitsche\\'s method for tangential conditions, while normal conditions were imposed strongly. Once the exact mass conservation was provided by the divergence free formulation, we focused on evaluating the differences between micropolar fluids and conventional fluids, to show the advantages of using the micropolar fluid model to capture the features of complex fluids. A square and an arc heat driven cavities were solved as test cases. A variation of the parameters of the model, along with the variation of Rayleigh number were performed for a better understanding of the system. The divergence free formulation was used to guarantee an accurate solution of the flow. This formulation was implemented using the framework PetIGA as a basis, using its parallel stuctures to achieve high scalability. The results of the square heat driven cavity test case are in good agreement with those reported earlier.

  13. Chain Assembly and Disassembly Processes Differently Affect the Conformational Space of Ubiquitin Chains.

    Science.gov (United States)

    Kniss, Andreas; Schuetz, Denise; Kazemi, Sina; Pluska, Lukas; Spindler, Philipp E; Rogov, Vladimir V; Husnjak, Koraljka; Dikic, Ivan; Güntert, Peter; Sommer, Thomas; Prisner, Thomas F; Dötsch, Volker

    2018-02-06

    Ubiquitination is the most versatile posttranslational modification. The information is encoded by linkage type as well as chain length, which are translated by ubiquitin binding domains into specific signaling events. Chain topology determines the conformational space of a ubiquitin chain and adds an additional regulatory layer to this ubiquitin code. In particular, processes that modify chain length will be affected by chain conformations as they require access to the elongation or cleavage sites. We investigated conformational distributions in the context of chain elongation and disassembly using pulsed electron-electron double resonance spectroscopy in combination with molecular modeling. Analysis of the conformational space of diubiquitin revealed conformational selection or remodeling as mechanisms for chain recognition during elongation or hydrolysis, respectively. Chain elongation to tetraubiquitin increases the sampled conformational space, suggesting that a high intrinsic flexibility of K48-linked chains may contribute to efficient proteasomal degradation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Velocity-space sensitivity of neutron spectrometry measurements

    DEFF Research Database (Denmark)

    Jacobsen, Asger Schou; Salewski, Mirko; Eriksson, J.

    2015-01-01

    Neutron emission spectrometry (NES) measures the energies of neutrons produced in fusion reactions. Here we present velocity-space weight functions for NES and neutron yield measurements. Weight functions show the sensitivity as well as the accessible regions in velocity space for a given range...... of the neutron energy spectrum. Combined with a calculated fast-ion distribution function, they determine the part of the distribution function producing detectable neutrons in a given neutron energy range. Furthermore, we construct a forward model based on weight functions capable of rapidly calculating neutron...... energy spectra. This forward model can be inverted and could thereby be used to directly measure the fast-ion phase-space distribution functions, possibly in combination with other fast-ion diagnostics. The presented methods and results can be applied to neutron energy spectra measured by any kind...

  15. Guiding exploration in conformational feature space with Lipschitz underestimation for ab-initio protein structure prediction.

    Science.gov (United States)

    Hao, Xiaohu; Zhang, Guijun; Zhou, Xiaogen

    2018-02-06

    Computing conformations which are 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. Consequently, the dimension of the protein conformational space should be reduced to a proper level, and an effective exploring algorithm should be proposed. In this paper, a plug-in method for guiding exploration in conformational feature space with Lipschitz underestimation (LUE) for ab-initio protein structure prediction is proposed. The conformational space is converted into ultrafast shape recognition (USR) feature space firstly. Based on the USR feature space, the conformational space can be further converted into Underestimation space according to Lipschitz estimation theory for guiding exploration. As a consequence of the use of underestimation model, the tight lower bound estimate information can be used for exploration guidance, the invalid sampling areas can be eliminated in advance, and the number of energy function evaluations can be reduced. The proposed method provides a novel technique to solve the exploring problem of protein conformational space. LUE is applied to differential evolution (DE) algorithm, and metropolis Monte Carlo(MMC) algorithm which is available in the Rosetta; When LUE is applied to DE and MMC, it will be screened by the underestimation method prior to energy calculation and selection. Further, LUE is compared with DE and MMC by testing on 15 small-to-medium structurally diverse proteins. Test results show that near-native protein structures with higher accuracy can be obtained more rapidly and efficiently with the use of LUE. Copyright © 2018 Elsevier Ltd. All rights reserved.

  16. Beamforming of Joint Polarization-Space Matched Filtering for Conformal Array

    Directory of Open Access Journals (Sweden)

    Lutao Liu

    2013-01-01

    Full Text Available Due to the polarization mismatch of the antenna, the received signal suffers from energy loss. The conventional beamforming algorithms could not be applied to the conformal array because of the varying curvature. In order to overcome the energy loss of the received signal, a novel joint polarization-space matched filtering algorithm for cylindrical conformal array is proposed. First, the snapshot data model of the conformal polarization sensitive array is analyzed. Second, the analytical expression of polarization sensitive array beamforming is derived. Linearly constrained minimum variance (LCMV beamforming technique is facilitated for the cylindrical conformal array. Third, the idea of joint polarization-space matched filtering is presented, and the principle of joint polarization-space matched filtering is discussed in detail. Theoretical analysis and computer simulation results verify that the conformal polarization sensitive array is more robust than the ordinary conformal array. The proposed algorithm can improve the performance when signal and interference are too close. It can enhance the signal-to-noise ratio (SNR by adjusting the polarization of the elements of the conformal array, which matches the polarization of the incident signal.

  17. A novel family of space-filling curves in their relation to chromosome conformation in eukaryotes

    Science.gov (United States)

    Smrek, Jan; Grosberg, Alexander Y.

    2013-12-01

    Spatial conformation of DNA chains during interphase in eukaryotic cell nucleus is relatively dense, yet unknotted and exhibits self-similar fractal properties. In this respect it resembles the space-filling curves of Hilbert, but differs in the experimentally accessible contact probability of distant loci. Here we construct space-filling curves with fractal domain boundaries of dimension close to that of the embedding space and show how these match the statistical properties and the contact probability of the DNA conformation. The present mathematical model should shed light on the statistical ensemble of unknotted dense polymers and ease the modeling of genome folding and related biological processes.

  18. Analytic solution for the space-time fractional Klein-Gordon and coupled conformable Boussinesq equations

    Science.gov (United States)

    Shallal, Muhannad A.; Jabbar, Hawraz N.; Ali, Khalid K.

    2018-03-01

    In this paper, we constructed a travelling wave solution for space-time fractional nonlinear partial differential equations by using the modified extended Tanh method with Riccati equation. The method is used to obtain analytic solutions for the space-time fractional Klein-Gordon and coupled conformable space-time fractional Boussinesq equations. The fractional complex transforms and the properties of modified Riemann-Liouville derivative have been used to convert these equations into nonlinear ordinary differential equations.

  19. Metamaterial-Backed Conformal Antennas for Space Exploration Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The high-permittivity substrate (er = 10.2) allows individual antenna patches to be made smaller and also mimics substrates (Si, SiC, GaAs, InP, GaN) used in MMIC...

  20. The Area Between Exchange Curves as a Measure of Conformational Differences in Hydrogen-Deuterium Exchange Mass Spectrometry Studies

    Science.gov (United States)

    Mazur, Sharlyn J.; Weber, Daniel P.

    2017-05-01

    Hydrogen-deuterium exchange mass spectrometry (HDX-MS) provides information about protein conformational mobility under native conditions. The area between exchange curves, A bec , a functional data analysis concept, was adapted to the interpretation of HDX-MS data and provides a useful measure of exchange curve dissimilarity for tests of significance. Importantly, for most globular proteins under native conditions, A bec values provide an estimate of the log ratio of exchange-competent fractions in the two states, and thus are related to differences in the free energy of microdomain unfolding.

  1. Molecular Simulation Uncovers the Conformational Space of the λ Cro Dimer in Solution

    Science.gov (United States)

    Ahlstrom, Logan S.; Miyashita, Osamu

    2011-01-01

    The significant variation among solved structures of the λ Cro dimer suggests its flexibility. However, contacts in the crystal lattice could have stabilized a conformation which is unrepresentative of its dominant solution form. Here we report on the conformational space of the Cro dimer in solution using replica exchange molecular dynamics in explicit solvent. The simulated ensemble shows remarkable correlation with available x-ray structures. Network analysis and a free energy surface reveal the predominance of closed and semi-open dimers, with a modest barrier separating these two states. The fully open conformation lies higher in free energy, indicating that it requires stabilization by DNA or crystal contacts. Most NMR models are found to be unstable conformations in solution. Intersubunit salt bridging between Arg4 and Glu53 during simulation stabilizes closed conformations. Because a semi-open state is among the low-energy conformations sampled in simulation, we propose that Cro-DNA binding may not entail a large conformational change relative to the dominant dimer forms in solution. PMID:22098751

  2. Coset spaces and Einstein manifolds with l-conformal Galilei symmetry

    Energy Technology Data Exchange (ETDEWEB)

    Chernyavsky, Dmitry, E-mail: chernyavsky@tpu.ru

    2016-10-15

    The group theoretic construction is applied to construct a novel dynamical realization of the l-conformal Galilei group in terms of geodesic equations on the coset space. A peculiar feature of the geodesics is that all their integrals of motion, including the accelerations, are functionally independent. The analysis in the recent work [Chernyavsky and Galajinsky (2016) [35

  3. Coset spaces and Einstein manifolds with l-conformal Galilei symmetry

    Directory of Open Access Journals (Sweden)

    Dmitry Chernyavsky

    2016-10-01

    Full Text Available The group theoretic construction is applied to construct a novel dynamical realization of the l-conformal Galilei group in terms of geodesic equations on the coset space. A peculiar feature of the geodesics is that all their integrals of motion, including the accelerations, are functionally independent. The analysis in the recent work [Chernyavsky and Galajinsky (2016 [35

  4. Isotope-Encoded Carboxyl Group Footprinting for Mass Spectrometry-Based Protein Conformational Studies

    Science.gov (United States)

    Zhang, Hao; Liu, Haijun; Blankenship, Robert E.; Gross, Michael L.

    2016-01-01

    We report an isotope-encoding method coupled with carboxyl-group footprinting to monitor protein conformational changes. The carboxyl groups of aspartic/glutamic acids and of the C-terminus of proteins can serve as reporters for protein conformational changes when labeled with glycine ethyl ester (GEE) mediated by carbodiimide. In the new development, isotope-encoded "heavy" and "light" GEE are used to label separately the two states of the orange carotenoid protein (OCP) from cyanobacteria. Two samples are mixed (1:1 ratio) and analyzed by a single LC-MS/MS experiment. The differences in labeling extent between the two states are represented by the ratio of the "heavy" and "light" peptides, providing information about protein conformational changes. Combining isotope-encoded MS quantitative analysis and carboxyl-group footprinting reduces the time of MS analysis and improves the sensitivity of GEE and other footprinting.

  5. Exploring the conformational space of cysteine by matrix isolation spectroscopy combined with near-infrared laser induced conformational change.

    Science.gov (United States)

    Najbauer, Eszter E; Bazsó, Gábor; Góbi, Sándor; Magyarfalvi, Gábor; Tarczay, György

    2014-02-27

    Six conformers of α-cysteine were identified by matrix isolation IR spectroscopy combined with NIR laser irradiation. Five of these conformers are identical with the five out of six conformers that have recently been identified by microwave spectroscopy. The sixth conformer observed in the present study is a short-lived conformer, which decays by H-atom tunneling; its half-life in a 12 K N2 matrix is (1.1 ± 0.5) × 10(3) s. This study proves that matrix isolation IR spectroscopy combined with NIR laser irradiation is a suitable method to identify conformers of a complex system for which computations predict several dozens of conformers, and that the reliability of this method for conformational assignment is comparable to that of microwave spectroscopy.

  6. Conformal metric optimization on surface (CMOS) for deformation and mapping in Laplace-Beltrami embedding space.

    Science.gov (United States)

    Shi, Yonggang; Lai, Rongjie; Gill, Raja; Pelletier, Daniel; Mohr, David; Sicotte, Nancy; Toga, Arthur W

    2011-01-01

    In this paper we develop a novel technique for surface deformation and mapping in the high-dimensional Laplace-Beltrami embedding space. The key idea of our work is to realize surface deformation in the embedding space via optimization of a conformal metric on the surface. Numerical techniques are developed for computing derivatives of the eigenvalues and eigenfunctions with respect to the conformal metric, which is then applied to compute surface maps in the embedding space by minimizing an energy function. In our experiments, we demonstrate the robustness of our method by applying it to map hippocampal atrophy of multiple sclerosis patients with depression on a data set of 109 subjects. Statistically significant results have been obtained that show excellent correlation with clinical variables. A comparison with the popular SPHARM tool has also been performed to demonstrate that our method achieves more significant results.

  7. Fluorine Substitution in Neurotransmitters: Microwave Spectroscopy and Modelling of the Conformational Space and Non Bonding Interactions

    Science.gov (United States)

    Melandri, S.; Maris, A.; Merloni, A.

    2011-06-01

    Fluorine substitution in molecules is a common practice in bio-organic chemistry in order to modulate physicochemical properties and biological activity of molecules and an increasing number of drugs on the market contain fluorine, the presence of which is often of major importance to modify pharmacokinetics properties and molecular activity. The rationale for such a strategy is that fluorine is generally a stronger electron acceptor than the other halogen atoms and its size is intermediate between that of hydrogen and oxygen. We have studied two fluorinated analogs of 2-phenylethylamine (PEA), the prototype molecule for adrenergic neurotransmitters, namely: 4-Fluoro (4FPEA) and 2-Fluoro-2-phenylethylamine (2FPEA) by Molecular Beam Fourier Transform Microwave Spectroscopy in the frequency range 6-18 GHz and ab initio calculations at the MP2/6311++G** level. The aim is to obtain information on the spatial arrangement of the ethylamine side chain and the effects of fluorination on the energy landscape. The conformational space is dominated by low energy gauche conformations stabilized by weak interactions between the aminic hydrogens and the electron cloud of the benzene ring and anti conformations higher in energy. In 2FPEA the presence of the fluorine atom almost duplicate the number of possible conformation with respect to 4FPEA. We observed two conformers of 4FPEA and five conformers of 2FPEA which have been classified with the guide provided by accurate ab initio calculations. The identification of the conformational species was helped by the analysis of the quadrupole hyperfine pattern which is greatly influenced by the orientation of the amino group and acts as a fingerprint for each conformation. The orientation of the dipole moment within the principal axis frame and the order of stability of the different conformations are other independent pieces of evidence for the unambiguous assignment and identification of the conformers. The order of stability was

  8. Characterizing rapid, activity-linked conformational transitions in proteins via sub-second hydrogen deuterium exchange mass spectrometry.

    Science.gov (United States)

    Resetca, Diana; Wilson, Derek J

    2013-11-01

    This review outlines the application of time-resolved electrospray ionization mass spectrometry (TRESI-MS) and hydrogen-deuterium exchange (HDX) to study rapid, activity-linked conformational transitions in proteins. The method is implemented on a microfluidic chip which incorporates all sample-handling steps required for a 'bottom-up' HDX workflow: a capillary mixer for sub-second HDX labeling, a static mixer for HDX quenching, a microreactor for rapid protein digestion, and on-chip electrospray. By combining short HDX labeling pulses with rapid digestion, this approach provides a detailed characterization of the structural transitions that occur during protein folding, ligand binding, post-translational modification and catalytic turnover in enzymes. This broad spectrum of applications in areas largely inaccessible to conventional techniques means that microfluidics-enabled TRESI-MS/HDX is a unique and powerful approach for investigating the dynamic basis of protein function. © 2013 FEBS.

  9. Conformational Analysis of Proteins in Highly Concentrated Solutions by Dialysis-Coupled Hydrogen/Deuterium Exchange Mass Spectrometry

    DEFF Research Database (Denmark)

    Houde, Damian; Esmail Nazari, Zeinab; Bou-Assaf, George M

    2016-01-01

    When highly concentrated, an antibody solution can exhibit unusual behaviors, which can lead to unwanted properties, such as increased levels of protein aggregation and unusually high viscosity. Molecular modeling, along with many indirect biophysical measurements, has suggested that the cause...... for these phenomena can be due to short range electrostatic and/or hydrophobic protein-protein interactions. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a useful tool for investigating protein conformation, dynamics, and interactions. However, "traditional" continuous dilution labeling HDX......-MS experiments have limited utility for the direct analysis of solutions with high concentrations of protein. Here, we present a dialysis-based HDX-MS (di-HDX-MS) method as an alternative HDX-MS labeling format, which takes advantage of passive dialysis rather than the classic dilution workflow. We applied...

  10. 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.

  11. Multiple Gas-Phase Conformations of a Synthetic Linear Poly(acrylamide) Polymer Observed Using Ion Mobility-Mass Spectrometry

    Science.gov (United States)

    Haler, Jean R. N.; Far, Johann; Aqil, Abdelhafid; Claereboudt, Jan; Tomczyk, Nick; Giles, Kevin; Jérôme, Christine; De Pauw, Edwin

    2017-08-01

    Ion mobility-mass spectrometry (IM-MS) has emerged as a powerful separation and identification tool to characterize synthetic polymer mixtures and topologies (linear, cyclic, star-shaped,…). Electrospray coupled to IM-MS already revealed the coexistence of several charge state-dependent conformations for a single charge state of biomolecules with strong intramolecular interactions, even when limited resolving power IM-MS instruments were used. For synthetic polymers, the sample's polydispersity allows the observation of several chain lengths. A unique collision cross-section (CCS) trend is usually observed when increasing the degree of polymerization (DP) at constant charge state, allowing the deciphering of different polymer topologies. In this paper, we report multiple coexisting CCS trends when increasing the DP at constant charge state for linear poly(acrylamide) PAAm in the gas phase. This is similar to observations on peptides and proteins. Biomolecules show in addition population changes when collisionally heating the ions. In the case of synthetic PAAm, fragmentation occurred before reaching the energy for conformation conversion. These observations, which were made on two different IM-MS instruments (SYNAPT G2 HDMS and high resolution multi-pass cyclic T-Wave prototype from Waters), limit the use of ion mobility for synthetic polymer topology interpretations to polymers where unique CCS values are observed for each DP at constant charge state. [Figure not available: see fulltext.

  12. Conformational isomerism and self-association of calixarene building blocks in non-polar solution studied by Fourier transform infrared spectrometry

    NARCIS (Netherlands)

    Lutz, Bert T.G.; Astarloa, Gonzalo; van der Maas, John H.; Janssen, R.G.; Janssen, Rob G.; Verboom, Willem; Reinhoudt, David

    1995-01-01

    In order to establish the conformational equilibrium of calix[6]arene derivatives, a series of phenolic building blocks differing in chain length (oligomers) have been studied in solution by Fourier transform infrared spectrometry (FT-IR). Different intramolecular OH ¿ X interactions have been

  13. Elucidation of conformer preferences for a hydrophobic antimicrobial peptide by vesicle capture-freeze-drying: a preparatory method coupled to ion mobility-mass spectrometry.

    Science.gov (United States)

    Patrick, John W; Gamez, Roberto C; Russell, David H

    2015-01-06

    A novel sample preparation method to probe the solution phase structure of dimerized Gramicidin A (GA) inserted into lipid vesicle bilayers is described. This method, termed vesicle capture-freeze-drying (VCFD), when coupled with electrospray ionization-ion mobility-mass spectrometry (ESI-IM-MS), successfully demonstrates the first evidence for the preservation of membrane-bound structure in the analysis of solution phase conformers retained into the gas phase. The extremely hydrophobic character of GA ensures that only membrane-bound conformations are captured and subsequently monitored when samples are prepared using VCFD, removing a barrier that has prevented previous attempts at direct analysis using mass spectrometry. Solution-phase physicochemical interactions of GA influenced by lipid acyl chain length and extent of acyl chain unsaturation can now be probed by monitoring the conformer preferences using IM-MS. Increasing the acyl chain length from 12 to 22 carbons yields [2GA + 2Na](2+) IM-MS profiles with reduced conformer microheterogeneity. POPC (16:0, 18:1 PC), a lipid possessing a single acyl chain unsaturation point, yields the highest abundance of the single stranded head to head (SSHH) conformer. Conformer preferences adopted in the lipid bilayer are maintained as GA dimers travel from the solution phase to fully desolvated gas-phase ions demonstrating that distributions observed using ESI-IM-MS unambiguously reflect the ensemble of conformers observed in the solution phase. VCFD-ESI-IM-MS yields novel biophysical insight into the influence of lipid bilayer membranes on conformer preferences and conformer heterogeneity of an important channel-forming membrane peptide.

  14. Effective Application of Bicelles for Conformational Analysis of G Protein-Coupled Receptors by Hydrogen/Deuterium Exchange Mass Spectrometry

    Science.gov (United States)

    Duc, Nguyen Minh; Du, Yang; Thorsen, Thor S.; Lee, Su Youn; Zhang, Cheng; Kato, Hideaki; Kobilka, Brian K.; Chung, Ka Young

    2015-05-01

    G protein-coupled receptors (GPCRs) have important roles in physiology and pathology, and 40% of drugs currently on the market target GPCRs for the treatment of various diseases. Because of their therapeutic importance, the structural mechanism of GPCR signaling is of great interest in the field of drug discovery. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a useful tool for analyzing ligand binding sites, the protein-protein interaction interface, and conformational changes of proteins. However, its application to GPCRs has been limited for various reasons, including the hydrophobic nature of GPCRs and the use of detergents in their preparation. In the present study, we tested the application of bicelles as a means of solubilizing GPCRs for HDX-MS studies. GPCRs (e.g., β2-adrenergic receptor [β2AR], μ-opioid receptor, and protease-activated receptor 1) solubilized in bicelles produced better sequence coverage (greater than 90%) than GPCRs solubilized in n-dodecyl-β-D-maltopyranoside (DDM), suggesting that bicelles are a more effective method of solubilization for HDX-MS studies. The HDX-MS profile of β2AR in bicelles showed that transmembrane domains (TMs) undergo lower deuterium uptake than intracellular or extracellular regions, which is consistent with the fact that the TMs are highly ordered and embedded in bicelles. The overall HDX-MS profiles of β2AR solubilized in bicelles and in DDM were similar except for intracellular loop 3. Interestingly, we detected EX1 kinetics, an important phenomenon in protein dynamics, at the C-terminus of TM6 in β2AR. In conclusion, we suggest the application of bicelles as a useful method for solubilizing GPCRs for conformational analysis by HDX-MS.

  15. Study of spontaneously broken conformal symmetry in curved space-times

    Energy Technology Data Exchange (ETDEWEB)

    Janson, M.M.

    1977-05-01

    Spontaneous breakdown of Weyl invariance (local scale invariance) in a conformally-invariant extension of a gauge model for weak and electromagnetic interactions is considered. The existence of an asymmetric vacuum for the Higgs field, phi, is seen to depend on the space-time structure via the Gursey-Penrose term, approximately phi/sup +/phi R, in the action. (R denotes the scalar curvature.) The effects of a prescribed space-time structure on spontaneously broken Weyl invariance is investigated. In a cosmological space-time, it is found that initially, in the primordial fireball, the symmetry must hold exactly. Spontaneous symmetry breaking (SSB) develops as the universe expands and cools. Consequences of this model include a dependence of G/sub F/, the effective weak interaction coupling strength, on ''cosmic time.'' It is seen to decrease monotonically; in the present epoch (G/sub F//G/sub F/)/sub TODAY/ approximately less than 10/sup -10/ (year)/sup -1/. The effects of the Schwarzschild geometry on SSB are explored. In the interior of a neutron star the Higgs vacuum expectation value, and consequently G/sub F/, is found to have a radial dependence. The magnitude of this variation does not warrant revision of present models of neutron star structures. Another perspective on the problem considered a theory of gravitation (conformal relativity) to be incorporated in the conformally invariant gauge model of weak and electromagnetic interactions. If SSB develops, the vacuum gravitational field equations are the Einstein field equations with a cosmological constant. The stability of the asymmetric vacuum solution is investigated to ascertain whether SSB can occur.

  16. Effects of sucrose and benzyl alcohol on GCSF conformational dynamics revealed by hydrogen deuterium exchange mass spectrometry.

    Science.gov (United States)

    Zhang, Jun; Banks, Douglas D; He, Feng; Treuheit, Michael J; Becker, Gerald W

    2015-05-01

    Protein stability, one of the major concerns for therapeutic protein development, can be optimized during process development by evaluating multiple formulation conditions. This can be a costly and lengthy procedure where different excipients and storage conditions are tested for their impact on protein stability. A better understanding of the effects of different formulation conditions at the molecular level will provide information on the local interactions within the protein leading to a more rational design of stable and efficacious formulations. In this study, we examined the roles of the excipients, sucrose and benzyl alcohol, on the conformational dynamics of recombinant human granulocyte colony stimulating factor using hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS). Under physiological pH and temperature, sucrose globally protects the whole molecule from deuterium uptake, whereas benzyl alcohol induces increased deuterium uptake of the regions within the α-helical bundle, with even larger extent. The HDX experiments described were incorporated a set of internal peptides (Zhang et al., 2012. Anal Chem 84:4942-4949) to monitor the differences in intrinsic exchange rates in different formulations. In addition, we discussed the feasibility of implementing HDX-MS with these peptide probes in protein formulation development. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

  17. 4D Flexible Atom-Pairs: An efficient probabilistic conformational space comparison for ligand-based virtual screening

    Science.gov (United States)

    2011-01-01

    Background The performance of 3D-based virtual screening similarity functions is affected by the applied conformations of compounds. Therefore, the results of 3D approaches are often less robust than 2D approaches. The application of 3D methods on multiple conformer data sets normally reduces this weakness, but entails a significant computational overhead. Therefore, we developed a special conformational space encoding by means of Gaussian mixture models and a similarity function that operates on these models. The application of a model-based encoding allows an efficient comparison of the conformational space of compounds. Results Comparisons of our 4D flexible atom-pair approach with over 15 state-of-the-art 2D- and 3D-based virtual screening similarity functions on the 40 data sets of the Directory of Useful Decoys show a robust performance of our approach. Even 3D-based approaches that operate on multiple conformers yield inferior results. The 4D flexible atom-pair method achieves an averaged AUC value of 0.78 on the filtered Directory of Useful Decoys data sets. The best 2D- and 3D-based approaches of this study yield an AUC value of 0.74 and 0.72, respectively. As a result, the 4D flexible atom-pair approach achieves an average rank of 1.25 with respect to 15 other state-of-the-art similarity functions and four different evaluation metrics. Conclusions Our 4D method yields a robust performance on 40 pharmaceutically relevant targets. The conformational space encoding enables an efficient comparison of the conformational space. Therefore, the weakness of the 3D-based approaches on single conformations is circumvented. With over 100,000 similarity calculations on a single desktop CPU, the utilization of the 4D flexible atom-pair in real-world applications is feasible. PMID:21733172

  18. 4D Flexible Atom-Pairs: An efficient probabilistic conformational space comparison for ligand-based virtual screening

    Directory of Open Access Journals (Sweden)

    Jahn Andreas

    2011-07-01

    Full Text Available Abstract Background The performance of 3D-based virtual screening similarity functions is affected by the applied conformations of compounds. Therefore, the results of 3D approaches are often less robust than 2D approaches. The application of 3D methods on multiple conformer data sets normally reduces this weakness, but entails a significant computational overhead. Therefore, we developed a special conformational space encoding by means of Gaussian mixture models and a similarity function that operates on these models. The application of a model-based encoding allows an efficient comparison of the conformational space of compounds. Results Comparisons of our 4D flexible atom-pair approach with over 15 state-of-the-art 2D- and 3D-based virtual screening similarity functions on the 40 data sets of the Directory of Useful Decoys show a robust performance of our approach. Even 3D-based approaches that operate on multiple conformers yield inferior results. The 4D flexible atom-pair method achieves an averaged AUC value of 0.78 on the filtered Directory of Useful Decoys data sets. The best 2D- and 3D-based approaches of this study yield an AUC value of 0.74 and 0.72, respectively. As a result, the 4D flexible atom-pair approach achieves an average rank of 1.25 with respect to 15 other state-of-the-art similarity functions and four different evaluation metrics. Conclusions Our 4D method yields a robust performance on 40 pharmaceutically relevant targets. The conformational space encoding enables an efficient comparison of the conformational space. Therefore, the weakness of the 3D-based approaches on single conformations is circumvented. With over 100,000 similarity calculations on a single desktop CPU, the utilization of the 4D flexible atom-pair in real-world applications is feasible.

  19. Differentiation of Compact and Extended Conformations of Di-Ubiquitin Conjugates with Lysine-Specific Isopeptide Linkages by Ion Mobility-Mass Spectrometry

    Science.gov (United States)

    Jung, Ji Eun; Pierson, Nicholas A.; Marquardt, Andreas; Scheffner, Martin; Przybylski, Michael; Clemmer, David E.

    2011-08-01

    Modification of ubiquitin, a key cellular regulatory polypeptide of 76 amino acids, to polyubiquitin conjugates by lysine-specific isopeptide linkage at one of its seven lysine residues has been recognized as a central pathway determining its biochemical properties and cellular functions. Structural details and differences of distinct lysine-isopeptidyl ubiquitin conjugates that reflect their different functions and reactivities, however, are only partially understood. Ion mobility spectrometry (IMS) combined with mass spectrometry (MS) has recently emerged as a powerful tool for probing conformations and topology involved in protein interactions by an electric field-driven separation of polypeptide ions through a drift gas. Here we report the conformational characterization and differentiation of Lys63- and Lys48-linked ubiquitin conjugates by IMS-MS. Lys63- and Lys48-linked di-ubiquitin conjugates were prepared by recombinant bacterial expression and by chemical synthesis using a specific chemical ligation strategy, and characterized by high-resolution Fourier transform ion cyclotron resonance mass spectrometry, circular dichroism spectroscopy, and molecular modeling. IMS-MS was found to be an effective tool for the identification of structural differences of ubiquitin complexes in the gas phase. The comparison of collision cross-sections of Lys63- and Lys48-linked di-ubiquitin conjugates showed a more elongated conformation of Lys63-linked di-ubiquitin. In contrast, the Lys48-linked di-ubiquitin conjugate showed a more compact conformation. The IMS-MS results are consistent with published structural data and a comparative molecular modeling study of the Lys63- and Lys48-linked conjugates. The results presented here suggest IMS techniques can provide information that complements MS measurements in differentiating higher-order polyubiquitins and other isomeric protein linkages.

  20. Using mass spectrometry and small molecule reagents to detect distinctive structural features of different prion conformations (strains)

    Science.gov (United States)

    A prion (PrPSc) is a conformer of a normal cellular prion protein (PrPC). Although they are isosequential, PrPSc is an infectious protein able to convert PrPC into the prion conformation and thereby propagate an infection. PrPC is monomeric while PrPSc is a multimer. PrPSc can adopt more than one co...

  1. Conformational Dynamics of DNA G-Quadruplex in Solution Studied by Kinetic Capillary Electrophoresis Coupled On-line with Mass Spectrometry

    Science.gov (United States)

    Berezovski, Maxim V

    2014-01-01

    Invited for this months cover is the group of Prof. Maxim V. Berezovski. The cover picture shows the two-dimensional separation of unfolded (green) and folded (red) forms of G-quadruplex (GQ) DNA. The first dimension is kinetic capillary electrophoresis (KCE) separation of unfolded and folded DNA with different K+ concentrations in solution; the second dimension is ion mobility mass spectrometry separation of DNA conformers in the gas phase. DNA folding into a compact GQ structure is mediated by K+ ions. For more details, see the Full Paper on p. 58 ff. PMID:24808989

  2. Probing the Conformational and Functional Consequences of Disulfide Bond Engineering in Growth Hormone by Hydrogen-Deuterium Exchange Mass Spectrometry Coupled to Electron Transfer Dissociation

    DEFF Research Database (Denmark)

    Seger, Signe T; Breinholt, Jens; Faber, Johan H

    2015-01-01

    Human growth hormone (hGH), and its receptor interaction, is essential for cell growth. To stabilize a flexible loop between helices 3 and 4, while retaining affinity for the hGH receptor, we have engineered a new hGH variant (Q84C/Y143C). Here, we employ hydrogen-deuterium exchange mass...... spectrometry (HDX-MS) to map the impact of the new disulfide bond on the conformational dynamics of this new hGH variant. Compared to wild type hGH, the variant exhibits reduced loop dynamics, indicating a stabilizing effect of the introduced disulfide bond. Furthermore, the disulfide bond exhibits longer...

  3. Conformational Space Annealing explained: A general optimization algorithm, with diverse applications

    Science.gov (United States)

    Joung, InSuk; Kim, Jong Yun; Gross, Steven P.; Joo, Keehyoung; Lee, Jooyoung

    2018-02-01

    Many problems in science and engineering can be formulated as optimization problems. One way to solve these problems is to develop tailored problem-specific approaches. As such development is challenging, an alternative is to develop good generally-applicable algorithms. Such algorithms are easy to apply, typically function robustly, and reduce development time. Here we provide a description for one such algorithm called Conformational Space Annealing (CSA) along with its python version, PyCSA. We previously applied it to many optimization problems including protein structure prediction and graph community detection. To demonstrate its utility, we have applied PyCSA to two continuous test functions, namely Ackley and Eggholder functions. In addition, in order to provide complete generality of PyCSA to any types of an objective function, we demonstrate the way PyCSA can be applied to a discrete objective function, namely a parameter optimization problem. Based on the benchmarking results of the three problems, the performance of CSA is shown to be better than or similar to the most popular optimization method, simulated annealing. For continuous objective functions, we found that, L-BFGS-B was the best performing local optimization method, while for a discrete objective function Nelder-Mead was the best. The current version of PyCSA can be run in parallel at the coarse grained level by calculating multiple independent local optimizations separately. The source code of PyCSA is available from http://lee.kias.re.kr.

  4. Electron capture dissociation and drift tube ion mobility-mass spectrometry coupled with site directed mutations provide insights into the conformational diversity of a metamorphic protein.

    Science.gov (United States)

    Harvey, Sophie R; Porrini, Massimiliano; Tyler, Robert C; MacPhee, Cait E; Volkman, Brian F; Barran, Perdita E

    2015-04-28

    Ion mobility mass spectrometry can be combined with data from top-down sequencing to discern adopted conformations of proteins in the absence of solvent. This multi-technique approach has particular applicability for conformationally dynamic systems. Previously, we demonstrated the use of drift tube ion mobility-mass spectrometry (DT IM-MS) and electron capture dissociation (ECD) to study the metamorphic protein lymphotactin (Ltn). Ltn exists in equilibrium between distinct monomeric (Ltn10) and dimeric (Ltn40) folds, both of which can be preserved and probed in the gas-phase. Here, we further test this mass spectrometric framework, by examining two site directed mutants of Ltn, designed to stabilise either distinct fold in solution, in addition to a truncated form consisting of a minimum model of structure for Ltn10. The truncated mutant has similar collision cross sections to the wild type (WT), for low charge states, and is resistant to ECD fragmentation. The monomer mutant (CC3) presents in similar conformational families as observed previously for the WT Ltn monomer. As with the WT, the CC3 mutant is resistant to ECD fragmentation at low charge states. The dimer mutant W55D is found here to exist as both a monomer and dimer. As a monomer W55D exhibits similar behaviour to the WT, but as a dimer presents a much larger charge state and collision cross section range than the WT dimer, suggesting a smaller interaction interface. In addition, ECD on the W55D mutant yields greater fragmentation than for the WT, suggesting a less stable β-sheet core. The results highlight the power of MS to provide insight into dynamic proteins, providing further information on each distinct fold of Ltn. In addition we observe differences in the fold stability following single or double point mutations. This approach, therefore, has potential to be a useful tool to screen for the structural effects of mutagenesis, even when sample is limited.

  5. Joint Space-Time Coherent Vibration Driven Conformational Transitions in a Single Molecule

    Science.gov (United States)

    Li, Shaowei; Chen, Siyu; Li, Jie; Wu, Ruqian; Ho, W.

    2017-10-01

    We report single-molecule conformational transitions with joint angstrom-femtosecond resolution by irradiating the junction of a scanning tunneling microscope with femtosecond laser pulses. An isolated pyrrolidine molecule adsorbed on a Cu(001) surface undergoes reversible transitions between two conformational states. The transition rate decays in time and exhibits sinusoidal oscillations with periods of specific molecular vibrations. The dynamics of this transition depends sensitively on the molecular environment, as exemplified by the effects of another molecule in proximity.

  6. Conformation-driven quantum interference effects mediated by through-space conjugation in self-assembled monolayers.

    Science.gov (United States)

    Carlotti, Marco; Kovalchuk, Andrii; Wächter, Tobias; Qiu, Xinkai; Zharnikov, Michael; Chiechi, Ryan C

    2016-12-20

    Tunnelling currents through tunnelling junctions comprising molecules with cross-conjugation are markedly lower than for their linearly conjugated analogues. This effect has been shown experimentally and theoretically to arise from destructive quantum interference, which is understood to be an intrinsic, electronic property of molecules. Here we show experimental evidence of conformation-driven interference effects by examining through-space conjugation in which π-conjugated fragments are arranged face-on or edge-on in sufficiently close proximity to interact through space. Observing these effects in the latter requires trapping molecules in a non-equilibrium conformation closely resembling the X-ray crystal structure, which we accomplish using self-assembled monolayers to construct bottom-up, large-area tunnelling junctions. In contrast, interference effects are completely absent in zero-bias simulations on the equilibrium, gas-phase conformation, establishing through-space conjugation as both of fundamental interest and as a potential tool for tuning tunnelling charge-transport in large-area, solid-state molecular-electronic devices.

  7. Conformation-driven quantum interference effects mediated by through-space conjugation in self-assembled monolayers

    Science.gov (United States)

    Carlotti, Marco; Kovalchuk, Andrii; Wächter, Tobias; Qiu, Xinkai; Zharnikov, Michael; Chiechi, Ryan C.

    2016-12-01

    Tunnelling currents through tunnelling junctions comprising molecules with cross-conjugation are markedly lower than for their linearly conjugated analogues. This effect has been shown experimentally and theoretically to arise from destructive quantum interference, which is understood to be an intrinsic, electronic property of molecules. Here we show experimental evidence of conformation-driven interference effects by examining through-space conjugation in which π-conjugated fragments are arranged face-on or edge-on in sufficiently close proximity to interact through space. Observing these effects in the latter requires trapping molecules in a non-equilibrium conformation closely resembling the X-ray crystal structure, which we accomplish using self-assembled monolayers to construct bottom-up, large-area tunnelling junctions. In contrast, interference effects are completely absent in zero-bias simulations on the equilibrium, gas-phase conformation, establishing through-space conjugation as both of fundamental interest and as a potential tool for tuning tunnelling charge-transport in large-area, solid-state molecular-electronic devices.

  8. Investigating changes in the gas-phase conformation of Antithrombin III upon binding of Arixtra using traveling wave ion mobility spectrometry (TWIMS).

    Science.gov (United States)

    Zhao, Yuejie; Singh, Arunima; Li, Lingyun; Linhardt, Robert J; Xu, Yongmei; Liu, Jian; Woods, Robert J; Amster, I Jonathan

    2015-10-21

    We validate the utility of ion mobility to measure protein conformational changes induced by the binding of glycosaminoglycan ligands, using the well characterized system of Antithrombin III (ATIII) and Arixtra, a pharmaceutical agent with heparin (Hp) activity. Heparin has been used as a therapeutic anticoagulant drug for several decades through its interaction with ATIII, a serine protease inhibitor that plays a central role in the blood coagulation cascade. This interaction induces conformational changes within ATIII that dramatically enhance the ATIII-mediated inhibition rate. Arixtra is the smallest synthetic Hp containing the specific pentasaccharide sequence required to bind with ATIII. Here we report the first travelling wave ion mobility mass spectrometry (TWIMS) investigation of the conformational changes in ATIII induced by its interaction with Arixtra. Native electrospray ionization mass spectrometry allowed the gentle transfer of the native topology of ATIII and ATIII-Arixtra complex. IM measurements of ATIII and ATIII-Arixtra complex showed a single structure, with well-defined collisional cross section (CCS) values. An average 3.6% increase in CCS of ATIII occurred as a result of its interaction with Arixtra, which agrees closely with the theoretical estimation of the change in CCS based on protein crystal structures. A comparison of the binding behavior of ATIII under both denaturing and non-denaturing conditions confirmed the significance of a folded tertiary structure of ATIII for its biological activity. A Hp oligosaccharide whose structure is similar to Arixtra but missing the 3-O sulfo group on the central glucosamine residue showed a dramatic decrease in binding affinity towards ATIII, but no change in the mobility behavior of the complex, consistent with prior studies that suggested that 3-O sulfation affects the equilibrium constant for binding to ATIII, but not the mode of interaction. In contrast, nonspecific binding by a Hp

  9. Modification of chemical and conformational properties of natural organic matter by click chemistry as revealed by ESI-Orbitrap mass spectrometry.

    Science.gov (United States)

    Nebbioso, Antonio; Piccolo, Alessandro

    2015-11-01

    A click reaction is reported here for the first time as a useful technique to control the conformational stability of natural organic matter (NOM) suprastructures. Click conjugates were successfully formed between a previously butynylated NOM hydrophobic fraction and a hydrophilic polyethylene glycol (PEG)-amino chain. The click products were shown by size exclusion chromatography (HPSEC) hyphenated with Orbitrap mass spectrometry (MS) in electrospray ionization (ESI) (+), while precursors were visible in ESI (-). Despite their increase in molecular weight, HPSEC elution of click conjugates occurred after that of precursors, thus showing their departure from the NOM supramolecular association. This indicates that the click-conjugated NOM molecules were varied in their hydrophilic and cationic character and lost the capacity to accommodate in the original hydrophobic suprastructures. The most abundant product had the C16H30O5N4 formula, a click conjugate of butanoic acid, while other products were short-chained (C4-C8) linear unsaturated and hydroxylated carboxylic acids. Tandem MS revealed formation of triazole rings in clicked conjugates and their two fragmentations at the ester and the C-N alkyl-aryl bonds. The behavior of NOM molecules modified by click chemistry confirms that hydrophobicity and ionic charge of humic molecules play a pivotal role in stabilizing intermolecular forces in NOM. Moreover, the versatility of the click reaction may become useful to decorate NOM molecules with a variety of substrates, in order to alter NOM conformational and chemical properties and diversify its applications in the environment.

  10. Different conformational dynamics of PDZ1 and PDZ2 in full-length EBP50 analyzed by hydrogen/deuterium exchange mass spectrometry.

    Science.gov (United States)

    Park, Ji Young; Duc, Nguyen Minh; Kim, Dong Kyun; Lee, Su Youn; Li, Sheng; Seo, Min-Duk; Woods, Virgil L; Chung, Ka Young

    2015-08-01

    Ezrin-radixin-moesin-binding protein 50 (EBP50) is a scaffolding protein expressed in polarized epithelial cells in various organs, including the liver, kidney, and small intestine, in which it regulates the trafficking and targeting cellular proteins. EBP50 contains two postsynaptic density-95/disk-large/ZO-1 homology (PDZ) domains (e.g., PDZ1 and PDZ2) and an ezrin/radixin/moesin-binding (EB) domain. PDZ domains are one of the major scaffolding domains regulating protein-protein interactions with critical biological roles in cell polarity, migration, proliferation, recognition, and cell-cell interaction. PDZ1 and PDZ2 in EBP50 have different ligand selectivity, although several high-resolution structural studies of isolated PDZ1 and PDZ2 showed similar structures. We studied the conformations of full-length EBP50 and isolated PDZ1 and PDZ2 using hydrogen/deuterium exchange mass spectrometry (HDX-MS). The deuterium uptake profiles of isolated PDZ1 and PDZ2 were similar to those of full-length EBP50. Interestingly, PDZ1 was more dynamic than PDZ2, and these PDZ domains underwent different conformational changes upon ligand binding. These results might explain the differences in ligand-selectivity between PDZ1 and PDZ2.

  11. Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data

    Directory of Open Access Journals (Sweden)

    Peter F. Stadler

    2013-09-01

    Full Text Available Polymers of hydrogen cyanide and their hydrolysis products constitute a plausible, but still poorly understood proposal for early prebiotic chemistry on Earth. HCN polymers are generated by the interplay of more than a dozen distinctive reaction mechanisms and form a highly complex mixture. Here we use a computational model based on graph grammars as a means of exploring the chemical spaces of HCN polymerization and hydrolysis. A fundamental issue is to understand the combinatorial explosion inherent in large, complex chemical systems. We demonstrate that experimental data, here obtained by mass spectrometry, and computationally predicted free energies together can be used to guide the exploration of the chemical space and makes it feasible to investigate likely pathways and chemical motifs even in potentially open-ended chemical systems.

  12. On the space of solutions of the Hořava theory at the kinetic-conformal point

    Science.gov (United States)

    Bellorín, Jorge; Restuccia, Alvaro

    2017-10-01

    The nonprojectable Hořava theory at the kinetic-conformal point is defined by setting a specific value of the coupling constant of the kinetic term of the Lagrangian. This formulation has two additional second class-constraints that eliminate the extra mode. We show that the space of solutions of this theory in the Hamiltonian formalism is bigger than the space of solutions in the original Lagrangian formalism. In the Hamiltonian formalism there are certain configurations for the Lagrange multipliers that lead to solutions that cannot be found in the original Lagrangian formulation. We show specific examples in vacuum and with a source. The solution with the source has homogeneous and isotropic spatial hypersurfaces. The enhancement of the space of solutions leaves the possibility that new solutions applicable to cosmology, or to other physical systems, can be found in the Hamiltonian formalism.

  13. Correspondence between nonrelativistic anti-de Sitter space and conformal field theory, and aging-gravity duality.

    Science.gov (United States)

    Minic, Djordje; Pleimling, Michel

    2008-12-01

    We point out that the recent discussion of nonrelativistic anti-de Sitter space and conformal field theory correspondence has a direct application in nonequilibrium statistical physics, a fact which has not been emphasized in the recent literature on the subject. In particular, we propose a duality between aging in systems far from equilibrium characterized by the dynamical exponent z=2 and gravity in a specific background. The key ingredient in our proposal is the recent geometric realization of the Schrödinger group. We also discuss the relevance of the proposed correspondence for the more general aging phenomena in systems where the value of the dynamical exponent is different from 2.

  14. Conformal Space Suit Antenna Development for Enhanced EVA Communications and Wearable Computer Applications Project

    Data.gov (United States)

    National Aeronautics and Space Administration — As NASA prepares for the Constellation Space Missions and Extra-Vehicular Activity (EVA) on the moon by 2018, astronauts will be required to spend more time exposed...

  15. Conformal Space Suit Antenna Development for Enhanced EVA Communications and Wearable Computer Applications Project

    Data.gov (United States)

    National Aeronautics and Space Administration — As NASA prepares for future space missions and the return to the moon by 2020, astronauts will be required to spend more time exposed to the hazards of performing...

  16. Conformable Thermoelectric Device for Waste Heat Scavenging in Space Applications Project

    Data.gov (United States)

    National Aeronautics and Space Administration — NASA space exploration missions stand to benefit from reliable means to conserve energy that is otherwise given off as waste heat. Thermoelectric generators have...

  17. Conformational space of the Pseudosaccharin allyl ether 3-(allyloxy)-1,2-benzisothiazole 1,1-dioxide in gas phase and in rare gas matrices.

    Science.gov (United States)

    Gómez-Zavaglia, Andrea; Kaczor, Agnieszka; Almeida, Rui; Cristiano, Maria de Lurdes S; Fausto, Rui

    2008-02-28

    In this work, the conformational space of the pseudosaccharyl ether 3-(allyloxy)-1,2-benzisothiazole 1,1-dioxide (ABID) has been studied by means of infrared spectroscopy and density functional theory (DFT) calculations. Five different low energy conformers (TSk, TC, GSk, GSk' and GC, with relative energies of 0.00, 1.97, 2.00, 3.82 and 6.02 kJ mol(-1), respectively) were found on the DFT(B3LYP)/6-311++G(3df,3pd) potential energy surface of the molecule, all of them differing in the conformation of the allyl substituent. According to the calculations, in the gaseous phase all conformers are significantly populated (TSk:TC:GSk:GSk':GC = 47%:16%:18%:12%:7%, at 350 K). In the cryogenic matrices, however, only the TSk and TC conformers exist due to isomerization from the higher energy gauche forms to the most stable trans isomers during deposition of the matrix (conformational cooling). The observed conformational cooling is in consonance with the low calculated energy barriers for the GSk --> TSk, GSk' --> TSk and GC --> TC isomerization processes. Results from annealing experiments in krypton matrix doubtlessly show that in this matrix the order of stability of the TSk and TC conformers is reversed, with the more planar TC form becoming the most stable conformer.

  18. Density-Dependent Conformable Space-time Fractional Diffusion-Reaction Equation and Its Exact Solutions

    Science.gov (United States)

    Hosseini, Kamyar; Mayeli, Peyman; Bekir, Ahmet; Guner, Ozkan

    2018-01-01

    In this article, a special type of fractional differential equations (FDEs) named the density-dependent conformable fractional diffusion-reaction (DDCFDR) equation is studied. Aforementioned equation has a significant role in the modelling of some phenomena arising in the applied science. The well-organized methods, including the \\exp (-φ (\\varepsilon )) -expansion and modified Kudryashov methods are exerted to generate the exact solutions of this equation such that some of the solutions are new and have been reported for the first time. Results illustrate that both methods have a great performance in handling the DDCFDR equation.

  19. Space and Time Resolved Detection of Platelet Activation and von Willebrand Factor Conformational Changes in Deep Suspensions.

    Science.gov (United States)

    Biasetti, Jacopo; Sampath, Kaushik; Cortez, Angel; Azhir, Alaleh; Gilad, Assaf A; Kickler, Thomas S; Obser, Tobias; Ruggeri, Zaverio M; Katz, Joseph

    2017-01-01

    Tracking cells and proteins' phenotypic changes in deep suspensions is critical for the direct imaging of blood-related phenomena in in vitro replica of cardiovascular systems and blood-handling devices. This paper introduces fluorescence imaging techniques for space and time resolved detection of platelet activation, von Willebrand factor (VWF) conformational changes, and VWF-platelet interaction in deep suspensions. Labeled VWF, platelets, and VWF-platelet strands are suspended in deep cuvettes, illuminated, and imaged with a high-sensitivity EM-CCD camera, allowing detection using an exposure time of 1 ms. In-house postprocessing algorithms identify and track the moving signals. Recombinant VWF-eGFP (rVWF-eGFP) and VWF labeled with an FITC-conjugated polyclonal antibody are employed. Anti-P-Selectin FITC-conjugated antibodies and the calcium-sensitive probe Indo-1 are used to detect activated platelets. A positive correlation between the mean number of platelets detected per image and the percentage of activated platelets determined through flow cytometry is obtained, validating the technique. An increase in the number of rVWF-eGFP signals upon exposure to shear stress demonstrates the technique's ability to detect breakup of self-aggregates. VWF globular and unfolded conformations and self-aggregation are also observed. The ability to track the size and shape of VWF-platelet strands in space and time provides means to detect pro- and antithrombotic processes.

  20. Different conformational dynamics of β-arrestin1 and β-arrestin2 analyzed by hydrogen/deuterium exchange mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Yun, Youngjoo; Kim, Dong Kyun [School of Pharmacy, Sungkyunkwan University, Suwon (Korea, Republic of); Seo, Min-Duk [College of Pharmacy & Department of Molecular Science and Technology, Ajou University, Suwon (Korea, Republic of); Kim, Kyeong-Man [College of Pharmacy, Chonnam National University, Gwang-Ju (Korea, Republic of); Chung, Ka Young, E-mail: kychung2@skku.edu [School of Pharmacy, Sungkyunkwan University, Suwon (Korea, Republic of)

    2015-01-30

    Highlights: • The conformational dynamics of β-arrestin1 or β-arrestin2 were analyzed by HDX-MS. • β-Strands II through IV were more dynamic in β-arrestin2 than in β-arrestin1. • The middle loop was less dynamic in β-arrestin2 than in β-arrestin1. • Upon pre-activation by the R169E mutation, β-arrestins became more dynamic. • Pre-activation affected a wider region of β-arrestin1 compared to β-arrestin2. - Abstract: Arrestins have important roles in G protein-coupled receptor (GPCR) signaling including desensitization of GPCRs and G protein-independent signaling. There have been four arrestins identified: arrestin1, arrestin2 (e.g. β-arrestin1), arrestin3 (e.g. β-arrestin2), and arrestin4. β-Arrestin1 and β-arrestin2 are ubiquitously expressed and regulate a broad range of GPCRs, while arrestin1 and arrestin4 are expressed in the visual system. Although the functions of β-arrestin1 and β-arrestin2 widely overlap, β-arrestin2 has broader receptor selectivity, and a few studies have suggested that β-arrestin1 and β-arrestin2 have distinct cellular functions. Here, we compared the conformational dynamics of β-arrestin1 and β-arrestin2 by hydrogen/deuterium exchange mass spectrometry (HDX-MS). We also used the R169E mutant as a pre-activation model system. HDX-MS data revealed that β-strands II through IV were more dynamic in β-arrestin2 in the basal state, while the middle loop was more dynamic in β-arrestin1. With pre-activation, both β-arrestin1 and β-arrestin2 became more flexible, but broader regions of β-arrestin1 became flexible compared to β-arrestin2. The conformational differences between β-arrestin1 and β-arrestin2 in both the basal and pre-activated states might determine their different receptor selectivities and different cellular functions.

  1. Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers.

    Science.gov (United States)

    Tyka, Michael D; Jung, Kenneth; Baker, David

    2012-12-05

    All-atom sampling is a critical and compute-intensive end stage to protein structural modeling. Because of the vast size and extreme ruggedness of conformational space, even close to the native structure, the high-resolution sampling problem is almost as difficult as predicting the rough fold of a protein. Here, we present a combination of new algorithms that considerably speed up the exploration of very rugged conformational landscapes and are capable of finding heretofore hidden low-energy states. The algorithm is based on a hierarchical workflow and can be parallelized on supercomputers with up to 128,000 compute cores with near perfect efficiency. Such scaling behavior is notable, as with Moore's law continuing only in the number of cores per chip, parallelizability is a critical property of new algorithms. Using the enhanced sampling power, we have uncovered previously invisible deficiencies in the Rosetta force field and created an extensive decoy training set for optimizing and testing force fields. Copyright © 2012 Wiley Periodicals, Inc.

  2. Towards matrix-free femtosecond-laser desorption mass spectrometry for in situ space research.

    Science.gov (United States)

    Moreno-García, Pavel; Grimaudo, Valentine; Riedo, Andreas; Tulej, Marek; Wurz, Peter; Broekmann, Peter

    2016-04-30

    There is an increasing interest in the quest for low molecular weight biomarkers that can be studied on extra-terrestrial objects by direct laser desorption mass spectrometry (LD-MS). Although molecular structure investigations have recently been carried out by direct LD-MS approaches, there is still a lack of suitable instruments for implementation on a spacecraft due to weight, size and power consumption demands. In this contribution we demonstrate the feasibility of LD-MS structural analysis of molecular species by a miniature laser desorption-ionization mass spectrometer (instrument name LMS) originally designed for in situ elemental and isotope analysis of solids in space research. Direct LD-MS studies with molecular resolution were carried out by means of a Laser Ablation/Ionization Mass Spectrometry (LIMS) technique. Two polymer samples served as model systems: neutral polyethylene glycol (PEG) and cationic polymerizates of imidazole and epichlorohydrin (IMEP). Optimal conditions for molecular fragmentation could be identified for both polymers by tuning the laser energy and the instrument-sample distance. PEG and IMEP polymers show sufficient stability over a relatively wide laser energy range. Under mild LD conditions only moderate fragmentation of the polymers takes place so that valuable structural characterization based on fragment ions can be achieved. As the applied laser pulse energy rises, the abundance of fragment ions increases, reaches a plateau and subsequently drops down due to more severe fragmentation and atomization of the polymers. At this final stage, usually referred to as laser ablation, only elemental/isotope analysis can be achieved. Our investigations demonstrate the versatility of the LMS instrument that can be tuned to favourable laser desorption conditions that successfully meet molecule-specific requirements and deliver abundant fragment ion signals with detailed structural information. Overall, the results show promise for use in

  3. Semi-automated screen for global protein conformational changes in solution by ion mobility spectrometry-massspectrometry combined with size-exclusion chromatography and differential hydrogen-deuterium exchange.

    Science.gov (United States)

    Pierson, Nicholas A; Makarov, Alexey A; Strulson, Christopher A; Mao, Yun; Mao, Bing

    2017-05-05

    Development of methodologies for studying protein higher-order structure in solution helps to establish a better understanding of the intrinsic link between protein conformational structure and biological function and activity. The goal of this study was to demonstrate a simultaneous screening approach for global protein conformational changes in solution through the combination of ion mobility spectrometry-mass spectrometry (IMS-MS) with differential hydrogen-deuterium exchange (ΔHDX) on the size-exclusion chromatography (SEC) platform in a single on-line workflow. A semi-automated experimental setup based on the use of SEC on-column conditions allowed for tracking of protein conformational changes in solution as a function of acetonitrile concentration. In this setup, the SEC protein elution data was complemented by the ΔHDX profile which showed global protein conformational changes as a difference in the number of deuterons exchanged to protons. The ΔHDX data, in turn, was complemented by the changes in the drift time by IMS-MS. All three orthogonal techniques were applied for studying global higher-order structure of the proteins ubiquitin, cytochrome c and myoglobin, in solution simultaneously. The described approach allows for the use of a crude sample (or mixture of proteins) and could be suitable for rapid comparison of protein batch-to-batch higher-order structure or for optimizing conditions for enzymatic reactions. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. D-Branes on ALE Spaces and the ADE Classification of Conformal Field Theories

    CERN Document Server

    Lerche, Wolfgang; Schweigert, C

    2002-01-01

    The spectrum of D2-branes wrapped on an ALE space of general ADE type is determined, by representing them as boundary states of N=2 superconformal minimal models. The stable quantum states have RR charges which precisely represent the gauge fields of the corresponding Lie algebra. This provides a simple and direct physical link between the ADE classification of N=2 superconformal field theories, and the corresponding root systems. An affine extension of this structure is also considered, whose boundary states represent the D2-branes plus additional D0-branes.

  5. Conformationally Constrained Histidines in the Design of Peptidomimetics: Strategies for the χ-Space Control

    Directory of Open Access Journals (Sweden)

    Adriano Mollica

    2011-05-01

    Full Text Available A successful design of peptidomimetics must come to terms with χ-space control. The incorporation of χ-space constrained amino acids into bioactive peptides renders the χ1 and χ2 torsional angles of pharmacophore amino acids critical for activity and selectivity as with other relevant structural features of the template. This review describes histidine analogues characterized by replacement of native α and/or β-hydrogen atoms with alkyl substituents as well as analogues with α, β-didehydro unsaturation or Cα-Cβ cyclopropane insertion (ACC derivatives. Attention is also dedicated to the relevant field of β-aminoacid chemistry by describing the synthesis of β2- and β3-models (β-hHis. Structural modifications leading to cyclic imino derivatives such as spinacine, aza-histidine and analogues with shortening or elongation of the native side chain (nor-histidine and homo-histidine, respectively are also described. Examples of the use of the described analogues to replace native histidine in bioactive peptides are also given.

  6. 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

  7. Conformal Carroll groups

    OpenAIRE

    Duval, C.; Gibbons, G W; Horvathy, P. A.

    2014-01-01

    Conformal extensions of Levy-Leblond's Carroll group, based on geometric properties analogous to those of Newton-Cartan space-time are proposed. The extensions are labelled by an integer $k$. This framework includes and extends our recent study of the Bondi-Metzner-Sachs (BMS) and Newman-Unti (NU) groups. The relation to Conformal Galilei groups is clarified. Conformal Carroll symmetry is illustrated by "Carrollian photons". Motion both in the Newton-Cartan and Carroll spaces may be related t...

  8. General relativistic models for rotating magnetized neutron stars in conformally flat space-time

    Science.gov (United States)

    Pili, A. G.; Bucciantini, N.; Del Zanna, L.

    2017-09-01

    The extraordinary energetic activity of magnetars is usually explained in terms of dissipation of a huge internal magnetic field of the order of 1015-16 G. How such a strong magnetic field can originate during the formation of a neutron star (NS) is still subject of active research. An important role can be played by fast rotation: if magnetars are born as millisecond rotators dynamo mechanisms may efficiently amplify the magnetic field inherited from the progenitor star during the collapse. In this case, the combination of rapid rotation and strong magnetic field determine the right physical condition not only for the development of a powerful jet-driven explosion, manifesting as a gamma-ray burst, but also for a copious gravitational waves emission. Strong magnetic fields are indeed able to induce substantial quadrupolar deformations in the star. In this paper, we analyse the joint effect of rotation and magnetization on the structure of a polytropic and axisymmetric NS, within the ideal magneto-hydrodynamic regime. We will consider either purely toroidal or purely poloidal magnetic field geometries. Through the sampling of a large parameter space, we generalize previous results in literature, inferring new quantitative relations that allow for a parametrization of the induced deformation, that takes into account also the effects due to the stellar compactness and the current distribution. Finally, in the case of purely poloidal field, we also discuss how different prescription on the surface charge distribution (a gauge freedom) modify the properties of the surrounding electrosphere and its physical implications.

  9. Conformational preludes to the latency transition in PAI-1 as determined by atomistic computer simulations and hydrogen/deuterium-exchange mass spectrometry

    DEFF Research Database (Denmark)

    Petersen, Michael; Madsen, Jeppe B; Jørgensen, Thomas J D

    2017-01-01

    as ligand binding in this region can accelerate or decelerate the conformational inactivation. Plasticity in this region may thus be mechanistically linked to the conformational change, possibly through facilitation of further unfolding of the hydrophobic core, as previously reported. This study provides...... a promising example of how computer simulations can help tether out mechanisms of serpin function and dysfunction at a spatial and temporal resolution that is far beyond the reach of any experiment....

  10. 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....

  11. Parallel Exploration of Interaction Space by BioID and Affinity Purification Coupled to Mass Spectrometry.

    Science.gov (United States)

    Hesketh, Geoffrey G; Youn, Ji-Young; Samavarchi-Tehrani, Payman; Raught, Brian; Gingras, Anne-Claude

    2017-01-01

    Complete understanding of cellular function requires knowledge of the composition and dynamics of protein interaction networks, the importance of which spans all molecular cell biology fields. Mass spectrometry-based proteomics approaches are instrumental in this process, with affinity purification coupled to mass spectrometry (AP-MS) now widely used for defining interaction landscapes. Traditional AP-MS methods are well suited to providing information regarding the temporal aspects of soluble protein-protein interactions, but the requirement to maintain protein-protein interactions during cell lysis and AP means that both weak-affinity interactions and spatial information is lost. A more recently developed method called BioID employs the expression of bait proteins fused to a nonspecific biotin ligase, BirA*, that induces in vivo biotinylation of proximal proteins. Coupling this method to biotin affinity enrichment and mass spectrometry negates many of the solubility and interaction strength issues inherent in traditional AP-MS methods, and provides unparalleled spatial context for protein interactions. Here we describe the parallel implementation of both BioID and FLAG AP-MS allowing simultaneous exploration of both spatial and temporal aspects of protein interaction networks.

  12. Separation and characterisation of beta2-microglobulin folding conformers by ion-exchange liquid chromatography and ion-exchange liquid chromatography-mass spectrometry.

    Science.gov (United States)

    Bertoletti, Laura; Regazzoni, Luca; Aldini, Giancarlo; Colombo, Raffaella; Abballe, Franco; Caccialanza, Gabriele; De Lorenzi, Ersilia

    2013-04-10

    In this work we present for the first time the use of ion-exchange liquid chromatography to separate the native form and a partially structured intermediate of the folding of the amyloidogenic protein beta2-microglobulin. Using a strong anion-exchange column that accounts for the differences in charge exposure of the two conformers, a LC-UV method is initially optimised in terms of mobile phase pH, composition and temperature. The preferred mobile phase conditions that afford useful information were found to be 35 mM ammonium formate, pH 7.4 at 25°C. The dynamic equilibrium of the two species is demonstrated upon increasing the concentration of acetonitrile in the protein sample. Then, the chromatographic method is transferred to MS detection and the respective charge state distributions of the separated conformers are identified. The LC-MS results demonstrate that one of the conformers is partially unfolded, compared with the native and more compact species. The correspondence with previous results obtained in free solution by capillary electrophoresis suggest that strong ion exchange LC-MS does not alter beta2-microglobulin conformation and maintains the dynamic equilibrium already observed between the native protein and its folding intermediate. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. Galilean conformal and superconformal symmetries

    Energy Technology Data Exchange (ETDEWEB)

    Lukierski, J., E-mail: lukier@ift.uni.wroc.pl [University of Wroclaw, Institute for Theoretical Physics (Poland)

    2012-10-15

    Firstly we discuss briefly three different algebras named as nonrelativistic (NR) conformal: Schroedinger, Galilean conformal, and infinite algebra of local NR conformal isometries. Further we shall consider in some detail Galilean conformal algebra (GCA) obtained in the limit c{yields}{infinity} from relativistic conformal algebraO(d+1, 2) (d-number of space dimensions). Two different contraction limits providing GCA and some recently considered realizations will be briefly discussed. Finally by considering NR contraction of D = 4 superconformal algebra the Galilei conformal superalgebra (GCSA) is obtained, in the formulation using complexWeyl supercharges.

  14. Joint estimation of 2D-DOA and frequency based on space-time matrix and conformal array.

    Science.gov (United States)

    Wan, Liang-Tian; Liu, Lu-Tao; Si, Wei-Jian; Tian, Zuo-Xi

    2013-01-01

    Each element in the conformal array has a different pattern, which leads to the performance deterioration of the conventional high resolution direction-of-arrival (DOA) algorithms. In this paper, a joint frequency and two-dimension DOA (2D-DOA) estimation algorithm for conformal array are proposed. The delay correlation function is used to suppress noise. Both spatial and time sampling are utilized to construct the spatial-time matrix. The frequency and 2D-DOA estimation are accomplished based on parallel factor (PARAFAC) analysis without spectral peak searching and parameter pairing. The proposed algorithm needs only four guiding elements with precise positions to estimate frequency and 2D-DOA. Other instrumental elements can be arranged flexibly on the surface of the carrier. Simulation results demonstrate the effectiveness of the proposed algorithm.

  15. 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...

  16. A comprehensive conformational space analysis of N-formyl-l-tryptophanamide system by using a genetic algorithm for multi-modal search.

    Science.gov (United States)

    El Guerdaoui, Anouar; Tijar, Rachida; El Merbouh, Brahim; Bourjila, Malika; El Bouzaidi, Rachid Drissi; El Gridani, Abderrahman

    2017-08-01

    The conformational space of protected amino acid HCO-Tryptophane-NH2 was explored by using a new optimization procedure, in order to localize the stable minima on its potential energy surface (PES). The genetic algorithm based on the Multi-Niche Crowding (MNC) technique was used initially to generate a set of optimized structures for title compound. Resulting structures from the genetic algorithm technique will be used hereafter as input conformers at a hierarchy of increasingly more accurate electronic structure calculations (RHF/6-31G+(d) and DFT/B3LYP/6-31G+(d) geometry optimizations). The lowest energy conformer γL(g+g+) presents a folded Backbone that is stabilized by strong hydrogen bond noted C7. This links the carbonyl oxygen of the formyl group and the hydrogen of the amine group. There are further interactions from one hand between the carbonyl oxygen of the formyl group and the neighboring CH group on the pyrrole ring and from other hand between the N-terminus hydrogen and the indole ring in accordance with the experimental results. This work includes also a comparison between the theoretical calculations and the experimental results of X-ray crystallography extracted from protein data bank (PDB). Copyright © 2017 Elsevier Inc. All rights reserved.

  17. WIZARD: AI in conformational analysis

    Science.gov (United States)

    Dolata, Daniel P.; Leach, Andrew R.; Prout, Keith

    1987-04-01

    A program which utilizes the techniques of Artificial Intelligence and Expert Systems to solve problems in the area of Conformational Analysis is described. The program searches conformational space in a systematic fashion, based on the technique known as heuristic state-space search. The program proceeds by recognizing conformational units, assigning one or more conformational templates to each unit, and joining them to form conformational suggestions. These suggestions are criticized to discover logical inconsistencies, and any resulting stresses are resolved. The resulting conformational suggestions are sometimes accurate enough for immediate use, or may be further refined by a numerical program. The latter combination is shown to be quite efficient compared to purely numerical conformational search techniques.

  18. Conformal block study and bounding OPE in conformal field theories

    CERN Document Server

    Yvernay, Pierre

    2015-01-01

    During the past few years, the re-emergence of conformal bootstrap as a numerical tool to solve conformal field theory allowed more precise estimation of several presumed conformal field theory among which we could cite the 3D Ising model. This work intends to provide insight on conformal blocks which are elementary objects in the conformal bootstrap approach. These are considered in Euclidian space where we study fields of all equal dimension. This study allows us to improve bounds derived in \\cite{OPEconv}.

  19. Transportation Conformity

    Science.gov (United States)

    This section provides information on: current laws, regulations and guidance, policy and technical guidance, project-level conformity, general information, contacts and training, adequacy review of SIP submissions

  20. Combined effects of f(R) gravity and conformally invariant Maxwell field on the extended phase space thermodynamics of higher-dimensional black holes

    Energy Technology Data Exchange (ETDEWEB)

    Mo, Jie-Xiong; Li, Gu-Qiang; Xu, Xiao-Bao [Lingnan Normal University, Institute of Theoretical Physics, Zhanjiang, Guangdong (China)

    2016-10-15

    In this paper, we investigate the thermodynamics of higher-dimensional f(R) black holes in the extended phase space. Both the analytic expressions and the numerical results for the possible critical physical quantities are obtained. It is proved that meaningful critical specific volume only exists when p is odd. This unique phenomenon may be attributed to the combined effect of f(R) gravity and conformally invariant Maxwell field. It is also shown that the ratio P{sub c}v{sub c}/T{sub c} differs from that of higher-dimensional charged AdS black holes in Einstein gravity. However, the ratio for four-dimensional f(R) black holes is the same as that of four-dimensional RN-AdS black holes, implying that f(R) gravity does not influence the ratio. So the ratio may be related to conformally invariant Maxwell field. To probe the phase transition, we derive the explicit expression of the Gibbs free energy with its graph plotted. A phase transition analogous to the van der Waals liquid-gas system takes place between the small black hole and the large black hole. Classical swallow tail behavior, characteristic of first-order phase transitions, can also be observed in the Gibbs free energy graph. Critical exponents are also calculated. It is shown that these exponents are exactly the same as those of other AdS black holes, implying that neither f(R) gravity nor conformally invariant Maxwell field influence the critical exponents. Since the investigated black hole solution depends on the form of the function f(R), we discuss in detail how our results put constraint on the form of the function f(R) and we also present a simple example. (orig.)

  1. 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.

  2. Combined effects of f(R) gravity and conformally invariant Maxwell field on the extended phase space thermodynamics of higher-dimensional black holes

    CERN Document Server

    Mo, Jie-Xiong; Xu, Xiao-Bao

    2016-01-01

    In this paper, we investigate the thermodynamics of higher-dimensional $f(R)$ black holes in the extended phase space. Both the analytic expressions and numerical results for the possible critical physical quantities are obtained. It is proved that meaningful critical specific volume only exists when $p$ is odd. This unique phenomenon may be attributed to the combined effect of $f(R)$ gravity and conformally invariant Maxwell field. It is also shown that the ratio $P_cv_c/T_c$ differs from that of higher dimensional charged AdS black holes in Einstein gravity. However, the ratio for four-dimensional $f(R)$ black holes is the same as that of four-dimensional RN-AdS black holes, implying that $f(R)$ gravity does not influence the ratio. So the ratio may be related to conformally invariant Maxwell field. To probe the phase transition, we derive the explicit expression of the Gibbs free energy with its graph plotted. Phase transition analogous to the van der Waals liquid-gas system take place between the small bl...

  3. Development of grazing incidence devices for space-borne time of flight mass spectrometry

    Science.gov (United States)

    Cadu, A.; Devoto, P.; Louarn, P.; Sauvaud, J.-A.

    2012-04-01

    Time of flight mass spectrometer is widely used to study space plasmas in planetary and solar missions. This space-borne instrument selects ions in function of their energy through an electrostatic analyzer. Particles are then post-accelerated to energies in the range of 20 keV to cross a carbon foil. At the foil exit, electrons are emitted and separated from ion beam in the time of flight section. A first detector (a Micro-Channel Plate or MCP) emits a start signal at electron arrival and a second one emits a stop signal at incident ion end of path. The time difference gives the speed of the particle and its mass can be calculated, knowing its initial energy. However, current instruments suffer from strong limitations. The post acceleration needs very high voltage power supplies which are heavy, have a high power consumption and imply technical constraints for the development. A typical instrument weighs from 5 to 6 kg, includes a 20 kV power supply, consumes a least 5 W and encounters corona effect and electrical breakdown problems. Moreover, despite the particle high energy range, scattering and straggling phenomena in the carbon foil significantly reduce the instrument overall resolution. Some methods, such as electrostatic focus lenses or reflectrons, really improve mass separation but global system efficiency remains very low because of the charge state dependence of such devices. The main purpose of our work is to replace carbon foil by grazing incidence MCP's - also known as MPO's, for Micro Pore Optics - for electron emission. Thus, incident particles would back-scatter onto the channel inner surface with an angle of a few degrees. With this solution, we can decrease dispersion sources and lower the power supplies to post accelerate ions. The result would be a lighter and simpler instrument with a substantial resolution improvement. We have first simulated MPO's behavior with TRIM and MARLOWE Monte-Carlo codes. Energy scattering and output angle computed

  4. New pilot for validation of automated analyses of organics by gas chromatography mass spectrometry (GCMS): application to space researches

    Science.gov (United States)

    Sternberg, Robert; Buch, Arnaud; Chazalnoel, Pascale; Geffroy, Claude; David, Marc

    The search for complex organic molecules in extraterrestrial environments, including important biomolecules such as amino acids and carboxylic acids, will require after an extraction a derivatization step to transform these organic compounds into species that are sufficiently volatile to be detected by gas chromatography mass spectrometry (GCMS). Current and future space missions, such as Mars Science Laboratory (MSL 2011, will include such derivatization method and thus a dedicated laboratory pilot is needed to validate protocols before launch of the probes. A new in situ generic Derivatization-Pyrolysis Unit (DPU) is presented. Derivatization is carried out in a 4 mL reactor placed on a GCMS injector for automated derivatization as well as for pre- and post treatment of the sample. The DPU unit is evaluated in terms of its technical features. The performances are illustrated with applications including conventional and in situ derivatization for using terrestrial Mars analog materials enriched by a 5 nmol amino acids solution. The DPU allows the analysis of a wide range of molecules to be detected and can be adapted to samples from any solid spatial object such as Mars, asteroids and comets. This pilot is a good basis for the validation of future generations of instruments, such as the Mars Organic Molecule Analyzer (MOMA) of the Exomars 2018 mission, dedicated to the search for organics in spatial environments.

  5. General Conformity

    Science.gov (United States)

    The General Conformity requirements ensure that the actions taken by federal agencies in nonattainment and maintenance areas do not interfere with a state’s plans to meet national standards for air quality.

  6. 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.

  7. 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.

  8. Families and degenerations of conformal field theories

    Energy Technology Data Exchange (ETDEWEB)

    Roggenkamp, D.

    2004-09-01

    In this work, moduli spaces of conformal field theories are investigated. In the first part, moduli spaces corresponding to current-current deformation of conformal field theories are constructed explicitly. For WZW models, they are described in detail, and sigma model realizations of the deformed WZW models are presented. The second part is devoted to the study of boundaries of moduli spaces of conformal field theories. For this purpose a notion of convergence of families of conformal field theories is introduced, which admits certain degenerated conformal field theories to occur as limits. To such a degeneration of conformal field theories, a degeneration of metric spaces together with additional geometric structures can be associated, which give rise to a geometric interpretation. Boundaries of moduli spaces of toroidal conformal field theories, orbifolds thereof and WZW models are analyzed. Furthermore, also the limit of the discrete family of Virasoro minimal models is investigated. (orig.)

  9. Reduction of space charge effects in inductively coupled plasma mass spectrometry using a supplemental electron source inside the skimmer: ion transmission and mass spectral characteristics

    Science.gov (United States)

    Praphairaksit; Houk

    2000-06-01

    An electron source consisting of a heated filament has been added to the skimmer to suppress space charge effects in inductively coupled plasma mass spectrometry (ICPMS). Electrons from this source can reduce the space charge repulsion between the positive ions in the ion beam. As a result, ion transmission efficiency and analyte ion sensitivities are significantly improved across the full mass range. MO+/M+ abundance ratios are not affected, M2+/M+ abundance ratios increase only slightly, and no new background ions are created by this electron injection technique.

  10. Determination of the solution-bound conformation of an amino acid binding protein by NMR paramagnetic relaxation enhancement: use of a single flexible paramagnetic probe with improved estimation of its sampling space.

    Science.gov (United States)

    Bermejo, Guillermo A; Strub, Marie-Paule; Ho, Chien; Tjandra, Nico

    2009-07-15

    We demonstrate the feasibility of elucidating the bound ("closed") conformation of a periplasmic binding protein, the glutamine-binding protein (GlnBP), in solution, using paramagnetic relaxation enhancements (PREs) arising from a single paramagnetic group. GlnBP consists of two globular domains connected by a hinge. Using the ligand-free ("open") conformation as a starting point, conjoined rigid-body/torsion-angle simulated annealing calculations were performed using backbone (1)H(N)-PREs as a major source of distance information. Paramagnetic probe flexibility was accounted for via a multiple-conformer representation. A conventional approach where the entire PRE data set is enforced at once during simulated annealing yielded poor results due to inappropriate conformational sampling of the probe. On the other hand, significant improvements in coordinate accuracy were obtained by estimating the probe sampling space prior to structure calculation. Such sampling is achieved by refining the ensemble of probe conformers with intradomain PREs only, keeping the protein backbone fixed in the open form. Subsequently, while constraining the probe to the previously found conformations, the domains are allowed to move relative to each other under the influence of the non-intradomain PREs, giving the hinge region torsional degrees of freedom. Thus, by partitioning the protocol into "probe sampling" and "backbone sampling" stages, structures significantly closer to the X-ray structure of ligand-bound GlnBP were obtained.

  11. Conformal Methods in General Relativity

    Science.gov (United States)

    Valiente Kroon, Juan A.

    2016-07-01

    List of symbols; Preface; 1. Introduction; Part I. Geometric Tools: 2. Differential Geometry; 3. Spacetime spinors; 4. Space spinors; 5. Conformal Geometry; Part II. General Relativity and Conformal Geometry: 6. Conformal extensions of exact solutions; 7. Asymptotic simplicity; 8. The conformal Einstein field equations; 9. Matter models; 10. Asymptotics; Part III. Methods of PDE Theory: 11. The conformal constraint equations; 12. Methods of the theory of hyperbolic differential equations; 13. Hyperbolic reductions; 14. Causality and the Cauchy problem in General Relativity; Part IV. Applications: 15. De Sitter-like spacetimes; 16. Minkowski-like spacetimes; 17. Anti-de Sitter-like spacetimes; 18. Characteristic problems for the conformal field equations; 19. Static solutions; 20. Spatial infinity; 21. Perspectives; References; Index.

  12. Sampling conformational space of intrinsically disordered proteins in explicit solvent: Comparison between well-tempered ensemble approach and solute tempering method.

    Science.gov (United States)

    Han, Mengzhi; Xu, Ji; Ren, Ying

    2017-03-01

    Intrinsically disordered proteins (IDPs) are a class of proteins that expected to be largely unstructured under physiological conditions. Due to their heterogeneous nature, experimental characterization of IDP is challenging. Temperature replica exchange molecular dynamics (T-REMD) is a widely used enhanced sampling method to probe structural characteristics of these proteins. However, its application has been hindered due to its tremendous computational cost, especially when simulating large systems in explicit solvent. Two methods, parallel tempering well-tempered ensemble (PT-WTE) and replica exchange with solute tempering (REST), have been proposed to alleviate the computational expense of T-REMD. In this work, we select three different IDP systems to compare the sampling characteristics and efficiencies of the two methods Both the two methods could efficiently sample the conformational space of IDP and yield highly consistent results for all the three IDPs. The efficiencies of the two methods: are compatible, with about 5-6 times better than the plain T-REMD. Besides, the advantages and disadvantages of each method are also discussed. Specially, the PT-WTE method could provide temperature dependent data of the system which could not be achieved by REST, while the REST method could readily be used to a part of the system, which is quite efficient to simulate some biological processes. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Gluon Amplitudes as 2d Conformal Correlators

    OpenAIRE

    Pasterski, Sabrina; Shao, Shu-Heng; Strominger, Andrew

    2017-01-01

    Recently, spin-one wavefunctions in four dimensions that are conformal primaries of the Lorentz group SL(2,C) were constructed. We compute low-point, tree-level gluon scattering amplitudes in the space of these conformal primary wavefunctions. The answers have the same conformal covariance as correlators of spin-one primaries in a 2d CFT. The BCFW recursion relation between three- and four-point gluon amplitudes is recast into this conformal basis.

  14. Recursion Relations for Conformal Blocks

    CERN Document Server

    Penedones, João; Yamazaki, Masahito

    2016-09-12

    In the context of conformal field theories in general space-time dimension, we find all the possible singularities of the conformal blocks as functions of the scaling dimension $\\Delta$ of the exchanged operator. In particular, we argue, using representation theory of parabolic Verma modules, that in odd spacetime dimension the singularities are only simple poles. We discuss how to use this information to write recursion relations that determine the conformal blocks. We first recover the recursion relation introduced in 1307.6856 for conformal blocks of external scalar operators. We then generalize this recursion relation for the conformal blocks associated to the four point function of three scalar and one vector operator. Finally we specialize to the case in which the vector operator is a conserved current.

  15. How constant momentum acceleration decouples energy and space focusing in distance-of-flight and time-of-flight mass spectrometries.

    Science.gov (United States)

    Dennis, Elise A; Gundlach-Graham, Alexander W; Enke, Christie G; Ray, Steven J; Carado, Anthony J; Barinaga, Charles J; Koppenaal, David W; Hieftje, Gary M

    2013-05-01

    Resolution in time-of-flight mass spectrometry (TOFMS) is ordinarily limited by the initial energy and space distributions within an instrument's acceleration region and by the length of the field-free flight zone. With gaseous ion sources, these distributions lead to systematic flight-time errors that cannot be simultaneously corrected with conventional static-field ion-focusing devices (i.e., an ion mirror). It is known that initial energy and space distributions produce non-linearly correlated errors in both ion velocity and exit time from the acceleration region. Here we reinvestigate an old acceleration technique, constant-momentum acceleration (CMA), to decouple the effects of initial energy and space distributions. In CMA, only initial ion energies (and not their positions) affect the velocity ions gain. Therefore, with CMA, the spatial distribution within the acceleration region can be manipulated without creating ion-velocity error. The velocity differences caused by a spread in initial ion energy can be corrected with an ion mirror. We discuss here the use of CMA and independent focusing of energy and space distributions for both distance-of-flight mass spectrometry (DOFMS) and TOFMS. Performance characteristics of our CMA-DOFMS and CMA-TOFMS instrument, fitted with a glow-discharge ionization source, are described. In CMA-DOFMS, resolving powers (FWHM) of greater than 1000 are achieved for atomic ions with a flight length of 285 mm. In CMA-TOFMS, only ions over a narrow range of m/z values can be energy-focused; however, the technique offers improved resolution for these focused ions, with resolving powers of greater than 2000 for a separation distance of 350 mm.

  16. Recent advancements in conformal gravity

    Science.gov (United States)

    O'Brien, James G.; Chaykov, Spasen S.; Dentico, Jeremy; Stulge, Modestas; Stefanski, Brian; Moss, Robert J.

    2017-05-01

    In recent years, due to the lack of direct observed evidence of cold dark matter, coupled with the shrinking parameter space to search for new dark matter particles, there has been increased interest in Alternative Gravitational theories. This paper, addresses three recent advances in conformal gravity, a fourth order renormalizable metric theory of gravitation originally formulated by Weyl, and later advanced by Mannheim and Kazanas. The first section of the paper applies conformal gravity to the rotation curves of the LITTLE THINGS survey, extending the total number of rotation curves successfully fit by conformal gravity to well over 200 individual data sets without the need for additional dark matter. Further, in this rotation curve study, we show how MOND and conformal gravity compare for each galaxy in the sample. Second, we look at the original Zwicky problem of applying the virial theorem to the Coma cluster in order to get an estimate for the cluster mass. However, instead of using the standard Newtonian potential, here we use the weak field approximation of conformal gravity. We show that in the conformal case we can get a much smaller mass estimate and thus there is no apparent need to include dark matter. We then show that this calculation is in agreement with the observational data from other well studied clusters. Last, we explore the calculation of the deflection of starlight through conformal gravity, as a first step towards applying conformal gravity to gravitaitonal lensing.

  17. A molecular mechanics study of the effect of substitution in position 1 on the conformational space of the oxytocin/vasopressin ring

    Science.gov (United States)

    Tarnowska, Monika; Liwo, Adam; Shenderovich, Mark D.; Liepiņa, Inta; Golbraikh, Alexander A.; Grzonka, Zbigniew; Tempczyk, Anna

    1993-12-01

    The effect of the substitution in position 1 on the low-energy conformations of the oxytocin/vasopressin 20-membered ring was investigated by means of molecular mechanics. Three representative substitutions were considered: β'-mercapto-β,β-dimethyl)propionic acid (Dmp), (β'-mercapto-β,β-cyclopentamethylene)propionic acid (Cpp), both forming strong antagonists, and (α,α-dimethyl-β-mercapto)propionic acid (α-Dmp), forming analogs of strongly reduced biological activity, with the β-mercaptopropionic (Mpa) residue taken as reference. Both ECEPP/2 (rigid valence geometry) and AMBER (flexible valence geometry) force fields were employed in the calculations. Three basic types of backbone conformations were taken into account which are distinguished by the type of β-turn at residues 3 and 4: β1/βIII, βII, and βI'/βIII', all types containing one or two intra-annular hydrogen bonds. The allowed (ring-closed) disulfide-bridge conformations were searched by an algorithm formulated in terms of scanning the disulfide-bridge torsional angle Cβ-S-S-Cβ. The ECEPP/2 and AMBER energies of the obtained conformations were found to be in reasonable agreement. Two of the low-energy conformers of the [Mpa1]-compound agreed very well with the cyclic part of the two conformers found in the crystal structure of [Mpa1]-oxytocin. An analysis of the effect of β-substitution on relative energies showed that the conformations with the N-C'-CH2-CH2 (ψ'1) and C'-CH2-CH2-S (ϰ'1) angles of the first residue around (-100°, 60°) and (100°, -60°) are not affected; this in most cases implies a left-handed disulfide bridge. In the case of α-substitution the allowed values of ψ'1 are close to ± 60°. This requirement, being in contradiction to the one concerning β-substitution, could explain the very low biological activity of the α-substituted analogs. The conformational preferences of substituted compounds can largely be explained by the analysis of local interactions

  18. Crystalline arrays of pairs of molecular rotors: correlated motion, rotational barriers, and space-inversion symmetry breaking due to conformational mutations.

    Science.gov (United States)

    Lemouchi, Cyprien; Iliopoulos, Konstantinos; Zorina, Leokadiya; Simonov, Sergey; Wzietek, Pawel; Cauchy, Thomas; Rodríguez-Fortea, Antonio; Canadell, Enric; Kaleta, Jiří; Michl, Josef; Gindre, Denis; Chrysos, Michael; Batail, Patrick

    2013-06-26

    The rod-like molecule bis((4-(4-pyridyl)ethynyl)bicyclo[2.2.2]oct-1-yl)buta-1,3-diyne, 1, contains two 1,4-bis(ethynyl)bicyclo[2.2.2]octane (BCO) chiral rotators linked by a diyne fragment and self-assembles in a one-dimensional, monoclinic C2/c centrosymmetric structure where two equilibrium positions with large occupancy imbalance (88% versus 12%) are identified on a single rotor site. Combining variable-temperature (70-300 K) proton spin-lattice relaxation, (1)H T1(-1), at two different (1)H Larmor frequencies (55 and 210 MHz) and DFT calculations of rotational barriers, we were able to assign two types of Brownian rotators with different activation energies, 1.85 and 6.1 kcal mol(-1), to the two (1)H spin-lattice relaxation processes on the single rotor site. On the basis of DFT calculations, the low-energy process has been assigned to adjacent rotors in a well-correlated synchronous motion, whereas the high-energy process is the manifestation of an abrupt change in their kinematics once two blades of adjacent rotors are seen to rub together. Although crystals of 1 should be second harmonic inactive, a large second-order optical response is recorded when the electric field oscillates in a direction parallel to the unique rotor axle director. We conclude that conformational mutations by torsional interconversion of the three blades of the BCO units break space-inversion symmetry in sequences of mutamers in dynamic equilibrium in the crystal in domains at a mesoscopic scale comparable with the wavelength of light used. A control experiment was performed with a crystalline film of a similar tetrayne molecule, 1,4-bis(3-((trimethylsilyl)ethynyl)bicyclo[1.1.1]pent-1-yl)buta-1,3-diyne, whose bicyclopentane units can rotate but are achiral and produce no second-order optical response.

  19. Non-conformable, partial and conformable transposition

    DEFF Research Database (Denmark)

    König, Thomas; Mäder, Lars Kai

    2013-01-01

    Although member states are obliged to transpose directives into domestic law in a conformable manner and receive considerable time for their transposition activities, we identify three levels of transposition outcomes for EU directives: conformable, partially conformable and non-conformable...... 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...

  20. An accurate method for microanalysis of carbon monoxide in putrid postmortem blood by head-space gas chromatography-mass spectrometry (HS/GC/MS).

    Science.gov (United States)

    Hao, Hongxia; Zhou, Hong; Liu, Xiaopei; Zhang, Zhong; Yu, Zhongshan

    2013-06-10

    Carbon monoxide (CO) may be the cause of more than half the fatal poisonings reported in many countries, with some of these cases under-reported or misdiagnosed by medical professionals. Therefore, an accurate and reliable analytical method to measure blood carboxyhemoglobin level (COHb%), in the 1% to lethal range, is essential for correct diagnosis. Herein a method was established, i.e. head-space gas chromatography-mass spectrometry (HS/GC/MS) that has numerous advantages over other techniques, such as UV spectrometry, for determination of COHb%. There was a linear relationship (R(2)=0. 9995) between the peak area for CO and the COHb% in blood. Using a molecular sieve-packed column, CO levels in the air down to 0.01% and COHb% levels in small blood samples down to 0.2% could be quantitated rapidly and accurately. Furthermore, this method showed good reproducibility with a relative standard deviation for COHb% of <1%. Therefore, this technique provides an accurate and reliable method for determining CO and COHb% levels and may prove useful for investigation of deaths potentially related to CO exposure. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  1. Structural selection by microsolvation: Conformational locking of tryptamine

    NARCIS (Netherlands)

    Schmitt, M.; Bohm, M.; Ratzer, C.; Vu, C.; Kalkman, L.; Meerts, W.L.

    2005-01-01

    The conformational space of tryptamine has been thoroughly investigated using rotationally resolved laser-induced fluorescence spectroscopy. Six conformers could be identified on the basis of the inertial parameters of several deuterated isotopomers. Upon attaching a single water molecule, the

  2. MeV-range velocity-space tomography from gamma-ray and neutron emission spectrometry measurements at JET

    DEFF Research Database (Denmark)

    Salewski, Mirko; Nocente, M.; Jacobsen, Asger Schou

    2017-01-01

    We demonstrate the measurement of a 2D MeV-range ion velocity distribution function by velocity-space tomography at JET. Deuterium ions were accelerated into the MeV-range by third harmonic ion cyclotron resonance heating. We made measurements with three neutron emission spectrometers and a high-...

  3. Supergravitational conformal Galileons

    Science.gov (United States)

    Deen, Rehan; Ovrut, Burt

    2017-08-01

    The worldvolume actions of 3+1 dimensional bosonic branes embedded in a five-dimensional bulk space can lead to important effective field theories, such as the DBI conformal Galileons, and may, when the Null Energy Condition is violated, play an essential role in cosmological theories of the early universe. These include Galileon Genesis and "bouncing" cosmology, where a pre-Big Bang contracting phase bounces smoothly to the presently observed expanding universe. Perhaps the most natural arena for such branes to arise is within the context of superstring and M -theory vacua. Here, not only are branes required for the consistency of the theory, but, in many cases, the exact spectrum of particle physics occurs at low energy. However, such theories have the additional constraint that they must be N = 1 supersymmetric. This motivates us to compute the worldvolume actions of N = 1 supersymmetric three-branes, first in flat superspace and then to generalize them to N = 1 supergravitation. In this paper, for simplicity, we begin the process, not within the context of a superstring vacuum but, rather, for the conformal Galileons arising on a co-dimension one brane embedded in a maximally symmetric AdS 5 bulk space. We proceed to N = 1 supersymmetrize the associated worldvolume theory and then generalize the results to N = 1 supergravity, opening the door to possible new cosmological scenarios

  4. Probing RNA native conformational ensembles with structural constraints

    DEFF Research Database (Denmark)

    Fonseca, Rasmus; van den Bedem, Henry; Bernauer, Julie

    2016-01-01

    substates, which are difficult to characterize experimentally and computationally. Here, we present an innovative, entirely kinematic computational procedure to efficiently explore the native ensemble of RNA molecules. Our procedure projects degrees of freedom onto a subspace of conformation space defined...... by distance constraints in the tertiary structure. The dimensionality reduction enables efficient exploration of conformational space. We show that the conformational distributions obtained with our method broadly sample the conformational landscape observed in NMR experiments. Compared to normal mode...

  5. On conformally related -waves

    Indian Academy of Sciences (India)

    Conformal transformations; conformal Killing vectors; -waves. Abstract. Brinkmann [1] has shown that conformally related distinct Ricci flat solutions are -waves. Brinkmann's result has been generalized to include the conformally invariant source terms. It has been shown that [4] if g i k and g ¯ i k ( = − 2 g i k , : a ...

  6. Integration of Affinity Selection-Mass Spectrometry and Functional Cell-Based Assays to Rapidly Triage Druggable Target Space within the NF-κB Pathway.

    Science.gov (United States)

    Kutilek, Victoria D; Andrews, Christine L; Richards, Matthew P; Xu, Zangwei; Sun, Tianxiao; Chen, Yiping; Hashke, Andrew; Smotrov, Nadya; Fernandez, Rafael; Nickbarg, Elliott B; Chamberlin, Chad; Sauvagnat, Berengere; Curran, Patrick J; Boinay, Ryan; Saradjian, Peter; Allen, Samantha J; Byrne, Noel; Elsen, Nathaniel L; Ford, Rachael E; Hall, Dawn L; Kornienko, Maria; Rickert, Keith W; Sharma, Sujata; Shipman, Jennifer M; Lumb, Kevin J; Coleman, Kevin; Dandliker, Peter J; Kariv, Ilona; Beutel, Bruce

    2016-07-01

    The primary objective of early drug discovery is to associate druggable target space with a desired phenotype. The inability to efficiently associate these often leads to failure early in the drug discovery process. In this proof-of-concept study, the most tractable starting points for drug discovery within the NF-κB pathway model system were identified by integrating affinity selection-mass spectrometry (AS-MS) with functional cellular assays. The AS-MS platform Automated Ligand Identification System (ALIS) was used to rapidly screen 15 NF-κB proteins in parallel against large-compound libraries. ALIS identified 382 target-selective compounds binding to 14 of the 15 proteins. Without any chemical optimization, 22 of the 382 target-selective compounds exhibited a cellular phenotype consistent with the respective target associated in ALIS. Further studies on structurally related compounds distinguished two chemical series that exhibited a preliminary structure-activity relationship and confirmed target-driven cellular activity to NF-κB1/p105 and TRAF5, respectively. These two series represent new drug discovery opportunities for chemical optimization. The results described herein demonstrate the power of combining ALIS with cell functional assays in a high-throughput, target-based approach to determine the most tractable drug discovery opportunities within a pathway. © 2016 Society for Laboratory Automation and Screening.

  7. CED: a conformational epitope database

    Directory of Open Access Journals (Sweden)

    Huang Jian

    2006-04-01

    Full Text Available Abstract Background Antigen epitopes provide valuable information useful for disease prevention, diagnosis, and treatment. Recently, more and more databases focusing on different types of epitopes have become available. Conformational epitopes are an important form of epitope formed by residues that are sequentially discontinuous but close together in three-dimensional space. These epitopes have implicit structural information, making them attractive for both theoretical and applied biomedical research. However, most existing databases focus on linear rather than conformational epitopes. Description We describe CED, a special database of well defined conformational epitopes. CED provides a collection of conformational epitopes and related information including the residue make up and location of the epitope, the immunological property of the epitope, the source antigen and corresponding antibody of the epitope. All entries in this database are manually curated from articles published in peer review journals. The database can be browsed or searched through a user-friendly web interface. Most epitopes in CED can also be viewed interactively in the context of their 3D structures. In addition, the entries are also hyperlinked to various databases such as Swiss-Prot, PDB, KEGG and PubMed, providing wide background information. Conclusion A conformational epitope database called CED has been developed as an information resource for investigators involved in both theoretical and applied immunology research. It complements other existing specialised epitope databases. The database is freely available at http://web.kuicr.kyoto-u.ac.jp/~ced

  8. Quantification of the aerosol direct radiative effect from smoke over clouds using passive space-borne spectrometry

    Science.gov (United States)

    de Graaf, M.; Stammes, P.; Tilstra, L. G.

    2013-05-01

    The solar radiative absorption by smoke layers above clouds is quantified, using the unique broad spectral range of the space-borne spectrometer Scanning Imaging Absorption Spectrometer for Atmospheric Chartography (SCIAMACHY) from the ultraviolet (UV) to the shortwave infrared (SWIR). Aerosol radiative effects in the UV are separated from cloud radiative effects in the shortwave infrared (SWIR). In the UV, aerosol absorption from smoke is strong, creating a strong signal in the measured reflectance. In the SWIR, absorbing and scattering effects from smoke are negligible, allowing the retrieval of cloud parameters from the measured spectrum using existing retrieval techniques. The spectral signature of the cloud can be modelled using a radiative transfer model (RTM) and the cloud parameters retrieved in the SWIR. In this way, the aerosol effects can be determined from the measured aerosol-polluted cloud shortwave spectrum and the modelled aerosol-unpolluted cloud shortwave spectrum. This can be used to derive the aerosol direct radiative effect (DRE) over marine clouds, independent of aerosol parameter retrievals, significantly improving the current accuracy of aerosol DRE estimates. Only cloud parameters are needed to model the aerosolunpolluted cloud reflectance, while the effects of the aerosol absorption are in the aerosol-polluted cloud reflectance measurements. In this paper we present a case study of the above method using SCIAMACHY data over the South Atlantic Ocean west of Africa on 13 August 2006, when a huge plume of smoke was present over persistent cloud fields. The aerosol DRE over clouds was as high as 128 ± 8 Wm-2 for this case, while the aerosol DRE over clouds averaged through August 2006 was found to be 23 ± 8 Wm-2 with a mean variation over the region in this month of 22 Wm-2.

  9. 14 CFR 21.130 - Statement of conformity.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false Statement of conformity. 21.130 Section 21... conformity. Each holder or licensee of a type certificate only, for a product manufactured in the United... Administrator a statement of conformity (FAA Form 317). This statement must be signed by an authorized person...

  10. 14 CFR 21.53 - Statement of conformity.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false Statement of conformity. 21.53 Section 21... CERTIFICATION PROCEDURES FOR PRODUCTS AND PARTS Type Certificates § 21.53 Statement of conformity. Link to an... conformity (FAA Form 317) to the Administrator for each aircraft engine and propeller presented to the...

  11. 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....

  12. 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.

  13. Identification and quantification of seven volatile n-nitrosamines in cosmetics using gas chromatography/chemical ionization-mass spectrometry coupled with head space-solid phase microextraction.

    Science.gov (United States)

    Choi, Na Rae; Kim, Yong Pyo; Ji, Won Hyun; Hwang, Geum-Sook; Ahn, Yun Gyong

    2016-01-01

    An analytical method was developed for the identification and quantification of seven volatile n-nitrosamines (n-nitrosodimethylamine [NDMA], n-nitrosoethylmethylamine [NMEA], n-nitrosodiethylamine [NDEA], n-nitrosodipropylamine [NDPA], n-nitrosodibutylamine [NDBA], n-nitrosopiperidine [NPIP], and n-nitrosopyrrolidine [NPYR]) in water insoluble cream type cosmetics. It was found that the head space-solid phase microextraction (HS-SPME) was suitable for extraction, clean up, and pre-concentration of n-nitrosamines in the cream type samples so its optimal conditions were investigated. Identification and quantification of n-nitrosamines using single quadrupole gas chromatography/mass spectrometry (GC/MS) in chemical ionization (CI) mode were carried out with accurate mass measurements. Their accurate masses of protonated molecular ions were obtained within 10 mDa of the theoretical masses when sufficiently high signal was acquired from the unique calibration method using mass and isotope accuracy. For the method validation of quantification, spiking experiments were carried out to determine the linearity, recovery, and method detection limit (MDL) using three deuterated internal standards. The average recovery was 79% within 20% relative standard deviation (RSD) at the concentration of 50 ng/g. MDLs ranged from 0.46 ng/g to 36.54 ng/g, which was satisfactory for the directive limit of 50 ng/g proposed by the European Commission (EC). As a result, it was concluded that the method could be provided for the accurate mass screening, confirmation, and quantification of n-nitrosamines when applied to cosmetic inspection. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Development and Evaluation of an Externally Air-Cooled Low-Flow torch and the Attenuation of Space Charge and Matrix Effects in Inductively Coupled Plasma Mass Spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Praphairaksit, Narong [Iowa State Univ., Ames, IA (United States)

    2000-09-12

    An externally air-cooled low-flow torch has been constructed and successfully demonstrated for applications in inductively coupled plasma mass spectrometry (ICP-MS). The torch is cooled by pressurized air flowing at ~70 L/min through a quartz air jacket onto the exterior of the outer tube. The outer gas flow rate and operating RF forward power are reduced considerably. Although plasmas can be sustained at the operating power as low as 400 W with a 2 L/min of outer gas flow, somewhat higher power and outer gas flows are advisable. A stable and analytical useful plasma can be obtained at 850 W with an outer gas flow rate of ~4 L/min. Under these conditions, the air-cooled plasma produces comparable sensitivities, doubly charged ion ratios, matrix effects and other analytical merits as those produced by a conventional torch while using significantly less argon and power requirements. Metal oxide ion ratios are slightly higher with the air-cooled plasma but can be mitigated by reducing the aerosol gas flow rate slightly with only minor sacrifice in analyte sensitivity. A methodology to alleviate the space charge and matrix effects in ICP-MS has been developed. A supplemental electron source adapted from a conventional electron impact ionizer is added to the base of the skimmer. Electrons supplied from this source downstream of the skimmer with suitable amount and energy can neutralize the positive ions in the beam extracted from the plasma and diminish the space charge repulsion between them. As a result, the overall ion transmission efficiency and consequent analyte ion sensitivities are significantly improved while other important analytical aspects, such as metal oxide ion ratio, doubly charged ion ratio and background ions remain relatively unchanged with the operation of this electron source. This technique not only improves the ion transmission efficiency but also minimizes the matrix effects drastically. The matrix-induced suppression of signal for even the most

  15. The decomposition of global conformal invariants

    CERN Document Server

    Alexakis, Spyros

    2012-01-01

    This book addresses a basic question in differential geometry that was first considered by physicists Stanley Deser and Adam Schwimmer in 1993 in their study of conformal anomalies. The question concerns conformally invariant functionals on the space of Riemannian metrics over a given manifold. These functionals act on a metric by first constructing a Riemannian scalar out of it, and then integrating this scalar over the manifold. Suppose this integral remains invariant under conformal re-scalings of the underlying metric. What information can one then deduce about the Riemannian scalar? Dese

  16. Scalar scattering via conformal higher spin exchange

    Energy Technology Data Exchange (ETDEWEB)

    Joung, Euihun [School of Physics and Astronomy,Seoul National University, Seoul 151-747 (Korea, Republic of); Gauge, Gravity & Strings, Center for Theoretical Physics of the Universe,Institute for Basic Sciences, Daejeon 34047 (Korea, Republic of); Nakach, Simon; Tseytlin, Arkady A. [Theoretical physics group, Blackett Laboratory,Imperial College London, SW7 2AZ (United Kingdom)

    2016-02-18

    Theories containing infinite number of higher spin fields require a particular definition of summation over spins consistent with their underlying symmetries. We consider a model of massless scalars interacting (via bilinear conserved currents) with conformal higher spin fields in flat space. We compute the tree-level four-scalar scattering amplitude using a natural prescription for summation over an infinite set of conformal higher spin exchanges and find that it vanishes. Independently, we show that the vanishing of the scalar scattering amplitude is, in fact, implied by the global conformal higher spin symmetry of this model. We also discuss one-loop corrections to the four-scalar scattering amplitude.

  17. Invariant classification of second-order conformally flat superintegrable systems

    Science.gov (United States)

    Capel, J. J.; Kress, J. M.

    2014-12-01

    In this paper we continue the work of Kalnins et al in classifying all second-order conformally-superintegrable (Laplace-type) systems over conformally flat spaces, using tools from algebraic geometry and classical invariant theory. The results obtained show, through Stäckel equivalence, that the list of known nondegenerate superintegrable systems over three-dimensional conformally flat spaces is complete. In particular, a seven-dimensional manifold is determined such that each point corresponds to a conformal class of superintegrable systems. This manifold is foliated by the nonlinear action of the conformal group in three dimensions. Two systems lie in the same conformal class if and only if they lie in the same leaf of the foliation. This foliation is explicitly described using algebraic varieties formed from representations of the conformal group. The proof of these results rely heavily on Gröbner basis calculations using the computer algebra software packages Maple and Singular.

  18. Conformal ghosts on the sphere

    Energy Technology Data Exchange (ETDEWEB)

    Vogeler, Kirsten

    2010-07-16

    This thesis is about the relation of geometry and logarithmic conformal field theories. I consider two different geometric settings: in part I the topological A-model with embedding x:R x S{sup 1}{yields}CP{sup 1}, and in part II conformal, fermionic ghosts on the torus. The A-model can be transformed such that the path integral yields a {delta} distribution on the moduli space of instantons. Integrating out the dependency on S{sup 1}, one obtains Morse theory on the universal cover LCP{sup 1} of loop space. Its low-energy state space can be derived perturbatively in cells of this manifold, and can be modelled by the representations of the chiral de Rham complex. Assuming that the representation theory of the A-model and the chiral de Rham complex are identical, I consider the chiral de Rham complex in the following. The state spaces are local, induced representations of the symmetry generated by the gradient vector field of the Morse function. According to a conjecture of E. Frenkel, A. Losev and N. Nekrasov, a generalization of these local representations as distributions on LCP{sup 1} leads to nonperturbative states of the theory. On these states, the Hamiltonian must be corrected by additional terms. I discuss the representation theory of the nonperturbative states and determine the terms which deform the Hamiltonian. They have a geometric significance as cohomology operators in a complex of globally extended local representation spaces. Eventually, I prove that a logarithmic extension of the chiral de Rham complex corresponds the additional terms in the Hamiltonian. The conformal, fermionic ghosts of part II transform in irreducible representations of the monodromy group Z{sub 2}. I show that the conformal field theory of these fields has to be logarithmically extended as soon as the representations of the monodromy group are allowed to move freely on the parameter space CP{sup 1} backslash {l_brace}0,1,{infinity}{r_brace} of the torus. The triplet model

  19. Conformal gravity and "gravitational bubbles"

    CERN Document Server

    Berezin, V A; Eroshenko, Yu N

    2015-01-01

    We describe the general structure of the spherically symmetric solutions in the Weyl conformal gravity. The corresponding Bach equations are derived for the special type of metrics, which can be considered as the representative of the general class. The complete set of the pure vacuum solutions, consisting of two classes, is found. The first one contains the solutions with constant two-dimensional curvature scalar, and the representatives are the famous Robertson--Walker metrics. We called one of them the "gravitational bubbles", which is compact and with zero Weyl tensor. These "gravitational bubbles" are the pure vacuum curved space-times (without any material sources, including the cosmological constant), which are absolutely impossible in General Relativity. This phenomenon makes it easier to create the universe from "nothing". The second class consists of the solutions with varying curvature scalar. We found its representative as the one-parameter family, which can be conformally covered by the thee-para...

  20. Conformal solids and holography

    Science.gov (United States)

    Esposito, A.; Garcia-Saenz, S.; Nicolis, A.; Penco, R.

    2017-12-01

    We argue that a SO( d) magnetic monopole in an asymptotically AdS space-time is dual to a d-dimensional strongly coupled system in a solid state. In light of this, it would be remiss of us not to dub such a field configuration solidon. In the presence of mixed boundary conditions, a solidon spontaneously breaks translations (among many other symmetries) and gives rise to Goldstone excitations on the boundary — the phonons of the solid. We derive the quadratic action for the boundary phonons in the probe limit and show that, when the mixed boundary conditions preserve conformal symmetry, the longitudinal and transverse sound speeds are related to each other as expected from effective field theory arguments. We then include backreaction and calculate the free energy of the solidon for a particular choice of mixed boundary conditions, corresponding to a relevant multi-trace deformation of the boundary theory. We find such free energy to be lower than that of thermal AdS. This suggests that our solidon undergoes a solid-to-liquid first order phase transition by melting into a Schwarzschild-AdS black hole as the temperature is raised.

  1. The multiple conformational charge states of zinc(II) coordination by 2His-2Cys oligopeptide investigated by ion mobility-mass spectrometry, density functional theory and theoretical collision cross sections.

    Science.gov (United States)

    Wagoner, Stephanie M; Deeconda, Manogna; Cumpian, Kayleah L; Ortiz, Rafael; Chinthala, Swetha; Angel, Laurence A

    2016-12-01

    Whether traveling wave ion mobility-mass spectrometry (IM-MS), B3LYP/LanL2DZ density functional theory, and ion size scaled Lennard-Jones (LJ) collision cross sections (CCS) from the B3LYP optimized structures could be used to determine the type of Zn(II) coordination by the oligopeptide acetyl-His1 -Cys2 -Gly3 -Pro4 -Tyr5 -His6 -Cys7 (amb5 ) was investigated. The IM-MS analyses of a pH titration of molar equivalents of Zn(II):amb5 showed that both negatively and positively charged complexes formed and coordination of Zn(II) increased as the His and Cys deprotonated near their pKa values. The B3LYP method was used to generate a series of alternative coordination structures to compare with the experimental results. The method predicted that the single negatively charged complex coordinated Zn(II) in a distorted tetrahedral geometry via the 2His-2Cys substituent groups, whereas, the double negatively charged and positively charged complexes coordinated Zn(II) via His, carbonyl oxygens and the C-terminus. The CCS of the B3LYP complexes were calculated using the LJ method and compared with those measured by IM-MS for the various charge state complexes. The LJ method provided CCS that agreed with five of the alternative distorted tetrahedral and trigonal bipyramidal coordinations for the doubly charged complexes, but provided CCS that were 15 to 31 Å2 larger than those measured by IM-MS for the singly charged complexes. Collision-induced dissociation of the Zn(II) complexes and a further pH titration study of amb5B , which included amidation of the C-terminus, suggested that the 2His-2Cys coordination was more significant than coordinations that included the C-terminus. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  2. Conformational stability of calreticulin

    DEFF Research Database (Denmark)

    Jørgensen, Charlotte S; Trandum, Christa; Larsen, Nanna Brink

    2005-01-01

    The conformational stability of calreticulin was investigated. Apparent unfolding temperatures (Tm) increased from 31 degrees C at pH 5 to 51 degrees C at pH 9, but electrophoretic analysis revealed that calreticulin oligomerized instead of unfolding. Structural analyses showed that the single C......-terminal alpha-helix was of major importance to the conformational stability of calreticulin....

  3. Conformational stability of calreticulin

    DEFF Research Database (Denmark)

    Jørgensen, C.S.; Trandum, C.; Larsen, N.

    2005-01-01

    The conformational stability of calreticulin was investigated. Apparent unfolding temperatures (T-m) increased from 31 degrees C at pH 5 to 51 degrees C at pH 9, but electrophoretic analysis revealed that calreticulin oligomerized instead of unfolding. Structural analyses showed that the single C......-terminal a-helix was of major importance to the conformational stability of calreticulin....

  4. Focused conformational sampling in proteins

    Science.gov (United States)

    Bacci, Marco; Langini, Cassiano; Vymětal, Jiří; Caflisch, Amedeo; Vitalis, Andreas

    2017-11-01

    A detailed understanding of the conformational dynamics of biological molecules is difficult to obtain by experimental techniques due to resolution limitations in both time and space. Computer simulations avoid these in theory but are often too short to sample rare events reliably. Here we show that the progress index-guided sampling (PIGS) protocol can be used to enhance the sampling of rare events in selected parts of biomolecules without perturbing the remainder of the system. The method is very easy to use as it only requires as essential input a set of several features representing the parts of interest sufficiently. In this feature space, new states are discovered by spontaneous fluctuations alone and in unsupervised fashion. Because there are no energetic biases acting on phase space variables or projections thereof, the trajectories PIGS generates can be analyzed directly in the framework of transition networks. We demonstrate the possibility and usefulness of such focused explorations of biomolecules with two loops that are part of the binding sites of bromodomains, a family of epigenetic "reader" modules. This real-life application uncovers states that are structurally and kinetically far away from the initial crystallographic structures and are also metastable. Representative conformations are intended to be used in future high-throughput virtual screening campaigns.

  5. Conformal Gauge Transformations in Thermodynamics

    Directory of Open Access Journals (Sweden)

    Alessandro Bravetti

    2015-09-01

    Full Text Available In this work, we show that the thermodynamic phase space is naturally endowed with a non-integrable connection, defined by all of those processes that annihilate the Gibbs one-form, i.e., reversible processes. We argue that such a connection is invariant under re-scalings of the connection one-form, whilst, as a consequence of the non-integrability of the connection, its curvature is not and, therefore, neither is the associated pseudo-Riemannian geometry. We claim that this is not surprising, since these two objects are associated with irreversible processes. Moreover, we provide the explicit form in which all of the elements of the geometric structure of the thermodynamic phase space change under a re-scaling of the connection one-form. We call this transformation of the geometric structure a conformal gauge transformation. As an example, we revisit the change of the thermodynamic representation and consider the resulting change between the two metrics on the thermodynamic phase space, which induce Weinhold’s energy metric and Ruppeiner’s entropy metric. As a by-product, we obtain a proof of the well-known conformal relation between Weinhold’s and Ruppeiner’s metrics along the equilibrium directions. Finally, we find interesting properties of the almost para-contact structure and of its eigenvectors, which may be of physical interest.

  6. Spaces

    Directory of Open Access Journals (Sweden)

    Maziar Nekovee

    2010-01-01

    Full Text Available Cognitive radio is being intensively researched as the enabling technology for license-exempt access to the so-called TV White Spaces (TVWS, large portions of spectrum in the UHF/VHF bands which become available on a geographical basis after digital switchover. Both in the US, and more recently, in the UK the regulators have given conditional endorsement to this new mode of access. This paper reviews the state-of-the-art in technology, regulation, and standardisation of cognitive access to TVWS. It examines the spectrum opportunity and commercial use cases associated with this form of secondary access.

  7. Mass spectrometry

    DEFF Research Database (Denmark)

    Nyvang Hartmeyer, Gitte; Jensen, Anne Kvistholm; Böcher, Sidsel

    2010-01-01

    Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is currently being introduced for the rapid and accurate identification of bacteria. We describe 2 MALDI-TOF MS identification cases - 1 directly on spinal fluid and 1 on grown bacteria. Rapidly obtained r...

  8. In vivo prediction of goat kids body composition from the deuterium oxide dilution space determined by isotope-ratio mass spectrometry.

    Science.gov (United States)

    Lerch, S; Lastel, M L; Grandclaudon, C; Brechet, C; Rychen, G; Feidt, C

    2015-09-01

    Deuterium oxide dilution space (DOS) determination is one of the most accurate methods for in vivo estimation of ruminant body composition. However, the time-consuming vacuum sublimation of blood preceding infrared spectroscopy analysis, which is traditionally used to determine deuterium oxide (DO) concentration, limits its current use. The use of isotope-ratio mass spectrometry (IRMS) to determine the deuterium enrichment and thus quantify DO in plasma could counteract this limitation by reducing the sample preparation for plasma deproteinisation through centrifugal filters. The aim of this study was to validate the DOS technique using IRMS in growing goat kids to establish in vivo prediction equations of body composition. Seventeen weaned male Alpine goat kids (8.6 wk old) received a hay-based diet supplemented with 2 types of concentrates providing medium ( = 9) or high ( = 8) energy levels. Kids were slaughtered at 14.0 ( = 1, medium-energy diet), 17.2 ( = 4, medium-energy diet, and = 4, high-energy diet), or 21.2 wk of age ( = 4, medium-energy diet, and = 4, high-energy diet). Two days before slaughter, DOS was determined after an intravenous injection of 0.2 g DO/kg body mass (BM) and the resulting study of DO dilution kinetics from 4 plasma samples (+5, +7, +29, and +31 h after injection). The deuterium enrichment was analyzed by IRMS. After slaughter, the gut contents were discarded, the empty body (EB) was minced, and EB water, lipid, protein, ash, and energy contents were measured by chemical analyses. Prediction equations for body components measured postmortem were computed from in vivo BM and DOS. The lack of postmortem variation of fat-free EB composition was confirmed (mean of 75.3% [SD 0.6] of water), and the proportion of lipids in the EB tended ( = 0.06) to be greater for the high-energy diet (13.1%) than for the medium-energy diet (11.1%). There was a close negative relationship (residual CV [rCV] = 3.9%, = 0.957) between EB water and lipid

  9. A Projective-to-Conformal Fefferman-Type Construction

    Science.gov (United States)

    Hammerl, Matthias; Sagerschnig, Katja; Šilhan, Josef; Taghavi-Chabert, Arman; Zádník, Vojtĕch

    2017-10-01

    We study a Fefferman-type construction based on the inclusion of Lie groups SL(n+1) into Spin(n+1,n+1). The construction associates a split-signature (n,n)-conformal spin structure to a projective structure of dimension n. We prove the existence of a canonical pure twistor spinor and a light-like conformal Killing field on the constructed conformal space. We obtain a complete characterisation of the constructed conformal spaces in terms of these solutions to overdetermined equations and an integrability condition on the Weyl curvature. The Fefferman-type construction presented here can be understood as an alternative approach to study a conformal version of classical Patterson-Walker metrics as discussed in recent works by Dunajski-Tod and by the authors. The present work therefore gives a complete exposition of conformal Patterson-Walker metrics from the viewpoint of parabolic geometry.

  10. Locally conformal symplectic manifolds

    Directory of Open Access Journals (Sweden)

    Izu Vaisman

    1985-01-01

    Full Text Available A locally conformal symplectic (l. c. s. manifold is a pair (M2n,Ω where M2n(n>1 is a connected differentiable manifold, and Ω a nondegenerate 2-form on M such that M=⋃αUα (Uα- open subsets. Ω/Uα=eσαΩα, σα:Uα→ℝ, dΩα=0. Equivalently, dΩ=ω∧Ω for some closed 1-form ω. L. c. s. manifolds can be seen as generalized phase spaces of Hamiltonian dynamical systems since the form of the Hamilton equations is, in fact, preserved by homothetic canonical transformations. The paper discusses first Hamiltonian vector fields, and infinitesimal automorphisms (i. a. on l. c. s. manifolds. If (M,Ω has an i. a. X such that ω(X≠0, we say that M is of the first kind and Ω assumes the particular form Ω=dθ−ω∧θ. Such an M is a 2-contact manifold with the structure forms (ω,θ, and it has a vertical 2-dimensional foliation V. If V is regular, we can give a fibration theorem which shows that M is a T2-principal bundle over a symplectic manifold. Particularly, V is regular for some homogeneous l. c. s, manifolds, and this leads to a general construction of compact homogeneous l. c. s, manifolds. Various related geometric results, including reductivity theorems for Lie algebras of i. a. are also given. Most of the proofs are adaptations of corresponding proofs in symplectic and contact geometry. The paper ends with an Appendix which states an analogous fibration theorem in Riemannian geometry.

  11. Multi-field conformal cosmological attractors

    Science.gov (United States)

    Kallosh, Renata; Linde, Andrei

    2013-12-01

    We describe a broad class of multi-field inflationary models with spontaneously broken conformal invariance. It generalizes the recently discovered class of cosmological attractors with a single inflaton field [1]. In the new multi-field theories, just as in the single-field models of [1], the moduli space has a boundary (Kähler cone) in terms of the original homogeneous conformal variables. Upon spontaneous breaking of the conformal invariance and switching to the Einstein frame, this boundary moves to infinity in terms of the canonically normalized inflaton field. This results in the exponential stretching and flattening of scalar potentials in the vicinity of the boundary of the moduli space, which makes even very steep potentials perfectly suitable for the slow-roll inflation. These theories, just like their single-field versions, typically lead to inflationary perturbations with ns = 1-2/N and r = 12/N2, where N is the number of e-foldings.

  12. Conformal expansions and renormalons

    CERN Document Server

    Brodsky, S J; Grunberg, G; Rathsman, J; Brodsky, Stanley J.; Gardi, Einan; Grunberg, Georges; Rathsman, Johan

    2001-01-01

    The coefficients in perturbative expansions in gauge theories are factoriallyincreasing, predominantly due to renormalons. This type of factorial increaseis not expected in conformal theories. In QCD conformal relations betweenobservables can be defined in the presence of a perturbative infraredfixed-point. Using the Banks-Zaks expansion we study the effect of thelarge-order behavior of the perturbative series on the conformal coefficients.We find that in general these coefficients become factorially increasing.However, when the factorial behavior genuinely originates in a renormalonintegral, as implied by a postulated skeleton expansion, it does not affect theconformal coefficients. As a consequence, the conformal coefficients willindeed be free of renormalon divergence, in accordance with previousobservations concerning the smallness of these coefficients for specificobservables. We further show that the correspondence of the BLM method with theskeleton expansion implies a unique scale-setting procedure. Th...

  13. Conformal expansions and renormalons

    CERN Document Server

    Gardi, E; Gardi, Einan; Grunberg, Georges

    2001-01-01

    The large-order behaviour of QCD is dominated by renormalons. On the other hand renormalons do not occur in conformal theories, such as the one describing the infrared fixed-point of QCD at small beta_0 (the Banks--Zaks limit). Since the fixed-point has a perturbative realization, all-order perturbative relations exist between the conformal coefficients, which are renormalon-free, and the standard perturbative coefficients, which contain renormalons. Therefore, an explicit cancellation of renormalons should occur in these relations. The absence of renormalons in the conformal limit can thus be seen as a constraint on the structure of the QCD perturbative expansion. We show that the conformal constraint is non-trivial: a generic model for the large-order behaviour violates it. We also analyse a specific example, based on a renormalon-type integral over the two-loop running-coupling, where the required cancellation does occur.

  14. Group Size and Conformity

    OpenAIRE

    Bond, Rod

    2005-01-01

    Abstract This paper reviews theory and research on the relationship between group size and conformity and presents a meta-analysis of 125 Asch-type conformity studies. It questions the assumption of a single function made in formal models of social influence and proposes instead that the function will vary depending on which social influence process predominates. It is argued that normative influence is lik...

  15. Conformable variational iteration method

    Directory of Open Access Journals (Sweden)

    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.

  16. Quantum massive conformal gravity

    Energy Technology Data Exchange (ETDEWEB)

    Faria, F.F. [Universidade Estadual do Piaui, Centro de Ciencias da Natureza, Teresina, PI (Brazil)

    2016-04-15

    We first find the linear approximation of the second plus fourth order derivative massive conformal gravity action. Then we reduce the linearized action to separated second order derivative terms, which allows us to quantize the theory by using the standard first order canonical quantization method. It is shown that quantum massive conformal gravity is renormalizable but has ghost states. A possible decoupling of these ghost states at high energies is discussed. (orig.)

  17. Delineating the conformal window

    DEFF Research Database (Denmark)

    Frandsen, Mads Toudal; Pickup, Thomas; Teper, Michael

    2011-01-01

    We identify and characterise the conformal window in gauge theories relevant for beyond the standard model building, e.g. Technicolour, using the criteria of metric confinement and causal analytic couplings, which are known to be consistent with the phase diagram of supersymmetric QCD from Seiberg...... duality. Using these criteria we find perturbation theory to be consistent throughout the predicted conformal window for several of these gauge theories and we discuss recent lattice results in the light of our findings....

  18. Holographic applications of logarithmic conformal field theories

    NARCIS (Netherlands)

    Grumiller, D.; Riedler, W.; Rosseel, J.; Zojer, T.

    2013-01-01

    We review the relations between Jordan cells in various branches of physics, ranging from quantum mechanics to massive gravity theories. Our main focus is on holographic correspondences between critically tuned gravity theories in anti-de Sitter space and logarithmic conformal field theories in

  19. Conformable Pressurized Structures : Design and Analysis

    NARCIS (Netherlands)

    Geuskens, F.J.J.M.M.

    2012-01-01

    There are many applications where volume needs to be pressurised within a geometrical space for which conventional pressure vessels do not provide suitable solutions. Applications are for example found in pressure cabins for Blended Wing Body Aircraft and conformable pressure vessels for an

  20. Logarithmic conformal field theory

    Science.gov (United States)

    Gainutdinov, Azat; Ridout, David; Runkel, Ingo

    2013-12-01

    Conformal field theory (CFT) has proven to be one of the richest and deepest subjects of modern theoretical and mathematical physics research, especially as regards statistical mechanics and string theory. It has also stimulated an enormous amount of activity in mathematics, shaping and building bridges between seemingly disparate fields through the study of vertex operator algebras, a (partial) axiomatisation of a chiral CFT. One can add to this that the successes of CFT, particularly when applied to statistical lattice models, have also served as an inspiration for mathematicians to develop entirely new fields: the Schramm-Loewner evolution and Smirnov's discrete complex analysis being notable examples. When the energy operator fails to be diagonalisable on the quantum state space, the CFT is said to be logarithmic. Consequently, a logarithmic CFT is one whose quantum space of states is constructed from a collection of representations which includes reducible but indecomposable ones. This qualifier arises because of the consequence that certain correlation functions will possess logarithmic singularities, something that contrasts with the familiar case of power law singularities. While such logarithmic singularities and reducible representations were noted by Rozansky and Saleur in their study of the U (1|1) Wess-Zumino-Witten model in 1992, the link between the non-diagonalisability of the energy operator and logarithmic singularities in correlators is usually ascribed to Gurarie's 1993 article (his paper also contains the first usage of the term 'logarithmic conformal field theory'). The class of CFTs that were under control at this time was quite small. In particular, an enormous amount of work from the statistical mechanics and string theory communities had produced a fairly detailed understanding of the (so-called) rational CFTs. However, physicists from both camps were well aware that applications from many diverse fields required significantly more

  1. Elucidation of Drug Metabolite Structural Isomers Using Molecular Modeling Coupled with Ion Mobility Mass Spectrometry.

    Science.gov (United States)

    Reading, Eamonn; Munoz-Muriedas, Jordi; Roberts, Andrew D; Dear, Gordon J; Robinson, Carol V; Beaumont, Claire

    2016-02-16

    Ion mobility-mass spectrometry (IM-MS) in combination with molecular modeling offers the potential for small molecule structural isomer identification by measurement of their gas phase collision cross sections (CCSs). Successful application of this approach to drug metabolite identification would facilitate resource reduction, including animal usage, and may benefit other areas of pharmaceutical structural characterization including impurity profiling and degradation chemistry. However, the conformational behavior of drug molecules and their metabolites in the gas phase is poorly understood. Here the gas phase conformational space of drug and drug-like molecules has been investigated as well as the influence of protonation and adduct formation on the conformations of drug metabolite structural isomers. The use of CCSs, measured from IM-MS and molecular modeling information, for the structural identification of drug metabolites has also been critically assessed. Detection of structural isomers of drug metabolites using IM-MS is demonstrated and, in addition, a molecular modeling approach has been developed offering rapid conformational searching and energy assessment of candidate structures which agree with experimental CCSs. Here it is illustrated that isomers must possess markedly dissimilar CCS values for structural differentiation, the existence and extent of CCS differences being ionization state and molecule dependent. The results present that IM-MS and molecular modeling can inform on the identity of drug metabolites and highlight the limitations of this approach in differentiating structural isomers.

  2. Conformal invariance of curvature perturbation

    CERN Document Server

    Gong, Jinn-Ouk; Park, Wan Il; Sasaki, Misao; Song, Yong-Seon

    2011-01-01

    We show that in the single component situation all perturbation variables in the comoving gauge are conformally invariant to all perturbation orders. Generally we identify a special time slicing, the uniform-conformal transformation slicing, where all perturbations are again conformally invariant to all perturbation orders. We apply this result to the delta N formalism, and show its conformal invariance.

  3. Conformal invariance of curvature perturbation

    Energy Technology Data Exchange (ETDEWEB)

    Gong, Jinn-Ouk [Theory Division, CERN, CH-1211 Genève 23 (Switzerland); Hwang, Jai-chan [Department of Astronomy and Atmospheric Sciences, Kyungpook National University, Daegu 702-701 (Korea, Republic of); Park, Wan Il; Sasaki, Misao; Song, Yong-Seon, E-mail: jinn-ouk.gong@cern.ch, E-mail: jchan@knu.ac.kr, E-mail: wipark@kias.re.kr, E-mail: misao@yukawa.kyoto-u.ac.jp, E-mail: ysong@kias.re.kr [Korea Institute for Advanced Study, Seoul 130-722 (Korea, Republic of)

    2011-09-01

    We show that in the single component situation all perturbation variables in the comoving gauge are conformally invariant to all perturbation orders. Generally we identify a special time slicing, the uniform-conformal transformation slicing, where all perturbations are again conformally invariant to all perturbation orders. We apply this result to the δN formalism, and show its conformal invariance.

  4. 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....

  5. A Novel, Low-Cost Conformable Lander Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The primary focus of this activity will be to outline a preliminary mechanical design for this conforming lander. Salient issues to be worked include (1) determining...

  6. Hot Conformal Gauge Theories

    DEFF Research Database (Denmark)

    Mojaza, Matin; Pica, Claudio; Sannino, Francesco

    2010-01-01

    in such a way that the theory develops a perturbative stable infrared fixed point at zero temperature. Due to large distance conformality we trade the coupling constant with its fixed point value and define a reduced free energy which depends only on the number of flavors, colors and matter representation. We...... show that the reduced free energy changes sign, at the second, fifth and sixth order in the coupling, when decreasing the number of flavors from the upper end of the conformal window. If the change in sign is interpreted as signal of an instability of the system then we infer a critical number...... of flavors. Surprisingly this number, if computed to the order g^2, agrees with previous predictions for the lower boundary of the conformal window for nonsupersymmetric gauge theories. The higher order results tend to predict a higher number of critical flavors. These are universal properties, i...

  7. New Fractional Complex Transform for Conformable Fractional Partial Differential Equations

    Directory of Open Access Journals (Sweden)

    Çenesiz Y.

    2016-12-01

    Full Text Available Conformable fractional complex transform is introduced in this paper for converting fractional partial differential equations to ordinary differential equations. Hence analytical methods in advanced calculus can be used to solve these equations. Conformable fractional complex transform is implemented to fractional partial differential equations such as space fractional advection diffusion equation and space fractional telegraph equation to obtain the exact solutions of these equations.

  8. Defining Low-Dimensional Projections to Guide Protein Conformational Sampling.

    Science.gov (United States)

    Novinskaya, Anastasia; Devaurs, Didier; Moll, Mark; Kavraki, Lydia E

    2017-01-01

    Exploring the conformational space of proteins is critical to characterize their functions. Numerous methods have been proposed to sample a protein's conformational space, including techniques developed in the field of robotics and known as sampling-based motion-planning algorithms (or sampling-based planners). However, these algorithms suffer from the curse of dimensionality when applied to large proteins. Many sampling-based planners attempt to mitigate this issue by keeping track of sampling density to guide conformational sampling toward unexplored regions of the conformational space. This is often done using low-dimensional projections as an indirect way to reduce the dimensionality of the exploration problem. However, how to choose an appropriate projection and how much it influences the planner's performance are still poorly understood issues. In this article, we introduce two methodologies defining low-dimensional projections that can be used by sampling-based planners for protein conformational sampling. The first method leverages information about a protein's flexibility to construct projections that can efficiently guide conformational sampling, when expert knowledge is available. The second method builds similar projections automatically, without expert intervention. We evaluate the projections produced by both methodologies on two conformational search problems involving three middle-size proteins. Our experiments demonstrate that (i) defining projections based on expert knowledge can benefit conformational sampling and (ii) automatically constructing such projections is a reasonable alternative.

  9. 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.

  10. Age and space distributions of monoterpenes in fresh needles of Picea abies (L) Karst. Determined by gas chromatography-mass spectrometry.

    Science.gov (United States)

    Holubová, V; Hrdlicka, P; Kubán, V

    2001-01-01

    Monoterpenes (alpha- and beta-pinene, delta-3-carene, camphene, alpha-phellandrene and limonene) were determined by Gas Chromatography-Mass Spectrometry in fresh needles of Picea abies (L) Karst. situated in three ecologically different regions of Moravia. Through the use of cryogenic grinding for critical sample homogenisation, solvent extraction with cold n-hexane, followed by GC analysis with mass detection, very low quantities of sample (0.1-0.3 g needles) could be processed, thus permitting a comparison of amounts of monoterpenes in needles of different ages and a determination of changes in concentrations of monoterpenes in needles at different locations on the tree. The amount of alpha-phellandrene decreased with the age of the needles, and the content of delta-3-carene was higher in apical branches compared to lateral ones.

  11. Deep Inelastic Scattering in Conformal QCD

    CERN Document Server

    Cornalba, Lorenzo; Penedones, Joao

    2010-01-01

    We consider the Regge limit of a CFT correlation function of two vector and two scalar operators, as appropriate to study small-x deep inelastic scattering in N=4 SYM or in QCD assuming approximate conformal symmetry. After clarifying the nature of the Regge limit for a CFT correlator, we use its conformal partial wave expansion to obtain an impact parameter representation encoding the exchange of a spin j Reggeon for any value of the coupling constant. The CFT impact parameter space is the three-dimensional hyperbolic space H3, which is the impact parameter space for high energy scattering in the dual AdS space. We determine the small-x structure functions associated to the exchange of a Reggeon. We discuss unitarization from the point of view of scattering in AdS and comment on the validity of the eikonal approximation. We then focus on the weak coupling limit of the theory where the amplitude is dominated by the exchange of the BFKL pomeron. Conformal invariance fixes the form of the vector impact factor a...

  12. Complete Mapping of Complex Disulfide Patterns with Closely-Spaced Cysteines by In-Source Reduction and Data-Dependent Mass Spectrometry

    DEFF Research Database (Denmark)

    Cramer, Christian N; Kelstrup, Christian D; Olsen, Jesper V

    2017-01-01

    bonds are present in complicated patterns. This includes the presence of disulfide bonds in nested patterns and closely spaced cysteines. Unambiguous mapping of such disulfide bonds typically requires advanced MS approaches. In this study, we exploited in-source reduction (ISR) of disulfide bonds during...... of individual disulfide bonds could be done in species containing closely spaced disulfide bonds. The strength of this methodology was demonstrated by complete mapping of all four disulfide bonds in lysozyme and all 17 disulfide bonds in human serum albumin, including nested disulfide bonds and motifs...

  13. Transportation Conformity Training and Presentations

    Science.gov (United States)

    EPA's OTAQ has provided multiple conformity training sessions in the past to assist state and local governments in implementing conformity requirements. As training information is prepared for other venues, it will be posted on this page.

  14. Dynamical spacetimes in conformal gravity

    National Research Council Canada - National Science Library

    Hongsheng Zhang; Yi Zhang; Xin-Zhou Li

    2017-01-01

    The conformal gravity remarkably boosts our prehension of gravity theories. We find a series of dynamical solutions in the W2-conformal gravity, including generalized Schwarzschild–Friedmann–Robertson–Walker (GSFRW...

  15. Multiscale conformal pattern transfer

    Science.gov (United States)

    Lodewijks, Kristof; Miljkovic, Vladimir; Massiot, Inès; Mekonnen, Addis; Verre, Ruggero; Olsson, Eva; Dmitriev, Alexandre

    2016-06-01

    We demonstrate a method for seamless transfer from a parent flat substrate of basically any lithographic top-down or bottom-up pattern onto essentially any kind of surface. The nano- or microscale patterns, spanning macroscopic surface areas, can be transferred with high conformity onto a large variety of surfaces when such patterns are produced on a thin carbon film, grown on top of a sacrificial layer. The latter allows lifting the patterns from the flat parent substrate onto a water-air interface to be picked up by the host surface of choice. We illustrate the power of this technique by functionalizing broad range of materials including glass, plastics, metals, rough semiconductors and polymers, highlighting the potential applications in in situ colorimetry of the chemistry of materials, anti-counterfeit technologies, biomolecular and biomedical studies, light-matter interactions at the nanoscale, conformal photovoltaics and flexible electronics.

  16. Multiscale conformal pattern transfer.

    Science.gov (United States)

    Lodewijks, Kristof; Miljkovic, Vladimir; Massiot, Inès; Mekonnen, Addis; Verre, Ruggero; Olsson, Eva; Dmitriev, Alexandre

    2016-06-22

    We demonstrate a method for seamless transfer from a parent flat substrate of basically any lithographic top-down or bottom-up pattern onto essentially any kind of surface. The nano- or microscale patterns, spanning macroscopic surface areas, can be transferred with high conformity onto a large variety of surfaces when such patterns are produced on a thin carbon film, grown on top of a sacrificial layer. The latter allows lifting the patterns from the flat parent substrate onto a water-air interface to be picked up by the host surface of choice. We illustrate the power of this technique by functionalizing broad range of materials including glass, plastics, metals, rough semiconductors and polymers, highlighting the potential applications in in situ colorimetry of the chemistry of materials, anti-counterfeit technologies, biomolecular and biomedical studies, light-matter interactions at the nanoscale, conformal photovoltaics and flexible electronics.

  17. Polymer Conformation under Confinement

    Directory of Open Access Journals (Sweden)

    Stavros Bollas

    2017-02-01

    Full Text Available The conformation of polymer chains under confinement is investigated in intercalated polymer/layered silicate nanocomposites. Hydrophilic poly(ethylene oxide/sodium montmorillonite, PEO/Na+-MMT, hybrids were prepared utilizing melt intercalation with compositions where the polymer chains are mostly within the ~1 nm galleries of the inorganic material. The polymer chains are completely amorphous in all compositions even at temperatures where the bulk polymer is highly crystalline. Attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR is utilized to investigate the conformation of the polymer chains over a broad range of temperatures from below to much higher than the bulk polymer melting temperature. A systematic increase of the gauche conformation relatively to the trans is found with decreasing polymer content both for the C–C and the C–O bonds that exist along the PEO backbone indicating that the severe confinement and the proximity to the inorganic surfaces results in a more disordered state of the polymer.

  18. Conformational Dynamics and Allostery in Pyruvate Kinase.

    Science.gov (United States)

    Donovan, Katherine A; Zhu, Shaolong; Liuni, Peter; Peng, Fen; Kessans, Sarah A; Wilson, Derek J; Dobson, Renwick C J

    2016-04-22

    Pyruvate kinase catalyzes the final step in glycolysis and is allosterically regulated to control flux through the pathway. Two models are proposed to explain how Escherichia coli pyruvate kinase type 1 is allosterically regulated: the "domain rotation model" suggests that both the domains within the monomer and the monomers within the tetramer reorient with respect to one another; the "rigid body reorientation model" proposes only a reorientation of the monomers within the tetramer causing rigidification of the active site. To test these hypotheses and elucidate the conformational and dynamic changes that drive allostery, we performed time-resolved electrospray ionization mass spectrometry coupled to hydrogen-deuterium exchange studies followed by mutagenic analysis to test the activation mechanism. Global exchange experiments, supported by thermostability studies, demonstrate that fructose 1,6-bisphosphate binding to the allosteric domain causes a shift toward a globally more dynamic ensemble of conformations. Mapping deuterium exchange to peptides within the enzyme highlight site-specific regions with altered conformational dynamics, many of which increase in conformational flexibility. Based upon these and mutagenic studies, we propose an allosteric mechanism whereby the binding of fructose 1,6-bisphosphate destabilizes an α-helix that bridges the allosteric and active site domains within the monomeric unit. This destabilizes the β-strands within the (β/α)8-barrel domain and the linked active site loops that are responsible for substrate binding. Our data are consistent with the domain rotation model but inconsistent with the rigid body reorientation model given the increased flexibility at the interdomain interface, and we can for the first time explain how fructose 1,6-bisphosphate affects the active site. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  19. Conformational Dynamics and Allostery in Pyruvate Kinase*

    Science.gov (United States)

    Donovan, Katherine A.; Zhu, Shaolong; Liuni, Peter; Peng, Fen; Kessans, Sarah A.; Wilson, Derek J.

    2016-01-01

    Pyruvate kinase catalyzes the final step in glycolysis and is allosterically regulated to control flux through the pathway. Two models are proposed to explain how Escherichia coli pyruvate kinase type 1 is allosterically regulated: the “domain rotation model” suggests that both the domains within the monomer and the monomers within the tetramer reorient with respect to one another; the “rigid body reorientation model” proposes only a reorientation of the monomers within the tetramer causing rigidification of the active site. To test these hypotheses and elucidate the conformational and dynamic changes that drive allostery, we performed time-resolved electrospray ionization mass spectrometry coupled to hydrogen-deuterium exchange studies followed by mutagenic analysis to test the activation mechanism. Global exchange experiments, supported by thermostability studies, demonstrate that fructose 1,6-bisphosphate binding to the allosteric domain causes a shift toward a globally more dynamic ensemble of conformations. Mapping deuterium exchange to peptides within the enzyme highlight site-specific regions with altered conformational dynamics, many of which increase in conformational flexibility. Based upon these and mutagenic studies, we propose an allosteric mechanism whereby the binding of fructose 1,6-bisphosphate destabilizes an α-helix that bridges the allosteric and active site domains within the monomeric unit. This destabilizes the β-strands within the (β/α)8-barrel domain and the linked active site loops that are responsible for substrate binding. Our data are consistent with the domain rotation model but inconsistent with the rigid body reorientation model given the increased flexibility at the interdomain interface, and we can for the first time explain how fructose 1,6-bisphosphate affects the active site. PMID:26879751

  20. Conformal Janus on Euclidean sphere

    Energy Technology Data Exchange (ETDEWEB)

    Bak, Dongsu [Physics Department, University of Seoul,Seoul 02504 (Korea, Republic of); B.W. Lee Center for Fields, Gravity & Strings, Institute for Basic Sciences,Daejeon 34047 (Korea, Republic of); Gustavsson, Andreas [School of Physics, Korea Institute for Advanced Study,Seoul 02455 (Korea, Republic of); Rey, Soo-Jong [School of Physics & Astronomy and Center for Theoretical Physics,Seoul National University,Seoul 08826 (Korea, Republic of); Center for Theoretical Physics, College of Physical Sciences, Sichuan University,Chengdu 610064 P.R. (China); B.W. Lee Center for Fields, Gravity & Strings, Institute for Basic Sciences,Daejeon 34047 (Korea, Republic of)

    2016-12-07

    We interpret Janus as an interface in a conformal field theory and study its properties. The Janus is created by an exactly marginal operator and we study its effect on the interface conformal field theory on the Janus. We do this by utilizing the AdS/CFT correspondence. We compute the interface free energy both from leading correction to the Euclidean action in the dual gravity description and from conformal perturbation theory in the conformal field theory. We find that the two results agree each other and that the interface free energy scales precisely as expected from the conformal invariance of the Janus interface.

  1. Conformal Invariance in the Long-Range Ising Model

    CERN Document Server

    Paulos, Miguel F; van Rees, Balt C; Zan, Bernardo

    2016-01-01

    We consider the question of conformal invariance of the long-range Ising model at the critical point. The continuum description is given in terms of a nonlocal field theory, and the absence of a stress tensor invalidates all of the standard arguments for the enhancement of scale invariance to conformal invariance. We however show that several correlation functions, computed to second order in the epsilon expansion, are nontrivially consistent with conformal invariance. We proceed to give a proof of conformal invariance to all orders in the epsilon expansion, based on the description of the long-range Ising model as a defect theory in an auxiliary higher-dimensional space. A detailed review of conformal invariance in the d-dimensional short-range Ising model is also included and may be of independent interest.

  2. Conformal invariance in the long-range Ising model

    Directory of Open Access Journals (Sweden)

    Miguel F. Paulos

    2016-01-01

    Full Text Available We consider the question of conformal invariance of the long-range Ising model at the critical point. The continuum description is given in terms of a nonlocal field theory, and the absence of a stress tensor invalidates all of the standard arguments for the enhancement of scale invariance to conformal invariance. We however show that several correlation functions, computed to second order in the epsilon expansion, are nontrivially consistent with conformal invariance. We proceed to give a proof of conformal invariance to all orders in the epsilon expansion, based on the description of the long-range Ising model as a defect theory in an auxiliary higher-dimensional space. A detailed review of conformal invariance in the d-dimensional short-range Ising model is also included and may be of independent interest.

  3. Conformal invariance in the long-range Ising model

    Energy Technology Data Exchange (ETDEWEB)

    Paulos, Miguel F. [CERN, Theory Group, Geneva (Switzerland); Rychkov, Slava, E-mail: slava.rychkov@lpt.ens.fr [CERN, Theory Group, Geneva (Switzerland); Laboratoire de Physique Théorique de l' École Normale Supérieure (LPTENS), Paris (France); Faculté de Physique, Université Pierre et Marie Curie (UPMC), Paris (France); Rees, Balt C. van [CERN, Theory Group, Geneva (Switzerland); Zan, Bernardo [Institute of Physics, Universiteit van Amsterdam, Amsterdam (Netherlands)

    2016-01-15

    We consider the question of conformal invariance of the long-range Ising model at the critical point. The continuum description is given in terms of a nonlocal field theory, and the absence of a stress tensor invalidates all of the standard arguments for the enhancement of scale invariance to conformal invariance. We however show that several correlation functions, computed to second order in the epsilon expansion, are nontrivially consistent with conformal invariance. We proceed to give a proof of conformal invariance to all orders in the epsilon expansion, based on the description of the long-range Ising model as a defect theory in an auxiliary higher-dimensional space. A detailed review of conformal invariance in the d-dimensional short-range Ising model is also included and may be of independent interest.

  4. Cosmological Perturbations in Conformal Gravity

    CERN Document Server

    Mannheim, Philip D

    2011-01-01

    We present the first steps needed for an analysis of the perturbations that occur in the cosmology associated with the conformal gravity theory. We discuss the implications of conformal invariance for perturbative coordinate gauge choices, and show that in the conformal theory the trace of the metric fluctuation kinematically decouples from the first-order gravitational fluctuation equations. We determine the equations that describe first-order metric fluctuations around the illustrative conformally flat de Sitter background. Via a conformal transformation we show that such fluctuations can be constructed from fluctuations around a flat background, even though the fluctuations themselves are associated with a perturbative geometry that is not itself conformal to flat. We extend the analysis to fluctuations around other cosmologically relevant backgrounds, such as the conformally-flat Robertson-Walker background, and find tensor fluctuations that grow far more rapidly than those that occur in the analogous sta...

  5. Conformance and Deviance

    DEFF Research Database (Denmark)

    Gjerdrum Pedersen, Esben Rahbek; Neergaard, Peter; Thusgaard Pedersen, Janni

    2013-01-01

    This paper analyses how large Danish companies are responding to new governmental regulation which requires them to report on corporate social responsibility (CSR). The paper is based on an analysis of 142 company annual reports required by the new Danish regulation regarding CSR reporting, plus ...... in CSR reporting practices. Finally, it is argued that non-conformance with the new regulatory requirements is not solely about conscious resistance but may also be caused by, for example, lack of awareness, resource limitations, misinterpretations, and practical difficulties....

  6. 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

  7. 14 CFR 314.3 - Conformity with subpart A of part 302.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 4 2010-01-01 2010-01-01 false Conformity with subpart A of part 302. 314.3 Section 314.3 Aeronautics and Space OFFICE OF THE SECRETARY, DEPARTMENT OF TRANSPORTATION (AVIATION PROCEEDINGS) PROCEDURAL REGULATIONS EMPLOYEE PROTECTION PROGRAM General § 314.3 Conformity with...

  8. 14 CFR 325.14 - Conformity with subpart A of part 302.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 4 2010-01-01 2010-01-01 false Conformity with subpart A of part 302. 325.14 Section 325.14 Aeronautics and Space OFFICE OF THE SECRETARY, DEPARTMENT OF TRANSPORTATION (AVIATION PROCEEDINGS) PROCEDURAL REGULATIONS ESSENTIAL AIR SERVICE PROCEDURES § 325.14 Conformity with...

  9. Noise kernels of stochastic gravity in conformally-flat spacetimes

    Science.gov (United States)

    Cho, H. T.; Hu, B. L.

    2015-03-01

    The central object in the theory of semiclassical stochastic gravity is the noise kernel, which is the symmetric two point correlation function of the stress-energy tensor. Using the corresponding Wightman functions in Minkowski, Einstein and open Einstein spaces, we construct the noise kernels of a conformally coupled scalar field in these spacetimes. From them we show that the noise kernels in conformally-flat spacetimes, including the Friedmann-Robertson-Walker universes, can be obtained in closed analytic forms by using a combination of conformal and coordinate transformations.

  10. Spectra of conformal sigma models

    Energy Technology Data Exchange (ETDEWEB)

    Tlapak, Vaclav

    2015-04-15

    In this thesis the spectra of conformal sigma models defined on (generalized) symmetric spaces are analysed. The spaces where sigma models are conformal without the addition of a Wess-Zumino term are supermanifolds, in other words spaces that include fermionic directions. After a brief review of the general construction of vertex operators and the background field expansion, we compute the diagonal terms of the one-loop anomalous dimensions of sigma models on semi-symmetric spaces. We find that the results are formally identical to the symmetric case. However, unlike for sigma models on symmetric spaces, off diagonal terms that lead to operator mixing are also present. These are not computed here. We then present a detailed analysis of the one-loop spectrum of the supersphere S{sup 3} {sup vertical} {sup stroke} {sup 2} sigma model as one of the simplest examples. The analysis illustrates the power and simplicity of the construction. We use this data to revisit a duality with the OSP(4 vertical stroke 2) Gross-Neveu model that was proposed by Candu and Saleur. With the help of a recent all-loop result for the anomalous dimension of (1)/(2)BPS operators of Gross-Neveu models, we are able to recover the entire zero-mode spectrum of the supersphere model. We also argue that the sigma model constraints and its equations of motion are implemented correctly in the Gross-Neveu model, including the one-loop data. The duality is further supported by a new all-loop result for the anomalous dimension of the ground states of the sigma model. However, higher-gradient operators cannot be completely recovered. It is possible that this discrepancy is related to a known instability of the sigma model. The instability of sigma models is due to symmetry preserving high-gradient operators that become relevant at arbitrarily small values of the coupling. This feature has been observed long ago in one-loop calculations of the O(N)-vector model and soon been realized to be a generic

  11. Tracing conformational changes in proteins

    OpenAIRE

    Haspel, Nurit; Moll, Mark; Baker, Matthew L; Chiu, Wah; Kavraki, Lydia E.

    2010-01-01

    Background Many proteins undergo extensive conformational changes as part of their functionality. Tracing these changes is important for understanding the way these proteins function. Traditional biophysics-based conformational search methods require a large number of calculations and are hard to apply to large-scale conformational motions. Results In this work we investigate the application of a robotics-inspired method, using backbone and limited side chain representation and a coarse grain...

  12. Application of head-space solid-phase microextraction coupled to comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry for the determination of multiple pesticide residues in tea samples.

    Science.gov (United States)

    Schurek, J; Portolés, T; Hajslova, J; Riddellova, K; Hernández, F

    2008-03-24

    A new method has been developed to detect 36 pesticides that may contaminate tea samples (green, black and fruit tea). The hyphenation of solid-phase microextraction in head-space mode with a comprehensive two-dimensional gas chromatography coupled with high-speed time-of-flight mass spectrometry (HS-SPME-GCxGC/TOF MS) proved to be a quick alternative to conventional GC/MS methodology which employs solvent-based extraction. The key parameters for controlling HS-SPME performance were optimized, including fiber coating type, temperature and absorption time settings and tea matrix modification by adding water. Quantification was carried out using matrix-matched calibration. The repeatability of measurements, expressed as relative standard deviation (R.S.D.), was less than 24% for all analytes. The limits of quantification ranged from 1 to 28 microgkg(-1). The optimized method was applied to analyze real life samples obtained from a retail market. Results generated by the new SPME procedure and those obtained by using a conventional one involving ethyl acetate extraction and high-performance gel permeation chromatography (HPGPC) clean up agreed with each other for positive (containing residue) samples.

  13. Conformal Fermi Coordinates

    CERN Document Server

    Dai, Liang; Schmidt, Fabian

    2015-01-01

    Fermi Normal Coordinates (FNC) are a useful frame for isolating the locally observable, physical effects of a long-wavelength spacetime perturbation. Their cosmological application, however, is hampered by the fact that they are only valid on scales much smaller than the horizon. We introduce a generalization that we call Conformal Fermi Coordinates (CFC). CFC preserve all the advantages of FNC, but in addition are valid outside the horizon. They allow us to calculate the coupling of long- and short-wavelength modes on all scales larger than the sound horizon of the cosmological fluid, starting from the epoch of inflation until today, by removing the complications of the second order Einstein equations to a large extent, and eliminating all gauge ambiguities. As an application, we present a calculation of the effect of long-wavelength tensor modes on small scale density fluctuations. We recover previous results, but clarify the physical content of the individual contributions in terms of locally measurable ef...

  14. Reflections on conformal spectra

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hyungrok; Kravchuk, Petr [Walter Burke Institute for Theoretical Physics, Caltech,Pasadena, California 91125 (United States); School of Natural Sciences, Institute for Advanced Study,Princeton, New Jersey 08540 (United States); Ooguri, Hirosi [Walter Burke Institute for Theoretical Physics, Caltech,Pasadena, California 91125 (United States); School of Natural Sciences, Institute for Advanced Study,Princeton, New Jersey 08540 (United States); Kavli Institute for the Physics and Mathematics of the Universe (WPI),University of Tokyo,Kashiwa 277-8583 (Japan)

    2016-04-29

    We use modular invariance and crossing symmetry of conformal field theory to reveal approximate reflection symmetries in the spectral decompositions of the partition function in two dimensions in the limit of large central charge and of the four-point function in any dimension in the limit of large scaling dimensions Δ{sub 0} of external operators. We use these symmetries to motivate universal upper bounds on the spectrum and the operator product expansion coefficients, which we then derive by independent techniques. Some of the bounds for four-point functions are valid for finite Δ{sub 0} as well as for large Δ{sub 0}. We discuss a similar symmetry in a large spacetime dimension limit. Finally, we comment on the analogue of the Cardy formula and sparse light spectrum condition for the four-point function.

  15. Conformal (In)Equality

    Science.gov (United States)

    Hyun, Young-Hwan; Kim, Yoonbai; Lee, Seokcheon

    2018-01-01

    The current accelerating expansion of the Universe is explained either by dark energy or by modified gravity theories. Both of them can explain exactly the same background evolution of the Universe, however this degeneracy may be broken when the observation of large scale structure formation is taken into account. Two observables are parameterized by the so-called dark energy equation of state, ω and the growth index parameter, γ. From these observed parameters, one may reconstruct the model parameters of the so-called scalar-tensor gravity theory, one of the modified gravity theories. Especially, the scalar-tensor gravity theory is described both in Jordan frame and in Einstein frame. If cosmological observations are interpreted in one frame, then all of the observables should also be interpreted in that frame. This explicitly shows conformal inequality of cosmological observables.

  16. Conformal (InEquality

    Directory of Open Access Journals (Sweden)

    Hyun Young-Hwan

    2018-01-01

    Full Text Available The current accelerating expansion of the Universe is explained either by dark energy or by modified gravity theories. Both of them can explain exactly the same background evolution of the Universe, however this degeneracy may be broken when the observation of large scale structure formation is taken into account. Two observables are parameterized by the so-called dark energy equation of state, ω and the growth index parameter, γ. From these observed parameters, one may reconstruct the model parameters of the so-called scalar-tensor gravity theory, one of the modified gravity theories. Especially, the scalar-tensor gravity theory is described both in Jordan frame and in Einstein frame. If cosmological observations are interpreted in one frame, then all of the observables should also be interpreted in that frame. This explicitly shows conformal inequality of cosmological observables.

  17. Reflections on Conformal Spectra

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    We use modular invariance and crossing symmetry of conformal field theory to reveal approximate reflection symmetries in the spectral decompositions of the partition function in two dimensions in the limit of large central charge and of the four-point function in any dimension in the limit of large scaling dimensions Δ0 of external operators. We use these symmetries to motivate universal upper bounds on the spectrum and the operator product expansion coefficients, which we then derive by independent techniques. Some of the bounds for four-point functions are valid for finite Δ0 as well as for large Δ0. We discuss a similar symmetry in a large spacetime dimension limit. Finally, we comment on the analogue of the Cardy formula and sparse light spectrum condition for the four-point function. (based on 1510.08772 with Kim & Ooguri). This seminar will be given via videolink

  18. Space space space

    CERN Document Server

    Trembach, Vera

    2014-01-01

    Space is an introduction to the mysteries of the Universe. Included are Task Cards for independent learning, Journal Word Cards for creative writing, and Hands-On Activities for reinforcing skills in Math and Language Arts. Space is a perfect introduction to further research of the Solar System.

  19. 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.

  20. Solvent Induced Conformational Kinetics (SICK)

    NARCIS (Netherlands)

    Jonkman, Leffert; Kommandeur, Jan

    1970-01-01

    Specific conformations of molecules may be induced by the solvent when a large free volume is associated with the oonformational change. The conformational energy barrier is then a property of the solvent, rather than of the molecule. Such effects are reported for several substituted

  1. Counselor Identity: Conformity or Distinction?

    Science.gov (United States)

    McLaughlin, Jerry E.; Boettcher, Kathryn

    2009-01-01

    The authors explore 3 debates in other disciplines similar to counseling's identity debate in order to learn about common themes and outcomes. Conformity, distinction, and cohesion emerged as common themes. They conclude that counselors should retain their distinctive, humanistic approach rather than conforming to the dominant, medical approach.

  2. Twisted geometries, twistors and conformal transformations

    CERN Document Server

    Långvik, Miklos

    2016-01-01

    The twisted geometries of spin network states are described by simple twistors, isomorphic to null twistors with a time-like direction singled out. The isomorphism depends on the Immirzi parameter, and reduces to the identity when the parameter goes to infinity. Using this twistorial representation we study the action of the conformal group SU(2,2) on the classical phase space of loop quantum gravity, described by twisted geometry. The generators of translations and conformal boosts do not preserve the geometric structure, whereas the dilatation generator does. It corresponds to a 1-parameter family of embeddings of T*SL(2,C) in twistor space, and its action preserves the intrinsic geometry while changing the extrinsic one - that is the boosts among polyhedra. We discuss the implication of this action from a dynamical point of view, and compare it with a discretisation of the dilatation generator of the continuum phase space, given by the Lie derivative of the group character. At leading order in the continuu...

  3. Biological insights from hydrogen exchange mass spectrometry.

    Science.gov (United States)

    Jaswal, Sheila S

    2013-06-01

    Over the past two decades, hydrogen exchange mass spectrometry (HXMS) has achieved the status of a widespread and routine approach in the structural biology toolbox. The ability of hydrogen exchange to detect a range of protein dynamics coupled with the accessibility of mass spectrometry to mixtures and large complexes at low concentrations result in an unmatched tool for investigating proteins challenging to many other structural techniques. Recent advances in methodology and data analysis are helping HXMS deliver on its potential to uncover the connection between conformation, dynamics and the biological function of proteins and complexes. This review provides a brief overview of the HXMS method and focuses on four recent reports to highlight applications that monitor structure and dynamics of proteins and complexes, track protein folding, and map the thermodynamics and kinetics of protein unfolding at equilibrium. These case studies illustrate typical data, analysis and results for each application and demonstrate a range of biological systems for which the interpretation of HXMS in terms of structure and conformational parameters provides unique insights into function. This article is part of a Special Issue entitled: Mass spectrometry in structural biology. Copyright © 2012 Elsevier B.V. All rights reserved.

  4. Imaging of conformational changes

    Energy Technology Data Exchange (ETDEWEB)

    Michl, Josef [Univ. of Colorado, Boulder, CO (United States)

    2016-03-13

    Control of intramolecular conformational change in a small number of molecules or even a single one by an application of an outside electric field defined by potentials on nearby metal or dielectric surfaces has potential applications in both 3-D and 2-D nanotechnology. Specifically, the synthesis, characterization, and understanding of designed solids with controlled built-in internal rotational motion of a dipole promises a new class of materials with intrinsic dielectric, ferroelectric, optical and optoelectronic properties not found in nature. Controlled rotational motion is of great interest due to its expected utility in phenomena as diverse as transport, current flow in molecular junctions, diffusion in microfluidic channels, and rotary motion in molecular machines. A direct time-resolved observation of the dynamics of motion on ps or ns time scale in a single molecule would be highly interesting but is also very difficult and has yet to be accomplished. Much can be learned from an easier but still challenging comparison of directly observed initial and final orientational states of a single molecule, which is the basis of this project. The project also impacts the understanding of surface-enhanced Raman spectroscopy (SERS) and single-molecule spectroscopic detection, as well as the synthesis of solid-state materials with tailored properties from designed precursors.

  5. At what chain length do unbranched alkanes prefer folded conformations?

    CERN Document Server

    Byrd, Jason N; Montgomery, John A

    2013-01-01

    Short unbranched alkanes are known to prefer linear conformations, while long unbranched alkanes are folded. It is not known with certainty at what chain length the linear conformation is no longer the global minimum. To clarify this point, we use {\\it ab initio} and density functional methods to compute the relative energies of the linear and hairpin alkane conformers for increasing chain lengths. Extensive electronic structure calculations are performed to obtain optimized geometries, harmonic frequencies and accurate single point energies for the selected alkane conformers from octane through octadecane. Benchmark CCSD(T)/cc-pVTZ single point calculations are performed for chains through tetradecane, while approximate methods are required for the longer chains up to octadecane. Using frozen natural orbitals to unambiguously truncate the virtual orbital space we are able to compute composite CCSD FNO(T) single point energies for all the chain lengths. This approximate composite method has significant comput...

  6. 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...

  7. In silico Exploration of the Conformational Universe of GPCRs.

    Science.gov (United States)

    Rodríguez-Espigares, Ismael; Kaczor, Agnieszka A; Selent, Jana

    2016-07-01

    The structural plasticity of G protein coupled receptors (GPCRs) leads to a conformational universe going from inactive to active receptor states with several intermediate states. Many of them have not been captured yet and their role for GPCR activation is not well understood. The study of this conformational space and the transition dynamics between different receptor populations is a major challenge in molecular biophysics. The rational design of effector molecules that target such receptor populations allows fine-tuning receptor signalling with higher specificity to produce drugs with safer therapeutic profiles. In this minireview, we outline highly conserved receptor regions which are considered determinant for the establishment of distinct receptor states. We then discuss in-silico approaches such as dimensionality reduction methods and Markov State Models to explore the GPCR conformational universe and exploit the obtained conformations through structure-based drug design. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Microchemical Analysis Of Space Operation Debris

    Science.gov (United States)

    Cummings, Virginia J.; Kim, Hae Soo

    1995-01-01

    Report discusses techniques used in analyzing debris relative to space shuttle operations. Debris collected from space shuttle, expendable launch vehicles, payloads carried by space shuttle, and payloads carried by expendable launch vehicles. Optical microscopy, scanning electron microscopy with energy-dispersive spectrometry, analytical electron microscopy with wavelength-dispersive spectrometry, and X-ray diffraction chosen as techniques used in examining samples of debris.

  9. Some Progress in Conformal Geometry

    Directory of Open Access Journals (Sweden)

    Sun-Yung A. Chang

    2007-12-01

    Full Text Available This is a survey paper of our current research on the theory of partial differential equations in conformal geometry. Our intention is to describe some of our current works in a rather brief and expository fashion. We are not giving a comprehensive survey on the subject and references cited here are not intended to be complete. We introduce a bubble tree structure to study the degeneration of a class of Yamabe metrics on Bach flat manifolds satisfying some global conformal bounds on compact manifolds of dimension 4. As applications, we establish a gap theorem, a finiteness theorem for diffeomorphism type for this class, and diameter bound of the $sigma_2$-metrics in a class of conformal 4-manifolds. For conformally compact Einstein metrics we introduce an eigenfunction compactification. As a consequence we obtain some topological constraints in terms of renormalized volumes.

  10. Steady states in conformal theories

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    A novel conjecture regarding the steady state behavior of conformal field theories placed between two heat baths will be presented. Some verification of the conjecture will be provided in the context of fluid dynamics and holography.

  11. Conformity Adequacy Review: Region 5

    Science.gov (United States)

    Resources are for air quality and transportation government and community leaders. Information on the conformity SIP adequacy/inadequacy of state implementation plans (SIPs) in EPA Region 5 (IL, IN, MI, OH, WI) is provided here.

  12. Analytical Aspects of Hydrogen Exchange Mass Spectrometry

    Science.gov (United States)

    Engen, John R.; Wales, Thomas E.

    2015-07-01

    This article reviews the analytical aspects of measuring hydrogen exchange by mass spectrometry (HX MS). We describe the nature of analytical selectivity in hydrogen exchange, then review the analytical tools required to accomplish fragmentation, separation, and the mass spectrometry measurements under restrictive exchange quench conditions. In contrast to analytical quantitation that relies on measurements of peak intensity or area, quantitation in HX MS depends on measuring a mass change with respect to an undeuterated or deuterated control, resulting in a value between zero and the maximum amount of deuterium that can be incorporated. Reliable quantitation is a function of experimental fidelity and to achieve high measurement reproducibility, a large number of experimental variables must be controlled during sample preparation and analysis. The method also reports on important qualitative aspects of the sample, including conformational heterogeneity and population dynamics.

  13. On conformal minimal 2-spheres in complex Grassmann manifold G ...

    Indian Academy of Sciences (India)

    They classified the minimal two-spheres immersed in CPn and proved the rigidity theorems of conformal minimal two-spheres in CPn, but some of these properties are not inherited when the ambient space is G(k, n), k ≥ 2. The pseudo- holomorphic two-spheres in G(k, n) were studied by Jiao and Peng [10], Jiao [11] and.

  14. QCD-instantons and conformal inversion symmetry

    Energy Technology Data Exchange (ETDEWEB)

    Klammer, D.

    2006-07-15

    Instantons are an essential and non-perturbative part of Quantum Chromodynamics, the theory of strong interactions. One of the most relevant quantities in the instanton calculus is the instanton-size distribution, which can be described on the one hand within the framework of instanton perturbation theory and on the other hand investigated numerically by means of lattice computations. A rapid onset of a drastic discrepancy between these respective results indicates that the underlying physics is not yet well understood. In this work we investigate the appealing possibility of a symmetry under conformal inversion of space-time leading to this deviation. The motivation being that the lattice data seem to be invariant under an inversion of the instanton size. Since the instanton solution of a given size turns into an anti-instanton solution having an inverted size under conformal inversion of space-time, we ask in a first investigation, whether this property is transferred to the quantum level. In order to introduce a new scale, which is indicated by the lattice data and corresponds to the average instanton size as inversion radius, we project the instanton calculus onto the four-dimensional surface of a five-dimensional sphere via stereographic projection. The radius of this sphere is associated with the average instanton size. The result for the instanton size-distribution projected onto the sphere agrees surprisingly well with the lattice data at qualitative level. The resulting symmetry under an inversion of the instanton size is almost perfect. (orig.)

  15. Conformational quiescence of ADAMTS-13 prevents proteolytic promiscuity.

    Science.gov (United States)

    South, K; Freitas, M O; Lane, D A

    2016-10-01

    Essentials Recently, ADAMTS-13 has been shown to undergo substrate induced conformation activation. Conformational quiescence of ADAMTS-13 may serve to prevent off-target proteolysis in plasma. Conformationally active ADAMTS-13 variants are capable of proteolysing the Aα chain of fibrinogen. This should be considered as ADAMTS-13 variants are developed as potential therapeutic agents. Click to hear Dr Zheng's presentation on structure function and cofactor-dependent regulation of ADAMTS-13 SUMMARY: Background Recent work has revealed that ADAMTS-13 circulates in a 'closed' conformation, only fully interacting with von Willebrand factor (VWF) following a conformational change. We hypothesized that this conformational quiescence also maintains the substrate specificity of ADAMTS-13 and that the 'open' conformation of the protease might facilitate proteolytic promiscuity. Objectives To identify a novel substrate for a constitutively active gain of function (GoF) ADAMTS-13 variant (R568K/F592Y/R660K/Y661F/Y665F). Methods Fibrinogen proteolysis was characterized using SDS PAGE and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Fibrin formation was monitored by turbidity measurements and fibrin structure visualized by confocal microscopy. Results ADAMTS-13 exhibits proteolytic activity against the Aα chain of human fibrinogen, but this is only manifest on its conformational activation. Accordingly, the GoF ADAMTS-13 variant and truncated variants such as MDTCS exhibit this activity. The cleavage site has been determined by LC-MS/MS to be Aα chain Lys225-Met226. Proteolysis of fibrinogen by GoF ADAMTS-13 impairs fibrin formation in plasma-based assays, alters clot structure and increases clot permeability. Although GoF ADAMTS-13 does not appear to proteolyse preformed cross-linked fibrin, its proteolytic activity against fibrinogen increases the susceptibility of fibrin to tissue-type plasminogen activator (t-PA)-induced lysis by plasmin and increases the

  16. Falsification of Mannheim's conformal gravity

    CERN Document Server

    Yoon, Youngsub

    2013-01-01

    We show that Mannheim's conformal gravity, whose potential has a term proportional to $1/r$ and another term proportional to $r$, doesn't reduce to Newtonian gravity at short distances. Therefore, despite the claim that it successfully explains galaxy rotation curves, it seems falsified by numerous Cavendish-type experiments performed at laboratories on Earth whose work haven't found any deviations from Newton's theory. Moreover, when Mannheim used his potential to fit the galaxy rotation curve, he used the Newtonian formula to calculate the effects of the term proportional to $1/r$, not the conformal gravity one. So, he lacked consistency. After all, he would not have been able to use the conformal gravity one either since it deviates so much from the Newtonian one, which the conformal gravity one should reduce to. We also give a couple of other similar reasons why Mannheim's conformal gravity is wrong. For example, the gravitational potential of conformal gravity doesn't reduce to the Newtonian one even in ...

  17. Absorption Mode FTICR Mass Spectrometry Imaging

    NARCIS (Netherlands)

    Smith, D.F.; Kilgour, D.P.A.; Konijnenburg, M.; O'Connor, P.B.; Heeren, R.M.A.|info:eu-repo/dai/nl/105188476

    2013-01-01

    Fourier transform ion cyclotron resonance mass spectrometry offers the highest mass resolving power for molecular imaging experiments. This high mass resolving power ensures that closely spaced peaks at the same nominal mass are resolved for proper image generation. Typically higher magnetic fields

  18. Conformational analysis of retinoids and restriction of their dynamics by retinoid-binding proteins

    NARCIS (Netherlands)

    vanAalten, DMF; deGroot, BL; Berendsen, HJC; Findlay, JBC

    1996-01-01

    An exhaustive sampling of the configurational space of all-trans retinol using a 0.1 mu s molecular-dynamics simulation is presented. The essential dynamics technique is used to describe the conformational changes in retinol using only three degrees of freedom, The different conformational states of

  19. Conformational analysis for some nonclassical antagonists of histamine H3 receptor

    Science.gov (United States)

    Borota, Ana; Mracec, Maria; Rad, Ramona; Ostopovici, Liliana; Mracec, Mircea

    A conformational search in vacuum for a series of 1,3-substituted pyrrolidine derivatives has been performed using the AMBER, AM1, PM3, and MNDO methods. Conformational analysis of the pyrrolidine ligands suggests that these compounds could have many conformers that populate the low-energy minima on the potential energy surface (PES). The conformational space occupied by the ligands is large and, in vacuum, the rotation barriers of different flexible bonds have energies between 0.5 and thousands of kcal/mol. By optimization, most conformers have energy barriers of 0-5 kcal/mol; thus, they could interconvert easily to obtain better interactions in the receptor active site. Optimized conformers having energy barriers of >5 kcal/mol display bad geometries with very large bond lengths and deformed rings. Shapes and heights of rotation barriers obtained through COSMO-AM1 single-point calculations in water are similar to those obtained from single-point calculations in vacuum. However, in water the energy barriers are lower, allowing most conformers to convert in other low-energy conformers. The best conformers in vacuum and in water are different: the gas phase best conformer has a helical shape, while the best conformer in water has an extended shape.

  20. Increased conformity offers diminishing returns for reducing total knee replacement wear.

    Science.gov (United States)

    Fregly, Benjamin J; Marquez-Barrientos, Carlos; Banks, Scott A; DesJardins, John D

    2010-02-01

    Wear remains a significant problem limiting the lifespan of total knee replacements (TKRs). Though increased conformity between TKR components has the potential to decrease wear, the optimal amount and planes of conformity have not been investigated. Furthermore, differing conformities in the medial and lateral compartments may provide designers the opportunity to address both wear and kinematic design goals simultaneously. This study used a computational model of a Stanmore knee simulator machine and a previously validated wear model to investigate this issue for simulated gait. TKR geometries with different amounts and planes of conformity on the medial and lateral sides were created and tested in two phases. The first phase utilized a wide range of sagittal and coronal conformity combinations to blanket a physically realistic design space. The second phase performed a focused investigation of the conformity conditions from the first phase to which predicted wear volume was sensitive. For the first phase, sagittal but not coronal conformity was found to have a significant effect on predicted wear volume. For the second phase, increased sagittal conformity was found to decrease predicted wear volume in a nonlinear fashion, with reductions gradually diminishing as conformity increased. These results suggest that TKR geometric design efforts aimed at minimizing wear should focus on sagittal rather than coronal conformity and that at least moderate sagittal conformity is desirable in both compartments.

  1. CONFORMANCE IMPROVEMENT USING GELS

    Energy Technology Data Exchange (ETDEWEB)

    Randall S. Seright

    2003-09-01

    This report describes work performed during the second year of the project, ''Conformance Improvement Using Gels.'' The project has two objectives. The first objective is to identify gel compositions and conditions that substantially reduce flow through fractures that allow direct channeling between wells, while leaving secondary fractures open so that high fluid injection and production rates can be maintained. The second objective is to optimize treatments in fractured production wells, where the gel must reduce permeability to water much more than that to oil. Pore-level images from X-ray computed microtomography were re-examined for Berea sandstone and porous polyethylene. This analysis suggests that oil penetration through gel-filled pores occurs by a gel-dehydration mechanism, rather than a gel-ripping mechanism. This finding helps to explain why aqueous gels can reduce permeability to water more than to oil. We analyzed a Cr(III)-acetate-HPAM gel treatment in a production well in the Arbuckle formation. The availability of accurate pressure data before, during, and after the treatment was critical for the analysis. After the gel treatment, water productivity was fairly constant at about 20% of the pre-treatment value. However, oil productivity was stimulated by a factor of 18 immediately after the treatment. During the six months after the treatment, oil productivity gradually decreased to approach the pre-treatment value. To explain this behavior, we proposed that the fracture area open to oil flow was increased substantially by the gel treatment, followed by a gradual closing of the fractures during subsequent production. For a conventional Cr(III)-acetate-HPAM gel, the delay between gelant preparation and injection into a fracture impacts the placement, leakoff, and permeability reduction behavior. Formulations placed as partially formed gels showed relatively low pressure gradients during placement, and yet substantially reduced the

  2. CONFORMANCE IMPROVEMENT USING GELS

    Energy Technology Data Exchange (ETDEWEB)

    Randall S. Seright

    2004-09-30

    This report describes work performed during the third and final year of the project, ''Conformance Improvement Using Gels.'' Corefloods revealed throughput dependencies of permeability reduction by polymers and gels that were much more prolonged during oil flow than water flow. This behavior was explained using simple mobility ratio arguments. A model was developed that quantitatively fits the results and predicts ''clean up'' times for oil productivity when production wells are returned to service after application of a polymer or gel treatment. X-ray computed microtomography studies of gels in strongly water-wet Berea sandstone and strongly oil-wet porous polyethylene suggested that oil penetration through gel-filled pores occurs by a gel-dehydration mechanism, rather than gel-ripping or gel-displacement mechanisms. In contrast, analysis of data from the University of Kansas suggests that the gel-ripping or displacement mechanisms are more important in more permeable, strongly water-wet sandpacks. These findings help to explain why aqueous gels can reduce permeability to water more than to oil under different conditions. Since cement is the most commonly used material for water shutoff, we considered when gels are preferred over cements. Our analysis and experimental results indicated that cement cannot be expected to completely fill (top to bottom) a vertical fracture of any width, except near the wellbore. For vertical fractures with apertures less than 4 mm, the cement slurry will simply not penetrate very far into the fracture. For vertical fractures with apertures greater than 4 mm, the slurry may penetrate a substantial distance into the bottom part of the fracture. However, except near the wellbore, the upper part of the fracture will remain open due to gravity segregation. We compared various approaches to plugging fractures using gels, including (1) varying polymer content, (2) varying placement (extrusion) rate

  3. Tomographic patient registration and conformal avoidance tomotherapy

    Science.gov (United States)

    Aldridge, Jennifer Stacy

    Development of tomotherapy has led to the emergence of several processes, providing the basis for many unique investigative opportunities. These processes include setup verification, tomographic verification, megavoltage dose reconstruction, and conformal avoidance tomotherapy. Setup verification and conformal avoidance tomotherapy, in particular, are two closely intertwined matters. In order to avoid critical structures located within or adjacent to indistinct tumor regions, accurate patient positioning from fraction to fraction must be ensured. With tomographic patient registration, a higher level of assurance is offered than with traditional positioning methods. Translational and rotational offsets are calculated directly from projection data using cross- correlation or fast Fourier transforms. Experiments assessing the algorithm's ability to calculate individual offsets were conducted using the University of Wisconsin's Tomotherapy Benchtop. These experiments indicate statistical errors within +/-1 mm for offsets up to approximately 20 mm, with maximum offset errors of about +/-2 mm for displacements up to 35 mm. The angular offset component is within +/-2°. To evaluate the registration process as a whole, experimental results from a few multi-parameter examples are also analyzed. With the development of tomographic patient registration in projection space, efforts to promote further sparing of critical structures are justified. Conformal avoidance tomotherapy has as its objective to treat an indistinct tumor region while conformally avoiding any normal critical structures in that region. To demonstrate the advantages of conformal avoidance tomotherapy, conventional and tomotherapy treatments are contrasted for both nasopharyngeal and breast carcinoma cases. For initial research efforts, computed tomography data sets of a human male and female were obtained via the ``Visible Human Project''. Since these data sets are on the order of hundreds of megabytes, both

  4. To conform or not to conform: spontaneous conformity diminishes the sensitivity to monetary outcomes.

    Science.gov (United States)

    Yu, Rongjun; Sun, Sai

    2013-01-01

    When people have different opinions in a group, they often adjust their own attitudes and behaviors to match the group opinion, known as social conformity. The affiliation account of normative conformity states that people conform to norms in order to 'fit in', whereas the accuracy account of informative conformity posits that the motive to learn from others produces herding. Here, we test another possibility that following the crowd reduces the experienced negative emotion when the group decision turns out to be a bad one. Using event related potential (ERP) combined with a novel group gambling task, we found that participants were more likely to choose the option that was predominately chosen by other players in previous trials, although there was little explicit normative pressure at the decision stage and group choices were not informative. When individuals' choices were different from others, the feedback related negativity (FRN), an ERP component sensitive to losses and errors, was enhanced, suggesting that being independent is aversive. At the outcome stage, the losses minus wins FRN effect was significantly reduced following conformity choices than following independent choices. Analyses of the P300 revealed similar patterns both in the response and outcome period. Our study suggests that social conformity serves as an emotional buffer that protects individuals from experiencing strong negative emotion when the outcomes are bad.

  5. To conform or not to conform: spontaneous conformity diminishes the sensitivity to monetary outcomes.

    Directory of Open Access Journals (Sweden)

    Rongjun Yu

    Full Text Available When people have different opinions in a group, they often adjust their own attitudes and behaviors to match the group opinion, known as social conformity. The affiliation account of normative conformity states that people conform to norms in order to 'fit in', whereas the accuracy account of informative conformity posits that the motive to learn from others produces herding. Here, we test another possibility that following the crowd reduces the experienced negative emotion when the group decision turns out to be a bad one. Using event related potential (ERP combined with a novel group gambling task, we found that participants were more likely to choose the option that was predominately chosen by other players in previous trials, although there was little explicit normative pressure at the decision stage and group choices were not informative. When individuals' choices were different from others, the feedback related negativity (FRN, an ERP component sensitive to losses and errors, was enhanced, suggesting that being independent is aversive. At the outcome stage, the losses minus wins FRN effect was significantly reduced following conformity choices than following independent choices. Analyses of the P300 revealed similar patterns both in the response and outcome period. Our study suggests that social conformity serves as an emotional buffer that protects individuals from experiencing strong negative emotion when the outcomes are bad.

  6. Galactic conformity measured in semi-analytic models

    Science.gov (United States)

    Lacerna, I.; Contreras, S.; González, R. E.; Padilla, N.; Gonzalez-Perez, V.

    2018-03-01

    We study the correlation between the specific star formation rate of central galaxies and neighbour galaxies, also known as `galactic conformity', out to 20 h^{-1} {Mpc} using three semi-analytic models (SAMs, one from L-GALAXIES and other two from GALFORM). The aim is to establish whether SAMs are able to show galactic conformity using different models and selection criteria. In all the models, when the selection of primary galaxies is based on an isolation criterion in real space, the mean fraction of quenched (Q) galaxies around Q primary galaxies is higher than that around star-forming primary galaxies of the same stellar mass. The overall signal of conformity decreases when we remove satellites selected as primary galaxies, but the effect is much stronger in GALFORM models compared with the L-GALAXIES model. We find this difference is partially explained by the fact that in GALFORM once a galaxy becomes a satellite remains as such, whereas satellites can become centrals at a later time in L-GALAXIES. The signal of conformity decreases down to 60 per cent in the L-GALAXIES model after removing central galaxies that were ejected from their host halo in the past. Galactic conformity is also influenced by primary galaxies at fixed stellar mass that reside in dark matter haloes of different masses. Finally, we explore a proxy of conformity between distinct haloes. In this case, the conformity is weak beyond ˜3 h^{-1} {Mpc} (conformity is directly related with a long-range effect.

  7. Conformal Window and Correlation Functions in Lattice Conformal QCD

    CERN Document Server

    Iwasaki, Y

    2012-01-01

    We discuss various aspects of Conformal Field Theories on the Lattice. We investigate the SU(3) gauge theory with Nf fermions in the fundamental representation. First we make a brief review of our previous works on the phase structure of lattice gauge theories in terms of the gauge coupling constant and the quark mass. We thereby clarify the reason why we conjecture that the conformal window is 7 = 1 exhibit the characteristics of the conformal function with IR cutoff, an exponential damping with power correction. Investigating our numerical data by a new method, the "micro-analysis" of propagators, we observe that our data are consistent with the picture that the Nf=7 case and the Nf=2 at T ~ 2Tc case are close to the meson unparticle model. On the other hand, the Nf=16 case and the Nf=2 at T= 10^2 ~10^5 Tc cases are close to the fermion unparticle model.

  8. 40 CFR 93.154 - Conformity analysis.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Conformity analysis. 93.154 Section 93...) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR FEDERAL IMPLEMENTATION PLANS Determining Conformity of General Federal Actions to State or Federal Implementation Plans § 93.154 Conformity analysis. Any Federal...

  9. Logarithmic conformal field theory: beyond an introduction

    Science.gov (United States)

    Creutzig, Thomas; Ridout, David

    2013-12-01

    of the underlying chiral algebra and the modular data pertaining to the characters of the representations. Each of the archetypal logarithmic conformal field theories is studied here by first determining its irreducible spectrum, which turns out to be continuous, as well as a selection of natural reducible, but indecomposable, modules. This is followed by a detailed description of how to obtain character formulae for each irreducible, a derivation of the action of the modular group on the characters, and an application of the Verlinde formula to compute the Grothendieck fusion rules. In each case, the (genuine) fusion rules are known, so comparisons can be made and favourable conclusions drawn. In addition, each example admits an infinite set of simple currents, hence extended symmetry algebras may be constructed and a series of bulk modular invariants computed. The spectrum of such an extended theory is typically discrete and this is how the triplet model \\mathfrak {W} (1,2) arises, for example. Moreover, simple current technology admits a derivation of the extended algebra fusion rules from those of its continuous parent theory. Finally, each example is concluded by a brief description of the computation of some bulk correlators, a discussion of the structure of the bulk state space, and remarks concerning more advanced developments and generalizations. The final part gives a very short account of the theory of staggered modules, the (simplest class of) representations that are responsible for the logarithmic singularities that distinguish logarithmic theories from their rational cousins. These modules are discussed in a generality suitable to encompass all the examples met in this review and some of the very basic structure theory is proven. Then, the important quantities known as logarithmic couplings are reviewed for Virasoro staggered modules and their role as fundamentally important parameters, akin to the three-point constants of rational conformal field

  10. Conformal geometry and quasiregular mappings

    CERN Document Server

    Vuorinen, Matti

    1988-01-01

    This book is an introduction to the theory of spatial quasiregular mappings intended for the uninitiated reader. At the same time the book also addresses specialists in classical analysis and, in particular, geometric function theory. The text leads the reader to the frontier of current research and covers some most recent developments in the subject, previously scatterd through the literature. A major role in this monograph is played by certain conformal invariants which are solutions of extremal problems related to extremal lengths of curve families. These invariants are then applied to prove sharp distortion theorems for quasiregular mappings. One of these extremal problems of conformal geometry generalizes a classical two-dimensional problem of O. Teichmüller. The novel feature of the exposition is the way in which conformal invariants are applied and the sharp results obtained should be of considerable interest even in the two-dimensional particular case. This book combines the features of a textbook an...

  11. Logarithmic exotic conformal Galilean algebras

    Energy Technology Data Exchange (ETDEWEB)

    Henkel, Malte, E-mail: Malte.henkel@univ-lorraine.fr [Groupe de Physique Statistique, Institut Jean Lamour (CNRS UMR 7198), Université de Lorraine Nancy, B.P. 70239, F-54506 Vandoeuvre-lès-Nancy Cedex (France); Hosseiny, Ali, E-mail: al_hosseiny@sbu.ac.ir [Department of Physics, Shahid Beheshti University, G.C. Evin, Tehran 19839 (Iran, Islamic Republic of); School of Particles and Accelerators, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran (Iran, Islamic Republic of); Rouhani, Shahin, E-mail: rouhani@ipm.ir [Department of Physics, Sharif University of Technology, P.O. Box 11165-9161, Tehran (Iran, Islamic Republic of); School of Particles and Accelerators, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran (Iran, Islamic Republic of)

    2014-02-15

    Logarithmic representations of the conformal Galilean algebra (CGA) and the Exotic Conformal Galilean algebra (ECGA) are constructed. This can be achieved by non-decomposable representations of the scaling dimensions or the rapidity indices, specific to conformal Galilean algebras. Logarithmic representations of the non-exotic CGA lead to the expected constraints on scaling dimensions and rapidities and also on the logarithmic contributions in the co-variant two-point functions. On the other hand, the ECGA admits several distinct situations which are distinguished by different sets of constraints and distinct scaling forms of the two-point functions. Two distinct realisations for the spatial rotations are identified as well. This is the first concrete example of a reducible, but non-decomposable representation, without logarithmic terms. Such cases had been anticipated before.

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

    Science.gov (United States)

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

    2013-10-28

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

  13. Social influence: compliance and conformity.

    Science.gov (United States)

    Cialdini, Robert B; Goldstein, Noah J

    2004-01-01

    This review covers recent developments in the social influence literature, focusing primarily on compliance and conformity research published between 1997 and 2002. The principles and processes underlying a target's susceptibility to outside influences are considered in light of three goals fundamental to rewarding human functioning. Specifically, targets are motivated to form accurate perceptions of reality and react accordingly, to develop and preserve meaningful social relationships, and to maintain a favorable self-concept. Consistent with the current movement in compliance and conformity research, this review emphasizes the ways in which these goals interact with external forces to engender social influence processes that are subtle, indirect, and outside of awareness.

  14. Epigenetic dominance of prion conformers.

    Directory of Open Access Journals (Sweden)

    Eri Saijo

    2013-10-01

    Full Text Available Although they share certain biological properties with nucleic acid based infectious agents, prions, the causative agents of invariably fatal, transmissible neurodegenerative disorders such as bovine spongiform encephalopathy, sheep scrapie, and human Creutzfeldt Jakob disease, propagate by conformational templating of host encoded proteins. Once thought to be unique to these diseases, this mechanism is now recognized as a ubiquitous means of information transfer in biological systems, including other protein misfolding disorders such as those causing Alzheimer's and Parkinson's diseases. To address the poorly understood mechanism by which host prion protein (PrP primary structures interact with distinct prion conformations to influence pathogenesis, we produced transgenic (Tg mice expressing different sheep scrapie susceptibility alleles, varying only at a single amino acid at PrP residue 136. Tg mice expressing ovine PrP with alanine (A at (OvPrP-A136 infected with SSBP/1 scrapie prions propagated a relatively stable (S prion conformation, which accumulated as punctate aggregates in the brain, and produced prolonged incubation times. In contrast, Tg mice expressing OvPrP with valine (V at 136 (OvPrP-V136 infected with the same prions developed disease rapidly, and the converted prion was comprised of an unstable (U, diffusely distributed conformer. Infected Tg mice co-expressing both alleles manifested properties consistent with the U conformer, suggesting a dominant effect resulting from exclusive conversion of OvPrP-V136 but not OvPrP-A136. Surprisingly, however, studies with monoclonal antibody (mAb PRC5, which discriminates OvPrP-A136 from OvPrP-V136, revealed substantial conversion of OvPrP-A136. Moreover, the resulting OvPrP-A136 prion acquired the characteristics of the U conformer. These results, substantiated by in vitro analyses, indicated that co-expression of OvPrP-V136 altered the conversion potential of OvPrP-A136 from the S to

  15. Plan-graph Based Heuristics for Conformant Probabilistic Planning

    Science.gov (United States)

    Ramakrishnan, Salesh; Pollack, Martha E.; Smith, David E.

    2004-01-01

    In this paper, we introduce plan-graph based heuristics to solve a variation of the conformant probabilistic planning (CPP) problem. In many real-world problems, it is the case that the sensors are unreliable or take too many resources to provide knowledge about the environment. These domains are better modeled as conformant planning problems. POMDP based techniques are currently the most successful approach for solving CPP but have the limitation of state- space explosion. Recent advances in deterministic and conformant planning have shown that plan-graphs can be used to enhance the performance significantly. We show that this enhancement can also be translated to CPP. We describe our process for developing the plan-graph heuristics and estimating the probability of a partial plan. We compare the performance of our planner PVHPOP when used with different heuristics. We also perform a comparison with a POMDP solver to show over a order of magnitude improvement in performance.

  16. Two-dimensional Minkowski causal automorphisms and conformal maps

    Science.gov (United States)

    Burgos, Juan Manuel

    2013-02-01

    Treating the two-dimensional Minkowski space as a Wick rotated version of the complex plane, we characterize the causal automorphisms in the two-dimensional Minkowski space as the Märzke-Wheeler maps of a certain class of observers. We also characterize the differentiable causal automorphisms of this space as the Minkowski conformal maps whose restriction to the time axis belongs to the class of observers mentioned above. We answer a recently raised question about whether causal automorphisms are characterized by their wave equation. As another application of the theory, we give a proper time formula for accelerated observers which solves the twin paradox in two-dimensional Minkowski spacetime.

  17. Conformal field theory between supersymmetry and indecomposable structures

    Energy Technology Data Exchange (ETDEWEB)

    Eberle, H.

    2006-07-15

    This thesis considers conformal field theory in its supersymmetric extension as well as in its relaxation to logarithmic conformal field theory. This thesis is concerned with the subspace of K3 compactifications which is not well known yet. In particular, we inspect the intersection point of the Z{sub 2} and Z{sub 4} orbifold subvarieties within the K3 moduli space, explicitly identify the two corresponding points on the subvarieties geometrically, and give an explicit isomorphism of the three conformal field theory models located at that point, a specific Z{sub 2} and Z{sub 4} orbifold model as well as the Gepner model (2){sup 4}. We also prove the orthogonality of the two subvarieties at the intersection point. This is the starting point for the programme to investigate generic points in K3 moduli space. We use the coordinate identification at the intersection point in order to relate the coordinates of both subvarieties and to explicitly calculate a geometric geodesic between the two subvarieties as well as its generator. A generic point in K3 moduli space can be reached by such a geodesic originating at a known model. We also present advances on the conformal field theoretic side of deformations along such a geodesic using conformal deformation theory. Moreover, we regard a relaxation of conformal field theory to logarithmic conformal field theory. In particular, we study general augmented c{sub p,q} minimal models which generalise the well-known (augmented) c{sub p,1} model series. We calculate logarithmic nullvectors in both types of models. But most importantly, we investigate the low lying Virasoro representation content and fusion algebra of two general augmented c{sub p,q} models, the augmented c{sub 2,3}=0 model as well as the augmented Yang-Lee model at c{sub 2,5}=-22/5. In particular, the true vacuum representation is rather given by a rank 1 indecomposable but not irreducible subrepresentation of a rank 2 representation. We generalise these generic

  18. Conformal coating value/risk assessment for Sandia satellite programs.

    Energy Technology Data Exchange (ETDEWEB)

    Russick, Edward Mark; Thayer, Gayle Echo

    2008-03-01

    Conformal coatings are used in space applications on printed circuit board (PCB) assemblies primarily as a protective barrier against environmental contaminants. Such coatings have been used at Sandia for decades in satellite applications including the GPS satellite program. Recently, the value of conformal coating has been questioned because it is time consuming (requiring a 5-6 week schedule allowance) and delays due to difficulty of repairs and rework performed afterward are troublesome. In an effort to find opportunities where assembly time can be reduced, a review of the literature as well as discussions with satellite engineers both within and external to Sandia regarding the value of conformal coating was performed. Several sources on the value of conformal coating, the functions it performs, and on whether coatings are necessary and should be used at all were found, though nearly all were based on anecdotal information. The first section of this report, titled 'Conformal Coating for Space Applications', summarizes the results of an initial risk-value assessment of the conformal coating process for Sandia satellite programs based on information gathered. In the process of collecting information to perform the assessment, it was necessary to obtain a comprehensive understanding of the entire satellite box assembly process. A production time-line was constructed and is presented in the second section of this report, titled 'Satellite Box Assembly', specifically to identify potential sources of time delays, manufacturing issues, and component failures related to the conformal coating process in relation to the box assembly. The time-line also allows for identification of production issues that were anecdotally attributed to the conformal coating but actually were associated with other production steps in the box assembly process. It was constructed largely in consultation with GPS program engineers with empirical knowledge of times required

  19. Youth Conformity Regarding Institutions and Media

    Directory of Open Access Journals (Sweden)

    Nikolay Ivantchev

    2012-10-01

    Full Text Available An experiment on conformity was carried out. The participants were 95 youths. The scale “Conformity – Autonomy” from I. Karagiozov’s questionnaire for locus of control (1998 was also used. The results indicated the prevalence of youth conformity regarding institutions and media. The different types of conformity were related to each other. The subjects’ gender and the experimentators’ gender mediated the connections between the both types of conformity. The female youths conformed more with institutions than the male youths, but there were not any significant gender differences in their conform behavior regarding media (magazines. More male youths conformed for the magazines when the experimentator was a woman. More female youths conformed for the magazines when the experimentator was a man.

  20. Fast, clash-free RNA conformational morphing using molecular junctions.

    Science.gov (United States)

    Héliou, Amélie; Budday, Dominik; Fonseca, Rasmus; van den Bedem, Henry

    2017-07-15

    Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. Despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groups of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation. The source code, binaries and data are available at https://simtk.org/home/kgs . amelie.heliou@polytechnique.edu or vdbedem@stanford.edu. Supplementary data are available at Bioinformatics online.

  1. 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.

  2. Conformation analysis of oligomeric flavanoids

    Science.gov (United States)

    Jan P. Steynberg; E. Vincent Brandt; Daneel Ferreira; Carin A. Helfer; Wayne L. Mattice; Dominika Gornik; Richard W. Hemingway

    1995-01-01

    The profisetinidins are the most important polyflavanoids of commerce, making up the major constituents of wattle and quebracho tannins. Within the dimeric profisetinidins, substantial complexity exists because of stereo-, regio, rotational and conformational isomers. Definition of the stereochemistry of the upper and lower flavan units, the location of the...

  3. Conformal symmetry and holographic cosmology

    NARCIS (Netherlands)

    Bzowski, A.W.

    2013-01-01

    This thesis presents a novel approach to cosmology using gauge/gravity duality. Analysis of the implications of conformal invariance in field theories leads to quantitative cosmological predictions which are in agreement with current data. Furthermore, holographic cosmology extends the theory of

  4. Free fructose is conformationally locked.

    Science.gov (United States)

    Cocinero, Emilio J; Lesarri, Alberto; Écija, Patricia; Cimas, Álvaro; Davis, Benjamin G; Basterretxea, Francisco J; Fernández, José A; Castaño, Fernando

    2013-02-20

    Fructose has been examined under isolation conditions using a combination of UV ultrafast laser vaporization and Fourier-transform microwave (FT-MW) spectroscopy. The rotational spectra for the parent, all (six) monosubstituted (13)C species, and two single D species reveal unambiguously that the free hexoketose is conformationally locked in a single dominant β-pyranose structure. This six-membered-chair skeleton adopts a (2)C(5) configuration (equivalent to (1)C(4) in aldoses). The free-molecule structure sharply contrasts with the furanose form observed in biochemically relevant polysaccharides, like sucrose. The structure of free fructose has been determined experimentally using substitution and effective structures. The enhanced stability of the observed conformation is primarily attributed to a cooperative network of five intramolecular O-H···O hydrogen bonds and stabilization of both endo and exo anomeric effects. Breaking a single intramolecular hydrogen bond destabilizes the free molecule by more than 10 kJ mol(-1). The structural results are compared to ribose, recently examined with rotational resolution, where six different conformations coexist with similar conformational energies. In addition, several DFT and ab initio methods and basis sets are benchmarked with the experimental data.

  5. Exceptional and Spinorial Conformal Windows

    DEFF Research Database (Denmark)

    Mojaza, Matin; Pica, Claudio; Ryttov, Thomas

    2012-01-01

    We study the conformal window of gauge theories containing fermionic matter fields, where the gauge group is any of the exceptional groups with the fermions transforming according to the fundamental and adjoint representations and the orthogonal groups where the fermions transform according...

  6. Anomalous Dimensions of Conformal Baryons

    DEFF Research Database (Denmark)

    Pica, Claudio; Sannino, Francesco

    2016-01-01

    We determine the anomalous dimensions of baryon operators for the three color theory as function of the number of massless flavours within the conformal window to the maximum known order in perturbation theory. We show that the anomalous dimension of the baryon is controllably small, within...

  7. Analyticity in spin in conformal theories

    Science.gov (United States)

    Caron-Huot, Simon

    2017-09-01

    Conformal theory correlators are characterized by the spectrum and three-point functions of local operators. We present a formula which extracts this data as an analytic function of spin. In analogy with a classic formula due to Froissart and Gribov, it is sensitive only to an "imaginary part" which appears after analytic continuation to Lorentzian signature, and it converges thanks to recent bounds on the high-energy Regge limit. At large spin, substituting in cross-channel data, the formula yields 1 /J expansions with controlled errors. In large- N theories, the imaginary part is saturated by single-trace operators. For a sparse spectrum, it manifests the suppression of bulk higher-derivative interactions that constitutes the signature of a local gravity dual in Anti-de-Sitter space.

  8. Molecular Imaging Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Kovac, S.

    2009-05-01

    Full Text Available Molecular imaging mass spectrometry (IMS is a recently developed method for direct determination of spatial distribution of biopolymers, preferably proteins on cell surface and tissues. Imaging mass spectrometry data are mainly based on Matrix-Assisted Laser Desorption/Ionization- Time of Flight (MALDI TOF. The MALDI TOF based imaging mass spectrometry was applied for determination of changes in kidney tissue of sensitive mice after poisoning with aristolochic acid I. The second application presented here were changes in the gastric tissue in mice after infection with Helicobacter pylori, as a model of gastric cancer in humans caused by this pathogen microorganism. Molecular imaging mass spectrometry can be applied in medicine, mostly for identification of candidate biomarkers for malignant and non-malignant diseases. Furthermore, imaging MS has almost unlimited capacity in agriculture, food technology and biotechnology, e. g. for monitoring, process development and quality control of manufactured tissue of animal, plant and microbial origin.

  9. Ion mobility spectrometry

    CERN Document Server

    Eiceman, GA

    2005-01-01

    Key Developments for Faster, More Precise Detection Capabilities Driven by the demand for the rapid and advanced detection of explosives, chemical and biological warfare agents, and narcotics, ion mobility spectrometry (IMS) undergone significant refinements in technology, computational capabilities, and understanding of the principles of gas phase ion chemistry and mobility. Beginning with a thorough discussion of the fundamental theories and physics of ion mobility, Ion Mobility Spectrometry, Second Edition describes the recent advances in instrumentation and newly

  10. Probing fibronectin conformation on a protein corona layer around nanoparticles.

    Science.gov (United States)

    Raoufi, Mohammad; Hajipour, Mohammad Javad; Kamali Shahri, Seyed Mehdi; Schoen, Ingmar; Linn, Uwe; Mahmoudi, Morteza

    2018-01-18

    Protein unfolding induced by nanoparticles (NPs) can lead to exposure of cryptic epitopes that might dictate biological identity and affect NP biological fate (e.g., blood circulation time, biodistribution, and tumor accumulation). Here, we monitor the conformation of fluorescence resonance energy transfer (FRET)-labelled fibronectin (FN) on corona-coated gold NPs. We found that the labelled FN proteins, which directly accessed the gold NP surface, underwent more pronounced conformational changes than those associated with the protein corona via protein-protein interactions. FRET and liquid chromatography-mass spectrometry analyses demonstrated that NP size/concentration, pH change, and the level of surface coverage by the corona can tune the accessibility of labelled FN to the gold NP surface. Although some subsequently adsorbing proteins accessed the NP surface thanks to incomplete surface coverage and protein exchange (the Vroman effect), most outer-layer proteins could not directly bind to the NP surface, blocked by pre-adsorbed corona layers. This finding was also partially confirmed by isothermal titration calorimetry (ITC) analysis. These results suggest the proof-of-concept that outermost-layer proteins with modestly changed conformation rather than unfolded proteins at the gold NP surface effectively create the NPs' biological identity, which might have important implications on biological fates of gold NPs.

  11. 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.

  12. Gel dosimetry for conformal radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Gambarini, G. [Department of Physics of the University and INFN, Milan (Italy)]. e-mail: grazia.gambarini@mi.infn.it

    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)

  13. 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.

  14. 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.

  15. Objective interpretation as conforming interpretation

    Directory of Open Access Journals (Sweden)

    Lidka Rodak

    2011-12-01

    Full Text Available The practical discourse willingly uses the formula of “objective interpretation”, with no regards to its controversial nature that has been discussed in literature.The main aim of the article is to investigate what “objective interpretation” could mean and how it could be understood in the practical discourse, focusing on the understanding offered by judicature.The thesis of the article is that objective interpretation, as identified with textualists’ position, is not possible to uphold, and should be rather linked with conforming interpretation. And what this actually implies is that it is not the virtue of certainty and predictability – which are usually associated with objectivity- but coherence that makes the foundation of applicability of objectivity in law.What could be observed from the analyses, is that both the phenomenon of conforming interpretation and objective interpretation play the role of arguments in the interpretive discourse, arguments that provide justification that interpretation is not arbitrary or subjective. With regards to the important part of the ideology of legal application which is the conviction that decisions should be taken on the basis of law in order to exclude arbitrariness, objective interpretation could be read as a question “what kind of authority “supports” certain interpretation”? that is almost never free of judicial creativity and judicial activism.One can say that, objective and conforming interpretation are just another arguments used in legal discourse.

  16. Electrophysiological precursors of social conformity.

    Science.gov (United States)

    Shestakova, Anna; Rieskamp, Jörg; Tugin, Sergey; Ossadtchi, Alexey; Krutitskaya, Janina; Klucharev, Vasily

    2013-10-01

    Humans often change their beliefs or behavior due to the behavior or opinions of others. This study explored, with the use of human event-related potentials (ERPs), whether social conformity is based on a general performance-monitoring mechanism. We tested the hypothesis that conflicts with a normative group opinion evoke a feedback-related negativity (FRN) often associated with performance monitoring and subsequent adjustment of behavior. The experimental results show that individual judgments of facial attractiveness were adjusted in line with a normative group opinion. A mismatch between individual and group opinions triggered a frontocentral negative deflection with the maximum at 200 ms, similar to FRN. Overall, a conflict with a normative group opinion triggered a cascade of neuronal responses: from an earlier FRN response reflecting a conflict with the normative opinion to a later ERP component (peaking at 380 ms) reflecting a conforming behavioral adjustment. These results add to the growing literature on neuronal mechanisms of social influence by disentangling the conflict-monitoring signal in response to the perceived violation of social norms and the neural signal of a conforming behavioral adjustment.

  17. Electrophysiological precursors of social conformity

    Science.gov (United States)

    Rieskamp, Jörg; Tugin, Sergey; Ossadtchi, Alexey; Krutitskaya, Janina; Klucharev, Vasily

    2013-01-01

    Humans often change their beliefs or behavior due to the behavior or opinions of others. This study explored, with the use of human event-related potentials (ERPs), whether social conformity is based on a general performance-monitoring mechanism. We tested the hypothesis that conflicts with a normative group opinion evoke a feedback-related negativity (FRN) often associated with performance monitoring and subsequent adjustment of behavior. The experimental results show that individual judgments of facial attractiveness were adjusted in line with a normative group opinion. A mismatch between individual and group opinions triggered a frontocentral negative deflection with the maximum at 200 ms, similar to FRN. Overall, a conflict with a normative group opinion triggered a cascade of neuronal responses: from an earlier FRN response reflecting a conflict with the normative opinion to a later ERP component (peaking at 380 ms) reflecting a conforming behavioral adjustment. These results add to the growing literature on neuronal mechanisms of social influence by disentangling the conflict-monitoring signal in response to the perceived violation of social norms and the neural signal of a conforming behavioral adjustment. PMID:22683703

  18. Conformational Study of Dibenzyl Ether

    Science.gov (United States)

    Hernandez-Castillo, Alicia O.; Abeysekera, Chamara; Hewett, Daniel M.; Zwier, Timothy S.

    2017-06-01

    Understanding the initial stages of polycyclic aromatic hydrocarbon (PAH) aggregation, the onset of soot formation, is an important goal on the pathway to cleaner combustion processes. PAHs with short alkyl chains, present in fuel-rich combustion environments, can undergo reactions that will chemically link aromatic rings together. One such example of a linked diaryl compound is dibenzyl ether, C_{6}H_{5}-CH_{2}-O-CH_{2}-C_{6}H_{5}. The -CH_{2}-O-CH_{2}- linkage has a length and flexibility well-suited to forming a π-stacked conformation between the two phenyl rings. In this talk, we will explore the single-conformation spectroscopy of dibenzyl ether under jet-cooled conditions in the gas phase. Laser-induced fluorescence, chirped pulse Fourier transform microwave (8-18 GHz region), and single-conformation infrared spectroscopy in the alkyl CH stretch region were all carried out on the molecule, thereby interrogating its full array of electronic, vibrational and rotational degrees of freedom. This work is the first step in a broader study to determine the extent of π-stacking in linked aryl compounds as a function of linkage and PAH size.

  19. Conformal anomaly and compactification of Kaluza--Klein models

    Energy Technology Data Exchange (ETDEWEB)

    Vasilevich, D.V.; Shtykov, N.N.

    1988-10-01

    An O (d)-invariant regularization of d-dimensional Kaluza--Klein models with scalar and fermion fields is proposed. The regularization preserves the power divergences and does not give inverse powers of the cutoff parameter in the conformal anomaly. The one-loop corrections to the trace of the energy--momentum tensor are calculated for internal spaces S/sup 2/, S/sup 4/, and S/sup 6/.

  20. Reinforcement learning signal predicts social conformity.

    NARCIS (Netherlands)

    Klucharev, V.; Hytonen, K.A.; Rijpkema, M.J.P.; Smidts, A.; Fernandez, G.S.E.

    2009-01-01

    We often change our decisions and judgments to conform with normative group behavior. However, the neural mechanisms of social conformity remain unclear. Here we show, using functional magnetic resonance imaging, that conformity is based on mechanisms that comply with principles of reinforcement

  1. Herding, Social Preferences and (Non-) Conformity

    OpenAIRE

    Luca Corazzini; Ben Greiner

    2005-01-01

    We study the role of social preferences and conformity in explaining herding behavior in anonymous risky environments. In an experiment similar to information cascade settings, but with no private information, we find no evidence for conformity. On the contrary, we observe a significant amount of non-conforming behavior, which cannot be attributed to errors.

  2. 40 CFR 52.2133 - General conformity.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 4 2010-07-01 2010-07-01 false General conformity. 52.2133 Section 52...) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS (CONTINUED) South Carolina § 52.2133 General conformity. The General Conformity regulations adopted into the South Carolina State Implementation Plan which...

  3. Conformity in Christ | Waaijman | Acta Theologica

    African Journals Online (AJOL)

    This essay investigates the notion of conformity in Christ as it is part of a comprehensive, multilayered process of transformation. In the first part it focuses on the process of transformation in creation, re-creation, conformity, love and glory. In the second part it discusses transformation in Christ by looking at conformation and ...

  4. 40 CFR 52.938 - General conformity.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 3 2010-07-01 2010-07-01 false General conformity. 52.938 Section 52...) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS Kentucky § 52.938 General conformity. The General Conformity regulations were submitted on November 10, 1995, and adopted into the Kentucky State...

  5. CONFORMITY IN CHRIST 1. THE TRANSFORMATION PROCESS

    African Journals Online (AJOL)

    This essay investigates the notion of conformity in Christ as it is part of a compre- hensive, multilayered process of transformation. In the first part it focuses on the process of transformation in creation, re-creation, conformity, love and glory. In the second part it discusses transformation in Christ by looking at conformation and ...

  6. 40 CFR 51.854 - Conformity analysis.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 2 2010-07-01 2010-07-01 false Conformity analysis. 51.854 Section 51... FOR PREPARATION, ADOPTION, AND SUBMITTAL OF IMPLEMENTATION PLANS Determining Conformity of General Federal Actions to State or Federal Implementation Plans § 51.854 Conformity analysis. Link to an...

  7. Conformational cooling dynamics in matrix-isolated 1,3-butanediol.

    Science.gov (United States)

    Rosado, Mário T S; Jesus, António J Lopes; Reva, Igor D; Fausto, Rui; Redinha, José S

    2009-07-02

    The complete conformational space of monomeric 1,3-butanediol has been characterized theoretically, and 73 unique stable conformers were found at the MP2/6-311++G(d,p) level. These were classified into nine families whose members share the same heavy atom backbone configurations and differ in the hydrogen atom orientations. The first and third most populated backbone families are governed by the formation of an intramolecular hydrogen bond; however, the second precludes this type of interaction and was frequently overlooked in previous studies. Its stability is determined by the relatively high entropy of its main conformers. The hydrogen bonding of four of the most important conformers was characterized by means of atoms in molecules (AIM, also known as QTAIM) and natural bond orbital (NBO) analyses. Using appropriate isodesmic reactions, hydrogen bonding energy stabilizations of 12-14 kJ mol(-1) have been found. Experimentally, monomeric molecules of 1,3-butanediol were isolated in low-temperature inert matrixes, and their infrared spectra were analyzed from the viewpoint of the conformational distribution. All the relevant transition states for the conformational interconversion reaction paths were characterized at the same level of theory to interpret the conformational cooling dynamics observed in the low-temperature matrixes. The energy barriers for rotation of the OH groups were calculated to be very low (conformers. Further increase in the substrate temperature (up to 40 K, Xe matrix) resulted in conformational cooling where the medium-height barriers (approximately 13 kJ mol(-1)) could be surmounted and all conformational population converted to the ground conformational state. Remarkably, this state turned to consist of two forms of the most stable hydrogen bonded family, which were predicted by calculations to be accidentally degenerated and were found in the annealed matrix in equal amounts. All of these experimentally observed conformational cooling

  8. Comparative modelling by restraint-based conformational sampling

    Directory of Open Access Journals (Sweden)

    Gore Swanand

    2008-01-01

    Full Text Available Abstract Background Although comparative modelling is routinely used to produce three-dimensional models of proteins, very few automated approaches are formulated in a way that allows inclusion of restraints derived from experimental data as well as those from the structures of homologues. Furthermore, proteins are usually described as a single conformer, rather than an ensemble that represents the heterogeneity and inaccuracy of experimentally determined protein structures. Here we address these issues by exploring the application of the restraint-based conformational space search engine, RAPPER, which has previously been developed for rebuilding experimentally defined protein structures and for fitting models to electron density derived from X-ray diffraction analyses. Results A new application of RAPPER for comparative modelling uses positional restraints and knowledge-based sampling to generate models with accuracies comparable to other leading modelling tools. Knowledge-based predictions are based on geometrical features of the homologous templates and rules concerning main-chain and side-chain conformations. By directly changing the restraints derived from available templates we estimate the accuracy limits of the method in comparative modelling. Conclusion The application of RAPPER to comparative modelling provides an effective means of exploring the conformational space available to a target sequence. Enhanced methods for generating positional restraints can greatly improve structure prediction. Generation of an ensemble of solutions that are consistent with both target sequence and knowledge derived from the template structures provides a more appropriate representation of a structural prediction than a single model. By formulating homologous structural information as sets of restraints we can begin to consider how comparative models might be used to inform conformer generation from sparse experimental data.

  9. Conformal symmetry inheritance in null fluid spacetimes

    CERN Document Server

    Tupper, B O J; Hall, G S; Coley, Alan A; Carot, J

    2003-01-01

    We define inheriting conformal Killing vectors for null fluid spacetimes and find the maximum dimension of the associated inheriting Lie algebra. We show that for non-conformally flat null fluid spacetimes, the maximum dimension of the inheriting algebra is seven and for conformally flat null fluid spacetimes the maximum dimension is eight. In addition, it is shown that there are two distinct classes of non-conformally flat generalized plane wave spacetimes which possess the maximum dimension, and one class in the conformally flat case.

  10. Conformational analysis of HAMLET, the folding variant of human alpha-lactalbumin associated with apoptosis.

    Science.gov (United States)

    Casbarra, Annarita; Birolo, Leila; Infusini, Giuseppe; Dal Piaz, Fabrizio; Svensson, Malin; Pucci, Piero; Svanborg, Catharina; Marino, Gennaro

    2004-05-01

    A combination of hydrogen/deuterium (H/D) exchange and limited proteolysis experiments coupled to mass spectrometry analysis was used to depict the conformation in solution of HAMLET, the folding variant of human alpha-lactalbumin, complexed to oleic acid, that induces apoptosis in tumor and immature cells. Although near- and far-UV CD and fluorescence spectroscopy were not able to discriminate between HAMLET and apo-alpha-lactalbumin, H/D exchange experiments clearly showed that they correspond to two distinct conformational states, with HAMLET incorporating a greater number of deuterium atoms than the apo and holo forms. Complementary proteolysis experiments revealed that HAMLET and apo are both accessible to proteases in the beta-domain but showed substantial differences in accessibility to proteases at specific sites. The overall results indicated that the conformational changes associated with the release of Ca2+ are not sufficient to induce the HAMLET conformation. Metal depletion might represent the first event to produce a partial unfolding in the beta-domain of alpha-lactalbumin, but some more unfolding is needed to generate the active conformation HAMLET, very likely allowing the protein to bind the C18:1 fatty acid moiety. On the basis of these data, a putative binding site of the oleic acid, which stabilizes the HAMLET conformation, is proposed.

  11. Conformal, Transparent Printed Antenna Developed for Communication and Navigation Systems

    Science.gov (United States)

    Lee, Richard Q.; Simons, Rainee N.

    1999-01-01

    Conformal, transparent printed antennas have advantages over conventional antennas in terms of space reuse and aesthetics. Because of their compactness and thin profile, these antennas can be mounted on video displays for efficient integration in communication systems such as palmtop computers, digital telephones, and flat-panel television displays. As an array of multiple elements, the antenna subsystem may save weight by reusing space (via vertical stacking) on photovoltaic arrays or on Earth-facing sensors. Also, the antenna could go unnoticed on automobile windshields or building windows, enabling satellite uplinks and downlinks or other emerging high-frequency communications.

  12. Ambient ionization mass spectrometry

    Science.gov (United States)

    Lebedev, A. T.

    2015-07-01

    Ambient ionization mass spectrometry emerged as a new scientific discipline only about ten years ago. A considerable body of information has been reported since that time. Keeping the sensitivity, performance and informativity of classical mass spectrometry methods, the new approach made it possible to eliminate laborious sample preparation procedures and triggered the development of miniaturized instruments to work directly in the field. The review concerns the theoretical foundations and design of ambient ionization methods. Their advantages and drawbacks, as well as prospects for application in chemistry, biology, medicine, environmetal analysis, etc., are discussed. The bibliography includes 194 references.

  13. The Biological Bases of Conformity

    Science.gov (United States)

    Morgan, T. J. H.; Laland, K. N.

    2012-01-01

    Humans are characterized by an extreme dependence on culturally transmitted information and recent formal theory predicts that natural selection should favor adaptive learning strategies that facilitate effective copying and decision making. One strategy that has attracted particular attention is conformist transmission, defined as the disproportionately likely adoption of the most common variant. Conformity has historically been emphasized as significant in the social psychology literature, and recently there have also been reports of conformist behavior in non-human animals. However, mathematical analyses differ in how important and widespread they expect conformity to be, and relevant experimental work is scarce, and generates findings that are both mutually contradictory and inconsistent with the predictions of the models. We review the relevant literature considering the causation, function, history, and ontogeny of conformity, and describe a computer-based experiment on human subjects that we carried out in order to resolve ambiguities. We found that only when many demonstrators were available and subjects were uncertain was subject behavior conformist. A further analysis found that the underlying response to social information alone was generally conformist. Thus, our data are consistent with a conformist use of social information, but as subjects’ behavior is the result of both social and asocial influences, the resultant behavior may not be conformist. We end by relating these findings to an embryonic cognitive neuroscience literature that has recently begun to explore the neural bases of social learning. Here conformist transmission may be a particularly useful case study, not only because there are well-defined and tractable opportunities to characterize the biological underpinnings of this form of social learning, but also because early findings imply that humans may possess specific cognitive adaptations for effective social learning. PMID:22712006

  14. Gauge choice in conformal gravity

    Science.gov (United States)

    Sultana, Joseph; Kazanas, Demosthenes

    2017-04-01

    In a recent paper, K. Horne examined the effect of a conformally coupled scalar field (referred to as Higgs field) on the Mannheim-Kazanas metric gμν, i.e. the static spherically symmetric metric within the context of conformal gravity, and studied its effect on the rotation curves of galaxies. He showed that for a Higgs field of the form S(r) = S0a/(r + a), where a is a radial length-scale, the equivalent Higgs-frame Mannheim-Kazanas metric \\tilde{g}_{μ ν } = Ω ^2 g_{μ ν }, with Ω = S(r)/S0, lacks the linear γr term, which has been employed in the fitting of the galactic rotation curves without the need to invoke dark matter. In this brief note, we point out that the representation of the Mannheim-Kazanas metric in a gauge, where it lacks the linear term, has already been presented by others, including Mannheim and Kazanas themselves, without the need to introduce a conformally coupled Higgs field. Furthermore, Horne argues that the absence of the linear term resolves the issue of light bending in the wrong direction, i.e. away from the gravitating mass, if γr > 0 in the Mannheim-Kazanas metric, a condition necessary to resolve the galactic dynamics in the absence of dark matter. In this case, we also point out that the elimination of the linear term is not even required because the sign of the γr term in the metric can be easily reversed by a simple gauge transformation, and also that the effects of this term are indeed too small to be observed.

  15. The Biological Bases of Conformity

    Directory of Open Access Journals (Sweden)

    Thomas Joshau Henry Morgan

    2012-06-01

    Full Text Available Humans are characterized by an extreme dependence on culturally transmitted information and recent formal theory predicts that natural selection should favour adaptive learning strategies that facilitate effective use of social information in decision making. One strategy that has attracted particular attention is conformist transmission, defined as the disproportionately likely adoption of the most common variant. Conformity has historically been emphasized as significant in the social psychology literature, and recently there have also been reports of conformist behaviour in nonhuman animals. However, mathematical analyses differ in how important and widespread they expect conformity to be, and relevant experimental work is scarce, and generates findings that are both mutually contradictory and inconsistent with the predictions of the models. We review the relevant literature considering the causation, function, history and ontogeny of conformity and describe a computer-based experiment on human subjects that we carried out in order to resolve ambiguities. We found that only when many demonstrators were available and subjects were uncertain was subject behaviour conformist. A further analysis found that the underlying response to social information alone was generally conformist. Thus, our data are consistent with a conformist use of social information, but as subject’s behaviour is the result of both social and asocial influences, the resultant behaviour may not be conformist. We end by relating these findings to an embryonic cognitive neuroscience literature that has recently begun to explore the neural bases of social learning. Here conformist transmission may be a particularly useful case study, not only because there are well-defined and tractable opportunities to characterize the biological underpinnings of this form of social learning, but also because early findings imply that humans may possess specific cognitive adaptations for

  16. The biological bases of conformity.

    Science.gov (United States)

    Morgan, T J H; Laland, K N

    2012-01-01

    Humans are characterized by an extreme dependence on culturally transmitted information and recent formal theory predicts that natural selection should favor adaptive learning strategies that facilitate effective copying and decision making. One strategy that has attracted particular attention is conformist transmission, defined as the disproportionately likely adoption of the most common variant. Conformity has historically been emphasized as significant in the social psychology literature, and recently there have also been reports of conformist behavior in non-human animals. However, mathematical analyses differ in how important and widespread they expect conformity to be, and relevant experimental work is scarce, and generates findings that are both mutually contradictory and inconsistent with the predictions of the models. We review the relevant literature considering the causation, function, history, and ontogeny of conformity, and describe a computer-based experiment on human subjects that we carried out in order to resolve ambiguities. We found that only when many demonstrators were available and subjects were uncertain was subject behavior conformist. A further analysis found that the underlying response to social information alone was generally conformist. Thus, our data are consistent with a conformist use of social information, but as subjects' behavior is the result of both social and asocial influences, the resultant behavior may not be conformist. We end by relating these findings to an embryonic cognitive neuroscience literature that has recently begun to explore the neural bases of social learning. Here conformist transmission may be a particularly useful case study, not only because there are well-defined and tractable opportunities to characterize the biological underpinnings of this form of social learning, but also because early findings imply that humans may possess specific cognitive adaptations for effective social learning.

  17. Prediction of conformationally dependent atomic multipole moments in carbohydrates.

    Science.gov (United States)

    Cardamone, Salvatore; Popelier, Paul L A

    2015-12-15

    The conformational flexibility of carbohydrates is challenging within the field of computational chemistry. This flexibility causes the electron density to change, which leads to fluctuating atomic multipole moments. Quantum Chemical Topology (QCT) allows for the partitioning of an "atom in a molecule," thus localizing electron density to finite atomic domains, which permits the unambiguous evaluation of atomic multipole moments. By selecting an ensemble of physically realistic conformers of a chemical system, one evaluates the various multipole moments at defined points in configuration space. The subsequent implementation of the machine learning method kriging delivers the evaluation of an analytical function, which smoothly interpolates between these points. This allows for the prediction of atomic multipole moments at new points in conformational space, not trained for but within prediction range. In this work, we demonstrate that the carbohydrates erythrose and threose are amenable to the above methodology. We investigate how kriging models respond when the training ensemble incorporating multiple energy minima and their environment in conformational space. Additionally, we evaluate the gains in predictive capacity of our models as the size of the training ensemble increases. We believe this approach to be entirely novel within the field of carbohydrates. For a modest training set size of 600, more than 90% of the external test configurations have an error in the total (predicted) electrostatic energy (relative to ab initio) of maximum 1 kJ mol(-1) for open chains and just over 90% an error of maximum 4 kJ mol(-1) for rings. © 2015 Wiley Periodicals, Inc.

  18. 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.

  19. Exploring conformational space using a mean field technique with ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    2007-06-21

    Jun 21, 2007 ... et al 1999; Daisuke Kihara et al 2001; Richard Bonneau and David Baker 2001; Hardin et al 2002; Moult et al. 2003; Youxing Qu et al 2004; Ginalski et al 2005; Bujnicki. J M 2006). Among these methods are those that attempt to use only the sequence (i.e. the chemical formula) of the molecule and physical ...

  20. Exploring conformational space using a mean field technique with ...

    Indian Academy of Sciences (India)

    2007-06-21

    Jun 21, 2007 ... The computational identification of all the low energy structures of a peptide given only its sequence is not an easy task even for small peptides, due to the multiple-minima problem and combinatorial explosion. We have developed an algorithm, called the MOLS technique, that addresses this problem, and ...

  1. Fourier Transform Mass Spectrometry.

    Science.gov (United States)

    Gross, Michael L.; Rempel, Don L.

    1984-01-01

    Discusses the nature of Fourier transform mass spectrometry and its unique combination of high mass resolution, high upper mass limit, and multichannel advantage. Examines its operation, capabilities and limitations, applications (ion storage, ion manipulation, ion chemistry), and future applications and developments. (JN)

  2. Miniaturization and Mass Spectrometry

    NARCIS (Netherlands)

    le Gac, S.; le Gac, Severine; van den Berg, Albert; van den Berg, A.; Unknown, [Unknown

    2009-01-01

    With this book we want to illustrate how two quickly growing fields of instrumentation and technology, both applied to life sciences, mass spectrometry and microfluidics (or microfabrication) naturally came to meet at the end of the last century and how this marriage impacts on several types of

  3. Exploring the conformational landscape of menthol, menthone, and isomenthone: A microwave study

    Science.gov (United States)

    Schmitz, David; Shubert, V.; Betz, Thomas; Schnell, Melanie

    2015-03-01

    The rotational spectra of the monoterpenoids menthol, menthone, and isomenthone are reported in the frequency range of 2-8.5GHz, obtained with broadband Fourier-transform microwave spectroscopy. For menthol only one conformation was identified under the cold conditions of the molecular jet, whereas three conformations were observed for menthone and one for isomenthone. The conformational space of the different molecules was extensively studied using quantum chemical calculations, and the results were compared with molecular parameters obtained by the measurements. Finally, a computer program is presented, which was developed to automatically identify different species in a dense broadband microwave spectrum using calculated ab initio rotational constants as input.

  4. Identifying multiple active conformations in the G protein-coupled receptor activation landscape using computational methods.

    Science.gov (United States)

    Dong, Sijia S; Goddard, William A; Abrol, Ravinder

    2017-01-01

    G protein-coupled receptors (GPCRs) are membrane proteins critical in cellular signaling, making them important targets for therapeutics. The activation of GPCRs is central to their function, requiring multiple conformations of the GPCRs in their activation landscape. To enable rational design of GPCR-targeting drugs, it is essential to obtain the ensemble of atomistic structures of GPCRs along their activation pathways. This is most challenging for structure determination experiments, making it valuable to develop reliable computational structure prediction methods. In particular, since the active-state conformations are higher in energy (less stable) than inactive-state conformations, they are difficult to stabilize. In addition, the computational methods are generally biased toward lowest energy structures by design and miss these high energy but functionally important conformations. To address this problem, we have developed a computationally efficient ActiveGEnSeMBLE method that systematically predicts multiple conformations that are likely in the GPCR activation landscape, including multiple active- and inactive-state conformations. ActiveGEnSeMBLE starts with a systematic coarse grid sampling of helix tilts/rotations (~13 trillion transmembrane domain conformations) and identifies multiple potential active-state energy wells, using the TM3-TM6 intracellular distance as a surrogate activation coordinate. These energy wells are then sampled locally using a finer grid in conformational space to find a locally minimized conformation in each energy well, which can be further relaxed using molecular dynamics (MD) simulations. This method, combining homology modeling, hierarchical complete conformational sampling, and nanosecond scale MD, provides one of the very few computational methods that predict multiple candidates for active-state conformations and is one of the most computationally affordable. © 2017 Elsevier Inc. All rights reserved.

  5. A quantitative measure for protein conformational heterogeneity.

    Science.gov (United States)

    Lyle, Nicholas; Das, Rahul K; Pappu, Rohit V

    2013-09-28

    Conformational heterogeneity is a defining characteristic of proteins. Intrinsically disordered proteins (IDPs) and denatured state ensembles are extreme manifestations of this heterogeneity. Inferences regarding globule versus coil formation can be drawn from analysis of polymeric properties such as average size, shape, and density fluctuations. Here we introduce a new parameter to quantify the degree of conformational heterogeneity within an ensemble to complement polymeric descriptors. The design of this parameter is guided by the need to distinguish between systems that couple their unfolding-folding transitions with coil-to-globule transitions and those systems that undergo coil-to-globule transitions with no evidence of acquiring a homogeneous ensemble of conformations upon collapse. The approach is as follows: Each conformation in an ensemble is converted into a conformational vector where the elements are inter-residue distances. Similarity between pairs of conformations is quantified using the projection between the corresponding conformational vectors. An ensemble of conformations yields a distribution of pairwise projections, which is converted into a distribution of pairwise conformational dissimilarities. The first moment of this dissimilarity distribution is normalized against the first moment of the distribution obtained by comparing conformations from the ensemble of interest to conformations drawn from a Flory random coil model. The latter sets an upper bound on conformational heterogeneity thus ensuring that the proposed measure for intra-ensemble heterogeneity is properly calibrated and can be used to compare ensembles for different sequences and across different temperatures. The new measure of conformational heterogeneity will be useful in quantitative studies of coupled folding and binding of IDPs and in de novo sequence design efforts that are geared toward controlling the degree of heterogeneity in unbound forms of IDPs.

  6. Two dimensional magnetic particle spectrometry.

    Science.gov (United States)

    Graeser, M; von Gladiss, A; Weber, M; Buzug, T M

    2017-05-07

    Magnetic particle spectrometry (MPS) is an excellent and straight forward method to determine the response of magnetic nanoparticles to an oscillating magnetic field. Such fields are applied in magnetic particle imaging (MPI). However, state of the art MPS devices lack the ability to excite particles in multidimensional field sequences that are present in MPI devices. Especially the particle behavior caused by Lissajous sequences cannot be measured with only one excitation direction. This work presents a new kind of MPS which features two excitation directions to overcome this limitation. Both field coils can drive AC as well as DC currents and are thereby able to emulate the field sequences for arbitrary spatial positions inside an MPI device. Since the DC currents can be switched very fast, the device can be used as system calibration unit and acquire system matrices in very short time. These are crucial for MPI image reconstruction. As the signal-to-noise-ratio provided by the MPS is approximately 1000 times higher than that of actual imaging devices, the time space analysis of particle signals is more precise and easier done. Four system matrices are presented in this paper which have been measured with the realized multidimensional MPS. Additionally, a time space comparison of the particle signal for Lissajous, radial and spiral trajectories is given.

  7. Reinforcement learning signal predicts social conformity.

    Science.gov (United States)

    Klucharev, Vasily; Hytönen, Kaisa; Rijpkema, Mark; Smidts, Ale; Fernández, Guillén

    2009-01-15

    We often change our decisions and judgments to conform with normative group behavior. However, the neural mechanisms of social conformity remain unclear. Here we show, using functional magnetic resonance imaging, that conformity is based on mechanisms that comply with principles of reinforcement learning. We found that individual judgments of facial attractiveness are adjusted in line with group opinion. Conflict with group opinion triggered a neuronal response in the rostral cingulate zone and the ventral striatum similar to the "prediction error" signal suggested by neuroscientific models of reinforcement learning. The amplitude of the conflict-related signal predicted subsequent conforming behavioral adjustments. Furthermore, the individual amplitude of the conflict-related signal in the ventral striatum correlated with differences in conforming behavior across subjects. These findings provide evidence that social group norms evoke conformity via learning mechanisms reflected in the activity of the rostral cingulate zone and ventral striatum.

  8. 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....

  9. Challenges of Agro-Food Standards Conformity

    DEFF Research Database (Denmark)

    Bolwig, Simon; Riisgaard, Lone; Gibbon, Peter

    2013-01-01

    a variety of programmes and projects aimed at supporting standards development and conformity. This article contributes to the critical literature discussing the challenges and potentials of standards conformity and supplies policy recommendations for future interventions. It reports the results...... of a research programme on standards conformity in East Africa. These demonstrate that most interventions underestimate the nature of the challenges faced and that significant impacts are achieved only under rather restricted conditions. The solutions lay not only in more selective support to standard...

  10. Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

    Science.gov (United States)

    Lapelosa, Mauro; Gallicchio, Emilio; Levy, Ronald M.

    2011-01-01

    The Binding Energy Distribution Analysis Method (BEDAM) is employed to compute the standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) with implicit solvation. Binding free energy estimates are in reasonably good agreement with experimental affinities. The conformations of the complexes identified by the simulations are in good agreement with crystallographic data, which was not used to restrain ligand orientations. The BEDAM method is based on λ -hopping Hamiltonian parallel Replica Exchange (HREM) molecular dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential, and multi-state free energy estimators (MBAR). Achieving converged and accurate results depends on all of these elements of the calculation. Convergence of the binding free energy is tied to the level of convergence of binding energy distributions at critical intermediate states where bound and unbound states are at equilibrium, and where the rate of binding/unbinding conformational transitions is maximal. This finding mirrors similar observations in the context of order/disorder transitions as for example in protein folding. Insights concerning the physical mechanism of ligand binding and unbinding are obtained. Convergence for the largest FK506 ligand is achieved only after imposing strict conformational restraints, which however require accurate prior structural knowledge of the structure of the complex. The analytical AGBNP2 model is found to underestimate the magnitude of the hydrophobic driving force towards binding in these systems characterized by loosely packed protein-ligand binding interfaces. Rescoring of the binding energies using a numerical surface area model corrects this deficiency. This study illustrates the complex interplay between energy models, exploration of conformational space, and free energy estimators needed to obtain robust estimates from binding free energy calculations. PMID:22368530

  11. Einstein gravity as a 3D conformally invariant theory

    CERN Document Server

    Gomes, Henrique; Koslowski, Tim

    2010-01-01

    We give an alternative description of the physical content of general relativity that does not require a Lorentz invariant spacetime. Instead, we find that gravity admits a dual description in terms of a theory where local size is irrelevant. The dual theory is invariant under foliation preserving 3-diffeomorphisms and 3D conformal transformations that preserve the 3-volume (for the spatially compact case). Locally, this symmetry is identical to that of Horava-Lifshitz gravity in the high energy limit but our theory is equivalent to Einstein gravity. Specifically, we find that the solutions of general relativity, in a gauge where the spatial hypersurfaces have constant mean extrinsic curvature, can be mapped to solutions of a particular gauge fixing of the dual theory. Moreover, this duality is not accidental. We provide a general geometric picture for our procedure that allows us to trade foliation invariance for conformal invariance. The dual theory provides a new proposal for the theory space of quantum gr...

  12. LAPLACE EQUATIONS, CONFORMAL SUPERINTEGRABILITY AND BÔCHER CONTRACTIONS

    Directory of Open Access Journals (Sweden)

    Ernest G. Kalnins

    2016-06-01

    Full Text Available Quantum superintegrable systems are solvable eigenvalue problems. Their solvability is due to symmetry, but the symmetry is often ``hidden''.The symmetry generators of 2nd order superintegrable systems in 2 dimensions close under commutation to define quadratic algebras, a generalization of Lie algebras. Distinct systems and their algebras are related by geometric limits, induced by generalized Inönü-Wigner Lie algebra contractions of the symmetry algebras of the underlying spaces. These have physical/geometric implications, such as the Askey scheme for hypergeometric orthogonal polynomials. The systems can be best understood by transforming them to Laplace conformally superintegrable systems and using ideas introduced in the 1894 thesis of Bôcher to study separable solutions of the wave equation. The contractions can be subsumed into contractions of the conformal algebra  so(4,C to itself. Here we announce main findings, with detailed classifications in papers under preparation.

  13. Universal entanglement and boundary geometry in conformal field theory

    Energy Technology Data Exchange (ETDEWEB)

    Herzog, Christopher P.; Huang, Kuo-Wei; Jensen, Kristan [C.N. Yang Institute for Theoretical Physics, Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794 (United States)

    2016-01-27

    Employing a conformal map to hyperbolic space cross a circle, we compute the universal contribution to the vacuum entanglement entropy (EE) across a sphere in even-dimensional conformal field theory. Previous attempts to derive the EE in this way were hindered by a lack of knowledge of the appropriate boundary terms in the trace anomaly. In this paper we show that the universal part of the EE can be treated as a purely boundary effect. As a byproduct of our computation, we derive an explicit form for the A-type anomaly contribution to the Wess-Zumino term for the trace anomaly, now including boundary terms. In d=4 and 6, these boundary terms generalize earlier bulk actions derived in the literature.

  14. Conformal bootstrap: non-perturbative QFT's under siege

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    [Exceptionally in Council Chamber] Originally formulated in the 70's, the conformal bootstrap is the ambitious idea that one can use internal consistency conditions to carve out, and eventually solve, the space of conformal field theories. In this talk I will review recent developments in the field which have boosted this program to a new level. I will present a method to extract quantitative informations in strongly-interacting theories, such as 3D Ising, O(N) vector model and even systems without a Lagrangian formulation. I will explain how these techniques have led to the world record determination of several critical exponents. Finally, I will review exact analytical results obtained using bootstrap techniques.

  15. Novel conformation of an RNA structural switch.

    Science.gov (United States)

    Kennedy, Scott D; Kierzek, Ryszard; Turner, Douglas H

    2012-11-20

    The RNA duplex, (5'GACGAGUGUCA)(2), has two conformations in equilibrium. The nuclear magnetic resonance solution structure reveals that the major conformation of the loop, 5'GAGU/3'UGAG, is novel and contains two unusual Watson-Crick/Hoogsteen GG pairs with G residues in the syn conformation, two A residues stacked on each other in the center of the helix with inverted sugars, and two bulged-out U residues. The structure provides a benchmark for testing approaches for predicting local RNA structure and a sequence that allows the design of a unique arrangement of functional groups and/or a conformational switch into nucleic acids.

  16. Rotational Spectroscopy Unveils Eleven Conformers of Adrenaline

    Science.gov (United States)

    Cabezas, C.; Cortijo, V.; Mata, S.; Lopez, J. C.; Alonso, J. L.

    2013-06-01

    Recent improvements in our LA-MB-FTMW instrumentation have allowed the characterization of eleven and eight conformers for the neurotransmitters adrenaline and noradrenaline respectively. The observation of this rich conformational behavior is in accordance with the recent observation of seven conformers for dopamine and in sharp contrast with the conformational reduction proposed for catecholamines. C. Cabezas, I. Peña, J. C. López, J. L. Alonso J. Phys. Chem. Lett. 2013, 4, 486. H. Mitsuda, M. Miyazaki, I. B. Nielsen, P. Carcabal,C. Dedonder, C. Jouvet, S. Ishiuchi, M. Fujii J. Phys. Chem. Lett. 2010, 1, 1130.

  17. A Framework for Online Conformance Checking

    DEFF Research Database (Denmark)

    Burattin, Andrea; Carmona, Josep

    2017-01-01

    Conformance checking – a branch of process mining – focuses on establishing to what extent actual executions of a process are in line with the expected behavior of a reference model. Current conformancechecking techniques only allow for a-posteriori analysis: the amount of (non-)conformant behavior...... is quantified after the completion of the process instance. In this paper we propose a framework for online conformance checking: not only do we quantify (non-)conformant behavior as the execution is running, we also restrict the computation to constant time complexity per event analyzed, thus enabling...

  18. Conformable eddy current array delivery

    Science.gov (United States)

    Summan, Rahul; Pierce, Gareth; Macleod, Charles; Mineo, Carmelo; Riise, Jonathan; Morozov, Maxim; Dobie, Gordon; Bolton, Gary; Raude, Angélique; Dalpé, Colombe; Braumann, Johannes

    2016-02-01

    The external surface of stainless steel containers used for the interim storage of nuclear material may be subject to Atmospherically Induced Stress Corrosion Cracking (AISCC). The inspection of such containers poses a significant challenge due to the large quantities involved; therefore, automating the inspection process is of considerable interest. This paper reports upon a proof-of-concept project concerning the automated NDT of a set of test containers containing artificially generated AISCCs. An Eddy current array probe with a conformable padded surface from Eddyfi was used as the NDT sensor and end effector on a KUKA KR5 arc HW robot. A kinematically valid cylindrical raster scan path was designed using the KUKA|PRC path planning software. Custom software was then written to interface measurement acquisition from the Eddyfi hardware with the motion control of the robot. Preliminary results and analysis are presented from scanning two canisters.

  19. Technidilaton at the conformal edge

    Science.gov (United States)

    Hashimoto, Michio; Yamawaki, Koichi

    2011-01-01

    Technidilaton (TD) was proposed long ago in the technicolor near criticality/conformality. To reveal the critical behavior of TD, we explicitly compute the nonperturbative contributions to the scale anomaly ⟨θμμ⟩ and to the technigluon condensate ⟨αGμν2⟩, which are generated by the dynamical mass m of the technifermions. Our computation is based on the (improved) ladder Schwinger-Dyson equation, with the gauge coupling α replaced by the two-loop running coupling α(μ) having the Caswell-Banks-Zaks infrared fixed point α*: α(μ)≃α=α* for the infrared region mHaba-Matsuzaki-Yamawaki. The decoupled TD can be a candidate of dark matter.

  20. Approaching Conformality with Ten Flavors

    Energy Technology Data Exchange (ETDEWEB)

    Appelquist, Thomas; Brower, Richard C.; Buchoff, Michael I.; Cheng, Michael; Cohen, Saul D.; Fleming, George T.; Kiskis, Joe; Lin, Meifeng; Na, Heechang; Neil, Ethan T.; Osborn, James C.

    2012-04-01

    We present first results for lattice simulations, on a single volume, of the low-lying spectrum of an SU(3) Yang-Mills gauge theory with N{sub f} = 10 light fermions in the fundamental representation. Fits to the fermion mass dependence of various observables are found to be globally consistent with the hypothesis that this theory is within or just outside the strongly-coupled edge of the conformal window, with mass anomalous dimension {gamma}* {approx} 1 over the range of scales simulated. We stress that we cannot rule out the possibility of spontaneous chiral-symmetry breaking at scales well below our infrared cutoff. We discuss important systematic effects, including finite-volume corrections, and consider directions for future improvement.

  1. Gravitomagnetic effects in conformal gravity

    CERN Document Server

    Said, Jackson Levi; Adami, Kristian Zarb

    2014-01-01

    Gravitomagnetic effects are characterized by two phenomena: first, the geodetic effect which describes the precession of the spin of a gyroscope in a free orbit around a massive object, second, the Lense-Thirring effect which describes the precession of the orbital plane about a rotating source mass. We calculate both these effects in the fourth-order theory of conformal Weyl gravity for the test case of circular orbits. We show that for the geodetic effect a linear term arises which may be interesting for high radial orbits, whereas for the Lense-Thirring effect the additional term has a diminishing effect for most orbits. Circular orbits are also considered in general leading up to a generalization of Kepler's third law.

  2. Phase transformation in conformational polymorphs of nimesulide.

    Science.gov (United States)

    Sanphui, Palash; Sarma, Bipul; Nangia, Ashwini

    2011-06-01

    Nimesulide is a nonsteroidal anti-inflammatory drug (NSAID) and a COX-2 inhibitor. The native crystal structure of nimesulide (or Form I) has been characterized in the literature by X-ray powder diffraction (XRPD) lines, whereas full three-dimensional coordinates are known for a second polymorph (Form II). A detailed structural characterization and phase stability of nimesulide polymorphs were carried out. Rod-like crystals of Form I (space group Pca2(1); number of symmetry-independent molecules, Z' = 2) were crystallized from EtOH concomitantly with Form II (C2/c, Z' = 1). These conformational polymorphs have different torsion angles at the phenoxy and sulfonamide groups. The crystal structures are stabilized by N-H · · · O hydrogen bonds and C-H · · · O, C-H · · · π interactions. Phase transition from the metastable Form (II) to the stable modification (I) was studied using differential scanning calorimetry, hot-stage microscopy, solid-state grinding, solvent-drop grinding, and slurry crystallization. The phase transition was monitored by infrared, Raman, and ss-nuclear magnetic resonance spectroscopy; and XRPD and single-crystal X-ray diffraction. The stable polymorph I was obtained in excess during solution crystallization, grinding, and slurry methods. Intrinsic dissolution and equilibrium solubility experiments showed that the metastable Form II dissolves much faster than the stable Form I. Copyright © 2011 Wiley-Liss, Inc.

  3. 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

  4. Conformations and Conformational Processes of Hexahydrobenzazocines by NMR and DFT Studies.

    Science.gov (United States)

    Musielak, Bogdan; Holak, Tad A; Rys, Barbara

    2015-09-18

    Conformational processes that occur in hexahydrobenzazocines have been studied with the (1)H and (13)C dynamic nuclear magnetic resonance (DNMR) spectroscopy. The coalescence effects are assigned to two different conformational processes: the ring-inversion of the ground-state conformations and the interconversion between two different conformers. The barriers for these processes are in the range of 42-52 and 42-43 kJ mol(-1), respectively. Molecular modeling on the density functional theory (DFT) level and the gauge invariant atomic orbitals (GIAO)-DFT calculations of isotropic shieldings and coupling constants for the set of low-energy conformations were compared with the experimental NMR data. The ground-state of all compounds in solution is the boat-chair (BC) conformation. The BC form adopts two different conformations because the nitrogen atom can be in the boat or chair parts of the BC structure. These two conformers are engaged in the interconversion process.

  5. Discovery of a novel conformational equilibrium in urokinase-type plasminogen activator.

    Science.gov (United States)

    Kromann-Hansen, Tobias; Louise Lange, Eva; Peter Sørensen, Hans; Hassanzadeh-Ghassabeh, Gholamreza; Huang, Mingdong; Jensen, Jan K; Muyldermans, Serge; Declerck, Paul J; Komives, Elizabeth A; Andreasen, Peter A

    2017-06-13

    Although trypsin-like serine proteases have flexible surface-exposed loops and are known to adopt higher and lower activity conformations, structural determinants for the different conformations have remained largely obscure. The trypsin-like serine protease, urokinase-type plasminogen activator (uPA), is central in tissue remodeling processes and also strongly implicated in tumor metastasis. We solved five X-ray crystal structures of murine uPA (muPA) in the absence and presence of allosteric molecules and/or substrate-like molecules. The structure of unbound muPA revealed an unsuspected non-chymotrypsin-like protease conformation in which two β-strands in the core of the protease domain undergoes a major antiparallel-to-parallel conformational transition. We next isolated two anti-muPA nanobodies; an active-site binding nanobody and an allosteric nanobody. Crystal structures of the muPA:nanobody complexes and hydrogen-deuterium exchange mass spectrometry revealed molecular insights about molecular factors controlling the antiparallel-to-parallel equilibrium in muPA. Together with muPA activity assays, the data provide valuable insights into regulatory mechanisms and conformational flexibility of uPA and trypsin-like serine proteases in general.

  6. A Multilevel Strategy for the Exploration of the Conformational Flexibility of Small Molecules.

    Science.gov (United States)

    Forti, Flavio; Cavasotto, Claudio N; Orozco, Modesto; Barril, Xavier; Luque, F Javier

    2012-05-08

    Predicting the conformational preferences of flexible compounds is still a challenging problem with important implications in areas such as molecular recognition and drug design. In this work, we describe a multilevel strategy to explore the conformational preferences of molecules. The method relies on the predominant-state approximation, which partitions the conformational space into distinct conformational wells. Moreover, it combines low-level (LL) methods for sampling the conformational minima and high-level (HL) techniques for calibrating their relative stability. In the implementation used in this study, the LL sampling is performed with the semiempirical RM1 Hamiltonian, and solvent effects are included using the RM1 version of the MST continuum solvation model. The HL refinement of the conformational wells is performed by combining geometry optimizations of the minima at the B3LYP (gas phase) or MST-B3LYP (solution) level, followed by single point MP2 computations using Dunning's augmented basis sets. Then, the effective free energy of a conformational well is estimated by combining the MP2 energy, supplemented with the MST-B3LYP solvation free energy for a conformational search in solution, with the local curvature of the well sampled at the semiempirical level. Applications of this strategy involve the exploration of the conformational preferences of 1,2-dichloroethane and neutral histamine in both the gas phase and water solution. Finally, the multilevel strategy is used to estimate the reorganization cost required for selecting the bioactive conformation of HIV reverse transcriptase inhibitors, which is estimated to be at most 1.3 kcal/mol.

  7. Spontaneous breaking of conformal invariance in theories of conformally coupled matter and Weyl gravity

    OpenAIRE

    Edery, A.; Fabbri, Luca; Paranjape, M. B.

    2006-01-01

    We study the theory of Weyl conformal gravity with matter degrees of freedom in a conformally invariant interaction. Specifically, we consider a triplet of scalar fields and SO(3) non-abelian gauge fields, i.e. the Georgi-Glashow model conformally coupled to Weyl gravity. We show that the equations of motion admit solutions spontaneously breaking the conformal symmetry and the gauge symmetry, providing a mechanism for supplying a scale in the theory. The vacuum solution corresponds to anti-de...

  8. PAS-cal: a generic recombinant peptide calibration standard for mass spectrometry.

    Science.gov (United States)

    Breibeck, Joscha; Serafin, Adam; Reichert, Andreas; Maier, Stefan; Küster, Bernhard; Skerra, Arne

    2014-08-01

    We describe the design, preparation, and mass-spectrometric characterization of a new recombinant peptide calibration standard with uniform biophysical and ionization characteristics for mass spectrometry. "PAS-cal" is an artificial polypeptide concatamer of peptide cassettes with varying lengths, each composed of the three small, chemically stable amino acids Pro, Ala, and Ser, which are interspersed by Arg residues to allow site-specific cleavage with trypsin. PAS-cal is expressed at high yields in Escherichia coli as a Small Ubiquitin-like MOdifier (SUMO) fusion protein, which is easily purified and allows isolation of the PAS-cal moiety after SUMO protease cleavage. Upon subsequent in situ treatment with trypsin, the PAS-cal polypeptide yields a set of four defined homogeneous peptides in the range from 2 to 8 kDa with equal mass spacing. ESI-MS analysis revealed a conveniently interpretable raw spectrum, which after deconvolution resulted in a very simple pattern of four peaks with similar ionization signals. MALDI-MS analysis of a PAS-cal peptide mixture comprising both the intact polypeptide and its tryptic fragments revealed not only the four standard peptides but also the singly and doubly charged states of the intact concatamer as well as di- and trimeric adduct ion species between the peptides, thus augmenting the observable m/z range. The advantageous properties of PAS-cal are most likely a result of the strongly hydrophilic and conformationally disordered PEG-like properties of the PAS sequences. Therefore, PAS-cal offers an inexpensive and versatile recombinant peptide calibration standard for mass spectrometry in protein/peptide bioanalytics and proteomics research, the composition of which may be further adapted to fit individual needs.

  9. 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

  10. Conformity to Peer Pressure in Preschool Children

    Science.gov (United States)

    Haun, Daniel B. M.; Tomasello, Michael

    2011-01-01

    Both adults and adolescents often conform their behavior and opinions to peer groups, even when they themselves know better. The current study investigated this phenomenon in 24 groups of 4 children between 4;2 and 4;9 years of age. Children often made their judgments conform to those of 3 peers, who had made obviously erroneous but unanimous…

  11. Group Cohesiveness, Deviation, Stress, and Conformity

    Science.gov (United States)

    1993-08-11

    productivity. ~ Relations, I. 599-519 . Blake , R. R., & Mouton , J. 5, (1961) . Conformity. resistance, and conversion. In I. A. Berg , & B. M. Bass...conversion ( Blake & HoutQn. 1961). Conformity without a true change in private acceptance has been termed compliance (Kiesler, 1969 ; Kiesler

  12. Chaotropes trigger conformational rearrangements differently in ...

    Indian Academy of Sciences (India)

    SHREYASI ASTHANA

    Abstract. Concanavalin A (ConA) is a plant lectin having industrial and biological applications. Concanavalin. A changes conformation upon exposure to different stress conditions, like exposure to sodium dodecyl sulphate, guanidine hydrochloride, varying hydronium ion potential, etc. The conformational changes were ...

  13. Asymptotic symmetry algebra of conformal gravity

    Science.gov (United States)

    Irakleidou, Maria; Lovrekovic, Iva

    2017-11-01

    We compute asymptotic symmetry algebras of conformal gravity. Due to more general boundary conditions allowed in conformal gravity in comparison to those in Einstein gravity, we can classify the corresponding algebras. The highest algebra for nontrivial boundary conditions is five dimensional and it leads to global geon solution with nonvanishing charges.

  14. Conformity to the Surviving Sepsis Campaign International ...

    African Journals Online (AJOL)

    They had moderate conformity rates for blood cultures prior to administering antibiotics (57%) and administration of antibiotics within first hour of recognition of septic shock (54%). There was high conformity rate to the glucose control policy (81%), use of protective lung strategy in acute lung injury/Acute respiratory distress ...

  15. Conformation of hindered piperidines: Spectroscopic evidence for ...

    Indian Academy of Sciences (India)

    Administrator

    C NMR; conformational analysis; boat forms. 1. Introduction. Many piperidine derivatives are found to possess pharmacological activity and form an essential part of the molecular structure of important drugs. 1. Most of the piperidine precursors are known to exist in chair conformation. Electron withdrawing groups. (–NO ...

  16. Future Directions of Structural Mass Spectrometry using Hydroxyl Radical Footprinting

    Energy Technology Data Exchange (ETDEWEB)

    J Kiselar; M Chance

    2011-12-31

    Hydroxyl radical protein footprinting coupled to mass spectrometry has been developed over the last decade and has matured to a powerful method for analyzing protein structure and dynamics. It has been successfully applied in the analysis of protein structure, protein folding, protein dynamics, and protein-protein and protein-DNA interactions. Using synchrotron radiolysis, exposure of proteins to a 'white' X-ray beam for milliseconds provides sufficient oxidative modification to surface amino acid side chains, which can be easily detected and quantified by mass spectrometry. Thus, conformational changes in proteins or protein complexes can be examined using a time-resolved approach, which would be a valuable method for the study of macromolecular dynamics. In this review, we describe a new application of hydroxyl radical protein footprinting to probe the time evolution of the calcium-dependent conformational changes of gelsolin on the millisecond timescale. The data suggest a cooperative transition as multiple sites in different molecular subdomains have similar rates of conformational change. These findings demonstrate that time-resolved protein footprinting is suitable for studies of protein dynamics that occur over periods ranging from milliseconds to seconds. In this review, we also show how the structural resolution and sensitivity of the technology can be improved as well. The hydroxyl radical varies in its reactivity to different side chains by over two orders of magnitude, thus oxidation of amino acid side chains of lower reactivity are more rarely observed in such experiments. Here we demonstrate that the selected reaction monitoring (SRM)-based method can be utilized for quantification of oxidized species, improving the signal-to-noise ratio. This expansion of the set of oxidized residues of lower reactivity will improve the overall structural resolution of the technique. This approach is also suggested as a basis for developing hypothesis

  17. Wormholes in conformal gravity arXiv

    CERN Document Server

    Hohmann, Manuel; Raidal, Martti; Veermäe, Hardi

    We present a new class of solutions for static spherically symmetric wormhole spacetimes in conformal gravity and outline a detailed method for their construction. As an explicit example, we construct a class of traversable and non-traversable wormholes that are locally conformal to Schwarzschild-(anti) de Sitter spacetimes. These wormhole spacetimes are exact vacuum solutions in, but not being limited to, Weyl gravity and conformal scalar-tensor theories. Importantly, the method implies that every conformal gravity theory with local field equations will trivially contain wormholes without the need for exotic matter. Applying those results on gravitational theories that possess conformal symmetry in the ultraviolet regime, the central singularities of black holes can be replaced with wormhole throats. We speculate on possible phenomenological consequences.

  18. Hydrogen Exchange Mass Spectrometry: Are We Out of the Quicksand?

    Science.gov (United States)

    Iacob, Roxana E.; Engen, John R.

    2012-06-01

    Although the use of hydrogen exchange (HX) mass spectrometry (MS) to study proteins and protein conformation is now over 20 years old, the perception lingers that it still has "issues." Is this method, in fact, still in the quicksand with many remaining obstacles to overcome? We do not think so. This critical insight addresses the "issues" and explores several broad questions including, have the limitations of HX MS been surmounted and has HX MS achieved "indispensable" status in the pantheon of protein structural analysis tools.

  19. Conformational structures in dry ionomers

    Science.gov (United States)

    Allahyarov, Elshad; Taylor, Philip

    2007-03-01

    The molecular architecture of polymer electrolyte membranes (PEM), which consist of hydrophobic and hydrophilic segments, leads to its own self-assembled structure through a partial phase segregation. Controlling these structures is necessary for improving the performance of fuel cells. We have used computer simulation to analyze the relationship between the hydrophilic cluster structure and the parameters describing the pendant side chains in dry Nafion-like materials. We investigate the morphology of a dry PEM system within different coarse-grained models: a free-proton model, a dipolar model for side chains, and a branched-chain model. We conclude that the free-proton model, where the proton-proton correlations are decoupled from the sulfonate-sulfonate correlations, has the potential to explain the experimentally observed conformational structures of PEM. We find that the geometry of domains with a high concentration of sulfonate groups depends only weakly on the form of the distance-dependent dielectric permittivity, but strongly depends on the partial charge and monomeric unit sequence distribution along the ionomer chain. We predict a nanophase separation with a lamellar-like morphology in ionomers carrying a divalent salt.

  20. Conformal invariance an introduction to loops, interfaces and stochastic Loewner evolution

    CERN Document Server

    Karevski, Dragi

    2012-01-01

    Conformal invariance has been a spectacularly successful tool in advancing our understanding of the two-dimensional phase transitions found in classical systems at equilibrium. This volume sharpens our picture of the applications of conformal invariance, introducing non-local observables such as loops and interfaces before explaining how they arise in specific physical contexts. It then shows how to use conformal invariance to determine their properties. Moving on to cover key conceptual developments in conformal invariance, the book devotes much of its space to stochastic Loewner evolution (SLE), detailing SLE’s conceptual foundations as well as extensive numerical tests. The chapters then elucidate SLE’s use in geometric phase transitions such as percolation or polymer systems, paying particular attention to surface effects. As clear and accessible as it is authoritative, this publication is as suitable for non-specialist readers and graduate students alike.

  1. Thermal corrections to Rényi entropies for conformal field theories

    Energy Technology Data Exchange (ETDEWEB)

    Herzog, Christopher P.; Nian, Jun [C. N. Yang Institute for Theoretical Physics, Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794 (United States)

    2015-06-03

    We compute thermal corrections to Rényi entropies of d dimensional conformal field theories on spheres. Consider the nth Rényi entropy for a cap of opening angle 2θ on S{sup d−1}. From a Boltzmann sum decomposition and the operator-state correspondence, the leading correction is related to a certain two-point correlation function of the operator (not equal to the identity) with smallest scaling dimension. More specifically, via a conformal map, the correction can be expressed in terms of the two-point function on a certain conical space with opening angle 2πn. In the case of free conformal field theories, this two-point function can be computed explicitly using the method of images. We perform the computation for the conformally coupled scalar. From the n→1 limit of our results, we extract the leading thermal correction to the entanglement entropy, reproducing results of arXiv:1407.1358.

  2. 47 CFR 2.1072 - Limitation on Declaration of Conformity.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Limitation on Declaration of Conformity. 2.1072... Conformity § 2.1072 Limitation on Declaration of Conformity. (a) The Declaration of Conformity signifies that...'s rules. (b) A Declaration of Conformity by the responsible party is effective until a termination...

  3. From vertex operator algebras to conformal nets and back

    OpenAIRE

    Carpi, Sebastiano; Kawahigashi, Yasuyuki; Longo, Roberto; Weiner, Mihály

    2015-01-01

    We consider unitary simple vertex operator algebras whose vertex operators satisfy certain energy bounds and a strong form of locality and call them strongly local. We present a general procedure which associates to every strongly local vertex operator algebra V a conformal net A_V acting on the Hilbert space completion of V and prove that the isomorphism class of A_V does not depend on the choice of the scalar product on V. We show that the class of strongly local vertex operator algebras is...

  4. PubChem3D: Similar conformers

    Directory of Open Access Journals (Sweden)

    Bolton Evan E

    2011-05-01

    Full Text Available Abstract Background PubChem is a free and open public resource for the biological activities of small molecules. With many tens of millions of both chemical structures and biological test results, PubChem is a sizeable system with an uneven degree of available information. Some chemical structures in PubChem include a great deal of biological annotation, while others have little to none. To help users, PubChem pre-computes "neighboring" relationships to relate similar chemical structures, which may have similar biological function. In this work, we introduce a "Similar Conformers" neighboring relationship to identify compounds with similar 3-D shape and similar 3-D orientation of functional groups typically used to define pharmacophore features. Results The first two diverse 3-D conformers of 26.1 million PubChem Compound records were compared to each other, using a shape Tanimoto (ST of 0.8 or greater and a color Tanimoto (CT of 0.5 or greater, yielding 8.16 billion conformer neighbor pairs and 6.62 billion compound neighbor pairs, with an average of 253 "Similar Conformers" compound neighbors per compound. Comparing the 3-D neighboring relationship to the corresponding 2-D neighboring relationship ("Similar Compounds" for molecules such as caffeine, aspirin, and morphine, one finds unique sets of related chemical structures, providing additional significant biological annotation. The PubChem 3-D neighboring relationship is also shown to be able to group a set of non-steroidal anti-inflammatory drugs (NSAIDs, despite limited PubChem 2-D similarity. In a study of 4,218 chemical structures of biomedical interest, consisting of many known drugs, using more diverse conformers per compound results in more 3-D compound neighbors per compound; however, the overlap of the compound neighbor lists per conformer also increasingly resemble each other, being 38% identical at three conformers and 68% at ten conformers. Perhaps surprising is that the average

  5. 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.

  6. Application of geometric algebra for the description of polymer conformations

    Science.gov (United States)

    Chys, Pieter

    2008-03-01

    In this paper a Clifford algebra-based method is applied to calculate polymer chain conformations. The approach enables the calculation of the position of an atom in space with the knowledge of the bond length (l), valence angle (θ), and rotation angle (φ) of each of the preceding bonds in the chain. Hence, the set of geometrical parameters {li,θi,φi} yields all the position coordinates pi of the main chain atoms. Moreover, the method allows the calculation of side chain conformations and the computation of rotations of chain segments. With these features it is, in principle, possible to generate conformations of any type of chemical structure. This method is proposed as an alternative for the classical approach by matrix algebra. It is more straightforward and its final symbolic representation considerably simpler than that of matrix algebra. Approaches for realistic modeling by means of incorporation of energetic considerations can be combined with it. This article, however, is entirely focused at showing the suitable mathematical framework on which further developments and applications can be built.

  7. Application of geometric algebra for the description of polymer conformations.

    Science.gov (United States)

    Chys, Pieter

    2008-03-14

    In this paper a Clifford algebra-based method is applied to calculate polymer chain conformations. The approach enables the calculation of the position of an atom in space with the knowledge of the bond length (l), valence angle (theta), and rotation angle (phi) of each of the preceding bonds in the chain. Hence, the set of geometrical parameters {l(i),theta(i),phi(i)} yields all the position coordinates p(i) of the main chain atoms. Moreover, the method allows the calculation of side chain conformations and the computation of rotations of chain segments. With these features it is, in principle, possible to generate conformations of any type of chemical structure. This method is proposed as an alternative for the classical approach by matrix algebra. It is more straightforward and its final symbolic representation considerably simpler than that of matrix algebra. Approaches for realistic modeling by means of incorporation of energetic considerations can be combined with it. This article, however, is entirely focused at showing the suitable mathematical framework on which further developments and applications can be built.

  8. Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods.

    Science.gov (United States)

    Abella, Jayvee R; Moll, Mark; Kavraki, Lydia E

    2017-10-16

    The ability to efficiently sample structurally diverse protein conformations allows one to gain a high-level view of a protein's energy landscape. Algorithms from robot motion planning have been used for conformational sampling, and several of these algorithms promote diversity by keeping track of "coverage" in conformational space based on the local sampling density. However, large proteins present special challenges. In particular, larger systems require running many concurrent instances of these algorithms, but these algorithms can quickly become memory intensive because they typically keep previously sampled conformations in memory to maintain coverage estimates. In addition, robotics-inspired algorithms depend on defining useful perturbation strategies for exploring the conformational space, which is a difficult task for large proteins because such systems are typically more constrained and exhibit complex motions. In this article, we introduce two methodologies for maintaining and enhancing diversity in robotics-inspired conformational sampling. The first method addresses algorithms based on coverage estimates and leverages the use of a low-dimensional projection to define a global coverage grid that maintains coverage across concurrent runs of sampling. The second method is an automatic definition of a perturbation strategy through readily available flexibility information derived from B-factors, secondary structure, and rigidity analysis. Our results show a significant increase in the diversity of the conformations sampled for proteins consisting of up to 500 residues when applied to a specific robotics-inspired algorithm for conformational sampling. The methodologies presented in this article may be vital components for the scalability of robotics-inspired approaches.

  9. Conformational Properties of β-PrP*

    Science.gov (United States)

    Hosszu, Laszlo L. P.; Trevitt, Clare R.; Jones, Samantha; Batchelor, Mark; Scott, David J.; Jackson, Graham S.; Collinge, John; Waltho, Jonathan P.; Clarke, Anthony R.

    2009-01-01

    Prion propagation involves a conformational transition of the cellular form of prion protein (PrPC) to a disease-specific isomer (PrPSc), shifting from a predominantly α-helical conformation to one dominated by β-sheet structure. This conformational transition is of critical importance in understanding the molecular basis for prion disease. Here, we elucidate the conformational properties of a disulfide-reduced fragment of human PrP spanning residues 91–231 under acidic conditions, using a combination of heteronuclear NMR, analytical ultracentrifugation, and circular dichroism. We find that this form of the protein, which similarly to PrPSc, is a potent inhibitor of the 26 S proteasome, assembles into soluble oligomers that have significant β-sheet content. The monomeric precursor to these oligomers exhibits many of the characteristics of a molten globule intermediate with some helical character in regions that form helices I and III in the PrPC conformation, whereas helix II exhibits little evidence for adopting a helical conformation, suggesting that this region is a likely source of interaction within the initial phases of the transformation to a β-rich conformation. This precursor state is almost as compact as the folded PrPC structure and, as it assembles, only residues 126–227 are immobilized within the oligomeric structure, leaving the remainder in a mobile, random-coil state. PMID:19369250

  10. Conformational properties of beta-PrP.

    Science.gov (United States)

    Hosszu, Laszlo L P; Trevitt, Clare R; Jones, Samantha; Batchelor, Mark; Scott, David J; Jackson, Graham S; Collinge, John; Waltho, Jonathan P; Clarke, Anthony R

    2009-08-14

    Prion propagation involves a conformational transition of the cellular form of prion protein (PrPC) to a disease-specific isomer (PrPSc), shifting from a predominantly alpha-helical conformation to one dominated by beta-sheet structure. This conformational transition is of critical importance in understanding the molecular basis for prion disease. Here, we elucidate the conformational properties of a disulfide-reduced fragment of human PrP spanning residues 91-231 under acidic conditions, using a combination of heteronuclear NMR, analytical ultracentrifugation, and circular dichroism. We find that this form of the protein, which similarly to PrPSc, is a potent inhibitor of the 26 S proteasome, assembles into soluble oligomers that have significant beta-sheet content. The monomeric precursor to these oligomers exhibits many of the characteristics of a molten globule intermediate with some helical character in regions that form helices I and III in the PrPC conformation, whereas helix II exhibits little evidence for adopting a helical conformation, suggesting that this region is a likely source of interaction within the initial phases of the transformation to a beta-rich conformation. This precursor state is almost as compact as the folded PrPC structure and, as it assembles, only residues 126-227 are immobilized within the oligomeric structure, leaving the remainder in a mobile, random-coil state.

  11. Conformational effects in photoelectron circular dichroism

    Science.gov (United States)

    Turchini, S.

    2017-12-01

    Photoelectron circular dichroism (PECD) is a novel type of spectroscopy, which presents surprising sensitivity to conformational effects in chiral systems. While classical photoelectron spectroscopy mainly responds to conformational effects in terms of energy level shifts, PECD provides a rich and detailed response to tiny changes in electronic and structural properties by means of the intensity dispersion of the circular dichroism as a function of photoelectron kinetic energy. In this work, the basics of PECD will be outlined, emphasizing the role of interference from the l,l+/- 1 outgoing partial wave of the photoelectron in the PECD transition matrix element, which is responsible for the extreme sensitivity to conformational effects. Examples using molecular systems and interfaces will shed light on the powerful application of PECD to classical conformational effects such as group substitution, isomerism, conformer population and clustering. Moreover, the PECD results will be reported in challenging new fields where conformations play a key role, such as vibrational effects, transient chirality and time- resolved experiments. To date, PECD has mostly been based on synchrotron radiation facilities, but it also has a future as a table-top lab experiment by means of multiphoton ionization. An important application of PECD as an analytical tool will be reported. The aim of this review is to illustrate that in PECD, the presence of conformational effects is essential for understanding a wide range of effects from a new perspective, making it different from classical spectroscopy.

  12. On functional representations of the conformal algebra

    Energy Technology Data Exchange (ETDEWEB)

    Rosten, Oliver J.

    2017-07-15

    Starting with conformally covariant correlation functions, a sequence of functional representations of the conformal algebra is constructed. A key step is the introduction of representations which involve an auxiliary functional. It is observed that these functionals are not arbitrary but rather must satisfy a pair of consistency equations corresponding to dilatation and special conformal invariance. In a particular representation, the former corresponds to the canonical form of the exact renormalization group equation specialized to a fixed point whereas the latter is new. This provides a concrete understanding of how conformal invariance is realized as a property of the Wilsonian effective action and the relationship to action-free formulations of conformal field theory. Subsequently, it is argued that the conformal Ward Identities serve to define a particular representation of the energy-momentum tensor. Consistency of this construction implies Polchinski's conditions for improving the energy-momentum tensor of a conformal field theory such that it is traceless. In the Wilsonian approach, the exactly marginal, redundant field which generates lines of physically equivalent fixed points is identified as the trace of the energy-momentum tensor. (orig.)

  13. Ensemble QSAR: a QSAR method based on conformational ensembles and metric descriptors.

    Science.gov (United States)

    Pissurlenkar, Raghuvir R S; Khedkar, Vijay M; Iyer, Radhakrishnan P; Coutinho, Evans C

    2011-07-30

    Quantitative structure-activity relationship (QSAR) is the most versatile tool in computer-assisted molecular design. One conceptual drawback seen in QSAR approaches is the "one chemical-one structure-one parameter value" dogma where the model development is based on physicochemical description for a single molecular conformation, while ignoring the rest of the conformational space. It is well known that molecules have several low-energy conformations populated at physiological temperature, and each conformer makes a significant impact on associated properties such as biological activity. At the level of molecular interaction, the dynamics around the molecular structure is of prime essence rather than the average structure. As a step toward understanding the role of these discrete microscopic states in biological activity, we have put together a theoretically rigorous and computationally tractable formalism coined as eQSAR. In this approach, the biological activity is modeled as a function of physicochemical description for a selected set of low-energy conformers, rather than that's for a single lowest energy conformation. Eigenvalues derived from the "Physicochemical property integrated distance matrices" (PD-matrices) that encompass both 3D structure and physicochemical properties, have been used as descriptors; is a novel addition. eQSAR is validated on three peptide datasets and explicitly elaborated for bradykinin-potentiating peptides. The conformational ensembles were generated by a simple molecular dynamics and consensus dynamics approaches. The eQSAR models are statistically significant and possess the ability to select the most biologically relevant conformation(s) with the relevant physicochemical attributes that have the greatest meaning for description of the biological activity. Copyright © 2011 Wiley Periodicals, Inc.

  14. 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.

  15. Conformal field theory with gauge symmetry

    CERN Document Server

    Ueno, Kenji

    2008-01-01

    This book presents a systematic approach to conformal field theory with gauge symmetry from the point of view of complex algebraic geometry. After presenting the basic facts of the theory of compact Riemann surfaces and the representation theory of affine Lie algebras in Chapters 1 and 2, conformal blocks for pointed Riemann surfaces with coordinates are constructed in Chapter 3. In Chapter 4 the sheaf of conformal blocks associated to a family of pointed Riemann surfaces with coordinates is constructed, and in Chapter 5 it is shown that this sheaf supports a projective flat connection-one of

  16. Conformable Fractional Nikiforov—Uvarov Method

    Science.gov (United States)

    Karayer, H.; Demirhan, D.; Büyükkılıç, F.

    2016-07-01

    We introduce conformable fractional Nikiforov—Uvarov (NU) method by means of conformable fractional derivative which is the most natural definition in non-integer calculus. Since, NU method gives exact eigenstate solutions of Schrödinger equation (SE) for certain potentials in quantum mechanics, this method is carried into the domain of fractional calculus to obtain the solutions of fractional SE. In order to demonstrate the applicability of the conformable fractional NU method, we solve fractional SE for harmonic oscillator potential, Woods—Saxon potential, and Hulthen potential.

  17. Conformal Gravity: Dark Matter and Dark Energy

    Directory of Open Access Journals (Sweden)

    Robert K. Nesbet

    2013-01-01

    Full Text Available This short review examines recent progress in understanding dark matter, dark energy, and galactic halos using theory that departs minimally from standard particle physics and cosmology. Strict conformal symmetry (local Weyl scaling covariance, postulated for all elementary massless fields, retains standard fermion and gauge boson theory but modifies Einstein–Hilbert general relativity and the Higgs scalar field model, with no new physical fields. Subgalactic phenomenology is retained. Without invoking dark matter, conformal gravity and a conformal Higgs model fit empirical data on galactic rotational velocities, galactic halos, and Hubble expansion including dark energy.

  18. Conformal invariance in quantum field theory

    CERN Document Server

    Todorov, Ivan T; Petkova, Valentina B

    1978-01-01

    The present volume is an extended and up-to-date version of two sets of lectures by the first author and it reviews more recent work. The notes aim to present a self-contained exposition of a constructive approach to conformal invariant quantum field theory. Other parts in application of the conformal group to quantum physics are only briefly mentioned. The relevant mathematical material (harmonic analysis on Euclidean conformal groups) is briefly summarized. A new exposition of physical applications is given, which includes an explicit construction of the vacuum operator product expansion for the free zero mass fields.

  19. Static validation of licence conformance policies

    DEFF Research Database (Denmark)

    Hansen, Rene Rydhof; Nielson, Flemming; Nielson, Hanne Riis

    2008-01-01

    Policy conformance is a security property gaining importance due to commercial interest like Digital Rights Management. It is well known that static analysis can be used to validate a number of more classical security policies, such as discretionary and mandatory access control policies, as well...... as communication protocols using symmetric and asymmetric cryptography. In this work we show how to develop a Flow Logic for validating the conformance of client software with respect to a licence conformance policy. Our approach is sufficiently flexible that it extends to fully open systems that can admit new...

  20. Large loop conformation sampling using the activation relaxation technique, ART-nouveau method.

    Science.gov (United States)

    St-Pierre, Jean-François; Mousseau, Normand

    2012-07-01

    We present an adaptation of the ART-nouveau energy surface sampling method to the problem of loop structure prediction. This method, previously used to study protein folding pathways and peptide aggregation, is well suited to the problem of sampling the conformation space of large loops by targeting probable folding pathways instead of sampling exhaustively that space. The number of sampled conformations needed by ART nouveau to find the global energy minimum for a loop was found to scale linearly with the sequence length of the loop for loops between 8 and about 20 amino acids. Considering the linear scaling dependence of the computation cost on the loop sequence length for sampling new conformations, we estimate the total computational cost of sampling larger loops to scale quadratically compared to the exponential scaling of exhaustive search methods. Copyright © 2012 Wiley Periodicals, Inc.

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

    Science.gov (United States)

    Bai, Fang; Liu, Xiaofeng; Li, Jiabo; Zhang, Haoyun; Jiang, Hualiang; Wang, Xicheng; Li, Honglin

    2010-11-04

    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. 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. By incorporating different energy terms with several empirical criteria, the MECBM method can produce more reasonable conformational ensemble with high accuracy but approximately the same

  2. Examining the Influence of Phosphorylation on Peptide Ion Structure by Ion Mobility Spectrometry-Mass Spectrometry

    Science.gov (United States)

    Glover, Matthew S.; Dilger, Jonathan M.; Acton, Matthew D.; Arnold, Randy J.; Radivojac, Predrag; Clemmer, David E.

    2016-05-01

    Ion mobility spectrometry-mass spectrometry (IMS-MS) techniques are used to study the general effects of phosphorylation on peptide structure. Cross sections for a library of 66 singly phosphorylated peptide ions from 33 pairs of positional isomers, and unmodified analogues were measured. Intrinsic size parameters (ISPs) derived from these measurements yield calculated collision cross sections for 85% of these phosphopeptide sequences that are within ±2.5% of experimental values. The average ISP for the phosphoryl group (0.64 ± 0.05) suggests that in general this moiety forms intramolecular interactions with the neighboring residues and peptide backbone, resulting in relatively compact structures. We assess the capability of ion mobility to separate positional isomers (i.e., peptide sequences that differ only in the location of the modification) and find that more than half of the isomeric pairs have >1% difference in collision cross section. Phosphorylation is also found to influence populations of structures that differ in the cis/ trans orientation of Xaa-Pro peptide bonds. Several sequences with phosphorylated Ser or Thr residues located N-terminally adjacent to Pro residues show fewer conformations compared to the unmodified sequences.

  3. Metric Measure Space as a Framework for Gravitation

    CERN Document Server

    Rahmanpour, Nafiseh

    2016-01-01

    In this manuscript, we show how conformal invariance can be incorporated in a classical theory of gravitation, in the context of metric measure space. Metric measure space involves a geometrical scalar $f$, dubbed as density function, which here appears as a conformal degree of freedom. In this framework, we present conformally invariant field equations, the relevant identities and geodesic equations. In metric measure space, the volume element and accordingly the operators with integral based definitions are modified. For instance, the divergence operator in this space differs from the Riemannian one. As a result, a gravitational theory formulated in this space has a generalized second Bianchi identity and a generalized conservation of energy-momentum tensor. It is shown how, by using the generalized identity for conservation of energy-momentum tensor, one can obtain a conformally invariant geodesic equation. By comparison of the geodesic equations in metric measure space with the Bohmian trajectories, in bo...

  4. Aluminized fiberglass insulation conforms to curved surfaces

    Science.gov (United States)

    1966-01-01

    Layers of fiber glass with outer reflective films of vacuum-deposited aluminum or other reflective metal, provide thermal insulation which conforms to curved surfaces. This insulation has good potential for cryogenic systems.

  5. Timed Safety Automata and Logic Conformance

    National Research Council Canada - National Science Library

    Young, Frank

    1999-01-01

    Timed Logic Conformance (TLC) is used to verify the behavioral and timing properties of detailed digital circuits against abstract circuit specifications when both are modeled as Timed Safety Automata (TSA...

  6. Conformal Carroll groups and BMS symmetry

    OpenAIRE

    Duval, C.; Gibbons, G W; Horvathy, P. A.

    2014-01-01

    The Bondi-Metzner-Sachs (BMS) group is shown to be the conformal extension of Levy-Leblond's "Carroll" group. Further extension to the Newman-Unti (NU) group is also discussed in the Carroll framework.

  7. General Information for Transportation and Conformity

    Science.gov (United States)

    Transportation conformity is required by the Clean Air Act section 176(c) (42 U.S.C. 7506(c)) to ensure that federal funding and approval are given to highway and transit projects that are consistent with SIP.

  8. Social conformity despite individual preferences for distinctiveness.

    Science.gov (United States)

    Smaldino, Paul E; Epstein, Joshua M

    2015-03-01

    We demonstrate that individual behaviours directed at the attainment of distinctiveness can in fact produce complete social conformity. We thus offer an unexpected generative mechanism for this central social phenomenon. Specifically, we establish that agents who have fixed needs to be distinct and adapt their positions to achieve distinctiveness goals, can nevertheless self-organize to a limiting state of absolute conformity. This seemingly paradoxical result is deduced formally from a small number of natural assumptions and is then explored at length computationally. Interesting departures from this conformity equilibrium are also possible, including divergence in positions. The effect of extremist minorities on these dynamics is discussed. A simple extension is then introduced, which allows the model to generate and maintain social diversity, including multimodal distinctiveness distributions. The paper contributes formal definitions, analytical deductions and counterintuitive findings to the literature on individual distinctiveness and social conformity.

  9. Reciprocity Outperforms Conformity to Promote Cooperation.

    Science.gov (United States)

    Romano, Angelo; Balliet, Daniel

    2017-10-01

    Evolutionary psychologists have proposed two processes that could give rise to the pervasiveness of human cooperation observed among individuals who are not genetically related: reciprocity and conformity. We tested whether reciprocity outperformed conformity in promoting cooperation, especially when these psychological processes would promote a different cooperative or noncooperative response. To do so, across three studies, we observed participants' cooperation with a partner after learning (a) that their partner had behaved cooperatively (or not) on several previous trials and (b) that their group members had behaved cooperatively (or not) on several previous trials with that same partner. Although we found that people both reciprocate and conform, reciprocity has a stronger influence on cooperation. Moreover, we found that conformity can be partly explained by a concern about one's reputation-a finding that supports a reciprocity framework.

  10. Film dosimetry in conformal radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Danciu, C.; Proimos, B.S. [Patras Univ. (Greece). Dept. of Medical Physics

    1995-12-01

    Dosimetry, through a film sandwiched in a transverse cross-section of a solid phantom, is a method of choice in Conformal Radiotherapy because: (a) the blackness (density) of the film at each point offers a measure of the total dose received at that point, and (b) the film is easily calibrated by exposing a film strip in the same cross-section, through a stationary field. The film must therefore have the following properties: (a) it must be slow, in order not to be overexposed, even at a therapeutic dose of 200 cGy, and (b) the response of the film (density versus dose curve) must be independent of the photon energy spectrum. A few slow films were compared. It was found that the Kodak X-Omat V for therapy verification was the best choice. To investigate whether the film response was independent of the photon energy, response curves for six depths, starting from the depth of maximum dose to the depth of 25 cm, in solid phantom were derived. The vertical beam was perpendicular to the anterior surface of the phantom, which was at the distance of 100 cm from the source and the field was 15x15 cm at that distance. This procedure was repeated for photon beams emitted by a Cobalt-60 unit, two 6 MV and 15 MV Linear Accelerators, as well as a 45 MV Betatron. For each of those four different beams the film response was the same for all six depths. The results, as shown in the diagrams, are very satisfactory. The response curve under a geometry similar to that actually applied, when the film is irradiated in a transverse cross-section of the phantom, was derived. The horizontal beam was almost parallel (angle of 85) to the plane of the film. The same was repeated with the central ray parallel to the film (angle 90) and at a distance of 1.5 cm from the horizontal film. The field size was again 15x15 at the lateral entrance surface of the beam. The response curves remained the same, as when the beam was perpendicular to the films.

  11. The Minkowski and conformal superspaces the classical and quantum descriptions

    CERN Document Server

    Fioresi, Rita

    2015-01-01

    This book is aimed at graduate students and researchers in physics and mathematics who seek to understand the basics of supersymmetry from a mathematical point of view. It provides a bridge between the physical and mathematical approaches to the superworld. The physicist who is devoted to learning the basics of supergeometry can find a friendly approach here, since only the concepts that are strictly necessary are introduced. On the other hand, the mathematician who wants to learn from physics will find that all the mathematical assumptions are firmly rooted in physical concepts. This may open up a channel of communication between the two communities working on different aspects of supersymmetry. Starting from special relativity and Minkowski space, the idea of conformal space and superspace is built step by step in a mathematically rigorous way, and always connecting with the ideas and notation used in physics. While the book is mainly devoted to these important physical examples of superspaces, it can also ...

  12. A novel conformational switch for electron transfer

    Indian Academy of Sciences (India)

    Administrator

    The soluble fraction of the sub-unit II cloned and over-expressed in E. coli has been studied as a model of the electron entry site (CuA) of cytochrome oxidase. The CuA site in the sub-unit II was found to exist in a pH induced conformational equilibrium with a high pH conformer being preferred at elevated temperatures.

  13. Does gender diversity promote non-conformity?

    OpenAIRE

    Amini, Makan; Ekström, Mathias; Ellingsen, Tore; Johannesson, Magnus; Strömsten, Fredrik

    2015-01-01

    Failure to express minority views may distort the behavior of company boards, committees, juries, and other decision-making bodies. Devising a new experimental procedure to measure such conformity in a judgment task, we compare the degree of conformity in groups with varying gender composition. Overall, our experiments offer little evidence that gender composition affects expression of minority views. A robust finding is that a subject's lack of ability predicts both a true propensity to acce...

  14. The research of conformal optical design

    Science.gov (United States)

    Li, Lin; Li, Yan; Huang, Yi-fan; Du, Bao-lin

    2009-07-01

    Conformal optical domes are characterized as having external more elongated optical surfaces that are optimized to minimize drag, increased missile velocity and extended operational range. The outer surface of the conformal domes typically deviate greatly from spherical surface descriptions, so the inherent asymmetry of conformal surfaces leads to variations in the aberration content presented to the optical sensor as it is gimbaled across the field of regard, which degrades the sensor's ability to properly image targets of interest and then undermine the overall system performance. Consequently, the aerodynamic advantages of conformal domes cannot be realized in practical systems unless the dynamic aberration correction techniques are developed to restore adequate optical imaging capabilities. Up to now, many optical correction solutions have been researched in conformal optical design, including static aberrations corrections and dynamic aberrations corrections. There are three parts in this paper. Firstly, the combination of static and dynamic aberration correction is introduced. A system for correcting optical aberration created by a conformal dome has an outer surface and an inner surface. The optimization of the inner surface is regard as the static aberration correction; moreover, a deformable mirror is placed at the position of the secondary mirror in the two-mirror all reflective imaging system, which is the dynamic aberration correction. Secondly, the using of appropriate surface types is very important in conformal dome design. Better performing optical systems can result from surface types with adequate degrees of freedom to describe the proper corrector shape. Two surface types and the methods of using them are described, including Zernike polynomial surfaces used in correct elements and user-defined surfaces used in deformable mirror (DM). Finally, the Adaptive optics (AO) correction is presented. In order to correct the dynamical residual aberration

  15. Effective Conformal Descriptions of Black Hole Entropy

    Directory of Open Access Journals (Sweden)

    Steven Carlip

    2011-07-01

    Full Text Available It is no longer considered surprising that black holes have temperatures and entropies. What remains surprising, though, is the universality of these thermodynamic properties: their exceptionally simple and general form, and the fact that they can be derived from many very different descriptions of the underlying microscopic degrees of freedom. I review the proposal that this universality arises from an approximate conformal symmetry, which permits an effective “conformal dual” description that is largely independent of the microscopic details.

  16. Divergence-type theory of conformal fields

    OpenAIRE

    Peralta-Ramos, J.; Calzetta, E.

    2009-01-01

    We present a nonlinear hydrodynamical description of a conformal plasma within the framework of divergence-type theories (DTTs), which are not based on a gradient expansion. We compare the equations of the DTT and the second-order theory (based on conformal invariants), for the case of Bjorken ow. The approach to ideal hydrodynamics is faster in the DTT, indicating that our results can be useful in the study of early-time dynamics in relativistic heavy-ion collisions.

  17. Tutorial appendix: structure preserving representation of euclidean motions through conformal geometric algebra

    NARCIS (Netherlands)

    Dorst, L.; Dorst, L.; Lasenby, J.

    2011-01-01

    Using conformal geometric algebra, Euclidean motions in n-D are represented as orthogonal transformations of a representational space of two extra dimensions, and a well-chosen metric. Orthogonal transformations are representable as multiple reflections, and by means of the geometric product this

  18. Diffusion and Signatures of Localization in Stochastic Conformal Field Theory

    Science.gov (United States)

    Bernard, Denis; Doyon, Benjamin

    2017-09-01

    We define a simple model of conformal field theory in random space-time environments, which we refer to as stochastic conformal field theory. This model accounts for the effects of dilute random impurities in strongly interacting critical many-body systems. On one hand, surprisingly, although impurities are separated by macroscopic distances, we find that the infinite-time steady state is factorized on microscopic lengths, a signature of the emergence of localization. The stationary state also displays vanishing energy current and strong uncorrelated spatial fluctuations of local observables. On the other hand, at finite times, the transient shows a crossover from ballistic to diffusive energy propagation. In this regime and a Markovian limit, concentrating on current-generating initial states with a temperature imbalance, we show that the energy current and density satisfy simple dissipative hydrodynamic equations. We describe the space-time scales at which nonequilibrium currents exist. We show that a light-cone effect subsists in the presence of impurities although a momentum burst propagates transiently on a diffusive scale only.

  19. Organic and Polymeric Semiconductors Enhanced by Noncovalent Conformational Locks.

    Science.gov (United States)

    Huang, Hui; Yang, Lei; Facchetti, Antonio; Marks, Tobin J

    2017-08-09

    Constructing highly planar, extended π-electron systems is an important strategy for achieving high-mobility organic semiconductors. In general, there are two synthetic strategies for achieving π-conjugated systems with high planarity. The conventional strategy connects neighboring aromatic rings through covalent bonds to restrict the rotation about single bonds. However, this usually requires a complex sequence of synthetic steps to achieve this target, which can be costly and labor-intensive. More recently, noncovalent through-space intramolecular interactions, which are defined here as noncovalent conformational locks, have been employed with great success to increase the planarity and rigidity of extended π-electron systems; this has become a well-known and important strategy to design and synthesize highly planar π-conjugated systems for organic electronics. This review offers a comprehensive and general summary of conjugated systems with such noncovalent conformational locks, including O···S, N···S, X···S (where X = Cl, Br, F), and H···S through-space interactions, together with analysis by density functional theory computation, X-ray diffraction, and microstructural characterization, as well as by evaluation of charge transport in organic thin-film transistors and solar cells.

  20. Capillary electrophoresis mass spectrometry based metabolomics

    Directory of Open Access Journals (Sweden)

    Alexander M. Buko

    2017-03-01

    Full Text Available Capillary electrophoresis–mass spectrometry (CE-MS is a powerful orthogonal technique capable of filling in gaps in the identification, quantitation and isomeric resolution of many small hydrophilic and charged metabolites. The metabolome is a large complex mixture of molecules for which not one technique nor a combination of techniques can optimally identify and measure it in it’s entirety. LC-MS, GC-MS and NMR have been the widely used for metabolomics for the past 20 years for a wide range of applications, each technique having shown uniqueness and advantages, for specific applications or target metabolic chemical space. CE-MS captures a unique metabolic chemical space beyond these standard methods providing another window into metabolomics profiling. This review will focus on the recent publications published within 2016 focusing on biotechnology and pharmaceutical applications of CE-MS.

  1. Laser-Cooling-Assisted Mass Spectrometry

    Science.gov (United States)

    Schneider, Christian; Schowalter, Steven J.; Chen, Kuang; Sullivan, Scott T.; Hudson, Eric R.

    2014-09-01

    Mass spectrometry is used in a wide range of scientific disciplines including proteomics, pharmaceutics, forensics, and fundamental physics and chemistry. Given this ubiquity, there is a worldwide effort to improve the efficiency and resolution of mass spectrometers. However, the performance of all techniques is ultimately limited by the initial phase-space distribution of the molecules being analyzed. Here, we dramatically reduce the width of this initial phase-space distribution by sympathetically cooling the input molecules with laser-cooled, cotrapped atomic ions, improving both the mass resolution and detection efficiency of a time-of-flight mass spectrometer by over an order of magnitude. Detailed molecular-dynamics simulations verify the technique and aid with evaluating its effectiveness. This technique appears to be applicable to other types of mass spectrometers.

  2. On being loud and proud: non-conformity and counter-conformity to group norms.

    Science.gov (United States)

    Hornsey, Matthew J; Majkut, Louise; Terry, Deborah J; McKimmie, Blake M

    2003-09-01

    Most experiments on conformity have been conducted in relation to judgments of physical reality; surprisingly few papers have experimentally examined the influence of group norms on social issues with a moral component. In response to this, participants were told that they were either in a minority or in a majority relative to their university group in terms of their attitudes toward recognition of gay couples in law (Expt 1: N = 205) and a government apology to Aborigines (Expt 2: N = 110). In both experiments, it was found that participants who had a weak moral basis for their attitude conformed to the group norm on private behaviours. In contrast, those who had a strong moral basis for their attitude showed non-conformity on private behaviours and counter-conformity on public behaviours. Incidences of non-conformity and counter-conformity are discussed with reference to theory and research on normative influence.

  3. Conformational proofreading: the impact of conformational changes on the specificity of molecular recognition.

    Directory of Open Access Journals (Sweden)

    Yonatan Savir

    Full Text Available To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve conformational changes. This raises a basic question: Does molecular recognition gain any advantage by such conformational changes? By introducing a simple statistical-mechanics approach, we study the effect of conformation and flexibility on the quality of recognition processes. Our model relates specificity to the conformation of the participant molecules and thus suggests a possible answer: Optimal specificity is achieved when the ligand is slightly off target; that is, a conformational mismatch between the ligand and its main target improves the selectivity of the process. This indicates that deformations upon binding serve as a conformational proofreading mechanism, which may be selected for via evolution.

  4. Conformal field theories and tensor categories. Proceedings

    Energy Technology Data Exchange (ETDEWEB)

    Bai, Chengming [Nankai Univ., Tianjin (China). Chern Institute of Mathematics; Fuchs, Juergen [Karlstad Univ. (Sweden). Theoretical Physics; Huang, Yi-Zhi [Rutgers Univ., Piscataway, NJ (United States). Dept. of Mathematics; Kong, Liang [Tsinghua Univ., Beijing (China). Inst. for Advanced Study; Runkel, Ingo; Schweigert, Christoph (eds.) [Hamburg Univ. (Germany). Dept. of Mathematics

    2014-08-01

    First book devoted completely to the mathematics of conformal field theories, tensor categories and their applications. Contributors include both mathematicians and physicists. Some long expository articles are especially suitable for beginners. The present volume is a collection of seven papers that are either based on the talks presented at the workshop ''Conformal field theories and tensor categories'' held June 13 to June 17, 2011 at the Beijing International Center for Mathematical Research, Peking University, or are extensions of the material presented in the talks at the workshop. These papers present new developments beyond rational conformal field theories and modular tensor categories and new applications in mathematics and physics. The topics covered include tensor categories from representation categories of Hopf algebras, applications of conformal field theories and tensor categories to topological phases and gapped systems, logarithmic conformal field theories and the corresponding non-semisimple tensor categories, and new developments in the representation theory of vertex operator algebras. Some of the papers contain detailed introductory material that is helpful for graduate students and researchers looking for an introduction to these research directions. The papers also discuss exciting recent developments in the area of conformal field theories, tensor categories and their applications and will be extremely useful for researchers working in these areas.

  5. The ABC of protein kinase conformations.

    Science.gov (United States)

    Möbitz, Henrik

    2015-10-01

    Due to their involvement in human diseases, protein kinases are an important therapeutic target class. Conformation is a key concept for understanding how functional activity, inhibition and sequence are linked. We assemble and annotate the mammalian structural kinome from the Protein Data Bank on the basis of a universal residue nomenclature. We identify a torsion angle around the Gly of the DFG-motif whose sharp distribution profile corresponds to three eclipsed conformations. This allows the definition a small set of clusters whose distribution shows a bias for the active conformation. A common rationale links the active and inactive state: stabilization of the active conformation, as well as inactivation by displacement of helix-αC or the DFG-motif is governed by the interaction between helix-αC and the DFG motif. In particular, the conformation of the DFG-motif is tightly correlated with the propensity of helix-αC displacement. Our analysis reveals detailed mechanisms for the displacement of helix-αC and the DFG and improves our understanding of the role of individual residues. By pooling conformations from the whole structural kinome, the energetic contributions of sequence and extrinsic factors can be estimated in free energy analyses. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Analytical halo model of galactic conformity

    Science.gov (United States)

    Pahwa, Isha; Paranjape, Aseem

    2017-09-01

    We present a fully analytical halo model of colour-dependent clustering that incorporates the effects of galactic conformity in a halo occupation distribution framework. The model, based on our previous numerical work, describes conformity through a correlation between the colour of a galaxy and the concentration of its parent halo, leading to a correlation between central and satellite galaxy colours at fixed halo mass. The strength of the correlation is set by a tunable 'group quenching efficiency', and the model can separately describe group-level correlations between galaxy colour (1-halo conformity) and large-scale correlations induced by assembly bias (2-halo conformity). We validate our analytical results using clustering measurements in mock galaxy catalogues, finding that the model is accurate at the 10-20 per cent level for a wide range of luminosities and length-scales. We apply the formalism to interpret the colour-dependent clustering of galaxies in the Sloan Digital Sky Survey (SDSS). We find good overall agreement between the data and a model that has 1-halo conformity at a level consistent with previous results based on an SDSS group catalogue, although the clustering data require satellites to be redder than suggested by the group catalogue. Within our modelling uncertainties, however, we do not find strong evidence of 2-halo conformity driven by assembly bias in SDSS clustering.

  7. Controlling complex networks with conformity behavior

    Science.gov (United States)

    Wang, Xu-Wen; Nie, Sen; Wang, Wen-Xu; Wang, Bing-Hong

    2015-09-01

    Controlling complex networks accompanied by common conformity behavior is a fundamental problem in social and physical science. Conformity behavior that individuals tend to follow the majority in their neighborhood is common in human society and animal communities. Despite recent progress in understanding controllability of complex networks, the existent controllability theories cannot be directly applied to networks associated with conformity. Here we propose a simple model to incorporate conformity-based decision making into the evolution of a network system, which allows us to employ the exact controllability theory to explore the controllability of such systems. We offer rigorous theoretical results of controllability for representative regular networks. We also explore real networks in different fields and some typical model networks, finding some interesting results that are different from the predictions of structural and exact controllability theory in the absence of conformity. We finally present an example of steering a real social network to some target states to further validate our controllability theory and tools. Our work offers a more realistic understanding of network controllability with conformity behavior and can have potential applications in networked evolutionary games, opinion dynamics and many other complex networked systems.

  8. Hyperphosphorylation of intrinsically disordered tau protein induces an amyloidogenic shift in its conformational ensemble.

    Directory of Open Access Journals (Sweden)

    Shaolong Zhu

    Full Text Available Tau is an intrinsically disordered protein (IDP whose primary physiological role is to stabilize microtubules in neuronal axons at all stages of development. In Alzheimer's and other tauopathies, tau forms intracellular insoluble amyloid aggregates known as neurofibrillary tangles, a process that appears in many cases to be preceded by hyperphosphorylation of tau monomers. Understanding the shift in conformational bias induced by hyperphosphorylation is key to elucidating the structural factors that drive tau pathology, however, as an IDP, tau is not amenable to conventional structural characterization. In this work, we employ a straightforward technique based on Time-Resolved ElectroSpray Ionization Mass Spectrometry (TRESI-MS and Hydrogen/Deuterium Exchange (HDX to provide a detailed picture of residual structure in tau, and the shifts in conformational bias induced by hyperphosphorylation. By comparing the native and hyperphosphorylated ensembles, we are able to define specific conformational biases that can easily be rationalized as enhancing amyloidogenic propensity. Representative structures for the native and hyperphosphorylated tau ensembles were generated by refinement of a broad sample of conformations generated by low-computational complexity modeling, based on agreement with the TRESI-HDX profiles.

  9. Topological Dissection of the Membrane Transport Protein Mhp1 Derived from Cysteine Accessibility and Mass Spectrometry.

    Science.gov (United States)

    Calabrese, Antonio N; Jackson, Scott M; Jones, Lynsey N; Beckstein, Oliver; Heinkel, Florian; Gsponer, Joerg; Sharples, David; Sans, Marta; Kokkinidou, Maria; Pearson, Arwen R; Radford, Sheena E; Ashcroft, Alison E; Henderson, Peter J F

    2017-09-05

    Cys accessibility and quantitative intact mass spectrometry (MS) analyses have been devised to study the topological transitions of Mhp1, the membrane protein for sodium-linked transport of hydantoins from Microbacterium liquefaciens. Mhp1 has been crystallized in three forms (outward-facing open, outward-facing occluded with substrate bound, and inward-facing open). We show that one natural cysteine residue, Cys327, out of three, has an enhanced solvent accessibility in the inward-facing (relative to the outward-facing) form. Reaction of the purified protein, in detergent, with the thiol-reactive N-ethylmalemide (NEM), results in modification of Cys327, suggesting that Mhp1 adopts predominantly inward-facing conformations. Addition of either sodium ions or the substrate 5-benzyl-l-hydantoin (L-BH) does not shift this conformational equilibrium, but systematic co-addition of the two results in an attenuation of labeling, indicating a shift toward outward-facing conformations that can be interpreted using conventional enzyme kinetic analyses. Such measurements can afford the Km for each ligand as well as the stoichiometry of ion-substrate-coupled conformational changes. Mutations that perturb the substrate binding site either result in the protein being unable to adopt outward-facing conformations or in a global destabilization of structure. The methodology combines covalent labeling, mass spectrometry, and kinetic analyses in a straightforward workflow applicable to a range of systems, enabling the interrogation of changes in a protein's conformation required for function at varied concentrations of substrates, and the consequences of mutations on these conformational transitions.

  10. S-Adenosylmethionine conformations in solution and in protein complexes: Conformational influences of the sulfonium group

    DEFF Research Database (Denmark)

    Markham, George D.; Norrby, Per-Ola; Bock, Charles W.

    2002-01-01

    calculations. Nuclear Overhauser effect measurements and computational results for AdoMet indicate a predominantly anti conformation about the glycosidic bond with a variety of conformations about the methionyl C-alpha-C-beta and C-beta-C-gamma bonds. An AdoMet conformation in which the positively charged....... In 20 reported structures of AdoMet-protein complexes, both anti and syn glycosidic torsional angles are found. The methionyl group typically adopts an extended conformation in complexes with enzymes that transfer the methyl group from the sulfonium center, but is more folded in complexes with proteins...

  11. Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules

    KAUST Repository

    Wang, Wei

    2017-10-06

    The function of complex biomolecular machines relies heavily on their conformational changes. Investigating these functional conformational changes is therefore essential for understanding the corresponding biological processes and promoting bioengineering applications and rational drug design. Constructing Markov State Models (MSMs) based on large-scale molecular dynamics simulations has emerged as a powerful approach to model functional conformational changes of the biomolecular system with sufficient resolution in both time and space. However, the rapid development of theory and algorithms for constructing MSMs has made it difficult for nonexperts to understand and apply the MSM framework, necessitating a comprehensive guidance toward its theory and practical usage. In this study, we introduce the MSM theory of conformational dynamics based on the projection operator scheme. We further propose a general protocol of constructing MSM to investigate functional conformational changes, which integrates the state-of-the-art techniques for building and optimizing initial pathways, performing adaptive sampling and constructing MSMs. We anticipate this protocol to be widely applied and useful in guiding nonexperts to study the functional conformational changes of large biomolecular systems via the MSM framework. We also discuss the current limitations of MSMs and some alternative methods to alleviate them.

  12. The chemistry of prions: small molecules, protein conformers and mass spectrometry

    Science.gov (United States)

    Background/Introduction. Prions propagate by converting a normal cellular isoform (PrPC) into the prion isoform (PrPSc) in a template-driven process. The lysines in PrPC are highly conserved and strongly influence prion propagation, based on studies using natural polymorphisms of PrPC and transg...

  13. Protein conformational landscapes: energy minimization and clustering of a long molecular dynamics trajectory.

    Science.gov (United States)

    Troyer, J M; Cohen, F E

    1995-09-01

    Using energy minimization and cluster analysis, we have analyzed a 1020 ps molecular dynamics trajectory of solvated bovine pancreatic trypsin inhibitor. Elucidation of conformational substates in this way both illustrates the degree of conformational convergence in the simulation and reduces the structural data to a tractable subset. The relative movement of structures upon energy minimization was used to estimate the sizes of features on the protein potential energy surface. The structures were analyzed using their pairwise root-mean-square C alpha deviations, which gave a global measure of conformational changes that would not be apparent by monitoring single degrees of freedom. At time scales of 0.1 ps, energy minimization detected sharp transitions between energy minima separated by 0.1 A rms deviation. Larger conformational clusters containing these smaller minima and separated by 0.25 A were seen at 1 ps time scales. Both of these small features of the conformational landscape were characterized by movements in loop regions associated with small, correlated backbone dihedral angle shifts. On a nanosecond time scale, the main features of the protein energy landscape were clusters separated by over 0.7 A rms deviation, with only seven of these substates visited over the 1 ns trajectory. These substrates, discernible both before and after energy minimization, differ mainly in a monotonic pivot of the loop residues 11-18 over the course of the simulation. This loop contains lysine 17, which specifically binds to trypsin in the active site. The trajectory did not return to previously visited clusters, indicating that this trajectory has not been shown to have completely sampled the conformational substates available to it. Because the apparent convergence to a single region of conformation space depends on both the time scale of observation and the size of the conformational features examined, convergence must be operationally defined within the context of the

  14. Protein-segment universe exhibiting transitions at intermediate segment length in conformational subspaces.

    Science.gov (United States)

    Ikeda, Kazuyoshi; Hirokawa, Takatsugu; Higo, Junichi; Tomii, Kentaro

    2008-08-13

    Many studies have examined rules governing two aspects of protein structures: short segments and proteins' structural domains. Nevertheless, the organization and nature of the conformational space of segments with intermediate length between short segments and domains remain unclear. Conformational spaces of intermediate length segments probably differ from those of short segments. We investigated the identification and characterization of the boundary(s) between peptide-like (short segment) and protein-like (long segment) distributions. We generated ensembles embedded in globular proteins comprising segments 10-50 residues long. We explored the relationships between the conformational distribution of segments and their lengths, and also protein structural classes using principal component analysis based on the intra-segment Calpha-Calpha atomic distances. Our statistical analyses of segment conformations and length revealed critical dual transitions in their conformational distribution with segments derived from all four structural classes. Dual transitions were identified with the intermediate phase between the short segments and domains. Consequently, protein segment universes were categorized. i) Short segments (10-22 residues) showed a distribution with a high frequency of secondary structure clusters. ii) Medium segments (23-26 residues) showed a distribution corresponding to an intermediate state of transitions. iii) Long segments (27-50 residues) showed a distribution converging on one huge cluster containing compact conformations with a smaller radius of gyration. This distribution reflects the protein structures' organization and protein domains' origin. Three major conformational components (radius of gyration, structural symmetry with respect to the N-terminal and C-terminal halves, and single-turn/two-turn structure) well define most of the segment universes. Furthermore, we identified several conformational components that were unique to each

  15. Protein-segment universe exhibiting transitions at intermediate segment length in conformational subspaces

    Directory of Open Access Journals (Sweden)

    Hirokawa Takatsugu

    2008-08-01

    Full Text Available Abstract Background Many studies have examined rules governing two aspects of protein structures: short segments and proteins' structural domains. Nevertheless, the organization and nature of the conformational space of segments with intermediate length between short segments and domains remain unclear. Conformational spaces of intermediate length segments probably differ from those of short segments. We investigated the identification and characterization of the boundary(s between peptide-like (short segment and protein-like (long segment distributions. We generated ensembles embedded in globular proteins comprising segments 10–50 residues long. We explored the relationships between the conformational distribution of segments and their lengths, and also protein structural classes using principal component analysis based on the intra-segment Cα-Cα atomic distances. Results Our statistical analyses of segment conformations and length revealed critical dual transitions in their conformational distribution with segments derived from all four structural classes. Dual transitions were identified with the intermediate phase between the short segments and domains. Consequently, protein segment universes were categorized. i Short segments (10–22 residues showed a distribution with a high frequency of secondary structure clusters. ii Medium segments (23���26 residues showed a distribution corresponding to an intermediate state of transitions. iii Long segments (27–50 residues showed a distribution converging on one huge cluster containing compact conformations with a smaller radius of gyration. This distribution reflects the protein structures' organization and protein domains' origin. Three major conformational components (radius of gyration, structural symmetry with respect to the N-terminal and C-terminal halves, and single-turn/two-turn structure well define most of the segment universes. Furthermore, we identified several

  16. A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.

    Directory of Open Access Journals (Sweden)

    Gregory D Friedland

    2009-05-01

    Full Text Available Conformational ensembles are increasingly recognized as a useful representation to describe fundamental relationships between protein structure, dynamics and function. Here we present an ensemble of ubiquitin in solution that is created by sampling conformational space without experimental information using "Backrub" motions inspired by alternative conformations observed in sub-Angstrom resolution crystal structures. Backrub-generated structures are then selected to produce an ensemble that optimizes agreement with nuclear magnetic resonance (NMR Residual Dipolar Couplings (RDCs. Using this ensemble, we probe two proposed relationships between properties of protein ensembles: (i a link between native-state dynamics and the conformational heterogeneity observed in crystal structures, and (ii a relation between dynamics of an individual protein and the conformational variability explored by its natural family. We show that the Backrub motional mechanism can simultaneously explore protein native-state dynamics measured by RDCs, encompass the conformational variability present in ubiquitin complex structures and facilitate sampling of conformational and sequence variability matching those occurring in the ubiquitin protein family. Our results thus support an overall relation between protein dynamics and conformational changes enabling sequence changes in evolution. More practically, the presented method can be applied to improve protein design predictions by accounting for intrinsic native-state dynamics.

  17. Quantum fluctuations in FRLW space-time

    OpenAIRE

    Rabochaya, Y.

    2015-01-01

    In this paper we study a quantum field theoretical approach, where a quantum probe is used to investigate the properties of generic non-flat FRLW space time. The fluctuations related to a massless conformal coupled scalar field defined on a space-time with horizon is identified with a probe and the procedure to measure the local temperature is presented.

  18. Supercharging with Trivalent Metal Ions in Native Mass Spectrometry

    Science.gov (United States)

    Flick, Tawnya G.; Williams, Evan R.

    2012-11-01

    Addition of 1.0 mM LaCl3 to aqueous ammonium acetate solutions containing proteins in their folded native forms can result in a significant increase in the molecular ion charging obtained with electrospray ionization as a result of cation adduction. In combination with m-nitrobenzyl alcohol, molecular ion charge states that are greater than the number of basic sites in the protein can be produced from these native solutions, even for lysozyme, which is conformationally constrained by four intramolecular disulfide bonds. Circular dichroism spectroscopy indicates that the conformation of ubiquitin is not measurably affected with up to 1.0 M LaCl3, but ion mobility data indicate that the high charge states that are formed when 1.0 mM LaCl3 is present are more unfolded than the low charge states formed without this reagent. These and other results indicate that the increased charging is a result of La3+ preferentially adducting onto compact or more native-like conformers during ESI and the gas-phase ions subsequently unfolding as a result of increased Coulomb repulsion. Electron capture dissociation of these high charge-state ions formed from these native solutions results in comparable sequence coverage to that obtained for ions formed from denaturing solutions without supercharging reagents, making this method a potentially powerful tool for obtaining structural information in native mass spectrometry.

  19. Structures of W(2.2 Lie conformal algebra

    Directory of Open Access Journals (Sweden)

    Yuan Lamei

    2016-01-01

    . In this paper, we study conformal derivations, central extensions and conformal modules for this Lie conformal algebra. Also, we compute the cohomology of this Lie conformal algebra with coefficients in its modules. In particular, we determine its cohomology with trivial coefficients both for the basic and reduced complexes.

  20. A note on fashion cycles, novelty and conformity

    OpenAIRE

    Alberti, Federica

    2013-01-01

    We develop a model in which novelty and conformity motivate fashion behavior. Fashion cycles occur if conformity is not too high. The duration of fashion cycles depends on individual-specific conformity, novelty, and the number of available styles. The use of individual-specific novelty and conformity allows us to also identify fashion leaders.

  1. 40 CFR 91.106 - Certificate of conformity.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Certificate of conformity. 91.106... Provisions § 91.106 Certificate of conformity. (a) Every manufacturer of a new marine SI engine produced... obtain a certificate of conformity covering each engine family. The certificate of conformity must be...

  2. 47 CFR 68.320 - Supplier's Declaration of Conformity.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 3 2010-10-01 2010-10-01 false Supplier's Declaration of Conformity. 68.320... Approval § 68.320 Supplier's Declaration of Conformity. (a) Supplier's Declaration of Conformity is a... Supplier's Declaration of Conformity attaches to all items subsequently marketed by the responsible party...

  3. 47 CFR 2.906 - Declaration of Conformity.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Declaration of Conformity. 2.906 Section 2.906... Conformity. (a) A Declaration of Conformity is a procedure where the responsible party, as defined in § 2.909... of Conformity attaches to all items subsequently marketed by the responsible party which are...

  4. 21 CFR 26.70 - Conformity assessment bodies.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Conformity assessment bodies. 26.70 Section 26.70...Frameworkâ Provisions § 26.70 Conformity assessment bodies. Each party recognizes that the conformity... conformity in relation to its requirements as specified in subpart B of this part. The parties shall specify...

  5. Bootstrapping Critical Ising Model on Three Dimensional Real Projective Space.

    Science.gov (United States)

    Nakayama, Yu

    2016-04-08

    Given conformal data on a flat Euclidean space, we use crosscap conformal bootstrap equations to numerically solve the Lee-Yang model as well as the critical Ising model on a three dimensional real projective space. We check the rapid convergence of our bootstrap program in two dimensions from the exact solutions available. Based on the comparison, we estimate that our systematic error on the numerically solved one-point functions of the critical Ising model on a three dimensional real projective space is less than 1%. Our method opens up a novel way to solve conformal field theories on nontrivial geometries.

  6. Conformal blocks and generalized Selberg integrals

    Energy Technology Data Exchange (ETDEWEB)

    Mironov, A., E-mail: mironov@lpi.r [Lebedev Physics Institute (Russian Federation); ITEP, Moscow (Russian Federation); Morozov, Al., E-mail: morozov@itep.r [ITEP, Moscow (Russian Federation); Morozov, And., E-mail: andrey.morozov@itep.r [ITEP, Moscow (Russian Federation); Physics Department, Moscow State University, Moscow (Russian Federation)

    2011-02-11

    Operator product expansion (OPE) of two operators in two-dimensional conformal field theory includes a sum over Virasoro descendants of other operator with universal coefficients, dictated exclusively by properties of the Virasoro algebra and independent of choice of the particular conformal model. In the free field model, these coefficients arise only with a special 'conservation' relation imposed on the three dimensions of the operators involved in OPE. We demonstrate that the coefficients for the three unconstrained dimensions arise in the free field formalism when additional Dotsenko-Fateev integrals are inserted between the positions of the two original operators in the product. If such coefficients are combined to form an n-point conformal block on Riemann sphere, one reproduces the earlier conjectured {beta}-ensemble representation of conformal blocks. The statement can also be regarded as a relation between the 3j-symbols of the Virasoro algebra and the slightly generalized Selberg integrals I{sub Y}, associated with arbitrary Young diagrams. The conformal blocks are multilinear combinations of such integrals and the AGT conjecture relates them to the Nekrasov functions which have exactly the same structure.

  7. Evolution of Conformity in Social Dilemmas.

    Directory of Open Access Journals (Sweden)

    Yali Dong

    Full Text Available People often deviate from their individual Nash equilibrium strategy in game experiments based on the prisoner's dilemma (PD game and the public goods game (PGG, whereas conditional cooperation, or conformity, is supported by the data from these experiments. In a complicated environment with no obvious "dominant" strategy, conformists who choose the average strategy of the other players in their group could be able to avoid risk by guaranteeing their income will be close to the group average. In this paper, we study the repeated PD game and the repeated m-person PGG, where individuals' strategies are restricted to the set of conforming strategies. We define a conforming strategy by two parameters, initial action in the game and the influence of the other players' choices in the previous round. We are particularly interested in the tit-for-tat (TFT strategy, which is the well-known conforming strategy in theoretical and empirical studies. In both the PD game and the PGG, TFT can prevent the invasion of non-cooperative strategy if the expected number of rounds exceeds a critical value. The stability analysis of adaptive dynamics shows that conformity in general promotes the evolution of cooperation, and that a regime of cooperation can be established in an AllD population through TFT-like strategies. These results provide insight into the emergence of cooperation in social dilemma games.

  8. Conformal blocks and generalized Selberg integrals

    Science.gov (United States)

    Mironov, A.; Morozov, Al.; Morozov, And.

    2011-02-01

    Operator product expansion (OPE) of two operators in two-dimensional conformal field theory includes a sum over Virasoro descendants of other operator with universal coefficients, dictated exclusively by properties of the Virasoro algebra and independent of choice of the particular conformal model. In the free field model, these coefficients arise only with a special “conservation” relation imposed on the three dimensions of the operators involved in OPE. We demonstrate that the coefficients for the three unconstrained dimensions arise in the free field formalism when additional Dotsenko-Fateev integrals are inserted between the positions of the two original operators in the product. If such coefficients are combined to form an n-point conformal block on Riemann sphere, one reproduces the earlier conjectured β-ensemble representation of conformal blocks. The statement can also be regarded as a relation between the 3j-symbols of the Virasoro algebra and the slightly generalized Selberg integrals I, associated with arbitrary Young diagrams. The conformal blocks are multilinear combinations of such integrals and the AGT conjecture relates them to the Nekrasov functions which have exactly the same structure.

  9. Arcjet Testing of Advanced Conformal Ablative TPS

    Science.gov (United States)

    Gasch, Matthew; Beck, Robin; Agrawal, Parul

    2014-01-01

    A conformable TPS over a rigid aeroshell has the potential to solve a number of challenges faced by traditional rigid TPS materials (such as tiled Phenolic Impregnated Carbon Ablator (PICA) system on MSL. The compliant (high strain to failure) nature of the conformable ablative materials will allow integration of the TPS with the underlying aeroshell structure much easier and enable monolithic-like configuration and larger segments (or parts) to be used. In May of 2013 the CA250 project executed an arcjet test series in the Ames IHF facility to evaluate a phenolic-based conformal system (named Conformal-PICA) over a range of test conditions from 40-400Wcm2. The test series consisted of four runs in the 13-inch diameter nozzle. Test models were based on SPRITE configuration (a 55-deg sphere cone), as it was able to provide a combination of required heat flux, pressure and shear within a single entry. The preliminary in-depth TC data acquired during that test series allowed a mid-fidelity thermal response model for conformal-PICA to be created while testing of seam models began to address TPS attachment and joining of multiple segments for future fabrication of large-scale aeroshells. Discussed in this paper are the results.

  10. Evolution of Conformity in Social Dilemmas.

    Science.gov (United States)

    Dong, Yali; Li, Cong; Tao, Yi; Zhang, Boyu

    2015-01-01

    People often deviate from their individual Nash equilibrium strategy in game experiments based on the prisoner's dilemma (PD) game and the public goods game (PGG), whereas conditional cooperation, or conformity, is supported by the data from these experiments. In a complicated environment with no obvious "dominant" strategy, conformists who choose the average strategy of the other players in their group could be able to avoid risk by guaranteeing their income will be close to the group average. In this paper, we study the repeated PD game and the repeated m-person PGG, where individuals' strategies are restricted to the set of conforming strategies. We define a conforming strategy by two parameters, initial action in the game and the influence of the other players' choices in the previous round. We are particularly interested in the tit-for-tat (TFT) strategy, which is the well-known conforming strategy in theoretical and empirical studies. In both the PD game and the PGG, TFT can prevent the invasion of non-cooperative strategy if the expected number of rounds exceeds a critical value. The stability analysis of adaptive dynamics shows that conformity in general promotes the evolution of cooperation, and that a regime of cooperation can be established in an AllD population through TFT-like strategies. These results provide insight into the emergence of cooperation in social dilemma games.

  11. Is non-conformity WEIRD? Cultural variation in adults' beliefs about children's competency and conformity.

    Science.gov (United States)

    Clegg, Jennifer M; Wen, Nicole J; Legare, Cristine H

    2017-03-01

    Cross-cultural comparisons provide critical insight into variation in reasoning about intelligence. In two studies, the authors used a novel methodology based on multivocal ethnography to assess the role of conformity in U.S. and Ni-Vanuatu adults' judgments of children's intelligence and, as a comparison trait, good behavior. In Study 1, there were cultural differences in the impact of conformity on U.S. and Ni-Vanuatu adults' judgments of children's intelligence and good behavior. When evaluating U.S. children only, U.S. adults were less likely to endorse high conformity children as intelligent, often citing creativity as a justification for their judgments. In contrast, Ni-Vanuatu adults were more likely to endorse Ni-Vanuatu high conformity children as intelligent. Ni-Vanuatu adults were also more likely to endorse high conformity children as well-behaved than U.S. adults. In Study 2, there were no effects of socioeconomic status on U.S. adults' evaluations of conformity. U.S. adults were less likely to endorse high conformity children as intelligent than Ni-Vanuatu adults. Taken together, the data demonstrate that beliefs about the relations between intelligence, conformity, and creativity vary within and across cultures. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  12. ConformRank: A conformity-based rank for finding top-k influential users

    Science.gov (United States)

    Wang, Qiyao; Jin, Yuehui; Cheng, Shiduan; Yang, Tan

    2017-05-01

    Finding influential users is a hot topic in social networks. For example, advertisers identify influential users to make a successful campaign. Retweeters forward messages from original users, who originally publish messages. This action is referred to as retweeting. Retweeting behaviors generate influence. Original users have influence on retweeters. Whether retweeters keep the same sentiment as original users is taken into consideration in this study. Influence is calculated based on conformity from emotional perspective after retweeting. A conformity-based algorithm, called ConformRank, is proposed to find top-k influential users, who make the most users keep the same sentiment after retweeting messages. Emotional conformity is introduced to denote how users conform to original users from the emotional perspective. Conforming weights are introduced to denote how two users keep the same sentiment after retweeting messages. Emotional conformity is applied for users and conforming weights are used for relations. Experiments were conducted on Sina Weibo. Experimental results show that users have larger influence when they publish positive messages.

  13. Exploring the conformational landscape of menthol, menthone, and isomenthone: A microwave study

    Directory of Open Access Journals (Sweden)

    David eSchmitz

    2015-03-01

    Full Text Available The rotational spectra of the monoterpenoids menthol, menthone, and isomenthone are reportedin the frequency range of 2−8.5GHz, obtained with broadband Fourier-transform microwave spectroscopy.For menthol only one conformation was identified under the cold conditions of the molecularjet, whereas three conformations were observed for menthone and one for isomenthone. Theconformational space of the different molecules was extensively studied using quantum chemicalcalculations, and the results were compared with molecular parameters obtained by the measurements.Finally, a computer program is presented, which was developed to automatically identifydifferent species in a dense broadband microwave spectrum using calculated ab initio rotationalconstants as input.

  14. JuliBootS: a hands-on guide to the conformal bootstrap

    CERN Document Server

    Paulos, Miguel F

    2014-01-01

    We introduce {\\tt JuliBootS}, a package for numerical conformal bootstrap computations coded in {\\tt Julia}. The centre-piece of {\\tt JuliBootS} is an implementation of Dantzig's simplex method capable of handling arbitrary precision linear programming problems with continuous search spaces. Current supported features include conformal dimension bounds, OPE bounds, and bootstrap with or without global symmetries. The code is trivially parallelizable on one or multiple machines. We exemplify usage extensively with several real-world applications. In passing we give a pedagogical introduction to the numerical bootstrap methods.

  15. Projective multiplets and hyperkähler cones in conformal supergravity

    Energy Technology Data Exchange (ETDEWEB)

    Butter, Daniel [Nikhef Theory Group, Science Park 105, 1098 XG Amsterdam (Netherlands)

    2015-06-24

    Projective superspace provides a natural framework for the construction of actions coupling hypermultiplets to conformal supergravity. We review how the off-shell actions are formulated in superspace and then discuss how to eliminate the infinite number of auxiliary fields to produce an on-shell N=2 supersymmetric sigma model, with the target space corresponding to a generic 4n-dimensional hyperkähler cone. We show how the component action coupling the hypermultiplets to conformal supergravity may be constructed starting from curved superspace. The superspace origin of the geometric data — the hyperkähler potential, complex structures, and any gauged isometries — is also addressed.

  16. Crossing symmetry in Alpha space

    CERN Document Server

    CERN. Geneva

    2017-01-01

    The conformal bootstrap program aims to catalog all conformal field theories (second-order phase transitions) in D dimensions. Despite its ambitious scope much progress has been made over the past decade, e.g. in computing critical exponents for the 3D O(N) models to high precision. At this stage, analytic methods to explore the CFT landscape are not as well developed. In this talk I will describe a new mathematical framework for the bootstrap known as "alpha space", which reduces crossing symmetry to a set of integral equations. Based on arXiv:1702.08471 (with Balt van Rees) and arXiv:1703.08159.

  17. Mass Spectrometry of Halopyrazolium Salts

    DEFF Research Database (Denmark)

    Larsen, Elfinn; Egsgaard, Helge; Pande, U. C.

    1983-01-01

    Eleven halogen substituted 1-methyl-2-phenylpyrazolium bromides or chlorides were investigated by field desorption, field ionization, and electron impact mass spectrometry. Dealkylation was found to be the predominant thermal decomposition. An exchange between covalent and ionic halogen prior...

  18. Spontaneous breaking of conformal invariance in theories of conformally coupled matter and Weyl gravity

    Energy Technology Data Exchange (ETDEWEB)

    Edery, A [Department of Physics, Bishop' s University, Lennoxville, QC J1M 1Z7 (Canada); Fabbri, Luca [Theory Group, INFN Section of Bologna, Department of physics, University of Bologna, Via Irnerio 46, C.A.P. 40126, Bologna (Italy); Paranjape, M B [Groupe de physique des particules, Universite de Montreal, C.P. 6128, succ. centre-ville, Montreal, QC H3C 3J7 (Canada)

    2006-11-21

    We study the theory of Weyl conformal gravity with matter degrees of freedom in a conformally invariant interaction. Specifically, we consider a triplet of scalar fields and SO(3) non-Abelian gauge fields, i.e. the Georgi-Glashow model conformally coupled to Weyl gravity. We show that the equations of motion admit solutions spontaneously breaking the conformal symmetry and the gauge symmetry, providing a mechanism for supplying a scale in the theory. The vacuum solution corresponds to anti-de Sitter spacetime, while localized soliton solutions correspond to magnetic monopoles in asymptotically anti-de Sitter spacetime. This mechanism strengthens the reasons for considering conformally invariant matter-gravity theory, which has shown promising indications concerning the problem of missing matter in galactic rotation curves.

  19. The conforming brain and deontological resolve.

    Directory of Open Access Journals (Sweden)

    Melanie Pincus

    Full Text Available Our personal values are subject to forces of social influence. Deontological resolve captures how strongly one relies on absolute rules of right and wrong in the representation of one's personal values and may predict willingness to modify one's values in the presence of social influence. Using fMRI, we found that a neurobiological metric for deontological resolve based on relative activity in the ventrolateral prefrontal cortex (VLPFC during the passive processing of sacred values predicted individual differences in conformity. Individuals with stronger deontological resolve, as measured by greater VLPFC activity, displayed lower levels of conformity. We also tested whether responsiveness to social reward, as measured by ventral striatal activity during social feedback, predicted variability in conformist behavior across individuals but found no significant relationship. From these results we conclude that unwillingness to conform to others' values is associated with a strong neurobiological representation of social rules.

  20. A mass-independent conformal quantum cloak

    Science.gov (United States)

    Lin, De-Hone

    2017-11-01

    An obstacle to constructing a quantum cloak with the transformation design method for steering a matter wave is the device involving the anisotropic modulation of the particle mass. It is the purpose of this paper to show that a narrow-acceptance-angle quantum cloak generated by a kind of conformal mapping could be mass-independent. This greatly simplifies the construction of the device since it can now be finished only by applying a potential field to a region of the shell. As demonstrations of the conclusion, an elliptical and a parabolic conformal quantum cloak are designed from the elliptical and parabolic coordinate systems. Their performance is inspected by probability currents. It is shown that the conformal devices can serve as novel splitters for a 2D matter wave. Finally, we discuss the difficulty of constructing a steering device from the hyperbolic coordinate system.

  1. Understanding Modern Magnets through Conformal Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Halbach, K.

    1989-10-27

    When I had to choose, within some narrow range, the topic of this paper, I received great help from a colleague in Berkeley and from Prof. Little when it was suggested that I should pick among the possible subjects of my talk the subject that Prof. Bloch would have enjoyed most. Since Prof. Bloch would prefer a scalpel over a sword every time, I hope and think that most people will approve my choice. When one intends to talk about a subject that is as old as conformal mapping and one does not want to lose the audience in a very short time, it is advisable to start by explaining both the motivation for the talk as well as the goals one has in mind when giving the talk. This particular talk has been motivated by the increasing frequency with which one hears, from people that ought to know better, statements like: 'Conformal mapping is really a thing of the past because of all the marvelous computer programs that we now have'. Even though, or more likely because, I have been intimately involved in the development of some large and widely used computer codes, I am deeply disturbed by such statements since they indicate a severe lack of understanding of the purpose of conformal mapping techniques, computers, and computer codes. In my view, conformal mapping can be an extremely powerful computational technique, and the easy availability of computers has made that aspect even more important now than it has been in the past. Additionally, and more importantly, conformal mapping can give very deep and unique insight into problems, giving often solutions to problems that can not be obtained with any other method, in particular not with computers. Wanting to demonstrate in particular the latter part, I set myself two goals for this talk: (1) I want to show with the help of a number of examples that conformal mapping is a unique and enormously powerful tool for thinking about, and solving, problems. Usually one has to write down only a few equations, and sometimes

  2. Black holes in massive conformal gravity

    Energy Technology Data Exchange (ETDEWEB)

    Myung, Yun Soo, E-mail: ysmyung@inje.ac.kr

    2014-03-07

    We analyze the classical stability of Schwarzschild black hole in massive conformal gravity which was recently proposed for another massive gravity model. This model in the Jordan frame is conformally equivalent to the Einstein–Weyl gravity in the Einstein frame. The coupled linearized Einstein equation is decomposed into the traceless and trace equation when one chooses 6m{sup 2}φ=δR. Solving the traceless equation exhibits unstable modes featuring the Gregory–Laflamme s-mode instability of five-dimensional black string, while we find no unstable modes when solving the trace equation. It is shown that the instability of the black hole in massive conformal gravity arises from the massiveness where the geometry of extra dimension trades for mass.

  3. Anisotropic stellar models admitting conformal motion

    Science.gov (United States)

    Banerjee, Ayan; Banerjee, Sumita; Hansraj, Sudan; Ovgun, Ali

    2017-04-01

    We address the problem of finding static and spherically symmetric anisotropic compact stars in general relativity that admit conformal motions. The study is framed in the language of f( R) gravity theory in order to expose opportunity for further study in the more general theory. Exact solutions of compact stars are found under the assumption that spherically symmetric spacetimes admit conformal motion with anisotropic matter distribution in nature. In this work, two cases have been studied for the existence of such solutions: first, we consider the model given by f(R)=R and then f(R)=aR+b . Finally, specific characteristics and physical properties have been explored analytically along with graphical representations for conformally symmetric compact stars in f( R) gravity.

  4. 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...

  5. Conformal transformation route to gravity's rainbow

    Science.gov (United States)

    He, Miao; Li, Ping; Wang, Zi-Liang; Ding, Jia-Cheng; Deng, Jian-Bo

    2018-02-01

    Conformal transformation as a mathematical tool has been used in many areas of gravitational physics. In this paper, we consider gravity's rainbow, in which the metric can be treated as a conformal rescaling of the original metric. By using the conformal transformation technique, we get a specific form of a modified Newton's constant and cosmological constant in gravity's rainbow, which implies that the total vacuum energy is dependent on probe energy. Moreover, the result shows that Einstein gravity's rainbow can be described by energy-dependent f(E,\\tilde{R}) gravity. At last, we study the f( R) gravity, when gravity's rainbow is considered, which can also be described as energy-dependent \\tilde{f}(E,\\tilde{R}) gravity.

  6. On conformal supergravity and harmonic superspace

    Energy Technology Data Exchange (ETDEWEB)

    Butter, Daniel [Nikhef Theory Group,Science Park 105, 1098 XG Amsterdam (Netherlands)

    2016-03-16

    This paper describes a fully covariant approach to harmonic superspace. It is based on the conformal superspace description of conformal supergravity and involves extending the supermanifold M{sup 4|8} by the tangent bundle of ℂP{sup 1}. The resulting superspace M{sup 4|8}×TℂP{sup 1} can be identified in a certain gauge with the conventional harmonic superspace M{sup 4|8}×S{sup 2}. This approach not only makes the connection to projective superspace transparent, but simplifies calculations in harmonic superspace significantly by eliminating the need to deal directly with supergravity prepotentials. As an application of the covariant approach, we derive from harmonic superspace the full component action for the sigma model of a hyperkähler cone coupled to conformal supergravity. Further applications are also sketched.

  7. Single homopolypeptide chains collapse into mechanically rigid conformations

    Science.gov (United States)

    Dougan, Lorna; Li, Jingyuan; Badilla, Carmen L.; Berne, B. J.; Fernandez, Julio M.

    2009-01-01

    Huntington's disease is linked to the insertion of glutamine (Q) in the protein huntingtin, resulting in polyglutamine (polyQ) expansions that self-associate to form aggregates. While polyQ aggregation has been the subject of intense study, a correspondingly thorough understanding of individual polyQ chains is lacking. Here we demonstrate a single molecule force-clamp technique that directly probes the mechanical properties of single polyQ chains. We have made polyQ constructs of varying lengths that span the length range of normal and diseased polyQ expansions. Each polyQ construct is flanked by the I27 titin module, providing a clear mechanical fingerprint of the molecule being pulled. Remarkably, under the application of force, no extension is observed for any of the polyQ constructs. This is in direct contrast with the random coil protein PEVK of titin, which readily extends under force. Our measurements suggest that polyQ chains form mechanically stable collapsed structures. We test this hypothesis by disrupting polyQ chains with insertions of proline residues and find that their mechanical extensibility is sensitive to the position of the proline interruption. These experiments demonstrate that polyQ chains collapse to form a heterogeneous ensemble of conformations that are mechanically resilient. We further use a heat-annealing molecular dynamics protocol to extensively search the conformation space and find that polyQ can exist in highly mechanically stable compact globular conformations. The mechanical rigidity of these collapsed structures may exceed the functional ability of eukaryotic proteasomes, resulting in the accumulation of undigested polyQ sequences in vivo. PMID:19549822

  8. Conformal interfaces between free boson orbifold theories

    Science.gov (United States)

    Becker, Melanie; Cabrera, Yaniel; Robbins, Daniel

    2017-09-01

    We construct a large class of conformal interfaces between two-dimensional c = 1 conformal field theories describing compact free bosons and their Z_2 orbifolds. The interfaces are obtained by constructing boundary states in the corresponding c = 2 product theories and applying the unfolding procedure. We compute the fusion products for all of these defects, and identify the invertible topological interfaces associated to global symmetries, the interfaces corresponding to marginal deformations, and the interfaces which map the untwisted sector of an orbifold to the invariant states of the parent theory.

  9. Conformity to peer pressure in preschool children

    OpenAIRE

    Haun, D.; Tomasello, M

    2011-01-01

    Both adults and adolescents often conform their behavior and opinions to peer groups, even when they themselves know better. The current study investigated this phenomenon in 24 groups of 4 children between 4;2 and 4;9 years of age. Children often made their judgments conform to those of 3 peers, who had made obviously erroneous but unanimous public judgments right before them. A follow-up study with 18 groups of 4 children between 4;0 and 4;6 years of age revealed that children did not chang...

  10. Spherical conformal models for compact stars

    Energy Technology Data Exchange (ETDEWEB)

    Takisa, P.M.; Maharaj, S.D.; Manjonjo, A.M.; Moopanar, S. [University of KwaZulu-Natal, Astrophysics and Cosmology Research Unit, School of Mathematics, Statistics and Computer Science, Durban (South Africa)

    2017-10-15

    We consider spherical exact models for compact stars with anisotropic pressures and a conformal symmetry. The conformal symmetry condition generates an integral relationship between the gravitational potentials. We solve this condition to find a new anisotropic solution to the Einstein field equations. We demonstrate that the exact solution produces a relativistic model of a compact star. The model generates stellar radii and masses consistent with PSR J1614-2230, Vela X1, PSR J1903+327 and Cen X-3. A detailed physical examination shows that the model is regular, well behaved and stable. The mass-radius limit and the surface red shift are consistent with observational constraints. (orig.)

  11. Geometry and conformations of benzenecarboxylic acids

    Directory of Open Access Journals (Sweden)

    IVAN GUTMAN

    2004-11-01

    Full Text Available The geometry, conformations and energy of mono-, di-, and tri-carboxylic derivatives of benzene were studied by means of the AM1 molecular-orbital method. Whereas the species having no carboxylic groups in the ortho-position (benzoic, isophthalic, terephthalic, and trimesic acids are planar in all their (stable conformations, those possessing carboxylic groups in the ortho-position (phthalic, 1,2,3-benzenetricarboxylic, and 1,2,4-benzenetricarboxylic acids assume a non-planar geometry, with one carboxyl group almost orthogonal to the plane of the benzene ring. Various rotamers of each of the studied benzenecarboxylic acids have nearly the same energy.

  12. Singularities, horizons, firewalls, and local conformal symmetry

    CERN Document Server

    Hooft, Gerard 't

    2015-01-01

    The Einstein-Hilbert theory of gravity can be rephrased by focusing on local conformal symmetry as an exact, but spontaneously broken symmetry of nature. The conformal component of the metric field is then treated as a dilaton field with only renormalizable interactions. This imposes constraints on the theory, which can also be viewed as demanding regularity of the action as the dilaton field variable tends to 0. In other words, we have constraints on the small distance behaviour. Our procedure appears to turn a black hole into a regular, topologically trivial soliton without singularities, horizons of firewalls, but many questions remain.

  13. Game Theory and Social Psychology: Conformity Games

    Science.gov (United States)

    Alessio, Danielle; Kilgour, D. Marc

    2011-11-01

    Game models can contribute to understanding of how social biases and pressures to conform can lead to puzzling behaviour in social groups. A model of the psychological biases false uniqueness and false consensus is set out. The model predicts the phenomenon of pluralistic ignorance, which is well-studied in social psychology, showing how it arises as a result of the prevalence of false uniqueness and the desire to conform. An efficient method is developed for finding Nash equilibria of the model under certain restrictions.

  14. Correct light deflection in Weyl conformal gravity

    Science.gov (United States)

    Cattani, Carlo; Scalia, Massimo; Laserra, Ettore; Bochicchio, Ivana; Nandi, Kamal K.

    2013-02-01

    The conformal gravity fit to observed galactic rotation curves requires γ>0. On the other hand, the conventional method for light deflection by galaxies gives a negative contribution to the Schwarzschild value for γ>0, which is contrary to observation. Thus, it is very important that the contribution to bending should in principle be positive, no matter how small its magnitude is. Here we show that the Rindler-Ishak method gives a positive contribution to Schwarzschild deflection for γ>0, as desired. We also obtain the exact local coupling term derived earlier by Sereno. These results indicate that conformal gravity can potentially test well against all astrophysical observations to date.

  15. Conformal invariants topics in geometric function theory

    CERN Document Server

    Ahlfors, Lars V

    2010-01-01

    Most conformal invariants can be described in terms of extremal properties. Conformal invariants and extremal problems are therefore intimately linked and form together the central theme of this classic book which is primarily intended for students with approximately a year's background in complex variable theory. The book emphasizes the geometric approach as well as classical and semi-classical results which Lars Ahlfors felt every student of complex analysis should know before embarking on independent research. At the time of the book's original appearance, much of this material had never ap

  16. Conformal metamaterial absorber for curved surface.

    Science.gov (United States)

    Jang, Youngsoo; Yoo, Minyeong; Lim, Sungjoon

    2013-10-07

    In this paper, three different unit cells are designed on the basis split-ring-cross resonators, and each unit cell has an absorption rate greater than 90% at incident angles of 0°, 30°, and 45°, respectively. They are non-periodically placed in three different zones on the curved surface. Therefore, the proposed conformal metamaterial absorber can achieve a high absorption rate. The performance of the proposed absorber is compared with that of a metallic curved surface and a conformal metamaterial absorber with the same unit cells.

  17. Raising a gender non-conforming child.

    Science.gov (United States)

    Wisnowski, Deborah L

    2011-10-01

    This article overviews the challenges parents face raising gender non-conforming children. The author is the mother of a fifteen year old gender non-conforming (GNC) child and co-founder of Stepping Stones Support Group which organizes support programs for families of GNC. The article discusses social challenges, educational challenges and internal conflicts the author has experienced while raising her child. The author also discusses the process of founding Stepping Stones and the importance having support has played in her and her child's life.

  18. Wilson loop invariants from WN conformal blocks

    Directory of Open Access Journals (Sweden)

    Oleg Alekseev

    2015-12-01

    Full Text Available Knot and link polynomials are topological invariants calculated from the expectation value of loop operators in topological field theories. In 3D Chern–Simons theory, these invariants can be found from crossing and braiding matrices of four-point conformal blocks of the boundary 2D CFT. We calculate crossing and braiding matrices for WN conformal blocks with one component in the fundamental representation and another component in a rectangular representation of SU(N, which can be used to obtain HOMFLY knot and link invariants for these cases. We also discuss how our approach can be generalized to invariants in higher-representations of WN algebra.

  19. Conformally coupled scalars, instantons and vacuum instability in AdS{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    De Haro, S. [King' s College London (United Kingdom). Dept. of Mathematics; Papadimitriou, I. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Petkou, A.C. [Crete Univ., Keraklion (Greece). Dept. of Physics

    2006-11-15

    We show that a scalar field conformally coupled to AdS gravity in four dimensions with a quartic self-interaction can be embedded into M-theory. The holographic effective action and effective potential are exactly calculated, allowing us to study non-perturbatively the stability of AdS{sub 4} in the presence of the conformally coupled scalar. It is shown that there exists a one-parameter family of conformal scalar boundary conditions for which the boundary theory has an unstable vacuum. In this case, the bulk theory has instanton solutions that mediate the decay of the AdS{sub 4} space. These results match nicely with the vacuum structure and the existence of instantons in an effective three-dimensional boundary model.

  20. Conformational analysis of the anomeric forms of kojibiose, nigerose, and maltose using MM3.

    Science.gov (United States)

    Dowd, M K; Zeng, J; French, A D; Reilly, P J

    1992-06-16

    Energy surfaces were computed for relative orientations of the relaxed pyranosyl rings of the two anomeric forms of kojibiose, nigerose, and maltose, the (1----2)-alpha, (1----3)-alpha, and (1----4)-alpha-linked D-glucosyl disaccharides, respectively. Twenty-four combinations of starting conformations of the rotatable side-groups were considered for each disaccharide. Optimized structures were calculated using MM3 on a 20 degree grid spacing of the torsional angles about the glycosidic bonds. The energy surfaces of the six disaccharides were similar in many respects but differed in detail within the low-energy regions. The maps also illustrate the importance of the exo-anomeric effect and linkage type in determining the conformational flexibility of disaccharides. Torsional conformations of known crystal structures of maltosyl-containing molecules lie in a lower MM3 energy range than previously reported.

  1. Conjugates of 1'-Aminoferrocene-1-carboxylic Acid and Proline: Synthesis, Conformational Analysis and Biological Evaluation

    Directory of Open Access Journals (Sweden)

    Monika Kovačević

    2014-08-01

    Full Text Available Our previous studies showed that alteration of dipeptides Y-Fca-Ala-OMe (III into Y-Ala-Fca-OMe (IV (Y = Ac, Boc; Fca = 1'-aminoferrocene-1-carboxylic acid significantly influenced their conformational space. The novel bioconjugates Y-Fca-Pro-OMe (1, Y = Ac; 2, Y = Boc and Y-Pro-Fca-OMe (3, Y = Boc; 4, Y = Ac have been prepared in order to investigate the influence of proline, a well-known turn-inducer, on the conformational properties of small organometallic peptides with an exchanged constituent amino acid sequences. For this purpose, peptides 1–4 were subjected to detailed spectroscopic analysis (IR, NMR, CD spectroscopy in solution. The conformation of peptide 3 in the solid state was determined. Furthermore, the ability of the prepared conjugates to inhibit the growth of estrogen receptor-responsive MCF-7 mammary carcinoma cells and HeLa cervical carcinoma cells was tested.

  2. On the advancements of conformal transformations and their associated symmetries in geometry and theoretical physics

    Energy Technology Data Exchange (ETDEWEB)

    Kastrup, H.A. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Theory Group

    2008-08-15

    The historical developments of conformal transformations and symmetries are sketched: Their origin from stereographic projections of the globe, their blossoming in two dimensions within the eld of analytic complex functions, the generic role of transformations by reciprocal radii in dimensions higher than two and their linearization in terms of polyspherical coordinates by Darboux, Weyl's attempt to extend General Relativity, the slow rise of nite dimensional conformal transformations in classical eld theories and the problem of their interpretation, then since about 1970 the rapid spread of their acceptance for asymptotic and structural problems in quantum eld theories and beyond, up to the current AdS=CFT conjecture. The occasion for the present article: hundred years ago Bateman and Cunningham discovered the form invariance of Maxwell's equations for electromagnetism with respect to conformal space-time transformations. (orig.)

  3. Structural changes of ultrasonicated bovine serum albumin revealed by hydrogen-deuterium exchange and mass spectrometry.

    Science.gov (United States)

    Zhang, Qiuting; Tu, Zongcai; Wang, Hui; Huang, Xiaoqin; Sha, Xiaomei; Xiao, Hui

    2014-11-01

    The structural changes of bovine serum albumin (BSA) under high-intensity ultrasonication were investigated by fluorescence spectroscopy and mass spectrometry. Evidence for the ultrasonication-induced conformational changes of BSA was provided by the intensity changes and maximum-wavelength shift in fluorescence spectrometry. Matrix-assisted laser desorption-ionization time-of-flight mass spectroscopy (MALDI-TOF MS) revealed the increased intensity of the peak at the charge state +5 and a newly emerged peak at charge state +6, indicating that the protein became unfolded after ultrasonication. Prevalent unfolding of BSA after ultrasonication was revealed by hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS). Increased intensity and duration of ultrasonication further promoted the unfolding of the protein. The unfolding induced by ultrasonication goes through an intermediate state similar to that induced by a low concentration of denaturant.

  4. Large- N volume independence in conformal and confining gauge theories

    Science.gov (United States)

    Ünsal, Mithat; Yaffe, Laurence G.

    2010-08-01

    Consequences of large N volume independence are examined in conformal and confining gauge theories. In the large N limit, gauge theories compactified on {mathbb{R}^{d - k}} × {left( {{S^1}} right)^k} are independent of the S 1 radii, provided the theory has unbroken center symmetry. In particular, this implies that a large N gauge theory which, on {mathbb{R}^d} , flowstoan IR fixed point, retains the infinite correlation length and other scale invariant properties of the decompactified theory even when compactified on {mathbb{R}^{d - k}} × {left( {{S^1}} right)^k} . In other words, finite volume effects are 1 /N suppressed. In lattice formulations of vector-like theories, this implies that numerical studies to determine the boundary between confined and conformal phases may be performed on one-site lattice models. In mathcal{N} = 4 supersymmetric Yang-Mills theory, the center symmetry realization is a matter of choice: the theory on {mathbb{R}^{4 - k}} × {left( {{S^1}} right)^k} has a moduli space which contains points with all possible realizations of center symmetry. Large N QCD with massive adjoint fermions and one or two compactified dimensions has a rich phase structure with an infinite number of phase transitions coalescing in the zero radius limit.

  5. Positive energy conditions in 4D conformal field theory

    Science.gov (United States)

    Farnsworth, Kara; Luty, Markus A.; Prilepina, Valentina

    2016-10-01

    We argue that all consistent 4D quantum field theories obey a spacetime-averaged weak energy inequality ≥ - C/L 4, where L is the size of the smearing region, and C is a positive constant that depends on the theory. If this condition is violated, the theory has states that are indistinguishable from states of negative total energy by any local measurement, and we expect instabilities or other inconsistencies. We apply this condition to 4D conformal field theories, and find that it places constraints on the OPE coefficients of the theory. The constraints we find are weaker than the "conformal collider" constraints of Hofman and Maldacena. In 3D CFTs, the only constraint we find is equivalent to the positivity of 2-point function of the energy-momentum tensor, which follows from unitarity. Our calculations are performed using momentum-space Wightman functions, which are remarkably simple functions of momenta, and may be of interest in their own right.

  6. Conformal field theories with infinitely many conservation laws

    CERN Document Server

    Todorov, Ivan

    2013-01-01

    Globally conformal invariant quantum field theories in a D-dimensional space-time (D even) have rational correlation functions and admit an infinite number of conserved (symmetric traceless) tensor currents. In a theory of a scalar field of dimension D-2 they were demonstrated to be generated by bilocal normal products of free massless scalar fields with an O(N), U(N), or Sp(2N) (global) gauge symmetry [BNRT]. Recently, conformal field theories "with higher spin symmetry" were considered for D=3 in [MZ] where a similar result was obtained (exploiting earlier study of CFT correlators). We suggest that the proper generalization of the notion of a 2D chiral algebra to arbitrary (even or odd) dimension is precisely a CFT with an infinite series of conserved currents. We shall recast and complement (part of) the argument of Maldacena and Zhiboedov into the framework of our earlier work. We extend to D=4 the auxiliary Weyl-spinor formalism developed in [GPY] for D=3. The free field construction only follows for D>3...

  7. Antibody side chain conformations are position-dependent.

    Science.gov (United States)

    Leem, Jinwoo; Georges, Guy; Shi, Jiye; Deane, Charlotte M

    2018-01-10

    Side chain prediction is an integral component of computational antibody design and structure prediction. Current antibody modelling tools use backbone-dependent rotamer libraries with conformations taken from general proteins. Here we present our antibody-specific rotamer library, where rotamers are binned according to their immunogenetics (IMGT) position, rather than their local backbone geometry. We find that for some amino acid types at certain positions, only a restricted number of side chain conformations are ever observed. Using this information, we are able to reduce the breadth of the rotamer sampling space. Based on our rotamer library, we built a side chain predictor, position-dependent antibody rotamer swapper (PEARS). On a blind test set of 95 antibody model structures, PEARS had the highest average χ 1 and χ1+2 accuracy (78.7% and 64.8%) compared to three leading backbone-dependent side chain predictors. Our use of IMGT position, rather than backbone ϕ/ψ, meant that PEARS was more robust to errors in the backbone of the model structure. PEARS also achieved the lowest number of side chain-side chain clashes. PEARS is freely available as a web application at http://opig.stats.ox.ac.uk/webapps/pears. © 2018 Wiley Periodicals, Inc.

  8. A first-order approach to conformal gravity

    CERN Document Server

    Zlosnik, T G

    2016-01-01

    We investigate whether a spontaneously-broken gauge theory of the group $SU(2,2)$ may be a genuine competitor to General Relativity. The basic ingredients of the theory are an $SU(2,2)$ gauge field $A_{\\mu}$ and a Higgs field $W$ in the adjoint representation of the group with the Higgs field producing the symmetry breaking $SU(2,2)\\rightarrow SO(1,3)\\times SO(1,1)$. The action for gravity is polynomial in $\\{A_{\\mu},W\\}$ and the field equations are first-order in derivatives of these fields. The new $SO(1,1)$ symmetry in the gravitational sector is interpreted in terms of an emergent scale symmetry and the recovery of conformalized General Relativity and fourth-order Weyl conformal gravity as limits of the theory- following imposition of Lagrangian constraints- is demonstrated. Maximally symmetric spacetime solutions to the full theory are found and stability of the theory around these solutions is investigated; it is shown that regions of the theory's parameter space describe perturbations identical to that...

  9. Conformal scaling and the size of m-hadrons

    Science.gov (United States)

    Del Debbio, Luigi; Zwicky, Roman

    2014-01-01

    The scaling laws in an IR theory are dictated by the critical exponents of relevant operators. We have investigated these scaling laws at leading order in two previous papers. In this work we investigate further consequences of the scaling laws, trying to identify potential signatures that could be studied by lattice simulations. From the first derivative of the form factor we derive the behavior of the mean charge radius of the hadronic states in the theory. We obtain ⟨rH2⟩˜m-2/(1+γm*) which is consistent with ⟨rH2⟩˜1/MH2. The mean charge radius can be used as an alternative observable to assess the size of the physical states, and hence finite size effects, in numerical simulations. Furthermore, we discuss the behavior of specific field correlators in coordinate space for the case of conformal, scale-invariant, and confining theories making use of selection rules in scaling dimensions and spin. We compute the scaling corrections to correlations functions by linearizing the renormalization group equations. We find that these corrections are potentially large close to the edge of the conformal window. As an application we compute the scaling correction to the formula MH˜m1/(1+γm*) directly through its associated correlator as well as through the trace anomaly. The two computations are shown to be equivalent through a generalization of the Feynman-Hellmann theorem for the fermion mass and the gauge coupling.

  10. Cluster secondary ion mass spectrometry microscope mode mass spectrometry imaging.

    Science.gov (United States)

    Kiss, András; Smith, Donald F; Jungmann, Julia H; Heeren, Ron M A

    2013-12-30

    Microscope mode imaging for secondary ion mass spectrometry is a technique with the promise of simultaneous high spatial resolution and high-speed imaging of biomolecules from complex surfaces. Technological developments such as new position-sensitive detectors, in combination with polyatomic primary ion sources, are required to exploit the full potential of microscope mode mass spectrometry imaging, i.e. to efficiently push the limits of ultra-high spatial resolution, sample throughput and sensitivity. In this work, a C60 primary source was combined with a commercial mass microscope for microscope mode secondary ion mass spectrometry imaging. The detector setup is a pixelated detector from the Medipix/Timepix family with high-voltage post-acceleration capabilities. The system's mass spectral and imaging performance is tested with various benchmark samples and thin tissue sections. The high secondary ion yield (with respect to 'traditional' monatomic primary ion sources) of the C60 primary ion source and the increased sensitivity of the high voltage detector setup improve microscope mode secondary ion mass spectrometry imaging. The analysis time and the signal-to-noise ratio are improved compared with other microscope mode imaging systems, all at high spatial resolution. We have demonstrated the unique capabilities of a C60 ion microscope with a Timepix detector for high spatial resolution microscope mode secondary ion mass spectrometry imaging. Copyright © 2013 John Wiley & Sons, Ltd.

  11. Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis

    Directory of Open Access Journals (Sweden)

    Kim Sunghwan

    2012-11-01

    -inactive from random and inactive spaces “on average”, although some assays show a noticeable separation between the non-inactive and random spaces when multiple conformers are used for each compound. The present study is a critical next step to understand effects of conformational diversity of the molecules upon the 3-D molecular similarity and its application to biological activity data analysis in PubChem. The results of this study may be helpful to build search and analysis tools that exploit 3-D molecular similarity between compounds archived in PubChem and other molecular libraries in a more efficient way.

  12. Study of the conformational change of adsorbed proteins on biomaterial surfaces using hydrogen-deuterium exchange with mass spectroscopy.

    Science.gov (United States)

    Kim, Jinku

    2016-05-01

    There is no doubt that protein adsorption plays a crucial role in determining biocompatibility of biomaterials. Despite the information of the identity and composition of blood plasma/serum proteins adsorbed on surfaces of biomaterials to understand which proteins are involved in blood/biomaterial interactions, it still does not provide information about the conformations and orientations of adsorbed protein, which are very important in determining biological responses to biomaterials. Therefore, our laboratory has developed an experimental technology to probe protein conformations on materials that is applicable to mixtures of proteins. Herein, the new application of hydrogen/deuterium (H/D) exchange combined with mass spectrometry was applied to determine conformational changes of adsorbed proteins at biomaterial surfaces. The results suggest that there may be a significant conformational change in adsorbed proteins at 'low' bulk concentrations that leads to a large change in the kinetics of H/D exchange as compared to 'high' bulk concentrations. This technique may eventually be useful for the study of the kinetics of protein conformational changes. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Influence of acid-induced conformational variability on protein separation in reversed phase high performance liquid chromatography.

    Science.gov (United States)

    Bobály, Balázs; Tóth, Eszter; Drahos, László; Zsila, Ferenc; Visy, Júlia; Fekete, Jenő; Vékey, Károly

    2014-01-17

    Influence of acid concentration in the mobile phase on protein separation was studied in a wide concentration range using trifluoroacetic acid (TFA) and formic acid (FA). At low, 0.001-0.01 (v/v%) TFA concentration and appropriate solvent strength proteins elute before the column's dead time. This is explained by the proteins having a structured, but relatively extended conformation in the eluent; and are excluded from the pores of the stationary phase. Above ca. 0.01-0.05 (v/v%) TFA concentration proteins undergo further conformational change, leading to a compact, molten globule-like structure, likely stabilized by ion pairing. Proteins in this conformation enter the pores and are retained on the column. The results suggest a pore exclusion induced separation related to protein conformation. This effect is influenced by the pH and type of acid used, and is likely to involve ion-pair formation. The TFA concentration needed to result in protein folding (and therefore to observe retention on the column) depends on the protein; and therefore can be utilized to improve chromatographic performance. Conformation change was monitored by circular dichroism spectroscopy and mass spectrometry; and it was shown that not only TFA but FA can also induce molten globule formation. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. Fast-ion energy resolution by one-step reaction gamma-ray spectrometry

    DEFF Research Database (Denmark)

    Salewski, Mirko; Nocente, M.; Gorini, G.

    2016-01-01

    The spectral broadening of γ-rays from fusion plasmas can be measured in high-resolution gamma-ray spectrometry (GRS). We derive weight functions that determine the observable velocity space and quantify the velocity-space sensitivity of one-step reaction high-resolution GRS measurements in magne...

  15. Mycobacterium tuberculosis acyl carrier protein synthase adopts two different pH-dependent structural conformations

    Energy Technology Data Exchange (ETDEWEB)

    Gokulan, Kuppan; Aggarwal, Anup; Shipman, Lance [Texas A& M University, College Station, TX 77843-3474 (United States); Besra, Gurdyal S. [University of Birmingham, Edgbaston, Birmingham B15 2TT (United Kingdom); Sacchettini, James C., E-mail: sacchett@tamu.edu [Texas A& M University, College Station, TX 77843-3474 (United States)

    2011-07-01

    Bacterial acyl carrier protein synthase plays an essential role in the synthesis of fatty acids, nonribosomal peptides and polyketides. In Mycobacterium tuberculosis, AcpS or group I phosphopentatheine transferase exhibits two different structural conformations depending upon the pH. The crystal structures of acyl carrier protein synthase (AcpS) from Mycobacterium tuberculosis (Mtb) and Corynebacterium ammoniagenes determined at pH 5.3 and pH 6.5, respectively, are reported. Comparison of the Mtb apo-AcpS structure with the recently reported structure of the Mtb AcpS–ADP complex revealed that AcpS adopts two different conformations: the orthorhombic and trigonal space-group structures show structural differences in the α2 helix and in the conformation of the α3–α4 connecting loop, which is in a closed conformation. The apo-AcpS structure shows electron density for the entire model and was obtained at lower pH values (4.4–6.0). In contrast, at a higher pH value (6.5) AcpS undergoes significant conformational changes, resulting in disordered regions that show no electron density in the AcpS model. The solved structures also reveal that C. ammoniagenes AcpS undergoes structural rearrangement in two regions, similar to the recently reported Mtb AcpS–ADP complex structure. In vitro reconstitution experiments show that AcpS has a higher post-translational modification activity between pH 4.4 and 6.0 than at pH values above 6.5, where the activity drops owing to the change in conformation. The results show that apo-AcpS and AcpS–ADP adopt different conformations depending upon the pH conditions of the crystallization solution.

  16. Design of conformal lens by drilling holes materials using quasi-conformal transformation optics.

    Science.gov (United States)

    Li, Shouliang; Zhang, Zhan; Wang, Junhong; He, Xianshi

    2014-10-20

    In this paper, based on quasi-conformal transformation optics, a 3D conformal lens made of isotropic and non-resonant metamaterial is designed, which can make a cylindrical conformal array behave similarly to a uniform linear array. After discussion and simplification in the two-dimensional model, we realize the proposed lens by utilizing drilling-hole material in the three-dimensional structure. The ring-like shape and forward-only radiation make it possible to equip the lens on a cylindrical device.

  17. A Formal Approach to Conformance Testing

    NARCIS (Netherlands)

    Tretmans, G.J.

    1992-01-01

    In order to assure successful communication between computer systems from different manufacturers, standardized communication protocols are being developed and specified. As a next step implementations of these protocols are needed that conform to these specifications. Testing is a way to check

  18. NMR studies of dynamic biomolecular conformational ensembles.

    Science.gov (United States)

    Torchia, Dennis A

    2015-02-01

    Multidimensional heteronuclear NMR approaches can provide nearly complete sequential signal assignments of isotopically enriched biomolecules. The availability of assignments together with measurements of spin relaxation rates, residual spin interactions, J-couplings and chemical shifts provides information at atomic resolution about internal dynamics on timescales ranging from ps to ms, both in solution and in the solid state. However, due to the complexity of biomolecules, it is not possible to extract a unique atomic-resolution description of biomolecular motions even from extensive NMR data when many conformations are sampled on multiple timescales. For this reason, powerful computational approaches are increasingly applied to large NMR data sets to elucidate conformational ensembles sampled by biomolecules. In the past decade, considerable attention has been directed at an important class of biomolecules that function by binding to a wide variety of target molecules. Questions of current interest are: "Does the free biomolecule sample a conformational ensemble that encompasses the conformations found when it binds to various targets; and if so, on what time scale is the ensemble sampled?" This article reviews recent efforts to answer these questions, with a focus on comparing ensembles obtained for the same biomolecules by different investigators. A detailed comparison of results obtained is provided for three biomolecules: ubiquitin, calmodulin and the HIV-1 trans-activation response RNA. Published by Elsevier B.V.

  19. Chaotropes trigger conformational rearrangements differently in ...

    Indian Academy of Sciences (India)

    However, the mechanism of denaturation varied with the studied conditions, like different SDS concentrations and hydronium ion potentials, wherein the proteinundergoes a conformational rearrangement from β-sheet to α-helix. Moreover, GdnHCl triggered complete denaturation of ConA into a predominantly random coil ...

  20. Black Hole Monodromy and Conformal Field Theory

    NARCIS (Netherlands)

    Castro, A.; Lapan, J.M.; Maloney, A.; Rodriguez, M.J.

    2013-01-01

    The analytic structure of solutions to the Klein-Gordon equation in a black hole background, as represented by monodromy data, is intimately related to black hole thermodynamics. It encodes the "hidden conformal symmetry" of a nonextremal black hole, and it explains why features of the inner event

  1. Attraction and Repulsion in Conformal Gravity

    CERN Document Server

    Phillips, Peter R

    2015-01-01

    We use numerical integration to solve the field equations of conformal gravity, assuming a metric that is static and spherically symmetric. Our solution is an extension of that found by Mannheim and Kazanas; it indicates, as expected, that gravitation in this model should be attractive on small scales and repulsive on large ones.

  2. Three dimensional conformal postoperative radiotherapy for ...

    African Journals Online (AJOL)

    Azza Helal

    2013-06-17

    Jun 17, 2013 ... Abbreviations: 3DCRT, three dimensional conformal radiotherapy;. OARs, organs at risk; DVPs, dose volume parameters; PTV, planning target volume; RT, radiation therapy; ACOD, Alexandria Clinical. Oncology Department; CT, computed tomography; ICRU, Interna- tional Commission on Radiation Units; ...

  3. Do Charge State Signatures Guarantee Protein Conformations?

    Science.gov (United States)

    Hall, Zoe; Robinson, Carol V.

    2012-07-01

    The extent to which proteins in the gas phase retain their condensed-phase structure is a hotly debated issue. Closely related to this is the degree to which the observed charge state reflects protein conformation. Evidence from electron capture dissociation, hydrogen/deuterium exchange, ion mobility, and molecular dynamics shows clearly that there is often a strong correlation between the degree of folding and charge state, with the most compact conformations observed for the lowest charge states. In this article, we address recent controversies surrounding the relationship between charge states and folding, focussing also on the manipulation of charge in solution and its effect on conformation. `Supercharging' reagents that have been used to effect change in charge state can promote unfolding in the electrospray droplet. However for several protein complexes, supercharging does not appear to perturb the structure in that unfolding is not detected. Consequently, a higher charge state does not necessarily imply unfolding. Whilst the effect of charge manipulation on conformation remains controversial, there is strong evidence that a folded, compact state of a protein can survive in the gas phase, at least on a millisecond timescale. The exact nature of the side-chain packing and secondary structural elements in these compact states, however, remains elusive and prompts further research.

  4. Hydrocarbon chain conformation in an intercalated surfactant ...

    Indian Academy of Sciences (India)

    trans conformation with most of the trans chain aligned parallel to the gallery walls. On lowering the temperature, molecular plane aligns parallel, so that the methylene chain lies flat, rigid and aligned to the confining surface. In the bilayer phase ...

  5. Polymer conformation during flow in porous media

    NARCIS (Netherlands)

    Kawale, D.; Bouwman, G.W.; Sachdev, S.; Zitha, P.L.J.; Kreutzer, M.T.; Rossen, W.R.; Boukany, P.

    2017-01-01

    Molecular conformations of individual polymers during flow through porous media are directly observed by single-DNA imaging in microfluidics. As the Weissenberg number increases during flow (Wi > 1), we observe two types of elastic instabilities: (a) stationary dead-zone and (b) time-dependant

  6. Entanglement Entropy in Warped Conformal Field Theories

    NARCIS (Netherlands)

    Castro, A.; Hofman, D.M.; Iqbal, N.

    We present a detailed discussion of entanglement entropy in (1+1)-dimensional Warped Conformal Field Theories (WCFTs). We implement the Rindler method to evaluate entanglement and Renyi entropies for a single interval and along the way we interpret our results in terms of twist field correlation

  7. Surveillance and Conformity in Competitive Youth Swimming

    Science.gov (United States)

    Lang, Melanie

    2010-01-01

    Underpinned by a Foucauldian analysis of sporting practices, this paper identifies the disciplinary mechanism of surveillance at work in competitive youth swimming. It highlights the ways in which swimmers and their coaches are subject to and apply this mechanism to produce embodied conformity to normative behaviour and obedient, docile bodies.…

  8. Conformational regulation of urokinase receptor function

    DEFF Research Database (Denmark)

    Gårdsvoll, Henrik; Jacobsen, Benedikte; Kriegbaum, Mette C

    2011-01-01

    PA per se into the hydrophobic ligand binding cavity of uPAR that modulates the function of this receptor. Based on these data, we now propose a model in which the inherent interdomain mobility in uPAR plays a major role in modulating its function. Particularly one uPAR conformation, which is stabilized...

  9. Conformity of Goods in International Sales

    DEFF Research Database (Denmark)

    Henschel, Rene Franz

    The Conformity of Goods in International Sales gives a systematic analysis of Article 35 in the United Nations Convention on Contracts for the International Sale of Goods (CISG). Based on a detailed analysis of the most important cases and leading academic writing, Article 35 is described...

  10. Food Place Profiling and the Conformity Paradox

    DEFF Research Database (Denmark)

    Therkelsen, Anette; Gyimóthy, Szilvia

    Drawing on earlier research on local food, terroir, authenticity, food narratives and conformity in branding efforts, we study the place branding strategies of four Danish coastal destinations, each focusing on profiling themselves as food places for tourists. Based on analyses of online food...

  11. Synthesis and conformational features of sym , ', ...

    Indian Academy of Sciences (India)

    A one pot reaction involving sym ,'-diarylthiourea and the respective arylamine in the presence of aq. KOH in nitrobenzene at ≥ 105°C afforded sym ,',"-triarylguanidine in fair to good yield and the products have been characterized. Sym ,',"-tri(4-tolyl)guanidine possesses (7) anti-anti conformation, sym ,' ...

  12. Conformation of hindered piperidines: Spectroscopic evidence for ...

    Indian Academy of Sciences (India)

    At room temperature the (3)-benzyl-(2),(6)-bis(aryl)piperidin-4-ones 1-4 exist in only one isomeric form whereas their -nitroso derivatives 5-8 exist in two isomeric forms. The preferred conformations of both the isomeric forms of nitrosamines were determined by comparison of the spectral data with those of the ...

  13. Testing of Advanced Conformal Ablative TPS

    Science.gov (United States)

    Gasch, Matthew; Agrawal, Parul; Beck, Robin

    2013-01-01

    In support of the CA250 project, this paper details the results of a test campaign that was conducted at the Ames Arcjet Facility, wherein several novel low density thermal protection (TPS) materials were evaluated in an entry like environment. The motivation for these tests was to investigate whether novel conformal ablative TPS materials can perform under high heat flux and shear environment as a viable alternative to rigid ablators like PICA or Avcoat for missions like MSL and beyond. A conformable TPS over a rigid aeroshell has the potential to solve a number of challenges faced by traditional rigid TPS materials (such as tiled Phenolic Impregnated Carbon Ablator (PICA) system on MSL, and honeycomb-based Avcoat on the Orion Multi Purpose Crew Vehicle (MPCV)). The compliant (high strain to failure) nature of the conformable ablative materials will allow better integration of the TPS with the underlying aeroshell structure and enable monolithic-like configuration and larger segments to be used in fabrication.A novel SPRITE1 architecture, developed by the researchers at NASA Ames was used for arcjet testing. This small probe like configuration with 450 spherecone, enabled us to test the materials in a combination of high heat flux, pressure and shear environment. The heat flux near the nose were in the range of 500-1000 W/sq cm whereas in the flank section of the test article the magnitudes were about 50 of the nose, 250-500W/sq cm range. There were two candidate conformable materials under consideration for this test series. Both test materials are low density (0.28 g/cu cm) similar to Phenolic Impregnated Carbon Ablator (PICA) or Silicone Impregnated Refractory Ceramic Ablator (SIRCA) and are comprised of: A flexible carbon substrate (Carbon felt) infiltrated with an ablative resin system: phenolic (Conformal-PICA) or silicone (Conformal-SICA). The test demonstrated a successful performance of both the conformable ablators for heat flux conditions between 50

  14. Circular Wilson loops in defect conformal field theory

    Science.gov (United States)

    Aguilera-Damia, Jeremías; Correa, Diego H.; Giraldo-Rivera, Victor I.

    2017-03-01

    We study a D3-D5 system dual to a conformal field theory with a codimension-one defect that separates regions where the ranks of the gauge groups differ by k. With the help of this additional parameter, as observed by Nagasaki, Tanida and Yamaguchi, one can define a double scaling limit in which the quantum corrections are organized in powers of λ/k 2, which should allow to extrapolate results between weak and strong coupling regimes. In particular we consider a radius R circular Wilson loop placed at a distance L, whose internal space orientation is given by an angle χ. We compute its vacuum expectation value and show that, in the double scaling limit and for small χ and small L/R, weak coupling results can be extrapolated to the strong coupling limit.

  15. Coulomb-gas approach for boundary conformal field theory

    Energy Technology Data Exchange (ETDEWEB)

    Kawai, Shinsuke E-mail: kawai@thphys.ox.ac.uk

    2002-05-20

    We present a construction of boundary states based on the Coulomb-gas formalism of Dotsenko and Fateev. It is shown that Neumann-like coherent states on the charged bosonic Fock space provide a set of boundary states with consistent modular properties. Such coherent states are characterised by the boundary charges, which are related to the number of bulk screening operators through the charge neutrality condition. We illustrate this using the Ising model as an example, and show that all of its known consistent boundary states are reproduced in our formalism. This method applies to c<1 minimal conformal theories and provides an unified computational tool for studying boundary states of such theories.

  16. Branes for Higgs phases and exact conformal field theories

    CERN Document Server

    Sfetsos, K

    1999-01-01

    We consider multicenter supergravity solutions corresponding to Higgs phases of supersymmetric Yang-Mills theories with Z_N symmetric vacuua. In certain energy regimes, we find a description in terms of a generalized wormhole solution that corresponds to the SL(2,R)/U(1) \\times SU(2)/U(1) exact conformal field theory. We show that U-dualities map these backgrounds to purely gravitational ones and comment on the relation to the black holes arising from intersecting D1 and D5 branes. We also discuss supersymmetric properties of the various solutions and the relation to 2-dim solitons, on flat space, of the reduced axion-dilaton-gravity equations. Finally, we address the problem of understanding other supergravity solutions from the multicenter ones. As prototype examples we use rotating D3 branes and NS5 and D5 branes associated to non-Abelian duals of 4-dim hyper-Kahler metrics with SO(3) isometry.

  17. Heterotic string solutions and coset conformal field theories

    CERN Document Server

    Giveon, Amit; Tseytlin, Arkady A

    1993-01-01

    We discuss solutions of the heterotic string theory which are analogous to bosonic and superstring backgrounds related to coset conformal field theories. A class of exact `left-right symmetric' solutions is obtained by supplementing the metric, antisymmetric tensor and dilaton of the superstring solutions by the gauge field background equal to the generalised Lorentz connection with torsion. As in the superstring case, these backgrounds are $\\a'$-independent, i.e. have a `semiclassical' form. The corresponding heterotic string sigma model is obtained from the combination of the (1,0) supersymmetric gauged WZNW action with the action of internal fermions coupled to the target space gauge field. The pure (1,0) supersymmetric gauged WZNW theory is anomalous and does not describe a consistent heterotic string solution. We also find (to the order $\\alpha'^3$) a two-dimensional perturbative heterotic string solution with the trivial gauge field background. To the leading order in $\\alpha'$ it coincides with the kno...

  18. Advanced Small Animal Conformal Radiation Therapy Device.

    Science.gov (United States)

    Sharma, Sunil; Narayanasamy, Ganesh; Przybyla, Beata; Webber, Jessica; Boerma, Marjan; Clarkson, Richard; Moros, Eduardo G; Corry, Peter M; Griffin, Robert J

    2017-02-01

    We have developed a small animal conformal radiation therapy device that provides a degree of geometrical/anatomical targeting comparable to what is achievable in a commercial animal irradiator. small animal conformal radiation therapy device is capable of producing precise and accurate conformal delivery of radiation to target as well as for imaging small animals. The small animal conformal radiation therapy device uses an X-ray tube, a robotic animal position system, and a digital imager. The system is in a steel enclosure with adequate lead shielding following National Council on Radiation Protection and Measurements 49 guidelines and verified with Geiger-Mueller survey meter. The X-ray source is calibrated following AAPM TG-61 specifications and mounted at 101.6 cm from the floor, which is a primary barrier. The X-ray tube is mounted on a custom-made "gantry" and has a special collimating assembly system that allows field size between 0.5 mm and 20 cm at isocenter. Three-dimensional imaging can be performed to aid target localization using the same X-ray source at custom settings and an in-house reconstruction software. The small animal conformal radiation therapy device thus provides an excellent integrated system to promote translational research in radiation oncology in an academic laboratory. The purpose of this article is to review shielding and dosimetric measurement and highlight a few successful studies that have been performed to date with our system. In addition, an example of new data from an in vivo rat model of breast cancer is presented in which spatially fractionated radiation alone and in combination with thermal ablation was applied and the therapeutic benefit examined.

  19. A Structural and Functional Comparison Between Infectious and Non-Infectious Autocatalytic Recombinant PrP Conformers.

    Directory of Open Access Journals (Sweden)

    Geoffrey P Noble

    2015-06-01

    Full Text Available Infectious prions contain a self-propagating, misfolded conformer of the prion protein termed PrPSc. A critical prediction of the protein-only hypothesis is that autocatalytic PrPSc molecules should be infectious. However, some autocatalytic recombinant PrPSc molecules have low or undetectable levels of specific infectivity in bioassays, and the essential determinants of recombinant prion infectivity remain obscure. To identify structural and functional features specifically associated with infectivity, we compared the properties of two autocatalytic recombinant PrP conformers derived from the same original template, which differ by >105-fold in specific infectivity for wild-type mice. Structurally, hydrogen/deuterium exchange mass spectrometry (DXMS studies revealed that solvent accessibility profiles of infectious and non-infectious autocatalytic recombinant PrP conformers are remarkably similar throughout their protease-resistant cores, except for two domains encompassing residues 91-115 and 144-163. Raman spectroscopy and immunoprecipitation studies confirm that these domains adopt distinct conformations within infectious versus non-infectious autocatalytic recombinant PrP conformers. Functionally, in vitro prion propagation experiments show that the non-infectious conformer is unable to seed mouse PrPC substrates containing a glycosylphosphatidylinositol (GPI anchor, including native PrPC. Taken together, these results indicate that having a conformation that can be specifically adopted by post-translationally modified PrPC molecules is an essential determinant of biological infectivity for recombinant prions, and suggest that this ability is associated with discrete features of PrPSc structure.

  20. A Structural and Functional Comparison Between Infectious and Non-Infectious Autocatalytic Recombinant PrP Conformers

    Science.gov (United States)

    Noble, Geoffrey P.; Wang, Daphne W.; Walsh, Daniel J.; Barone, Justin R.; Miller, Michael B.; Nishina, Koren A.; Li, Sheng; Supattapone, Surachai

    2015-01-01

    Infectious prions contain a self-propagating, misfolded conformer of the prion protein termed PrPSc. A critical prediction of the protein-only hypothesis is that autocatalytic PrPSc molecules should be infectious. However, some autocatalytic recombinant PrPSc molecules have low or undetectable levels of specific infectivity in bioassays, and the essential determinants of recombinant prion infectivity remain obscure. To identify structural and functional features specifically associated with infectivity, we compared the properties of two autocatalytic recombinant PrP conformers derived from the same original template, which differ by >105-fold in specific infectivity for wild-type mice. Structurally, hydrogen/deuterium exchange mass spectrometry (DXMS) studies revealed that solvent accessibility profiles of infectious and non-infectious autocatalytic recombinant PrP conformers are remarkably similar throughout their protease-resistant cores, except for two domains encompassing residues 91-115 and 144-163. Raman spectroscopy and immunoprecipitation studies confirm that these domains adopt distinct conformations within infectious versus non-infectious autocatalytic recombinant PrP conformers. Functionally, in vitro prion propagation experiments show that the non-infectious conformer is unable to seed mouse PrPC substrates containing a glycosylphosphatidylinositol (GPI) anchor, including native PrPC. Taken together, these results indicate that having a conformation that can be specifically adopted by post-translationally modified PrPC molecules is an essential determinant of biological infectivity for recombinant prions, and suggest that this ability is associated with discrete features of PrPSc structure. PMID:26125623

  1. Hierarchical sampling for metastable conformers determines biomolecular recognition: the case of malectin and diglucosylated N-glycan interactions.

    Science.gov (United States)

    Mamidi, Ashalatha Sreshty; Surolia, Avadhesha

    2015-01-01

    Structural information over the entire course of binding interactions based on the analyses of energy landscapes is described, which provides a framework to understand the events involved during biomolecular recognition. Conformational dynamics of malectin's exquisite selectivity for diglucosylated N-glycan (Dig-N-glycan), a highly flexible oligosaccharide comprising of numerous dihedral torsion angles, are described as an example. For this purpose, a novel approach based on hierarchical sampling for acquiring metastable molecular conformations constituting low-energy minima for understanding the structural features involved in a biologic recognition is proposed. For this purpose, four variants of principal component analysis were employed recursively in both Cartesian space and dihedral angles space that are characterized by free energy landscapes to select the most stable conformational substates. Subsequently, k-means clustering algorithm was implemented for geometric separation of the major native state to acquire a final ensemble of metastable conformers. A comparison of malectin complexes was then performed to characterize their conformational properties. Analyses of stereochemical metrics and other concerted binding events revealed surface complementarity, cooperative and bidentate hydrogen bonds, water-mediated hydrogen bonds, carbohydrate-aromatic interactions including CH-π and stacking interactions involved in this recognition. Additionally, a striking structural transition from loop to β-strands in malectin CRD upon specific binding to Dig-N-glycan is observed. The interplay of the above-mentioned binding events in malectin and Dig-N-glycan supports an extended conformational selection model as the underlying binding mechanism.

  2. Conformational epitope mapping of Pru du 6, a major allergen from almond nut.

    Science.gov (United States)

    Willison, LeAnna N; Zhang, Qian; Su, Mengna; Teuber, Suzanne S; Sathe, Shridhar K; Roux, Kenneth H

    2013-10-01

    Tree nuts are a widely consumed food. Although enjoyed safely by most individuals, allergic reactions to tree nuts, including almond, are not uncommon. Almond prunin (Pru du 6), an 11S globulin (legumin), is an abundant nut seed protein and a major allergen. Conformational epitope mapping studies of prunin have been performed with a murine monoclonal antibody (mAb) 4C10. This mAb reacts with non-reduced but not reduced prunin in immunoblotting assays, indicating the recognition of a conformational epitope. 4C10 competes with patient IgE, as assessed by ELISA, indicating clinical significance of the epitope. To characterize the 4C10 epitope, hydrogen/deuterium exchange (HDX) monitored by 14.5 T Fourier transform ion cyclotron resonance mass spectrometry (MS) was performed on the native prunin-4C10 complex and on uncomplexed native prunin. Several epitope candidate peptides that differ in deuterium uptake between the complexed and uncomplexed forms were identified. The epitope was further mapped by analyzing chimeric molecules incorporating segments of the homologous soybean allergen, Gly m 6, in immunoassays. These data indicate that the 4C10 epitope overlaps with a subset of patient IgE binding epitopes on almond prunin and further supports HDX-MS as a valid technique for mapping conformational epitopes. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. 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

    2018-01-14

    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.

  4. 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.

  5. Coincidence gamma-ray spectrometry

    DEFF Research Database (Denmark)

    Markovic, Nikola; Roos, Per; Nielsen, Sven Poul

    2017-01-01

    events are recorded in a list mode file with their timestamp and energy, enabling coincidence identification and spectrum manipulation in post-processing. When coincidence gamma-spectrometry is used for cascade emitting nuclides, coincident signals can be extracted thus significantly reducing......Gamma-ray spectrometry with high-purity germanium (HPGe) detectors is often the technique of choice in an environmental radioactivity laboratory. When measuring environmental samples associated activities are usually low so an important parameter that describes the performance of the spectrometer...... for a nuclide of interest is the minimum detectable activity (MDA). There are many ways for lowering the MDAs in gamma spectrometry. Recently, developments of fast and compact digital acquisition systems have led to growing number of multiple HPGe detector spectrometers. In these applications all detected...

  6. Mass spectrometry. [in organic chemistry

    Science.gov (United States)

    Burlingame, A. L.; Shackleton, C. H. L.; Howe, I.; Chizhov, O. S.

    1978-01-01

    A review of mass spectrometry in organic chemistry is given, dealing with advances in instrumentation and computer techniques, selected topics in gas-phase ion chemistry, and applications in such fields as biomedicine, natural-product studies, and environmental pollution analysis. Innovative techniques and instrumentation are discussed, along with chromatographic-mass spectrometric on-line computer techniques, mass spectral interpretation and management techniques, and such topics in gas-phase ion chemistry as electron-impact ionization and decomposition, photoionization, field ionization and desorption, high-pressure mass spectrometry, ion cyclotron resonance, and isomerization reactions of organic ions. Applications of mass spectrometry are examined with respect to bio-oligomers and their constituents, biomedically important substances, microbiology, environmental organic analysis, and organic geochemistry.

  7. Advances in Clinical Mass Spectrometry.

    Science.gov (United States)

    French, D

    Although mass spectrometry has been used clinically for decades, the advent of immunoassay technology moved the clinical laboratory to more labor saving automated platforms requiring little if any sample preparation. It became clear, however, that immunoassays lacked sufficient sensitivity and specificity necessary for measurement of certain analytes or for measurement of analytes in specific patient populations. This limitation prompted clinical laboratories to revisit mass spectrometry which could additionally be used to develop assays for which there was no commercial source. In this chapter, the clinical applications of mass spectrometry in therapeutic drug monitoring, toxicology, and steroid hormone analysis will be reviewed. Technologic advances and new clinical applications will also be discussed. © 2017 Elsevier Inc. All rights reserved.

  8. Symposium on accelerator mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    None

    1981-01-01

    The area of accelerator mass spectrometry has expanded considerably over the past few years and established itself as an independent and interdisciplinary research field. Three years have passed since the first meeting was held at Rochester. A Symposium on Accelerator Mass Spectrometry was held at Argonne on May 11-13, 1981. In attendance were 96 scientists of whom 26 were from outside the United States. The present proceedings document the program and excitement of the field. Papers are arranged according to the original program. A few papers not presented at the meeting have been added to complete the information on the status of accelerator mass spectrometry. Individual papers were prepared separately for the data base.

  9. Isotope ratio analysis by Orbitrap mass spectrometry

    Science.gov (United States)

    Eiler, J. M.; Chimiak, L. M.; Dallas, B.; Griep-Raming, J.; Juchelka, D.; Makarov, A.; Schwieters, J. B.

    2016-12-01

    Several technologies are being developed to examine the intramolecular isotopic structures of molecules (i.e., site-specific and multiple substitution), but various limitations in sample size and type or (for IRMS) resolution have so far prevented the creation of a truly general technique. We will discuss the initial findings of a technique based on Fourier transform mass spectrometry, using the Thermo Scientific Q Exactive GC — an instrument that contains an Orbitrap mass analyzer. Fourier transform mass spectrometry is marked by exceptionally high mass resolutions (the Orbitrap reaches M/∆M in the range 250,000-1M in the mass range of greatest interest, 50-200 amu). This allows for resolution of a large range of nearly isobaric interferences for isotopologues of volatile and semi-volatile compounds (i.e., involving isotopes of H, C, N, O and S). It also provides potential to solve very challenging mass resolution problems for isotopic analysis of other, heavier elements. Both internal and external experimental reproducibilities of isotope ratio analyses using the Orbitrap typically conform to shot-noise limits down to levels of 0.2 ‰ (1SE), and routinely in the range 0.5-1.0 ‰, with similar accuracy when standardized to concurrently run reference materials. Such measurements can be made without modifications to the ion optics of the Q Exactive GC, but do require specially designed sample introduction devices to permit sample/standard comparison and long integration times. The sensitivity of the Q Exactive GC permits analysis of sub-nanomolar samples and quantification of multiply-substituted species. The site-specific capability of this instrument arises from the fact that mass spectra of molecular analytes commonly contain diverse fragment ion species, each of which samples a specific sub-set of molecular sites. We will present applications of this technique to the biological and abiological chemistry of amino acids, forensic identification of

  10. Single-Molecule FRET States, Conformational Interchange, and Conformational Selection by Dye Labels in Calmodulin.

    Science.gov (United States)

    DeVore, Matthew S; Braimah, Adebayo; Benson, David R; Johnson, Carey K

    2016-05-19

    We investigate the roles of measurement time scale and the nature of the fluorophores in the FRET states measured for calmodulin, a calcium signaling protein known to undergo pronounced conformational changes. The measured FRET distributions depend markedly on the measurement time scale (nanosecond or microsecond). Comparison of FRET distributions measured by donor fluorescence decay with FRET distributions recovered from single-molecule burst measurements binned over time scales of 90 μs to 1 ms reveals conformational averaging over the intervening time regimes. We find further that, particularly in the presence of saturating Ca(2+), the nature of the measured single-molecule FRET distribution depends markedly on the identity of the FRET pair. The results suggest interchange between conformational states on time scales of hundreds of microseconds or less. Interaction with a fluorophore such as the dye Texas Red alters both the nature of the measured FRET distributions and the dynamics of conformational interchange. The results further suggest that the fluorophore may not be merely a benign reporter of protein conformations in FRET studies, but may in fact alter the conformational landscape.

  11. Serum Albumin Domain Structures in Human Blood Serum by Mass Spectrometry and Computational Biology.

    Science.gov (United States)

    Belsom, Adam; Schneider, Michael; Fischer, Lutz; Brock, Oliver; Rappsilber, Juri

    2016-03-01

    Chemical cross-linking combined with mass spectrometry has proven useful for studying protein-protein interactions and protein structure, however the low density of cross-link data has so far precluded its use in determining structures de novo. Cross-linking density has been typically limited by the chemical selectivity of the standard cross-linking reagents that are commonly used for protein cross-linking. We have implemented the use of a heterobifunctional cross-linking reagent, sulfosuccinimidyl 4,4'-azipentanoate (sulfo-SDA), combining a traditional sulfo-N-hydroxysuccinimide (sulfo-NHS) ester and a UV photoactivatable diazirine group. This diazirine yields a highly reactive and promiscuous carbene species, the net result being a greatly increased number of cross-links compared with homobifunctional, NHS-based cross-linkers. We present a novel methodology that combines the use of this high density photo-cross-linking data with conformational space search to investigate the structure of human serum albumin domains, from purified samples, and in its native environment, human blood serum. Our approach is able to determine human serum albumin domain structures with good accuracy: root-mean-square deviation to crystal structure are 2.8/5.6/2.9 Å (purified samples) and 4.5/5.9/4.8Å (serum samples) for domains A/B/C for the first selected structure; 2.5/4.9/2.9 Å (purified samples) and 3.5/5.2/3.8 Å (serum samples) for the best out of top five selected structures. Our proof-of-concept study on human serum albumin demonstrates initial potential of our approach for determining the structures of more proteins in the complex biological contexts in which they function and which they may require for correct folding. Data are available via ProteomeXchange with identifier PXD001692. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Cluster secondary ion mass spectrometry microscope mode mass spectrometry imaging

    NARCIS (Netherlands)

    Kiss, A.; Smith, D.F.; Jungmann, JH|info:eu-repo/dai/nl/351240020; Heeren, R.M.A.|info:eu-repo/dai/nl/105188476

    2013-01-01

    RATIONALE: Microscope mode imaging for secondary ion mass spectrometry is a technique with the promise of simultaneous high spatial resolution and high-speed imaging of biomolecules from complex surfaces. Technological developments such as new position-sensitive detectors, in combination with

  13. Gauge Natural Formulation of Conformal Theory of Gravity

    CERN Document Server

    Campigotto, M

    2014-01-01

    We consider conformal gravity as a gauge natural theory. We study its conservation laws and superpotentials. We also consider the Mannheim and Kazanas spherically symmetric vacuum solution and discuss conserved quantities associated to conformal and diffeomorphism symmetries.

  14. Conformal Killing Vectors Of Plane Symmetric Four Dimensional Lorentzian Manifolds

    CERN Document Server

    Khan, Suhail; Bokhari, Ashfaque H; Khan, Gulzar Ali; Mathematics, Department of; Peshawar, University of; Pakhtoonkhwa, Peshawar Khyber; Pakistan.,; Petroleum, King Fahd University of; Minerals,; 31261, Dhahran; Arabia, Saudi

    2015-01-01

    In this paper, we investigate conformal Killing's vectors (CKVs) admitted by some plane symmetric spacetimes. Ten conformal Killing's equations and their general forms of CKVs are derived along with their conformal factor. The existence of conformal Killing's symmetry imposes restrictions on the metric functions. The conditions imposing restrictions on these metric functions are obtained as a set of integrability conditions. Considering the cases of time-like and inheriting CKVs, we obtain spacetimes admitting plane conformal symmetry. Integrability conditions are solved completely for some known non-conformally flat and conformally flat classes of plane symmetric spacetimes. A special vacuum plane symmetric spacetime is obtained, and it is shown that for such a metric CKVs are just the homothetic vectors (HVs). Among all the examples considered, there exists only one case with a six dimensional algebra of special CKVs admitting one proper CKV. In all other examples of non-conformally flat metrics, no proper ...

  15. Bcl-2 Conformational Change as an Indicator of Chemotherapy Response

    National Research Council Canada - National Science Library

    Zhang, Xiao-kung

    2005-01-01

    .... We propose that Bcl-2 undergoes a conformational change in response to chemotherapeutic agents in breast cancer cells in vitro and in vivo and that a Bcl-2-conformation-sensitive antibody can be used...

  16. Peer influence: Neural mechanisms underlying in-group conformity

    National Research Council Canada - National Science Library

    Stallen, Mirre; Smidts, Ale; Sanfey, Alan

    2013-01-01

    .... 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...

  17. Conformity of nurse prescribing to care needs: nurses' understanding

    National Research Council Canada - National Science Library

    Marília Silveira Faeda; Márcia Galan Perroca

    2017-01-01

    Submission: 04-07-2016 Approval: 11-02-2016 ABSTRACT Objective: investigate the understanding of nurses on nurse prescribing conformity to the care needs of hospitalized patients and factors associated with that conformity. Method...

  18. Applying the tools of chemistry (mass spectrometry and covalent modification by small molecule reagents) to the detection of prions and the study of their structure

    Science.gov (United States)

    Prions are molecular pathogens, able to convert a normal cellular prion protein PrPC into a prion PrPSc. The information necessary for this conversion is contained in the conformation of PrPSc. Mass spectrometry and small-molecule covalent reactions have recently been used to study prions. This w...

  19. Sites involved in intra- and interdomain allostery associated with the activation of factor VIIa pinpointed by hydrogen-deuterium exchange and electron transfer dissociation mass spectrometry

    DEFF Research Database (Denmark)

    Song, Hongjian; Olsen, Ole H; Persson, Egon

    2014-01-01

    enhancement remain elusive. Here we have applied hydrogen/deuterium exchange mass spectrometry coupled to electron transfer dissociation to pinpoint individual residues in the heavy chain of FVIIa whose conformation and/or local interaction pattern changes when the enzyme transitions to the active form...

  20. Supersymmetric gauge theories, quantization of M{sub flat}, and conformal field theory

    Energy Technology Data Exchange (ETDEWEB)

    Teschner, J.; Vartanov, G.S.

    2013-02-15

    We propose a derivation of the correspondence between certain gauge theories with N=2 supersymmetry and conformal field theory discovered by Alday, Gaiotto and Tachikawa in the spirit of Seiberg-Witten theory. Based on certain results from the literature we argue that the quantum theory of the moduli spaces of flat SL(2,R)-connections represents a nonperturbative ''skeleton'' of the gauge theory, protected by supersymmetry. It follows that instanton partition functions can be characterized as solutions to a Riemann-Hilbert type problem. In order to solve it, we describe the quantization of the moduli spaces of flat connections explicitly in terms of two natural sets of Darboux coordinates. The kernel describing the relation between the two pictures represents the solution to the Riemann Hilbert problem, and is naturally identified with the Liouville conformal blocks.

  1. Attomole quantitation of protein separations with accelerator mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Vogel, J S; Grant, P G; Buccholz, B A; Dingley, K; Turteltaub, K W

    2000-12-15

    Quantification of specific proteins depends on separation by chromatography or electrophoresis followed by chemical detection schemes such as staining and fluorophore adhesion. Chemical exchange of short-lived isotopes, particularly sulfur, is also prevalent despite the inconveniences of counting radioactivity. Physical methods based on isotopic and elemental analyses offer highly sensitive protein quantitation that has linear response over wide dynamic ranges and is independent of protein conformation. Accelerator mass spectrometry quantifies long-lived isotopes such as 14C to sub-attomole sensitivity. We quantified protein interactions with small molecules such as toxins, vitamins, and natural biochemicals at precisions of 1-5% . Micro-proton-induced-xray-emission quantifies elemental abundances in separated metalloprotein samples to nanogram amounts and is capable of quantifying phosphorylated loci in gels. Accelerator-based quantitation is a possible tool for quantifying the genome translation into proteome.

  2. Charging of Proteins in Native Mass Spectrometry

    Science.gov (United States)

    Susa, Anna C.; Xia, Zijie; Tang, Henry Y. H.; Tainer, John A.; Williams, Evan R.

    2017-02-01

    Factors that influence the charging of protein ions formed by electrospray ionization from aqueous solutions in which proteins have native structures and function were investigated. Protein ions ranging in molecular weight from 12.3 to 79.7 kDa and pI values from 5.4 to 9.6 were formed from different solutions and reacted with volatile bases of gas-phase basicities higher than that of ammonia in the cell of a Fourier-transform ion cyclotron resonance mass spectrometer. The charge-state distribution of cytochrome c ions formed from aqueous ammonium or potassium acetate is the same. Moreover, ions formed from these two solutions do not undergo proton transfer to 2-fluoropyridine, which is 8 kcal/mol more basic than ammonia. These results provide compelling evidence that proton transfer between ammonia and protein ions does not limit protein ion charge in native electrospray ionization. Both circular dichroism and ion mobility measurements indicate that there are differences in conformations of proteins in pure water and aqueous ammonium acetate, and these differences can account for the difference in the extent of charging and proton-transfer reactivities of protein ions formed from these solutions. The extent of proton transfer of the protein ions with higher gas-phase basicity bases trends with how closely the protein ions are charged to the value predicted by the Rayleigh limit for spherical water droplets approximately the same size as the proteins. These results indicate that droplet charge limits protein ion charge in native mass spectrometry and are consistent with these ions being formed by the charged residue mechanism.

  3. Conformational changes of fibrinogen after adsorption.

    Science.gov (United States)

    Clarke, Matthew L; Wang, Jie; Chen, Zhan

    2005-11-24

    The adsorption behavior of fibrinogen to two biomedical polyurethanes and a perfluorinated polymer has been investigated. Changes in the secondary structure of adsorbed fibrinogen were monitored using attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) and sum frequency generation vibrational spectroscopy (SFG). SFG measurements were performed in the amide I range as well as in the C-H/N-H stretching range. Amide I signals from SFG demonstrate that fibrinogen has post-adsorption conformational changes that are dependent upon the polymer surface properties. For example, strong attenuation of the amide I and N-H stretching signals with increasing residence time was observed for fibrinogen adsorbed to poly(ether urethane) but not for the other two polymers. This change is not readily observed by ATR-FTIR. Differences in the observed spectral changes for fibrinogen adsorbed to each polymer are explained by different initial binding mechanisms and post-adsorption conformational changes.

  4. Spinor product computations for protein conformations.

    Science.gov (United States)

    Chys, Pieter; Chacón, Pablo

    2012-08-05

    Spinor operators in geometric algebra (GA) can efficiently describe conformational changes of proteins by ordered products that act on individual bonds and represent their net rotations. Backward propagation through the protein backbone yields all rotational spinor axes in advance allowing the efficient computation of atomic coordinates from internal coordinates. The introduced mathematical framework enables to efficiently manipulate and generate protein conformations to any arbitrary degree. Moreover, several new formulations in the context of rigid body motions are added. Emphasis is placed on the intimate relationship between spinors and quaternions, which can be recovered from within the GA approach. The spinor methodology is implemented and tested versus the state of the art algorithms for both protein construction and coordinate updating. Spinor calculations have a smaller computational cost and turn out to be slightly faster than current alternatives. Copyright © 2012 Wiley Periodicals, Inc.

  5. Problems with Mannheim's conformal gravity program

    Science.gov (United States)

    Yoon, Youngsub

    2013-07-01

    We show that Mannheim’s conformal gravity program, whose potential has a term proportional to 1/r and another term proportional to r, does not reduce to Newtonian gravity at short distances, unless one assumes undesirable singularities of the mass density of the proton. Therefore, despite the claim that it successfully explains galaxy rotation curves, unless one assumes the singularities, it seems to be falsified by numerous Cavendish-type experiments performed at laboratories on Earth whose work have not found any deviations from Newton’s theory. Moreover, it can be shown that as long as the total mass of the proton is positive, Mannheim’s conformal gravity program leads to negative linear potential, which is problematic from the point of view of fitting galaxy rotation curves, which necessarily requires positive linear potential.

  6. The conformational musings of a medicinal chemist.

    Science.gov (United States)

    Finch, Harry

    2014-03-01

    Structure-based drug design strategies based on X-ray crystallographic data of ligands bound to biological targets or computationally derived pharmacophore models have been introduced over the past 25 years or so. These have now matured and are deeply embedded in the drug discovery process in most pharmaceutical and biotechnology companies where they continue to play a major part in the discovery of new medicines and drug candidates. Newly developed NMR methods can now provide a full description of the conformations in which ligands exist in free solution, crucially allowing those that are dominant to be identified. Integrating experimentally determined conformational information on active and inactive molecules in drug discovery programmes, alongside the existing techniques, should have a major impact on the success of drug discovery. Copyright © 2013 Elsevier Ltd. All rights reserved.

  7. Conformational biosensor for diagnosis of prion diseases.

    Science.gov (United States)

    Tcherkasskaya, Olga; Davidson, Eugene A; Schmerr, Mary Jo; Orser, Cindy S

    2005-05-01

    A fluorescence technology to monitor the proliferation of amyloidogenic neurological disorders is proposed. A crude brain homogenate (0.01%) from animals infected with a transmissible spongiform encephalopathy is employed as a catalytic medium initiating conformational changes in 520 nM polypeptide biosensors (Tris/trifluoroethanol 50% mixture at pH 7). The fluorescence methods utilize pyrene residues covalently attached to the peptide ends. The coil-to-beta-strand transitions in biosensor molecules cause elevation of a distinct fluorescence band of the pyrene aggregates (i.e. excimers). This approach enables the detection of infectious prion proteins at fmol, does not require antibody binding or protease treatment. Technology might be adopted for diagnosing a large variety of conformational disorders as well as for generic high-throughput screening of the amyloidogenic potential in plasma.

  8. Investigating the Interaction between the Neonatal Fc Receptor and Monoclonal Antibody Variants by Hydrogen/Deuterium Exchange Mass Spectrometry

    DEFF Research Database (Denmark)

    Jensen, Pernille Foged; Larraillet, Vincent; Schlothauer, Tilman

    2015-01-01

    in understanding and modulating the IgG-FcRn interaction to optimize antibody pharmacokinetics and ultimately improve efficacy and safety. Here we studied the interaction between a full-length human IgG1 and human FcRn via hydrogen/deuterium exchange mass spectrometry and targeted electron transfer dissociation......-type glycosylated IgG. Our results provide new molecular insight into the IgG-FcRn interaction and illustrate the capability of hydrogen/deuterium exchange mass spectrometry to advance structural proteomics by providing detailed information on the conformation and dynamics of large protein complexes in solution....

  9. A Dynamic Epistemic Framework for Conformant Planning

    Directory of Open Access Journals (Sweden)

    Quan Yu

    2016-06-01

    Full Text Available In this paper, we introduce a lightweight dynamic epistemic logical framework for automated planning under initial uncertainty. We reduce plan verification and conformant planning to model checking problems of our logic. We show that the model checking problem of the iteration-free fragment is PSPACE-complete. By using two non-standard (but equivalent semantics, we give novel model checking algorithms to the full language and the iteration-free language.

  10. Conformal Dynamics of Precursors to Fracture

    OpenAIRE

    Barra, Felipe; Herrera, Mauricio; Procaccia, Itamar

    2002-01-01

    An exact integro-differential equation for the conformal map from the unit circle to the boundary of an evolving cavity in a stressed 2-dimensional solid is derived. This equation provides an accurate description of the dynamics of precursors to fracture when surface diffusion is important. The solution predicts the creation of sharp grooves that eventually lead to material failure via rapid fracture. Solutions of the new equation are demonstrated for the dynamics of an elliptical cavity and ...

  11. Redox-Dependent Conformational Switching of Diphenylacetylenes

    Directory of Open Access Journals (Sweden)

    Ian M. Jones

    2014-07-01

    Full Text Available Herein we describe the design and synthesis of a redox-dependent single-molecule switch. Appending a ferrocene unit to a diphenylacetylene scaffold gives a redox-sensitive handle, which undergoes reversible one-electron oxidation, as demonstrated by cyclic voltammetry analysis. 1H-NMR spectroscopy of the partially oxidized switch and control compounds suggests that oxidation to the ferrocenium cation induces a change in hydrogen bonding interactions that results in a conformational switch.

  12. Theoretical studies on the conformations of selenamides

    Indian Academy of Sciences (India)

    Unknown

    Abstract. Ab initio HF/6-31+G*, MP2/6-31+G*, B3LYP/6-31+G* level calculations have been performed on HSe–NH2 to estimate the Se–N rotational barriers and. N-inversion barriers. Two conformers have been found with syn and anti arrangement of the NH2 hydrogens with respect to Se–H bond. The N inversion barriers ...

  13. The Relationship of Conformity and Memory

    OpenAIRE

    Rogayeh Mohammadi, Gholam Hossein Javanmard

    2015-01-01

    Some theorists believe that the brain was evolved under the influence of the community and for the community. So it seems that social function has priority on pure cognitive in the brain. The purpose of this research was to study the relationship between conformity and general memory. The current study is a descriptive-correlational research by using prediction (regression) method. For doing this, 167 students were selected via the multistage cluster method from Bonab and Tabriz Payam Noor un...

  14. Abelian conformal field theory and determinant bundles

    DEFF Research Database (Denmark)

    Andersen, Jørgen Ellegaard; Ueno, K.

    2007-01-01

    are up to a scale the same as the curvature of the connections constructed in [14, 16]. We study the sewing construction for nodal curves and its explicit relation to the constructed connections. Finally we construct preferred holomorphic sections of these line bundles and analyze their behaviour near...... nodal curves. These results are used in [4] to construct modular functors form the conformal field theories given in [14, 16] by twisting with an appropriate factional power of this Abelian theory....

  15. Boundary conditions in conformal and integrable theories

    CERN Document Server

    Petkova, V B

    2000-01-01

    The study of boundary conditions in rational conformal field theories is not only physically important. It also reveals a lot on the structure of the theory ``in the bulk''. The same graphs classify both the torus and the cylinder partition functions and provide data on their hidden ``quantum symmetry''. The Ocneanu triangular cells -- the 3j-symbols of these symmetries, admit various interpretations and make a link between different problems.

  16. Opinion Dynamics and Wisdom under Conformity

    OpenAIRE

    Buechel, Berno; Hellmann, Tim; Kölßner, Stefan

    2014-01-01

    We present a model of opinion formation where individuals repeatedly engage in discussion and update their opinion in a social network similarly to the DeGroot model. Abstracting from the standard assumption that individuals always report their opinion truthfully, agents in our model may state an opinion that differs from their true opinion. The incentive to do so is induced by agents' preferences for conformity. We model opinion formation as a dynamic process and identify conditions for conv...

  17. Scale factor duality for conformal cyclic cosmologies

    Energy Technology Data Exchange (ETDEWEB)

    Silva, University Camara da; Lima, A.L. Alves; Sotkov, G.M. [Departamento de Física - CCE,Universidade Federal de Espirito Santo, 29075-900, Vitoria ES (Brazil)

    2016-11-16

    The scale factor duality is a symmetry of dilaton gravity which is known to lead to pre-big-bang cosmologies. A conformal time version of the scale factor duality (SFD) was recently implemented as a UV/IR symmetry between decelerated and accelerated phases of the post-big-bang evolution within Einstein gravity coupled to a scalar field. The problem investigated in the present paper concerns the employment of the conformal time SFD methods to the construction of pre-big-bang and cyclic extensions of these models. We demonstrate that each big-bang model gives rise to two qualitatively different pre-big-bang evolutions: a contraction/expansion SFD model and Penrose’s Conformal Cyclic Cosmology (CCC). A few examples of SFD symmetric cyclic universes involving certain gauged Kähler sigma models minimally coupled to Einstein gravity are studied. We also describe the specific SFD features of the thermodynamics and the conditions for validity of the generalized second law in the case of Gauss-Bonnet (GB) extension of these selected CCC models.

  18. Spherically symmetric conformal gravity and "gravitational bubbles"

    CERN Document Server

    Berezin, V A; Eroshenko, Yu N

    2016-01-01

    The general structure of the spherically symmetric solutions in the Weyl conformal gravity is described. The corresponding Bach equation are derived for the special type of metrics, which can be considered as the representative of the general class. The complete set of the pure vacuum solutions is found. It consists of two classes. The first one contains the solutions with constant two-dimensional curvature scalar of our specific metrics, and the representatives are the famous Robertson-Walker metrics. One of them we called the "gravitational bubbles", which is compact and with zero Weyl tensor. The second class is more general, with varying curvature scalar. We found its representative as the one-parameter family. It appears that it can be conformally covered by the thee-parameter Mannheim-Kazanas solution. We also investigated the general structure of the energy-momentum tensor in the spherical conformal gravity and constructed the vectorial equation that reveals clearly the same features of non-vacuum solu...

  19. Compact conformations of human protein disulfide isomerase.

    Directory of Open Access Journals (Sweden)

    Shang Yang

    Full Text Available Protein disulfide isomerase (PDI composed of four thioredoxin-like domains a, b, b', and a', is a key enzyme catalyzing oxidative protein folding in the endoplasmic reticulum. Large scale molecular dynamics simulations starting from the crystal structures of human PDI (hPDI in the oxidized and reduced states were performed. The results indicate that hPDI adopts more compact conformations in solution than in the crystal structures, which are stabilized primarily by inter-domain interactions, including the salt bridges between domains a and b' observed for the first time. A prominent feature of the compact conformations is that the two catalytic domains a and a' can locate close enough for intra-molecular electron transfer, which was confirmed by the characterization of an intermediate with a disulfide between the two domains. Mutations, which disrupt the inter-domain interactions, lead to decreased reductase activity of hPDI. Our molecular dynamics simulations and biochemical experiments reveal the intrinsic conformational dynamics of hPDI and its biological impact.

  20. Scale factor duality for conformal cyclic cosmologies

    Science.gov (United States)

    Camara da Silva, U.; Alves Lima, A. L.; Sotkov, G. M.

    2016-11-01

    The scale factor duality is a symmetry of dilaton gravity which is known to lead to pre-big-bang cosmologies. A conformal time version of the scale factor duality (SFD) was recently implemented as a UV/IR symmetry between decelerated and accelerated phases of the post-big-bang evolution within Einstein gravity coupled to a scalar field. The problem investigated in the present paper concerns the employment of the conformal time SFD methods to the construction of pre-big-bang and cyclic extensions of these models. We demonstrate that each big-bang model gives rise to two qualitatively different pre-big-bang evolutions: a contraction/expansion SFD model and Penrose's Conformal Cyclic Cosmology (CCC). A few examples of SFD symmetric cyclic universes involving certain gauged Kähler sigma models minimally coupled to Einstein gravity are studied. We also describe the specific SFD features of the thermodynamics and the conditions for validity of the generalized second law in the case of Gauss-Bonnet (GB) extension of these selected CCC models.