WorldWideScience

Sample records for ligand-stabilized conformational states

  1. Long-lived charge-separated states in ligand-stabilized silver clusters

    KAUST Repository

    Pelton, Matthew

    2012-07-25

    Recently developed synthesis methods allow for the production of atomically monodisperse clusters of silver atoms stabilized in solution by aromatic thiol ligands, which exhibit intense absorption peaks throughout the visible and near-IR spectral regions. Here we investigated the time-dependent optical properties of these clusters. We observed two kinetic processes following ultrafast laser excitation of any of the absorption peaks: a rapid decay, with a time constant of 1 ps or less, and a slow decay, with a time constant that can be longer than 300 ns. Both time constants decrease as the polarity of the solvent increases, indicating that the two processes correspond to the formation and recombination, respectively, of a charge-separated state. The long lifetime of this state and the broad optical absorption spectrum mean that the ligand-stabilized silver clusters are promising materials for solar energy harvesting. © 2012 American Chemical Society.

  2. Multiple conformations of proteins in native state

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Examples of protein sequences that can adopt multiple native states are recently accumulated. Characterization of the protein multiple conformations will have important implications for our understanding of the relationship between structure and function, and their folding kinetics. In present review, the experimental evidence for the existence of multiple conformations in the native state of proteins, the molecular basis and the biological significance of multiple conformations of proteins are focused.

  3. Testing Conformal Theory:. 3-STATE Potts

    Science.gov (United States)

    Barkema, G. T.; McCabe, J.; Wydro, T.

    2001-04-01

    Conformal theory predictions and Monte Carlo measurements of structure constants in 3-state Potts model were reviewed. The results provide a direct confirmation of the quality of conformal theory predictions of universal 3-point amplitudes. The prediction of these type of universal amplitudes sparked much of the original interest in conformal models, but are almost untested outside of the Ising model. Structure constants, C123, are universal amplitudes that define 3-point correlations, i.e., = C123/ |X12|2(Δ1+Δ2-Δ3)·× cyclic perms. To predict the values of these universal numbers, one constructs a 4-point correlation as a sum of products of conformal blocks and then, determines coefficients that weight the sum by demanding that the 4-point correlation satisfy a bootstrap equation. The bootstrap equation imposes consistency of the 4-point correlation with operator product expansions in multiple channels. The 3-state Potts model was chosen, because this model is easy of simulate. But, this Potts model has an added complication, i.e., a discrete Z3 symmetry at criticality. The discrete symmetry had to be implemented to calculate structure constants. Conformal theory predicted that Cσσσ = 1.092 and Cɛσσ* = 0.546. Monte Carlo simulations were performed on 500 × 500 lattices on which sample configurations were generated by the cluster algorithm of Wolff. To obtain the structure constants both 2-point and 3-point correlations were measured. The 2-point correlations fixed non-universal normalizatons. The quality of the Monte-Carlo methods were tested by measuring structure constants of the Ising model-good agreement with known results was found. For 3-state Potts, the simulations found that Cσσσ = 1.116 ± 0.14 and Cɛσσ* = 0.61 ± 0.06. These results provide striking agreement with predictions and a confirmation of conformal field theory.

  4. Solid state conformational classification of eight-membered rings

    DEFF Research Database (Denmark)

    Pérez, J.; García, L.; Kessler, M.

    2005-01-01

    A statistical classification of the solid state conformation in the title complexes using data retrieved from the Cambridge Structural Database (CSD) has been made. Phosphate and phosphinate complexes show a chair conformation preferably. In phosphonate complexes, the most frequent conformations...

  5. Protein Conformational Populations and Functionally Relevant Sub-states

    Energy Technology Data Exchange (ETDEWEB)

    Agarwal, Pratul K [ORNL; Burger, Virginia [University of Pittsburgh School of Medicine, Pittsburgh PA; Savol, Andrej [University of Pittsburgh School of Medicine, Pittsburgh PA; Ramanathan, Arvind [ORNL; Chennubhotla, Chakra [University of Pittsburgh School of Medicine, Pittsburgh PA

    2013-01-01

    Functioning proteins do not remain fixed in a unique structure, but instead they sample a range of conformations facilitated by motions within the protein. Even in the native state, a protein exists as a collection of interconverting conformations driven by thermodynamic fluctuations. Motions on the fast time scale allow a protein to sample conformations in the nearby area of its conformational landscape, while motions on slower time scales give it access to conformations in distal areas of the landscape. Emerging evidence indicates that protein landscapes contain conformational substates with dynamic and structural features that support the designated function of the protein. Nuclear magnetic resonance (NMR) experiments provide information about conformational ensembles of proteins. X-ray crystallography allows researchers to identify the most populated states along the landscape, and computational simulations give atom-level information about the conformational substates of different proteins. This ability to characterize and obtain quantitative information about the conformational substates and the populations of proteins within them is allowing researchers to better understand the relationship between protein structure and dynamics and the mechanisms of protein function. In this Account, we discuss recent developments and challenges in the characterization of functionally relevant conformational populations and substates of proteins. In some enzymes, the sampling of functionally relevant conformational substates is connected to promoting the overall mechanism of catalysis. For example, the conformational landscape of the enzyme dihydrofolate reductase has multiple substates, which facilitate the binding and the release of the cofactor and substrate and catalyze the hydride transfer. For the enzyme cyclophilin A, computational simulations reveal that the long time scale conformational fluctuations enable the enzyme to access conformational substates that allow

  6. Irregular conformal states and spectral curve: Irregular matrix model approach

    CERN Document Server

    Rim, Chaiho

    2016-01-01

    We present recent developments of irregular conformal conformal states. Irregular vertex operators and their adjoint are used to define the irregular conformal states and their Inner product. Free field formalism can be augmented by screening operators which provide more degrees of freedom. The inner product is conveniently given as partition function of a irregular matrix model. (Deformed) spectral curve is the loop equation of the matrix model at Nekrasov-Shatashivili limit. We present the details of analytic structure of the spectral curve for Virasoso symmetry and its extensions, W-symmetry and super-symmetry.

  7. Rotational KMS states and type I conformal nets

    CERN Document Server

    Longo, Roberto

    2016-01-01

    We consider KMS states on a local conformal net on the unit circle with respect to rotations. We prove that, if the conformal net is of type I, namely if it admits only type I DHR representations, then the extremal KMS states are the Gibbs states in an irreducible representation. Completely rational nets, the U(1)-current net, the Virasoro nets and their finite tensor products are shown to be of type I. In the completely rational case, we also give a direct proof that all factorial KMS states are Gibbs states.

  8. P. Mackay on Conformism, Non-Conformism and Anti-Conformism in the Culture of the United States, ed. by A. Balasopoulos et al.

    OpenAIRE

    2009-01-01

    Conformism, Non-Conformism and Anti-Conformism in the Culture of the United States. European Views of the United States. Vol. 1. Eds. Antonis Balasopoulos, Gesa Mackenthun and Theodora Tsimpouki. Heidelberg: Universitätverlag, 2008. pp. 330. ISBN 978-3-8253-5479-4.   This volume comes out of the 2006 EAAS Conference hosted by the University of Cyprus. The book explores expressions of conformism, non-conformism, and anti-conformism in American culture from the nineteenth century to the presen...

  9. P. Mackay on Conformism, Non-Conformism and Anti-Conformism in the Culture of the United States, ed. by A. Balasopoulos et al.

    Directory of Open Access Journals (Sweden)

    2009-02-01

    Full Text Available Conformism, Non-Conformism and Anti-Conformism in the Culture of the United States. European Views of the United States. Vol. 1. Eds. Antonis Balasopoulos, Gesa Mackenthun and Theodora Tsimpouki. Heidelberg: Universitätverlag, 2008. pp. 330. ISBN 978-3-8253-5479-4.  This volume comes out of the 2006 EAAS Conference hosted by the University of Cyprus. The book explores expressions of conformism, non-conformism, and anti-conformism in American culture from the nineteenth century to the present....

  10. Molecular motions and conformational transition between different conformational states of HIV-1 gp120 envelope glycoprotein

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The HIV-1 gp120 exterior envelope glycoprotein undergoes a series of conformational rearrangements while sequentially interacting with the receptor CD4 and coreceptor CCR5 or CXCR4 on the surface of host cells to initiate virus entry. Both the crystal structures of the HIV-1 gp120 core bound by the CD4 and antigen 17b and the SIV gp120 core prebound by CD4 are known. Despite the wealth of knowledge on these static snapshots of molecular conformations, the details of molecular motions involved in conformational transition that are crucial to intervention remain elusive. We presented comprehensive comparative analyses of the dynamics behaviors of the gp120 in its CD4-complexed, CD4-free and CD4-unliganded states based on the homology models with modeled V3 and V4 loops by means of CONCOORD computer simulation to generate ensembles of feasible protein structures that were subsequently analysed by essential dynamics analyses to identify preferred concerted motions. The revealed collective fluctuations are dominated by complex modes of combinational motions of the rotation/twisting, flexing/closure, and shortness/elongation between or within the inner, outer, and bridging-sheet domains, and these modes are related to the CD4 association and HIV neutralization avoidance. Further essential subspace overlap analyses were performed to quantitatively distinguish the preference for conformational transitions between the three states, revealing that the unliganded gp120 has a greater potential to translate its conformation into the conformational state adopted by the CD4-complexed gp120 than by the CD4-free gp120, whereas the CD4-free gp120 has a greater potential to translate its conformation into the unliganded state than the CD4-complexed gp120 does. These dy-namics data of gp120 in its different conformations are helpful in understanding the relationship be-tween the molecular motion/conformational transition and the function of gp120, and in gp120-structure-based subunit

  11. Nanobody stabilization of G protein coupled receptor conformational states

    Science.gov (United States)

    Steyaert, Jan; K Kobilka, Brian

    2011-01-01

    Remarkable progress has been made in the field of G protein coupled receptor (GPCR) structural biology during the past four years. Several obstacles to generating diffraction quality crystals of GPCRs have been overcome by combining innovative methods ranging from protein engineering to lipid-based screens and microdiffraction technology. The initial GPCR structures represent energetically stable inactive-state conformations. However, GPCRs signal through different G protein isoforms or G protein-independent effectors upon ligand binding suggesting the existence of multiple ligand-specific active states. These active-state conformations are unstable in the absence of specific cytosolic signaling partners representing new challenges for structural biology. Camelid single chain antibody fragments (nanobodies) show promise for stabilizing active GPCR conformations and as chaperones for crystallogenesis. PMID:21782416

  12. Modular Hamiltonian for Excited States in Conformal Field Theory.

    Science.gov (United States)

    Lashkari, Nima

    2016-07-22

    We present a novel replica trick that computes the relative entropy of two arbitrary states in conformal field theory. Our replica trick is based on the analytic continuation of partition functions that break the Z_{n} replica symmetry. It provides a method for computing arbitrary matrix elements of the modular Hamiltonian corresponding to excited states in terms of correlation functions. We show that the quantum Fisher information in vacuum can be expressed in terms of two-point functions on the replica geometry. We perform sample calculations in two-dimensional conformal field theories.

  13. Modular Hamiltonian of Excited States in Conformal Field Theory

    CERN Document Server

    Lashkari, Nima

    2015-01-01

    We present a novel replica trick that computes the relative entropy of two arbitrary states in conformal field theory. Our replica trick is based on the analytic continuation of partition functions that break the replica Z_n symmetry. It provides a method for computing arbitrary matrix elements of the modular Hamiltonian corresponding to excited states in terms of correlation functions. We show that the quantum Fisher information in vacuum can be expressed in terms of two-point functions on the replica geometry. We perform sample calculations in two-dimensional conformal field theories.

  14. Selective Electrocatalytic Activity of Ligand Stabilized Copper Oxide Nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Kauffman, Douglas R; Ohodnicki, Paul R; Kail, Brian W; Matranga, Christopher

    2011-01-01

    Ligand stabilization can influence the surface chemistry of Cu oxide nanoparticles (NPs) and provide unique product distributions for electrocatalytic methanol (MeOH) oxidation and CO{sub 2} reduction reactions. Oleic acid (OA) stabilized Cu{sub 2}O and CuO NPs promote the MeOH oxidation reaction with 88% and 99.97% selective HCOH formation, respectively. Alternatively, CO{sub 2} is the only reaction product detected for bulk Cu oxides and Cu oxide NPs with no ligands or weakly interacting ligands. We also demonstrate that OA stabilized Cu oxide NPs can reduce CO{sub 2} into CO with a {approx}1.7-fold increase in CO/H{sub 2} production ratios compared to bulk Cu oxides. The OA stabilized Cu oxide NPs also show 7.6 and 9.1-fold increases in CO/H{sub 2} production ratios compared to weakly stabilized and non-stabilized Cu oxide NPs, respectively. Our data illustrates that the presence and type of surface ligand can substantially influence the catalytic product selectivity of Cu oxide NPs.

  15. Conformational states of the full-length glucagon receptor

    Science.gov (United States)

    Yang, Linlin; Yang, Dehua; de Graaf, Chris; Moeller, Arne; West, Graham M.; Dharmarajan, Venkatasubramanian; Wang, Chong; Siu, Fai Y.; Song, Gaojie; Reedtz-Runge, Steffen; Pascal, Bruce D.; Wu, Beili; Potter, Clinton S.; Zhou, Hu; Griffin, Patrick R.; Carragher, Bridget; Yang, Huaiyu; Wang, Ming-Wei; Stevens, Raymond C.; Jiang, Hualiang

    2015-07-01

    Class B G protein-coupled receptors are composed of an extracellular domain (ECD) and a seven-transmembrane (7TM) domain, and their signalling is regulated by peptide hormones. Using a hybrid structural biology approach together with the ECD and 7TM domain crystal structures of the glucagon receptor (GCGR), we examine the relationship between full-length receptor conformation and peptide ligand binding. Molecular dynamics (MD) and disulfide crosslinking studies suggest that apo-GCGR can adopt both an open and closed conformation associated with extensive contacts between the ECD and 7TM domain. The electron microscopy (EM) map of the full-length GCGR shows how a monoclonal antibody stabilizes the ECD and 7TM domain in an elongated conformation. Hydrogen/deuterium exchange (HDX) studies and MD simulations indicate that an open conformation is also stabilized by peptide ligand binding. The combined studies reveal the open/closed states of GCGR and suggest that glucagon binds to GCGR by a conformational selection mechanism.

  16. Nanobody stabilization of G protein coupled receptor conformational states

    OpenAIRE

    Steyaert, Jan; K Kobilka, Brian

    2011-01-01

    Remarkable progress has been made in the field of G protein coupled receptor (GPCR) structural biology during the past four years. Several obstacles to generating diffraction quality crystals of GPCRs have been overcome by combining innovative methods ranging from protein engineering to lipid-based screens and microdiffraction technology. The initial GPCR structures represent energetically stable inactive-state conformations. However, GPCRs signal through different G protein isoforms or G pro...

  17. Twisted boundary states in c=1 coset conformal field theories

    CERN Document Server

    Ishikawa, H; Ishikawa, Hiroshi; Yamaguchi, Atsushi

    2003-01-01

    We study the mutual consistency of twisted boundary conditions in the coset conformal field theory G/H. We calculate the overlap of the twisted boundary states of G/H with the untwisted ones, and show that the twisted boundary states are consistently defined in the diagonal modular invariant. The overlap of the twisted boundary states is expressed by the branching functions of a twisted affine Lie algebra. As a check of our argument, we study the diagonal coset theory so(2n)_1 \\oplus so(2n)_1/so(2n)_2, which is equivalent with the orbifold S^1/\\Z_2. We construct the boundary states twisted by the automorphisms of the unextended Dynkin diagram of so(2n), and show their mutual consistency by identifying their counterpart in the orbifold. For the triality of so(8), the twisted states of the coset theory correspond to neither the Neumann nor the Dirichlet boundary states of the orbifold and yield the conformal boundary states that preserve only the Virasoro algebra.

  18. 78 FR 57335 - Approval and Promulgation of Implementation Plans; State of Missouri; Conformity of General...

    Science.gov (United States)

    2013-09-18

    ... AGENCY 40 CFR Part 52 Approval and Promulgation of Implementation Plans; State of Missouri; Conformity of... conformity rule in its entirety to bring it into compliance with the Federal general conformity rule which was updated in the Federal Register on April 5, 2010. General conformity regulations prohibit...

  19. 77 FR 38199 - Determining Conformity of Federal Actions to State or Federal Implementation Plans

    Science.gov (United States)

    2012-06-27

    ... From the Federal Register Online via the Government Publishing Office ] ENVIRONMENTAL PROTECTION AGENCY 40 CFR Part 93 Determining Conformity of Federal Actions to State or Federal Implementation Plans... conformity purposes, the budget(s) shall not be used to satisfy the requirements of this section....

  20. Energy levels and quantum states of [Leu]enkephalin conformations based on theoretical and experimental investigations

    Energy Technology Data Exchange (ETDEWEB)

    Abdali, Salim; Jensen, Morten O; Bohr, Henrik [Quantum Protein Centre (QUP), Department of Physics, Bldg. 309, Technical University of Denmark, DK-2800 Kgs. Lyngby (Denmark)

    2003-05-14

    This paper describes a theoretical and experimental study of [Leu]enkephalin conformations with respect to the quantum states of the atomic structure of the peptide. Results from vibrational absorption measurements and quantum calculations are used to outline a quantum picture and to assign vibrational modes to the different conformations. The energy landscape of the conformations is reported as a function of a Hamming distance in Ramachandran space. Molecular dynamics simulations reveal a pronounced stability of the so-called single-bend low-energy conformation, which supports the derived quantum picture of this peptide.

  1. Exploring the conformational states and rearrangements of Yarrowia lipolytica Lipase.

    Science.gov (United States)

    Bordes, Florence; Barbe, Sophie; Escalier, Pierre; Mourey, Lionel; André, Isabelle; Marty, Alain; Tranier, Samuel

    2010-10-06

    We report the 1.7 Å resolution crystal structure of the Lip2 lipase from Yarrowia lipolytica in its closed conformation. The Lip2 structure is highly homologous to known structures of the fungal lipase family (Thermomyces lanuginosa, Rhizopus niveus, and Rhizomucor miehei lipases). However, it also presents some unique features that are described and discussed here in detail. Structural differences, in particular in the conformation adopted by the so-called lid subdomain, suggest that the opening mechanism of Lip2 may differ from that of other fungal lipases. Because the catalytic activity of lipases is strongly dependent on structural rearrangement of this mobile subdomain, we focused on elucidating the molecular mechanism of lid motion. Using the x-ray structure of Lip2, we carried out extensive molecular-dynamics simulations in explicit solvent environments (water and water/octane interface) to characterize the major structural rearrangements that the lid undergoes under the influence of solvent or upon substrate binding. Overall, our results suggest a two-step opening mechanism that gives rise first to a semi-open conformation upon adsorption of the protein at the water/organic solvent interface, followed by a further opening of the lid upon substrate binding.

  2. Conformation-Selective Resonant Photoelectron Spectroscopy via Dipole-Bound States of Cold Anions.

    Science.gov (United States)

    Huang, Dao-Ling; Liu, Hong-Tao; Ning, Chuan-Gang; Wang, Lai-Sheng

    2015-06-18

    Molecular conformation is important in chemistry and biochemistry. Conformers connected by low energy barriers can only be observed at low temperatures and are difficult to be separated. Here we report a new method to obtain conformation-selective spectroscopic information about dipolar molecular radicals via dipole-bound excited states of the corresponding anions cooled in a cryogenic ion trap. We observed two conformers of cold 3-hydroxyphenoxide anions [m-HO(C6H4)O(-)] in high-resolution photoelectron spectroscopy and measured different electron affinities, 18,850(8) and 18,917(5) cm(-1), for the syn and anti 3-hydroxyphenoxy radicals, respectively. We also observed dipole-bound excited states for m-HO(C6H4)O(-) with different binding energies for the two conformers due to the different dipole moments of the corresponding 3-hydroxyphenoxy radicals. Excitations to selected vibrational levels of the dipole-bound states result in conformation-selective photoelectron spectra. This method should be applicable to conformation-selective spectroscopic studies of any anions with dipolar neutral cores.

  3. Evaluation of copolymer conformation states of vinylchloride-maleic anhydride

    Science.gov (United States)

    Ivanov, A. A.

    2016-11-01

    The quantum-chemical analysis and experimental study of alternating vinylchloride-maleic anhydride (VC-MA) copolymer macromolecules with polymerization degree 600 have been carried out. The VC-MA copolymer in solvents of different nature undergoes cycloanhydride-enol tautomerism and the macromolecules take the form of corrugated sticks according to viscometric measurements. The computer simulation has shown that the segment with polymerization degree n < 18 (model compound) is not a helix and rolls while if n = 18 the conformations get distorted. The model molecule optimal structure comprising a random sequence of alternating units of comonomers and their enol tautomers with minimal system total energy has been found by the semiempirical parametric method PM3.

  4. Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States.

    Science.gov (United States)

    Witek, Jagna; Keller, Bettina G; Blatter, Markus; Meissner, Axel; Wagner, Trixie; Riniker, Sereina

    2016-08-22

    The membrane permeability of cyclic peptides and peptidomimetics, which are generally larger and more complex than typical drug molecules, is likely strongly influenced by the conformational behavior of these compounds in polar and apolar environments. The size and complexity of peptides often limit their bioavailability, but there are known examples of peptide natural products such as cyclosporin A (CsA) that can cross cell membranes by passive diffusion. CsA is an undecapeptide with seven methylated backbone amides. Its crystal structure shows a "closed" twisted β-pleated sheet conformation with four intramolecular hydrogen bonds that is also observed in NMR measurements of CsA in chloroform. When binding to its target cyclophilin, on the other hand, CsA adopts an "open" conformation without intramolecular hydrogen bonds. In this study, we attempted to sample the complete conformational space of CsA in chloroform and in water by molecular dynamics simulations in order to better understand its conformational behavior in these two environments and to rationalize the good membrane permeability of CsA observed experimentally. From 10 μs molecular dynamics simulations in each solvent, Markov state models were constructed to characterize the metastable conformational states. The model in chloroform is compared to nuclear Overhauser effect NMR spectroscopy data reported in this study and taken from the literature. The conformational landscapes in the two solvents show significant overlap but also clearly distinct features.

  5. Sulphate removal induces a major conformational change in Leishmania mexicana pyruvate kinase in the crystalline state.

    Science.gov (United States)

    Tulloch, Lindsay B; Morgan, Hugh P; Hannaert, Véronique; Michels, Paul A M; Fothergill-Gilmore, Linda A; Walkinshaw, Malcolm D

    2008-11-14

    We report X-ray structures of pyruvate kinase from Leishmania mexicana (LmPYK) that are trapped in different conformations. These, together with the previously reported structure of LmPYK in its inactive (T-state) conformation, allow comparisons of three different conformers of the same species of pyruvate kinase (PYK). Four new site point mutants showing the effects of side-chain alteration at subunit interfaces are also enzymatically characterised. The LmPYK tetramer crystals grown with ammonium sulphate as precipitant adopt an active-like conformation, with sulphate ions at the active and effector sites. The sulphates occupy positions similar to those of the phosphates of ligands bound to active (R-state) and constitutively active (nonallosteric) PYKs from several species, and provide insight into the structural roles of the phosphates of the substrates and effectors. Crystal soaking in sulphate-free buffers was found to induce major conformational changes in the tetramer. In particular, the unwinding of the Aalpha6' helix and the inward hinge movement of the B domain are coupled with a significant widening (4 A) of the tetramer caused by lateral movement of the C domains. The two new LmPYK structures and the activity studies of site point mutations described in this article are consistent with a developing picture of allosteric activity in which localised changes in protein flexibility govern the distribution of conformer families adopted by the tetramer in its active and inactive states.

  6. Drugging specific conformational states of GPCRs: challenges and opportunities for computational chemistry.

    Science.gov (United States)

    Martí-Solano, Maria; Schmidt, Denis; Kolb, Peter; Selent, Jana

    2016-04-01

    Current advances in structural biology for membrane proteins support the existence of multiple Gprotein-coupled receptor (GPCR) conformations. These conformations can be associated to particular receptor states with definite coupling and signaling capacities. Drugging such receptor states represents an opportunity to discover a new generation of GPCR drugs with unprecedented specificity. However, exploiting recently available structural information to develop these drugs is still challenging. In this context, computational structure-based approaches can inform such drug development. In this review, we examine the potential of these approaches and the challenges they will need to overcome to guide the rational discovery of drugs targeting specific GPCR states.

  7. Conformational instability of the lowest triplet state of the benzene nucleus: I. The unsubstituted molecule

    NARCIS (Netherlands)

    van der Waals, J.H.; van Hemert, M.C.; Buma, W.J.

    1990-01-01

    Experiments on benzene have established that its lowest triplet state (3B1u) is conformationally unstable owing to vibronic coupling with the next higher state (3E1u). This instability was found to be critically dependent on the influence of a crystal field. An analogous vibronic coupling is to be

  8. Determination of Leu Side-Chain Conformations in Excited Protein States by NMR Relaxation Dispersion

    NARCIS (Netherlands)

    Hansen, D. Flemming; Neudecker, Philipp; Vallurupalli, Pramodh; Mulder, Frans A. A.; Kay, Lewis E.

    2010-01-01

    Fits of Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion profiles allow extraction of the kinetics and thermodynamics of exchange reactions that interconvert highly populated, ground state and low Populated, excited state conformers. Structural information is also available in the form of chem

  9. Conformational instability of the lowest triplet state of the benzene nucleus: I. The unsubstituted molecule

    NARCIS (Netherlands)

    J.H. van der Waals; M.C. van Hemert; W.J. Buma

    1990-01-01

    Experiments on benzene have established that its lowest triplet state (3B1u) is conformationally unstable owing to vibronic coupling with the next higher state (3E1u). This instability was found to be critically dependent on the influence of a crystal field. An analogous vibronic coupling is to be e

  10. Higher-point conformal blocks and entanglement entropy in heavy states

    Energy Technology Data Exchange (ETDEWEB)

    Banerjee, Pinaki [Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113 (India); Datta, Shouvik [Institut für Theoretische Physik, ETH Zürich, CH-8093 Zürich (Switzerland); Sinha, Ritam [Department of Theoretical Physics, Tata Institute of Fundamental Research,Mumbai 400005 (India)

    2016-05-23

    We consider conformal blocks of two heavy operators and an arbitrary number of light operators in a (1+1)-d CFT with large central charge. Using the monodromy method, these higher-point conformal blocks are shown to factorize into products of 4-point conformal blocks in the heavy-light limit for a class of OPE channels. This result is reproduced by considering suitable worldline configurations in the bulk conical defect geometry. We apply the CFT results to calculate the entanglement entropy of an arbitrary number of disjoint intervals for heavy states. The corresponding holographic entanglement entropy calculated via the minimal area prescription precisely matches these results from CFT. Along the way, we briefly illustrate the relation of these conformal blocks to Riemann surfaces and their associated moduli space.

  11. Higher-point conformal blocks and entanglement entropy in heavy states

    CERN Document Server

    Banerjee, Pinaki; Sinha, Ritam

    2016-01-01

    We consider conformal blocks of two heavy operators and an arbitrary number of light operators in a (1+1)-d CFT with large central charge. Using the monodromy method, these higher-point conformal blocks are shown to factorize into products of 4-point conformal blocks in the heavy-light limit for a class of OPE channels. This result is reproduced by considering suitable worldline configurations in the bulk conical defect geometry. We apply the CFT results to calculate the entanglement entropy of an arbitrary number of disjoint intervals for heavy states. The corresponding holographic entanglement entropy calculated via the minimal area prescription precisely matches these results from CFT. Along the way, we briefly illustrate the relation of these conformal blocks to Riemann surfaces and their associated moduli space.

  12. Relative entropy of excited states in two dimensional conformal field theories

    CERN Document Server

    Sárosi, Gábor

    2016-01-01

    We study the relative entropy and the trace square distance, both of which measure the distance between reduced density matrices of two excited states in two dimensional conformal field theories. We find a general formula for the relative entropy between two primary states with the same conformal dimension in the limit of a single small interval and find that in this case the relative entropy is proportional to the trace square distance. We check our general formulae by calculating the relative entropy between two generalized free fields and the trace square distance between the spin and disorder operators of the critical Ising model. We also give the leading term of the relative entropy in the small interval expansion when the two operators have different conformal dimensions. This turns out to be universal when the CFT has no primaires lighter than the stress tensor. The result reproduces the previously known special cases.

  13. Emergent Conformal Symmetry and Geometric Transport Properties of Quantum Hall States on Singular Surfaces

    Science.gov (United States)

    Can, T.; Chiu, Y. H.; Laskin, M.; Wiegmann, P.

    2016-12-01

    We study quantum Hall states on surfaces with conical singularities. We show that the electronic fluid at the cone tip possesses an intrinsic angular momentum, which is due solely to the gravitational anomaly. We also show that quantum Hall states behave as conformal primaries near singular points, with a conformal dimension equal to the angular momentum. Finally, we argue that the gravitational anomaly and conformal dimension determine the fine structure of the electronic density at the conical point. The singularities emerge as quasiparticles with spin and exchange statistics arising from adiabatically braiding conical singularities. Thus, the gravitational anomaly, which appears as a finite size correction on smooth surfaces, dominates geometric transport on singular surfaces.

  14. Cyclophilin A inhibition: targeting transition-state-bound enzyme conformations for structure-based drug design.

    Science.gov (United States)

    Nagaraju, Mulpuri; McGowan, Lauren C; Hamelberg, Donald

    2013-02-25

    Human Cyclophilin A (CypA) catalyzes cis-trans isomerization of the prolyl peptide ω-bond in proteins and is involved in many subcellular processes. CypA has, therefore, been identified as a potential drug target in many diseases, and the development of potent inhibitors with high selectivity is a key objective. In computer-aided drug design, selectivity is improved by taking into account the inherent flexibility of the receptor. However, the relevant receptor conformations to focus on in order to develop highly selective inhibitors are not always obvious from available X-ray crystal structures or ensemble of conformations generated using molecular dynamics simulations. Here, we show that the conformation of the active site of CypA varies as the substrate configuration changes during catalytic turnover. We have analyzed the principal modes of the active site dynamics of CypA from molecular dynamics simulations to show that similar ensembles of enzyme conformations recognize diverse inhibitors and bind the different configurations of the peptide substrate. Small nonpeptidomimetic inhibitors with varying activity are recognized by enzyme ensembles that are similar to those that tightly bind the transition state and cis configurations of the substrate. Our results suggest that enzyme-substrate ensembles are more relevant in structure-based drug design for CypA than free enzyme. Of the vast conformational space of the free enzyme, the enzyme conformations of the tightly bound enzyme-substrate complexes are the most important for catalysis. Therefore, functionalizing lead compounds to optimize their interactions with the enzyme's conformational ensemble bound to the substrate in the cis or the transition state could lead to more potent inhibitors.

  15. Driving Calmodulin Protein towards Conformational Shift by Changing Ionization States of Select Residues

    Science.gov (United States)

    Negi, Sunita; Rana Atilgan, Ali; Atilgan, Canan

    2012-12-01

    Proteins are complex systems made up of many conformational sub-states which are mainly determined by the folded structure. External factors such as solvent type, temperature, pH and ionic strength play a very important role in the conformations sampled by proteins. Here we study the conformational multiplicity of calmodulin (CaM) which is a protein that plays an important role in calcium signaling pathways in the eukaryotic cells. CaM can bind to a variety of other proteins or small organic compounds, and mediates different physiological processes by activating various enzymes. Binding of calcium ions and proteins or small organic molecules to CaM induces large conformational changes that are distinct to each interacting partner. In particular, we discuss the effect of pH variation on the conformations of CaM. By using the pKa values of the charged residues as a basis to assign protonation states, the conformational changes induced in CaM by reducing the pH are studied by molecular dynamics simulations. Our current view suggests that at high pH, barrier crossing to the compact form is prevented by repulsive electrostatic interactions between the two lobes. At reduced pH, not only is barrier crossing facilitated by protonation of residues, but also conformations which are on average more compact are attained. The latter are in accordance with the fluorescence resonance energy transfer experiment results of other workers. The key events leading to the conformational change from the open to the compact conformation are (i) formation of a salt bridge between the N-lobe and the linker, stabilizing their relative motions, (ii) bending of the C-lobe towards the N-lobe, leading to a lowering of the interaction energy between the two-lobes, (iii) formation of a hydrophobic patch between the two lobes, further stabilizing the bent conformation by reducing the entropic cost of the compact form, (iv) sharing of a Ca+2 ion between the two lobes.

  16. Bounds for State Degeneracies in 2D Conformal Field Theory

    CERN Document Server

    Hellerman, Simeon

    2010-01-01

    In this note we explore the application of modular invariance in 2-dimensional CFT to derive universal bounds for quantities describing certain state degeneracies, such as the thermodynamic entropy, or the number of marginal operators. We show that the entropy at inverse temperature 2 pi satisfies a universal lower bound, and we enumerate the principal obstacles to deriving upper bounds on entropies or quantum mechanical degeneracies for fully general CFTs. We then restrict our attention to infrared stable CFT with moderately low central charge, in addition to the usual assumptions of modular invariance, unitarity and discrete operator spectrum. For CFT in the range c_left + c_right < 48 with no relevant operators, we are able to prove an upper bound on the thermodynamic entropy at inverse temperature 2 pi. Under the same conditions we also prove that a CFT can have a number of marginal deformations no greater than ((c_left + c_right) / (48 - c_left - c_right)) e^(4 Pi) - 2.

  17. 78 FR 57267 - Approval and Promulgation of Implementation Plans; State of Missouri; Conformity of General...

    Science.gov (United States)

    2013-09-18

    ... (44 U.S.C. 3501 et seq.); is certified as not having a significant economic impact on a substantial... revision amends rule 10 CSR 10-6.300 Conformity of General Federal Actions to State Implementation Plans... affect the stringency of the SIP or adversely impact air quality. II. Have the requirements for approval...

  18. NMR analysis of native-state protein conformational flexibility by hydrogen exchange.

    Science.gov (United States)

    Hernández, Griselda; LeMaster, David M

    2009-01-01

    The rate of hydrogen exchange for the most protected amides of a protein is widely used to provide an estimate of global conformational stability by analyzing the exchange kinetics in the unfolded state in terms of model peptide exchange rates. The exchange behavior of the other amides of the protein which do not exchange via a global unfolding mechanism can provide insight into the smaller-scale conformational transitions that facilitate access to solvent as required for the exchange reaction. However, since the residual tertiary structure in the exchange-competent conformation can modulate the chemistry of the exchange reaction, equilibrium values estimated from normalization with model peptide rates are open to question. To overcome this limitation, the most robust approaches utilize differential analyses as a function of experimental variables such as denaturant concentration, temperature, pH, and mutational variation. Practical aspects of these various differential analysis techniques are considered with illustrations drawn from the literature.

  19. Interplay between singlet and triplet excited states in a conformationally locked donor–acceptor dyad

    KAUST Repository

    Filatov, Mikhail A.

    2015-10-13

    The synthesis and photophysical characterization of a palladium(II) porphyrin – anthracene dyad bridged via short and conformationally rigid bicyclo[2.2.2]octadiene spacer were achieved. A spectroscopic investigation of the prepared molecule in solution has been undertaken to study electronic energy transfer in excited singlet and triplet states between the anthracene and porphyrin units. By using steady-state and time-resolved photoluminescence spectroscopy it was shown that excitation of the singlet excited state of the anthracene leads to energy transfer to the lower-lying singlet state of porphyrin. Alternatively, excitation of the porphyrin followed by intersystem crossing to the triplet state leads to very fast energy transfer to the triplet state of anthracene. The rate of this energy transfer has been determined by transient absorption spectroscopy. Comparative studies of the dynamics of triplet excited states of the dyad and reference palladium octaethylporphyrin (PdOEP) have been performed.

  20. Designing molecular dynamics simulations to shift populations of the conformational states of calmodulin.

    Directory of Open Access Journals (Sweden)

    Ayse Ozlem Aykut

    Full Text Available We elucidate the mechanisms that lead to population shifts in the conformational states of calcium-loaded calmodulin (Ca(2+-CaM. We design extensive molecular dynamics simulations to classify the effects that are responsible for adopting occupied conformations available in the ensemble of NMR structures. Electrostatic interactions amongst the different regions of the protein and with its vicinal water are herein mediated by lowering the ionic strength or the pH. Amino acid E31, which is one of the few charged residues whose ionization state is highly sensitive to pH differences in the physiological range, proves to be distinctive in its control of population shifts. E31A mutation at low ionic strength results in a distinct change from an extended to a compact Ca(2+-CaM conformation within tens of nanoseconds, that otherwise occur on the time scales of microseconds. The kinked linker found in this particular compact form is observed in many of the target-bound forms of Ca(2+-CaM, increasing the binding affinity. This mutation is unique in controlling C-lobe dynamics by affecting the fluctuations between the EF-hand motif helices. We also monitor the effect of the ionic strength on the conformational multiplicity of Ca(2+-CaM. By lowering the ionic strength, the tendency of nonspecific anions in water to accumulate near the protein surface increases, especially in the vicinity of the linker. The change in the distribution of ions in the vicinal layer of water allows N- and C- lobes to span a wide variety of relative orientations that are otherwise not observed at physiological ionic strength. E31 protonation restores the conformations associated with physiological environmental conditions even at low ionic strength.

  1. Folding and unfolding of a triple-branch DNA molecule with four conformational states

    CERN Document Server

    Engel, Sandra; Forns, Nuria; Maass, Philipp; Ritort, Felix; 10.1080/14786435.2011.557671

    2011-01-01

    Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational states by pulling experiments with optical tweezers and theoretical modelling. Three distinct force rips associated with different transitions between the conformational states are observed in the folding and unfolding trajectories. By applying transition rate theory to a free energy model of the molecule, probability distributions for the first rupture forces of the different transitions are calculated. Good agreement of the theoretical predictions with the experimental findings is achieved. Furthermore, due to our specific design of the molecule, we found a useful method to identify permanently frayed molecules by estimating the number of opened basepairs from the measured force jump values.

  2. Preparation of Low Entropy Correlated Many-body States via Conformal Cooling Quenches

    CERN Document Server

    Zaletel, Michael P; Yao, Norman Y

    2016-01-01

    We analyze a method for preparing low-entropy many-body states in isolated quantum optical systems of atoms, ions and molecules. Our approach is based upon shifting entropy between different regions of a system by spatially modulating the magnitude of the effective Hamiltonian. We conduct two case studies, on a topological spin chain and the spinful fermionic Hubbard model, focusing on the key question: can a "conformal cooling quench" remove sufficient entropy within experimentally accessible timescales? Finite temperature, time-dependent matrix product state calculations reveal that even moderately sized "bath" regions can remove enough energy and entropy density to expose coherent low temperature physics. The protocol is particularly natural in systems with long-range interactions such lattice-trapped polar molecules and Rydberg dressed atoms where the magnitude of the Hamiltonian scales directly with the density. To this end, we propose a simple implementation of conformal cooling quenches in a dilutely-f...

  3. Solid-State Conformational Flexibility at Work: Zipping and Unzipping within a Cyclic Peptoid Single Crystal.

    Science.gov (United States)

    Meli, Alessandra; Macedi, Eleonora; De Riccardis, Francesco; Smith, Vincent J; Barbour, Leonard J; Izzo, Irene; Tedesco, Consiglia

    2016-04-01

    A peptidomimetic compound undergoes a reversible single-crystal-to-single-crystal transformation upon guest release/uptake with the transformation involving a drastic conformational change. The extensive and reversible alteration in the solid state is connected to the formation of an unprecedented "CH-π zipper" which can reversibly open and close (through the formation of CH-π interactions), thus allowing for guest sensing.

  4. Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome

    OpenAIRE

    2009-01-01

    Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria by means of reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here, we report the crystal structure of the Q188L mutant of Pseudomonas aeruginosa bacteriophytochrome (PaBphP) photosensory core module, which exhibits altered photoconversion behavior and different crystal packing from wild type. We observe two distinct chromophore conformations in the Q188L ...

  5. Conformational dynamics of a protein in the folded and the unfolded state

    Energy Technology Data Exchange (ETDEWEB)

    Fitter, Joerg

    2003-08-01

    In a quasielastic neutron scattering experiment, the picosecond dynamics of {alpha}-amylase was investigated for the folded and the unfolded state of the protein. In order to ensure a reasonable interpretation of the internal protein dynamics, the protein was measured in D{sub 2}O-buffer solution. The much higher structural flexibility of the pH induced unfolded state as compared to the native folded state was quantified using a simple analytical model, describing a local diffusion inside a sphere. In terms of this model the conformational volume, which is explored mainly by confined protein side-chain movements, is parameterized by the radius of a sphere (folded state, r=1.2 A; unfolded state, 1.8 A). Differences in conformational dynamics between the folded and the unfolded state of a protein are of fundamental interest in the field of protein science, because they are assumed to play an important role for the thermodynamics of folding/unfolding transition and for protein stability.

  6. A dualistic conformational response to substrate binding in the human serotonin transporter reveals a high affinity state for serotonin

    DEFF Research Database (Denmark)

    Bjerregaard, Henriette; Severinsen, Kasper; Said, Saida

    2015-01-01

    Serotonergic neurotransmission is modulated by the membrane-embedded serotonin transporter (SERT). SERT mediates the reuptake of serotonin into the presynaptic neurons. Conformational changes in SERT occur upon binding of ions and substrate and are crucial for translocation of serotonin across...... that were sensitized to detect a more outward-facing conformation of SERT. We found a novel high affinity outward-facing conformational state of the human SERT induced by serotonin. The ionic requirements for this new conformational response to serotonin mirror the ionic requirements for translocation...

  7. pH-dependent transient conformational states control optical properties in cyan fluorescent protein.

    Science.gov (United States)

    Laricheva, Elena N; Goh, Garrett B; Dickson, Alex; Brooks, Charles L

    2015-03-04

    A recently engineered mutant of cyan fluorescent protein (WasCFP) that exhibits pH-dependent absorption suggests that its tryptophan-based chromophore switches between neutral (protonated) and charged (deprotonated) states depending on external pH. At pH 8.1, the latter gives rise to green fluorescence as opposed to the cyan color of emission that is characteristic for the neutral form at low pH. Given the high energy cost of deprotonating the tryptophan at the indole nitrogen, this behavior is puzzling, even if the stabilizing effect of the V61K mutation in proximity to the protonation/deprotonation site is considered. Because of its potential to open new avenues for the development of optical sensors and photoconvertible fluorescent proteins, a mechanistic understanding of how the charged state in WasCFP can possibly be stabilized is thus important. Attributed to the dynamic nature of proteins, such understanding often requires knowledge of the various conformations adopted, including transiently populated conformational states. Transient conformational states triggered by pH are of emerging interest and have been shown to be important whenever ionizable groups interact with hydrophobic environments. Using a combination of the weighted-ensemble sampling method and explicit-solvent constant pH molecular dynamics (CPHMD(MSλD)) simulations, we have identified a solvated transient state, characterized by a partially open β-barrel where the chromophore pKa of 6.8 is shifted by over 20 units from that of the closed form (6.8 and 31.7, respectively). This state contributes a small population at low pH (12% at pH 6.1) but becomes dominant at mildly basic conditions, contributing as much as 53% at pH 8.1. This pH-dependent population shift between neutral (at pH 6.1) and charged (at pH 8.1) forms is thus responsible for the observed absorption behavior of WasCFP. Our findings demonstrate the conditions necessary to stabilize the charged state of the WasCFP chromophore

  8. Relative entropy of excited states in conformal field theories of arbitrary dimensions

    CERN Document Server

    Sárosi, Gábor

    2016-01-01

    Extending our previous work, we study the relative entropy between the reduced density matrices obtained from globally excited states in conformal field theories of arbitrary dimensions. We find a general formula in the small subsystem size limit. When one of the states is the vacuum of the CFT, our result matches with the holographic entanglement entropy computations in the corresponding bulk geometries, including AdS black branes. We also discuss the first asymmetric part of the relative entropy and comment on some implications of the results on the distinguishability of black hole microstates in AdS/CFT.

  9. Conformational Toggling of Yeast Iso-1-Cytochrome c in the Oxidized and Reduced States

    Science.gov (United States)

    Yang, Zhongzheng; Zhu, Jing; Ying, Tianlei; Jiang, Xianwang; Zhang, Xu; Wu, Houming; Liu, Maili; Tan, Xiangshi; Cao, Chunyang; Huang, Zhong-Xian

    2011-01-01

    To convert cyt c into a peroxidase-like metalloenzyme, the P71H mutant was designed to introduce a distal histidine. Unexpectedly, its peroxidase activity was found even lower than that of the native, and that the axial ligation of heme iron was changed to His71/His18 in the oxidized state, while to Met80/His18 in the reduced state, characterized by UV-visible, circular dichroism, and resonance Raman spectroscopy. To further probe the functional importance of Pro71 in oxidation state dependent conformational changes occurred in cyt c, the solution structures of P71H mutant in both oxidation states were determined. The structures indicate that the half molecule of cyt c (aa 50–102) presents a kind of “zigzag riveting ruler” structure, residues at certain positions of this region such as Pro71, Lys73 can move a big distance by altering the tertiary structure while maintaining the secondary structures. This finding provides a molecular insight into conformational toggling in different oxidation states of cyt c that is principle significance to its biological functions in electron transfer and apoptosis. Structural analysis also reveals that Pro71 functions as a key hydrophobic patch in the folding of the polypeptide of the region (aa 50–102), to prevent heme pocket from the solvent. PMID:22087268

  10. Real-Time Radar-Based Tracking and State Estimation of Multiple Non-Conformant Aircraft

    Science.gov (United States)

    Cook, Brandon; Arnett, Timothy; Macmann, Owen; Kumar, Manish

    2017-01-01

    In this study, a novel solution for automated tracking of multiple unknown aircraft is proposed. Many current methods use transponders to self-report state information and augment track identification. While conformant aircraft typically report transponder information to alert surrounding aircraft of its state, vehicles may exist in the airspace that are non-compliant and need to be accurately tracked using alternative methods. In this study, a multi-agent tracking solution is presented that solely utilizes primary surveillance radar data to estimate aircraft state information. Main research challenges include state estimation, track management, data association, and establishing persistent track validity. In an effort to realize these challenges, techniques such as Maximum a Posteriori estimation, Kalman filtering, degree of membership data association, and Nearest Neighbor Spanning Tree clustering are implemented for this application.

  11. Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Xiaojing; Kuk, Jane; Moffat, Keith; (UC)

    2009-09-16

    Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria by means of reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here, we report the crystal structure of the Q188L mutant of Pseudomonas aeruginosa bacteriophytochrome (PaBphP) photosensory core module, which exhibits altered photoconversion behavior and different crystal packing from wild type. We observe two distinct chromophore conformations in the Q188L crystal structure that we identify with the Pfr and Pr states. The Pr/Pfr compositions, varying from crystal to crystal, seem to correlate with light conditions under which the Q188L crystals are cryoprotected. We also compare all known Pr and Pfr structures. Using site-directed mutagenesis, we identify residues that are involved in stabilizing the 15Ea (Pfr) and 15Za (Pr) configurations of the biliverdin chromophore. Specifically, Ser-261 appears to be essential to form a stable Pr state in PaBphP, possibly by means of its interaction with the propionate group of ring C. We propose a 'flip-and-rotate' model that summarizes the major conformational differences between the Pr and Pfr states of the chromophore and its binding pocket.

  12. Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome.

    Science.gov (United States)

    Yang, Xiaojing; Kuk, Jane; Moffat, Keith

    2009-09-15

    Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria by means of reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here, we report the crystal structure of the Q188L mutant of Pseudomonas aeruginosa bacteriophytochrome (PaBphP) photosensory core module, which exhibits altered photoconversion behavior and different crystal packing from wild type. We observe two distinct chromophore conformations in the Q188L crystal structure that we identify with the Pfr and Pr states. The Pr/Pfr compositions, varying from crystal to crystal, seem to correlate with light conditions under which the Q188L crystals are cryoprotected. We also compare all known Pr and Pfr structures. Using site-directed mutagenesis, we identify residues that are involved in stabilizing the 15Ea (Pfr) and 15Za (Pr) configurations of the biliverdin chromophore. Specifically, Ser-261 appears to be essential to form a stable Pr state in PaBphP, possibly by means of its interaction with the propionate group of ring C. We propose a "flip-and-rotate" model that summarizes the major conformational differences between the Pr and Pfr states of the chromophore and its binding pocket.

  13. Cβ-H stretching vibration as a new probe for conformation of n-propanol in gaseous and liquid states.

    Science.gov (United States)

    Yu, Yuanqin; Wang, Yuxi; Hu, Naiyin; Lin, Ke; Zhou, Xiaoguo; Liu, Shilin

    2016-04-21

    The development of potential probes to identify molecular conformation is essential in organic and biological chemistry. In this work, we investigated a site-specific C-H stretching vibration as a conformational probe for a model compound, 1,1,3,3,3-deuterated n-propanol (CD3CH2CD2OH), using stimulated photoacoustic Raman spectroscopy in the gas phase and conventional spontaneous Raman spectroscopy in the liquid state. Along with quantum chemistry calculations, the experiment shows that the CH2 symmetric stretching mode at the β-carbon position is very sensitive to the conformational structure of n-propanol and can serve as a new probe for all five of its conformers. Compared with the O-H stretching vibration, a well-established conformational sensor for n-propanol, the Cβ-H stretching vibration presented here shows better conformational resolution in the liquid state. Furthermore, using this probe, we investigated the conformational preference of n-propanol in pure liquid and in dilute water solution. It is revealed that in pure liquid, n-propanol molecules prefer the trans-OH conformation, and in dilute water solution, this preference is enhanced, indicating that the water molecules play a role of further stabilizing the trans-OH n-propanol conformers. This leads to conformational evolution that n-propanol molecules with gauche-OH structure are transferred to the trans-OH structure upon diluting with water. These results not only provide important information on structures of n-propanol in different environments, but also demonstrate the potential of the C-H stretching vibration as a new tool for conformational analysis. This is especially important when considering that hydrocarbon chains are structural units in organic and biological molecules.

  14. Structure and conformational dynamics of molecules in the excited electronic states: theory and experiment

    Science.gov (United States)

    Godunov, I. A.; Bataev, V. A.; Maslov, D. V.; Yakovlev, N. N.

    2016-12-01

    The structure of conformational non-rigid molecules in the excited electronic states are investigated by joint theoretical and experimental methods. The theoretical part of work consist of two stages. In first stage the ab initio quantum-chemical calculations are carried out using high level methods. In second stage the vibrational problems of the various dimensions are solved by variational method for vibrations of large amplitude. In experimental part of work the vibronic spectra are investigated: gas-phase absorption and also, fluorescence excitation spectra of jet-cooled molecules. Some examples are considered.

  15. On the ambiguity of conformational states: A B&S-LEUS simulation study of the helical conformations of decaalanine in water

    Science.gov (United States)

    Bieler, Noah S.; Hünenberger, Philippe H.

    2015-04-01

    Estimating the relative stabilities of different conformational states of a (bio-)molecule using molecular dynamics simulations involves two challenging problems: the conceptual problem of how to define the states of interest and the technical problem of how to properly sample these states, along with achieving a sufficient number of interconversion transitions. In this study, the two issues are addressed in the context of a decaalanine peptide in water, by considering the 310-, α-, and π-helical states. The simulations rely on the ball-and-stick local-elevation umbrella-sampling (B&S-LEUS) method. In this scheme, the states are defined as hyperspheres (balls) in a (possibly high dimensional) collective-coordinate space and connected by hypercylinders (sticks) to ensure transitions. A new object, the pipe, is also introduced here to handle curvilinear pathways. Optimal sampling within the so-defined space is ensured by confinement and (one-dimensional) memory-based biasing potentials associated with the three different kinds of objects. The simulation results are then analysed in terms of free energies using reweighting, possibly relying on two distinct sets of collective coordinates for the state definition and analysis. The four possible choices considered for these sets are Cartesian coordinates, hydrogen-bond distances, backbone dihedral angles, or pairwise sums of successive backbone dihedral angles. The results concerning decaalanine underline that the concept of conformational state may be extremely ambiguous, and that its tentative absolute definition as a free-energy basin remains subordinated to the choice of a specific analysis space. For example, within the force-field employed and depending on the analysis coordinates selected, the 310-helical state may refer to weakly overlapping collections of conformations, differing by as much as 25 kJ mol-1 in terms of free energy. As another example, the π-helical state appears to correspond to a free

  16. Binding of vanadium compounds perturbs conformation and aggregation state of insulin

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The interactions between zinc-free insulin and vanadium compounds, NaVO3, VO(acac)2 and VO(ma)2, have been investigated by fluorescence spectroscopy, circular dichroism (CD) and Fourier-transformed infrared (FT-IR) spectroscopy. The results showed that binding of vanadium compounds produced a static quenching of the intrinsic fluorescence of insulin. The apparent association constants were determined to be (0.17±0.01)×104 L*mol-1 for NaVO3, (2.8±0.2)×104 L*mol-1 for VO(acac)2, and (4.0±0.1)×104 L*mol-1 for VO(ma)2, respectively. The light scattering intensity of insulin decreased upon incubation with the vanadium compounds, suggesting the disaggregation of insulin. The attenuation of the band at 273 nm of insulin CD spectra also supported the disaggregation of insulin observed above. A new band at 1650~1653 cm-1 appeared in the FT-IR spectra of insulin upon incubation with the vanadium compounds, indicating the formation of an α-helix structure at B (9-19) motif. This α-helix structure suggests a structural change of insulin from an extended conformation (T state) to a helical conformation (R state), which is essential for binding of insulin to its receptor. In conclusion, binding of vanadium compounds results in conformational changes and disaggregation of insulin. These changes might account for the enhancement of binding affinity for insulin to its receptor in the presence of vanadium compounds.

  17. Conformational responses to changes in the state of ionization of titrable groups in proteins

    Science.gov (United States)

    Richman, Daniel Eric

    Electrostatic energy links the structural properties of proteins with some of their important biological functions, including catalysis, energy transduction, and binding and recognition. Accurate calculation of electrostatic energy is essential for predicting and for analyzing function from structure. All proteins have many ionizable residues at the protein-water interface. These groups tend to have ionization equilibria (pK a values) shifted slightly relative to their values in water. In contrast, groups buried in the hydrophobic interior usually have highly anomalous p Ka values. These shifts are what structure-based calculations have to reproduce to allow examination of contributions from electrostatics to stability, solubility and interactions of proteins. Electrostatic energies are challenging to calculate accurately because proteins are heterogeneous dielectric materials. Any individual ionizable group can experience very different local environments with different dielectric properties. The studies in this thesis examine the hypothesis that proteins reorganize concomitant with changes in their state of ionization. It appears that the pKa value measured experimentally reflects the average of pKa values experienced in the different electrostatic environments corresponding to different conformational microstates. Current computational models fail to sample conformational reorganization of the backbone correctly. Staphyloccocal nuclease (SNase) was used as a model protein in nuclear magnetic resonance (NMR) spectroscopy studies to characterize the conformational rearrangements of the protein coupled to changes in the ionization state of titrable groups. One set of experiments tests the hypothesis that proton binding to surface Asp and Glu side chains drives local unfolding by stabilizing less-native, more water-solvated conformations in which the side chains have normalized pKa values. Increased backbone flexibility in the ps-ns timescale, hydrogen bond (H

  18. Two conformational states in D-shaped DNA: Effects of local denaturation

    Science.gov (United States)

    Lee, O.-Chul; Kim, Cheolhee; Kim, Jae-Yeol; Lee, Nam Ki; Sung, Wokyung

    2016-06-01

    The bending of double-stranded(ds) DNA on the nano-meter scale plays a key role in many cellular processes such as nucleosome packing, transcription-control, and viral-genome packing. In our recent study, a nanometer-sized dsDNA bent into a D shape was formed by hybridizing a circular single-stranded(ss) DNA and a complementary linear ssDNA. Our fluorescence resonance energy transfer (FRET) measurement of D-DNA revealed two types of conformational states: a less-bent state and a kinked state, which can transform into each other. To understand the origin of the two deformed states of D-DNA, here we study the presence of open base-pairs in the ds portion by using the breathing-DNA model to simulate the system. We provide strong evidence that the two states are due to the emergence of local denaturation, i.e., a bubble in the middle and two forks at ends of the dsDNA portion. We also study the system analytically and find that the free-energy landscape is bistable with two minima representative of the two states. The kink and fork sizes estimated by the analytical calculation are also in excellent agreement with the results of the simulation. Thus, this combined experimental-simulation-analytical study corroborates that highly bent D-DNA reduces bending stress via local denaturation.

  19. Properties of an Inward-Facing State of LeuT: Conformational Stability and Substrate Release

    OpenAIRE

    Grouleff, Julie; Søndergaard, Siri; Koldsø, Heidi; Schiøtt, Birgit

    2015-01-01

    The leucine transporter (LeuT) is a bacterial homolog of the human monoamine transporters, which are important pharmaceutical targets. There are no high-resolution structures of the human transporters available; however, LeuT has been crystallized in several different conformational states. Recently, an inward-facing conformation of LeuT was solved revealing an unexpectedly large movement of transmembrane helix 1a (TM1a). We have performed molecular dynamics simulations of the mutated and wil...

  20. Structural Dynamics and Conformational Equilibria of SERCA Regulatory Proteins in Membranes by Solid-State NMR Restrained Simulations

    Science.gov (United States)

    De Simone, Alfonso; Mote, Kaustubh R.; Veglia, Gianluigi

    2014-01-01

    Solid-state NMR spectroscopy is emerging as a powerful approach to determine structure, topology, and conformational dynamics of membrane proteins at the atomic level. Conformational dynamics are often inferred and quantified from the motional averaging of the NMR parameters. However, the nature of these motions is difficult to envision based only on spectroscopic data. Here, we utilized restrained molecular dynamics simulations to probe the structural dynamics, topology and conformational transitions of regulatory membrane proteins of the calcium ATPase SERCA, namely sarcolipin and phospholamban, in explicit lipid bilayers. Specifically, we employed oriented solid-state NMR data, such as dipolar couplings and chemical shift anisotropy measured in lipid bicelles, to refine the conformational ensemble of these proteins in lipid membranes. The samplings accurately reproduced the orientations of transmembrane helices and showed a significant degree of convergence with all of the NMR parameters. Unlike the unrestrained simulations, the resulting sarcolipin structures are in agreement with distances and angles for hydrogen bonds in ideal helices. In the case of phospholamban, the restrained ensemble sampled the conformational interconversion between T (helical) and R (unfolded) states for the cytoplasmic region that could not be observed using standard structural refinements with the same experimental data set. This study underscores the importance of implementing NMR data in molecular dynamics protocols to better describe the conformational landscapes of membrane proteins embedded in realistic lipid membranes. PMID:24940774

  1. Conformational states and recognition of amyloidogenic peptides of human insulin-degrading enzyme.

    Science.gov (United States)

    McCord, Lauren A; Liang, Wenguang G; Dowdell, Evan; Kalas, Vasilios; Hoey, Robert J; Koide, Akiko; Koide, Shohei; Tang, Wei-Jen

    2013-08-20

    Insulin-degrading enzyme (IDE) selectively degrades the monomer of amyloidogenic peptides and contributes to clearance of amyloid β (Aβ). Thus, IDE retards the progression of Alzheimer's disease. IDE possesses an enclosed catalytic chamber that engulfs and degrades its peptide substrates; however, the molecular mechanism of IDE function, including substrate access to the chamber and recognition, remains elusive. Here, we captured a unique IDE conformation by using a synthetic antibody fragment as a crystallization chaperone. An unexpected displacement of a door subdomain creates an ~18-Å opening to the chamber. This swinging-door mechanism permits the entry of short peptides into the catalytic chamber and disrupts the catalytic site within IDE door subdomain. Given the propensity of amyloidogenic peptides to convert into β-strands for their polymerization into amyloid fibrils, they also use such β-strands to stabilize the disrupted catalytic site resided at IDE door subdomain for their degradation by IDE. Thus, action of the swinging door allows IDE to recognize amyloidogenicity by substrate-induced stabilization of the IDE catalytic cleft. Small angle X-ray scattering (SAXS) analysis revealed that IDE exists as a mixture of closed and open states. These open states, which are distinct from the swinging door state, permit entry of larger substrates (e.g., Aβ, insulin) to the chamber and are preferred in solution. Mutational studies confirmed the critical roles of the door subdomain and hinge loop joining the N- and C-terminal halves of IDE for catalysis. Together, our data provide insights into the conformational changes of IDE that govern the selective destruction of amyloidogenic peptides.

  2. Selection of conformational states in self-assembled surface structures formed from an oligo(naphthylene-ethynylene) 3-bit binary switch

    Science.gov (United States)

    Ning, Y.; Cramer, J. R.; Nuermaimaiti, A.; Svane, K.; Yu, M.; Lægsgaard, E.; Besenbacher, F.; Xue, Q.-K.; Ma, X.; Hammer, B.; Gothelf, K. V.; Linderoth, T. R.

    2015-03-01

    Supra-molecular self-assembly on surfaces often involves molecular conformational flexibility which may act to enrich the variation and complexity of the structures formed. However, systematic and explicit investigations of how molecular conformational states are selected in surface self-assembly processes are relatively scarce. Here, we use a combination of high-resolution scanning tunneling microscopy and Density Functional Theory (DFT) calculations to investigate self-assembly for a custom-designed molecule capable of assuming eight distinct surface conformations (four enantiomeric pairs). The conformations result from binary positions of n = 3 naphtalene units on a linear oligo(naphthylene-ethynylene) backbone. On Au(111), inter-molecular interactions involving carboxyl and bulky tert-butyl-phenyl functional groups induce the molecules to form two ordered phases with brick-wall and lamella structure, respectively. These structures each involve molecules in two conformational states, and there is a clear separation between the conformers involved in the two types of structures. On Cu(111), individual molecules isolated by carboxylate-substrate binding show a distribution involving all possible conformational states. Together these observations imply selection and adaptation of conformational states upon molecular self-assembly. From DFT modeling and statistical analysis of the molecular conformations, the observed selection of conformational states is attributed to steric interaction between the naphthalene units. The present study enhances our understanding of how ordering and selection of molecular conformations is controlled by intermolecular interactions in a complex situation with many distinct conformational states for the participating molecules.

  3. Voltage Dependence of Conformational Dynamics and Subconducting States of VDAC-1.

    Science.gov (United States)

    Briones, Rodolfo; Weichbrodt, Conrad; Paltrinieri, Licia; Mey, Ingo; Villinger, Saskia; Giller, Karin; Lange, Adam; Zweckstetter, Markus; Griesinger, Christian; Becker, Stefan; Steinem, Claudia; de Groot, Bert L

    2016-09-20

    The voltage-dependent anion channel 1 (VDAC-1) is an important protein of the outer mitochondrial membrane that transports energy metabolites and is involved in apoptosis. The available structures of VDAC proteins show a wide β-stranded barrel pore, with its N-terminal α-helix (N-α) bound to its interior. Electrophysiology experiments revealed that voltage, its polarity, and membrane composition modulate VDAC currents. Experiments with VDAC-1 mutants identified amino acids that regulate the gating process. However, the mechanisms for how these factors regulate VDAC-1, and which changes they trigger in the channel, are still unknown. In this study, molecular dynamics simulations and single-channel experiments of VDAC-1 show agreement for the current-voltage relationships of an "open" channel and they also show several subconducting transient states that are more cation selective in the simulations. We observed voltage-dependent asymmetric distortions of the VDAC-1 barrel and the displacement of particular charged amino acids. We constructed conformational models of the protein voltage response and the pore changes that consistently explain the protein conformations observed at opposite voltage polarities, either in phosphatidylethanolamine or phosphatidylcholine membranes. The submicrosecond VDAC-1 voltage response shows intrinsic structural changes that explain the role of key gating amino acids and support some of the current gating hypotheses. These voltage-dependent protein changes include asymmetric barrel distortion, its interaction with the membrane, and significant displacement of N-α amino acids.

  4. Conformal anisotropic relativistic charged fluid spheres with a linear equation of state

    Science.gov (United States)

    Esculpi, M.; Alomá, E.

    2010-06-01

    We obtain two new families of compact solutions for a spherically symmetric distribution of matter consisting of an electrically charged anisotropic fluid sphere joined to the Reissner-Nordstrom static solution through a zero pressure surface. The static inner region also admits a one parameter group of conformal motions. First, to study the effect of the anisotropy in the sense of the pressures of the charged fluid, besides assuming a linear equation of state to hold for the fluid, we consider the tangential pressure p ⊥ to be proportional to the radial pressure p r , the proportionality factor C measuring the grade of anisotropy. We analyze the resulting charge distribution and the features of the obtained family of solutions. These families of solutions reproduce for the value C=1, the conformal isotropic solution for quark stars, previously obtained by Mak and Harko. The second family of solutions is obtained assuming the electrical charge inside the sphere to be a known function of the radial coordinate. The allowed values of the parameters pertained to these solutions are constrained by the physical conditions imposed. We study the effect of anisotropy in the allowed compactness ratios and in the values of the charge. The Glazer’s pulsation equation for isotropic charged spheres is extended to the case of anisotropic and charged fluid spheres in order to study the behavior of the solutions under linear adiabatic radial oscillations. These solutions could model some stage of the evolution of strange quark matter fluid stars.

  5. Conformational properties of the unfolded state of Im7 in nondenaturing conditions.

    Science.gov (United States)

    Pashley, Clare L; Morgan, Gareth J; Kalverda, Arnout P; Thompson, Gary S; Kleanthous, Colin; Radford, Sheena E

    2012-02-17

    The unfolded ensemble in aqueous solution represents the starting point of protein folding. Characterisation of this species is often difficult since the native state is usually predominantly populated at equilibrium. Previous work has shown that the four-helix protein, Im7 (immunity protein 7), folds via an on-pathway intermediate. While the transition states and folding intermediate have been characterised in atomistic detail, knowledge of the unfolded ensemble under the same ambient conditions remained sparse. Here, we introduce destabilising amino acid substitutions into the sequence of Im7, such that the unfolded state becomes predominantly populated at equilibrium in the absence of denaturant. Using far- and near-UV CD, fluorescence, urea titration and heteronuclear NMR experiments, we show that three amino acid substitutions (L18A-L19A-L37A) are sufficient to prevent Im7 folding, such that the unfolded state is predominantly populated at equilibrium. Using measurement of chemical shifts, (15)N transverse relaxation rates and sedimentation coefficients, we show that the unfolded species of L18A-L19A-L37A deviates significantly from random-coil behaviour. Specifically, we demonstrate that this unfolded species is compact (R(h)=25 Å) relative to the urea-denatured state (R(h)≥30 Å) and contains local clusters of hydrophobic residues in regions that correspond to the four helices in the native state. Despite these interactions, there is no evidence for long-range stabilising tertiary interactions or persistent helical structure. The results reveal an unfolded ensemble that is conformationally restricted in regions of the polypeptide chain that ultimately form helices I, II and IV in the native state.

  6. Changes in the conformational state of hemoglobin in hemodialysed patients with chronic renal failure.

    Science.gov (United States)

    Pieniazek, Anna; Gwozdzinski, Krzysztof

    2015-01-01

    The aim of this study was to evaluate the properties of internal components of erythrocytes in chronic renal failure (CRF) patients undergoing hemodialysis (HD) in comparison to control subjects. For investigation of conformational state of hemoglobin and nonheme proteins (NHP) the maleimide spin label (MSL) in electron paramagnetic resonance (EPR) was applied. The studies were performed using MSL in whole cells and hemolysate as well as proteins separated by ion exchange chromatography and checked by electrophoresis. Additionally the level of -SH groups in hemolysate and isolated internal proteins of CRF erythrocytes was determined using 4,4'-dithiodipyridine. All measurements were performed before and after hemodialysis. Oxidative stress accompanying CRF/hemodialysed patients caused a significant decrease in the mobility of internal components inside erythrocytes indicated by MSL (P hemoglobins and internal nonheme proteins in erythrocytes of CRF patients.

  7. 2D fractional supersymmetry for rational conformal field theory application for third-integer spin states

    CERN Document Server

    Pérez, A; Simon, P; de Traubenberg, M Rausch

    1996-01-01

    A 2D- fractional supersymmetry theory is algebraically constructed. The Lagrangian is derived using an adapted superspace including, in addition to a scalar field, two fields with spins 1/3,2/3. This theory turns out to be a rational conformal field theory. The symmetry of this model goes beyond the super Virasoro algebra and connects these third-integer spin states. Besides the stress-momentum tensor, we obtain a supercurrent of spin 4/3. Cubic relations are involved in order to close the algebra; the basic algebra is no longer a Lie or a super-Lie algebra. The central charge of this model is found to be 4/3. Finally, we analyse the form that a local invariant action should take.

  8. 2D fractional supersymmetry for rational conformal field theory: application for third-integer spin states

    Energy Technology Data Exchange (ETDEWEB)

    Perez, A. [Strasbourg-1 Univ., 67 (France). Lab. de Physique Theorique; Rausch de Traubenberg, M. [Strasbourg-1 Univ., 67 (France). Lab. de Physique Theorique]|[Centre de Recherches Nucleaires, Bat. 40/II, 67037 Strasbourg Cedex 2 (France); Simon, P. [Strasbourg-1 Univ., 67 (France). Lab. de Physique Theorique

    1996-12-23

    A 2D fractional supersymmetry theory is algebraically constructed. The Lagrangian is derived using an adapted superspace including, in addition to a scalar field, two fields with spins 1/3,2/3. This theory turns out to be a rational conformal field theory. The symmetry of this model goes beyond the super-Virasoro algebra and connects these third-integer spin states. Besides the stress-momentum tensor, we obtain a supercurrent of spin 4/3. Cubic relations are involved in order to close the algebra; the basic algebra is no longer a Lie or a super-Lie algebra. The central charge of this model is found to be 5/3. Finally, we analyze the form that a local invariant action should take. (orig.).

  9. Conjugation of cytochrome c with hydrogen titanate nanotubes: novel conformational state with implications for apoptosis

    Energy Technology Data Exchange (ETDEWEB)

    Ray, Moumita; Mazumdar, Shyamalava [Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005 (India); Chatterjee, Sriparna; Das, Tanmay; Bhattacharyya, Somnath; Ayyub, Pushan, E-mail: somnath@tifr.res.in, E-mail: pushan@tifr.res.in, E-mail: shyamal@tifr.res.in [Department of Condensed Matter Physics and Materials Science, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005 (India)

    2011-10-14

    We show that hydrogen titanate (H{sub 2}Ti{sub 3}O{sub 7}) nanotubes form strongly associated reversible nano-bio-conjugates with the vital respiratory protein, cytochrome c. Resonance Raman spectroscopy along with direct electrochemical studies indicate that in this nano-bio-conjugate, cytochrome c exists in an equilibrium of two conformational states with distinctly different formal redox potentials and coordination geometries of the heme center. The nanotube-conjugated cytochrome c also showed enhanced peroxidase activity similar to the membrane-bound protein that is believed to be an apoptosis initiator. This suggests that such a nanotube-cytochrome c conjugate may be a good candidate for cancer therapy applications.

  10. Neural-network analysis of the vibrational spectra of N-acetyl L-alanyl N '-methyl amide conformational states

    DEFF Research Database (Denmark)

    Bohr, Henrik; Frimand, Kenneth; Jalkanen, Karl J.

    2001-01-01

    data for a given conformer of the molecule by interpolation. Finally the neural network performances are used to monitor a sensitivity analysis of the importance of secondary structures and the influence of the solvent. The neural network is shown to be good in distinguishing the different conformers...... dichroism (VCD), Raman spectra, and Raman optical activity (ROA) intensities. The large changes due to hydration in the structures, and the relative stability of the conformer, reflected in the VA, VCD, Raman spectra, and ROA spectra observed experimentally, are reproduced by the DFT calculations. A neural...... network has been constructed for reproducing the inverse scattering data (we infer the structural coordinates from spectroscopic data) that the DFT method could produce. The purpose of the network has also been to generate the large set of conformational states associated with each set of spectroscopic...

  11. Renyi entanglement entropies of descendant states in critical systems with boundaries: conformal field theory and spin chains

    Science.gov (United States)

    Taddia, Luca; Ortolani, Fabio; Pálmai, Tamás

    2016-09-01

    We discuss the Renyi entanglement entropies of descendant states in critical one-dimensional systems with boundaries, that map to boundary conformal field theories in the scaling limit. We unify the previous conformal-field-theory approaches to describe primary and descendant states in systems with both open and closed boundaries. We provide universal expressions for the first two descendants in the identity family. We apply our technique to critical systems belonging to different universality classes with non-trivial boundary conditions that preserve conformal invariance, and find excellent agreement with numerical results obtained for finite spin chains. We also demonstrate that entanglement entropies are a powerful tool to resolve degeneracy of higher excited states in critical lattice models.

  12. Structural heterogeneity of the μ-opioid receptor’s conformational ensemble in the apo state

    Science.gov (United States)

    Sena, Diniz M.; Cong, Xiaojing; Giorgetti, Alejandro; Kless, Achim; Carloni, Paolo

    2017-04-01

    G-protein coupled receptors (GPCRs) are the largest and most pharmaceutically relevant family of membrane proteins. Here, fully unbiased, enhanced sampling simulations of a constitutively active mutant (CAM) of a class A GPCR, the μ-opioid receptor (μOR), demonstrates repeated transitions between the inactive (IS) and active-like (AS-L) states. The interconversion features typical activation/inactivation patterns involving established conformational rearrangements of conserved residues. By contrast, wild-type μOR remains in IS during the same course of simulation, consistent with the low basal activity of the protein. The simulations point to an important role of residue W2936.48 at the “toggle switch” in the mutation-induced constitutive activation. Such role has been already observed for other CAMs of class A GPCRs. We also find a significantly populated intermediate state, rather similar to IS. Based on the remarkable accord between simulations and experiments, we suggest here that this state, which has escaped so far experimental characterization, might constitute an early step in the activation process of the apo μOR CAM.

  13. Parent Hamiltonians for lattice Halperin states from free-boson conformal field theories

    Directory of Open Access Journals (Sweden)

    Anna Hackenbroich

    2017-03-01

    Full Text Available We introduce a family of many-body quantum states that describe interacting spin one-half hard-core particles with bosonic or fermionic statistics on arbitrary one- and two-dimensional lattices. The wave functions at lattice filling fraction ν=2/(2m+1 are derived from deformations of the Wess–Zumino–Witten model su(31 and are related to the (m+1,m+1,m Halperin fractional quantum Hall states. We derive long-range SU(2 invariant parent Hamiltonians for these states which in two dimensions are chiral t–J–V models with additional three-body interaction terms. In one dimension we obtain a generalisation to open chains of a periodic inverse-square t–J–V model proposed in [25]. We observe that the gapless low-energy spectrum of this model and its open-boundary generalisation can be described by rapidity sets with the same generalised Pauli exclusion principle. A two-component compactified free boson conformal field theory is identified as the low-energy effective theory for the periodic inverse-square t–J–V model.

  14. Entanglement entropy of excited states in conformal perturbation theory and the Einstein equation

    CERN Document Server

    Speranza, Antony J

    2016-01-01

    For a conformal field theory (CFT) deformed by a relevant operator, the entanglement entropy of a ball-shaped region may be computed as a perturbative expansion in the coupling. A similar perturbative expansion exists for excited states near the vacuum. Using these expansions, this work investigates the behavior of excited state entanglement entropies of small, ball-shaped regions. The motivation for these calculations is Jacobson's recent work on the equivalence of the Einstein equation and the hypothesis of maximal vacuum entropy [arXiv:1505.04753], which relies on a conjecture stating that the behavior of these entropies is sufficiently similar to a CFT. In addition to the expected type of terms which scale with the ball radius as $R^d$, the entanglement entropy calculation gives rise to terms scaling as $R^{2\\Delta}$, where $\\Delta$ is the dimension of the deforming operator. When $\\Delta\\leq\\frac{d}{2}$, the latter terms dominate the former, and suggest that a modification to the conjecture is needed.

  15. R\\'enyi entanglement entropies of descendant states in critical systems with boundaries: conformal field theory and spin chains

    CERN Document Server

    Taddia, Luca; Pálmai, Tamás

    2016-01-01

    We discuss the R\\'enyi entanglement entropies of descendant states in critical one-dimensional systems with boundaries, that map to boundary conformal field theories (CFT) in the scaling limit. We unify the previous CFT approaches to describe primary and descendant states in systems with both open and closed boundaries. We apply the technique to critical systems belonging to different universality classes with non-trivial boundary conditions that preserve conformal invariance, and compare the results to numerical data obtained on finite spin chains.

  16. Steady-state brain glucose transport kinetics re-evaluated with a four-state conformational model

    Directory of Open Access Journals (Sweden)

    João M N Duarte

    2009-10-01

    Full Text Available Glucose supply from blood to brain occurs through facilitative transporter proteins. A near linear relation between brain and plasma glucose has been experimentally determined and described by a reversible model of enzyme kinetics. A conformational four-state exchange model accounting for trans-acceleration and asymmetry of the carrier was included in a recently developed multi-compartmental model of glucose transport. Based on this model, we demonstrate that brain glucose (Gbrain as function of plasma glucose (Gplasma can be described by a single analytical equation namely comprising three kinetic compartments: blood, endothelial cells and brain. Transport was described by four parameters: apparent half saturation constant Kt, apparent maximum rate constant Tmax, glucose consumption rate CMRglc, and the iso-inhibition constant Kii that suggests Gbrain as inhibitor of the isomerisation of the unloaded carrier. Previous published data, where Gbrain was quantified as a function of plasma glucose by either biochemical methods or NMR spectroscopy, were used to determine the aforementioned kinetic parameters. Glucose transport was characterized by Kt ranging from 1.5 to 3.5 mM, Tmax/CMRglc from 4.6 to 5.6, and Kii from 51 to 149 mM. It was noteworthy that Kt was on the order of a few mM, as previously determined from the reversible model. The conformational four-state exchange model of glucose transport into the brain includes both efflux and transport inhibition by Gbrain, predicting that Gbrain eventually approaches a maximum concentration. However, since Kii largely exceeds Gplasma, iso-inhibition is unlikely to be of substantial importance for plasma glucose below 25 mM. As a consequence, the reversible model can account for most experimental observations under euglycaemia and moderate cases of hypo- and hyperglycaemia.

  17. Influence of the Mixing State of tert- Butyl Alcohol-water Mixtures on the Conformation of Bovine Serum Albumin

    Institute of Scientific and Technical Information of China (English)

    MA,Lin; WANG,Xu; XU,Li; HE,Wei-Ren; WEI,Zhi-Qiang; LIN,Rui-Sen

    2008-01-01

    The hydrodynamic radii of bovine serum albumin (BSA) in TBA-water mixtures were determined by dynamic light scattering measurements and utilized to investigate the conformational change of BSA in TBA-water mixtures, together with the analysis of the fluorescence spectra and UV-vis absorption spectra of BSA. Meanwhile, static light scattering measurements were used to probe the mixing state of the binary mixtures of TBA-water and the ternary mixtures of BSA-TBA-water and its influence on the conformation of the protein. A close relationship between the mixing state of TBA-water mixtures and the conformation of BSA was observed. The mixing state of TBA-water mixture at a low concentration was characterized by the clathrate hydrate of TBA caged by water molecules and it was found that hydrophobic binding of TBA to nonpolar groups of BSA in general destabilized the native structure of the protein, however, addition of a small amount of TBA attenuated the hydrophobic interactions among nonpolar groups of the protein and promoted a more ordered conformation. The results clearly showed that clustering of TBA at a high concentration reduced the effectiveness on destabilization of the compact conformation of proteins.

  18. Multiple conformational states in retrospective virtual screening - homology models vs. crystal structures: beta-2 adrenergic receptor case study.

    Science.gov (United States)

    Mordalski, Stefan; Witek, Jagna; Smusz, Sabina; Rataj, Krzysztof; Bojarski, Andrzej J

    2015-01-01

    Distinguishing active from inactive compounds is one of the crucial problems of molecular docking, especially in the context of virtual screening experiments. The randomization of poses and the natural flexibility of the protein make this discrimination even harder. Some of the recent approaches to post-docking analysis use an ensemble of receptor models to mimic this naturally occurring conformational diversity. However, the optimal number of receptor conformations is yet to be determined. In this study, we compare the results of a retrospective screening of beta-2 adrenergic receptor ligands performed on both the ensemble of receptor conformations extracted from ten available crystal structures and an equal number of homology models. Additional analysis was also performed for homology models with up to 20 receptor conformations considered. The docking results were encoded into the Structural Interaction Fingerprints and were automatically analyzed by support vector machine. The use of homology models in such virtual screening application was proved to be superior in comparison to crystal structures. Additionally, increasing the number of receptor conformational states led to enhanced effectiveness of active vs. inactive compounds discrimination. For virtual screening purposes, the use of homology models was found to be most beneficial, even in the presence of crystallographic data regarding the conformational space of the receptor. The results also showed that increasing the number of receptors considered improves the effectiveness of identifying active compounds by machine learning methods. Graphical abstractComparison of machine learning results obtained for various number of beta-2 AR homology models and crystal structures.

  19. Energy levels and quantum states of [Leu]enkephalin conformations based on theoretical and experimental investigations

    DEFF Research Database (Denmark)

    Abdali, Salim; Jensen, Morten Østergaard; Bohr, Henrik

    2003-01-01

    This paper describes a theoretical and experimental study of [Leu]enkephalin conformations with respect to the quantum estates of the atomic structure of the peptide. Results from vibrational absorption measurements and quantum calculations are used to outline a quantum picture and to assign...... vibrational modes to the different conformations. The energy landscape of the conformations is reported as a function of a Hamming distance in Ramachandran space. Molecular dynamics simulations reveal a pronounced stability of the so-called single-bend low-energy conformation, which supports the derived...... quantum picture of this peptide....

  20. Conformational Transformation Exhibited by the Peptide Extracted from Crystalline Region of Bombyx mori Silk Fibroin in Solid and Solution States

    Institute of Scientific and Technical Information of China (English)

    YAO Ju-Ming; ZHANG Guo-Qing; LEI Cai-Hong

    2006-01-01

    The conformational transformation of a 30-residue peptide H(Ala-Gly-Ser-Gly-Ala-Gly)5OH, i.e., (AGSGAG)5,extracted from highly crystalline region of Bombyx mori (B. mori) silk fibroin was described by using the high resolution solid state 13C NMR, and CD spectroscopies. Based on the conformation-dependent 13C NMR chemical shifts of the Ala, Gly and Ser residues and the line-shape analysis of the conformation sensitive Ala Cβ resonance,the peptide revealed a strong preference for silk Ⅱ structural form, i.e., an antiparallel β-sheet structure (φ=-140±20° and ψ= 135±20°) in solid state. On the contrary, the CD spectra of this peptide in the two non-native hexafluorinated fibre spinning solvents, hexafluoroisopropanol (HFIP) and hexafluoroacetone (HFA), exhibited the existence of an unusual tightly-folded conformation resembling 310-helix (φ=-60±20° and ψ=- 30 ± 20°), as judged from the R ratio of [θ]222/[θ]203 in HFIP solution, whereas a dynamically averaged unordered structure in HFA. Taken together, the information inclined to hypothesis that the primary structure of the highly crystalline regions of B. mori silk fibroin may be easily accessible to the large conformational changes, which in turn may be critical for facilitating the structural transformation from unprocessed silk fibroin (silk Ⅰ form) to processed silk fiber (silk Ⅱ form).

  1. Selection of conformational states in surface self-assembly for a molecule with eight possible pairs of surface enantiomers

    DEFF Research Database (Denmark)

    Nuermaimaiti, Ajiguli; Schultz-Falk, Vickie; Lind Cramer, Jacob

    2016-01-01

    Self-assembly of a molecule with many distinct conformational states, resulting in eight possible pairs of surface enantiomers, is investigated on a Au(111) surface under UHV conditions. The complex molecule is equipped with alkyl and carboxyl moieties to promote controlled self-assembly of lamel...

  2. Applications of neural network prediction of conformational states for small peptides from spectra and of fold classes

    DEFF Research Database (Denmark)

    Bohr, Henrik; Røgen, Peter; Jalkanen, Karl J.

    2001-01-01

    Electronic structures of small peptides were calculated 'ab initio' with the help of Density Functional Theory (DFT) and molecular dynamics that rendered a set of conformational states of the peptides. For the structures of these states it was possible to derive atomic polar tensors that allowed us...... to construct vibrational spectra for each of the conformational states with low energy. From the spectra, neural networks could be trained to distinguish between the various states and thus be able to generate a larger set of relevant structures and their relation to secondary structures of the peptides....... The calculations were done both with solvent atoms (up to ten water molecules) and without, and hence the neural networks could be used to monitor the influence of the solvent on hydrogen bond formation. The calculations at this stage only involved very short peptide fragments of a few alanine amino acids...

  3. Probing conformational states of glutaryl-CoA dehydrogenase by fragment screening

    Energy Technology Data Exchange (ETDEWEB)

    Begley, Darren W.; Davies, Douglas R.; Hartley, Robert C.; Hewitt, Stephen N.; Rychel, Amanda L.; Myler, Peter J.; Van Voorhis, Wesley C.; Staker, Bart L.; Stewart, Lance J. (Emerald)

    2014-10-02

    Glutaric acidemia type 1 is an inherited metabolic disorder which can cause macrocephaly, muscular rigidity, spastic paralysis and other progressive movement disorders in humans. The defects in glutaryl-CoA dehydrogenase (GCDH) associated with this disease are thought to increase holoenzyme instability and reduce cofactor binding. Here, the first structural analysis of a GCDH enzyme in the absence of the cofactor flavin adenine dinucleotide (FAD) is reported. The apo structure of GCDH from Burkholderia pseudomallei reveals a loss of secondary structure and increased disorder in the FAD-binding pocket relative to the ternary complex of the highly homologous human GCDH. After conducting a fragment-based screen, four small molecules were identified which bind to GCDH from B. pseudomallei. Complex structures were determined for these fragments, which cause backbone and side-chain perturbations to key active-site residues. Structural insights from this investigation highlight differences from apo GCDH and the utility of small-molecular fragments as chemical probes for capturing alternative conformational states of preformed protein crystals.

  4. Changes in the Conformational State of Hemoglobin in Hemodialysed Patients with Chronic Renal Failure

    Directory of Open Access Journals (Sweden)

    Anna Pieniazek

    2015-01-01

    Full Text Available The aim of this study was to evaluate the properties of internal components of erythrocytes in chronic renal failure (CRF patients undergoing hemodialysis (HD in comparison to control subjects. For investigation of conformational state of hemoglobin and nonheme proteins (NHP the maleimide spin label (MSL in electron paramagnetic resonance (EPR was applied. The studies were performed using MSL in whole cells and hemolysate as well as proteins separated by ion exchange chromatography and checked by electrophoresis. Additionally the level of –SH groups in hemolysate and isolated internal proteins of CRF erythrocytes was determined using 4,4′-dithiodipyridine. All measurements were performed before and after hemodialysis. Oxidative stress accompanying CRF/hemodialysed patients caused a significant decrease in the mobility of internal components inside erythrocytes indicated by MSL (P < 0.02. The significant decrease in mobility of spin labeled HbA1c and HbA both before and after HD (P < 0.0002 as well as in nonheme proteins before hemodialysis (P < 0.05 versus control was indicated. Decrease in mobility of internal components of erythrocytes was accompanied by loss of thiols before and after hemodialysis versus control in NHP (P < 0.05, HbA1c (P < 0.0002, and HbA (P < 0.0005. These findings showed oxidative influence of hemodialysis on hemoglobins and internal nonheme proteins in erythrocytes of CRF patients.

  5. Dielectric relaxation and the conformer equilibrium in the liquid and glassy states of β- D-fructose

    Science.gov (United States)

    Tombari, E.; Cardelli, C.; Salvetti, G.; Johari, G. P.

    2001-01-01

    To investigate the ionic and molecular dynamics in the liquid and glassy states of β- D-fructose, its dielectric relaxation spectra (12 Hz-500 kHz) and dynamic heat capacity (3.33 mHz) have been measured from 5 K above its melting point through the vitrification range, by allowing sufficient time for attainment of the conformer (or chemical) equilibria. Effects of the change in the conformer population on thermal cycling has been further studied. The dielectric behavior of liquid β- D-fructose is characteristically different from that of other molecular liquids in three ways: (i) the contribution to orientation polarization associated with the fast relaxation process, which persists in the glassy state, is relatively high in the liquid state of β- D-fructose; (ii) this contribution decreases with temperature exceptionally rapidly on cooling; and (iii) the difference in the rates of the two process is exceptionally large. The dynamic heat capacity change through the vitrification region is ˜160 J/(mol K), and is spread over ˜20 K range, and the enthalpy relaxation time is ˜50 s at 383 K. Transformation of β-pyranose to other conformers and other conformer transformation equilibria change on thermal cycling with the result that the overall relaxation rate increases at T>315 K and decreases at T<315 K. The relaxation spectrum becomes broader, the dc conductivity increases and the rate of the Johari-Goldstein relaxation whose Arrhenius energy is 42.1 kJ/mol increases.

  6. A reduced-amide inhibitor of Pin1 binds in a conformation resembling a twisted-amide transition state.

    Science.gov (United States)

    Xu, Guoyan G; Zhang, Yan; Mercedes-Camacho, Ana Y; Etzkorn, Felicia A

    2011-11-08

    The mechanism of the cell cycle regulatory peptidyl prolyl isomerase (PPIase), Pin1, was investigated using reduced-amide inhibitors designed to mimic the twisted-amide transition state. Inhibitors, R-pSer-Ψ[CH(2)N]-Pro-2-(indol-3-yl)ethylamine, 1 [R = fluorenylmethoxycarbonyl (Fmoc)] and 2 (R = Ac), of Pin1 were synthesized and bioassayed. Inhibitor 1 had an IC(50) value of 6.3 μM, which is 4.5-fold better for Pin1 than our comparable ground-state analogue, a cis-amide alkene isostere-containing inhibitor. The change of Fmoc to Ac in 2 improved aqueous solubility for structural determination and resulted in an IC(50) value of 12 μM. The X-ray structure of the complex of 2 bound to Pin1 was determined to 1.76 Å resolution. The structure revealed that the reduced amide adopted a conformation similar to the proposed twisted-amide transition state of Pin1, with a trans-pyrrolidine conformation of the prolyl ring. A similar conformation of substrate would be destabilized relative to the planar amide conformation. Three additional reduced amides, with Thr replacing Ser and l- or d-pipecolate (Pip) replacing Pro, were slightly weaker inhibitors of Pin1.

  7. Assessing the native state conformational distribution of ubiquitin by peptide acidity.

    Science.gov (United States)

    Hernández, Griselda; Anderson, Janet S; LeMaster, David M

    2010-12-01

    At equilibrium, every energetically feasible conformation of a protein occurs with a non-zero probability. Quantitative analysis of protein flexibility is thus synonymous with determining the proper Boltzmann-weighting of this conformational distribution. The exchange reactivity of solvent-exposed amide hydrogens greatly varies with conformation, while the short-lived peptide anion intermediate implies an insensitivity to the dynamics of conformational motion. Amides that are well-exposed in model conformational ensembles of ubiquitin vary a million-fold in exchange rates which continuum dielectric methods can predict with an rmsd of 3. However, the exchange rates for many of the more rarely exposed amides are markedly overestimated in the PDB-deposited 2K39 and 2KN5 ubiquitin ensembles, while the 2NR2 ensemble predictions are largely consistent with those of the Boltzmann-weighted conformational distribution sampled at the level of 1%. The correlation between the fraction of solvent-accessible conformations for a given amide hydrogen and the exchange rate constant for that residue provides a useful monitor of the degree of completeness with which a given ensemble has sampled the energetically accessible conformational space. These exchange predictions correlate with the degree to which each ensemble deviates from a set of 46 ubiquitin X-ray structures. Kolmogorov-Smirnov analysis for the distribution of intra- and inter-ensemble pairwise structural rmsd values assisted the identification of a subensemble of 2K39 that eliminates the overestimations of hydrogen exchange rates observed for the full ensemble. The relative merits of incorporating experimental restraints into the conformational sampling process are compared to using these restraints as filters to select subpopulations consistent with the experimental data.

  8. Temperature-accelerated molecular dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain.

    Science.gov (United States)

    Selwa, Edithe; Huynh, Tru; Ciccotti, Giovanni; Maragliano, Luca; Malliavin, Thérèse E

    2014-10-01

    The catalytic domain of the adenyl cyclase (AC) toxin from Bordetella pertussis is activated by interaction with calmodulin (CaM), resulting in cAMP overproduction in the infected cell. In the X-ray crystallographic structure of the complex between AC and the C terminal lobe of CaM, the toxin displays a markedly elongated shape. As for the structure of the isolated protein, experimental results support the hypothesis that more globular conformations are sampled, but information at atomic resolution is still lacking. Here, we use temperature-accelerated molecular dynamics (TAMD) simulations to generate putative all-atom models of globular conformations sampled by CaM-free AC. As collective variables, we use centers of mass coordinates of groups of residues selected from the analysis of standard molecular dynamics (MD) simulations. Results show that TAMD allows extended conformational sampling and generates AC conformations that are more globular than in the complexed state. These structures are then refined via energy minimization and further unrestrained MD simulations to optimize inter-domain packing interactions, thus resulting in the identification of a set of hydrogen bonds present in the globular conformations.

  9. Multiple conformational states and gate opening of outer membrane protein TolC revealed by molecular dynamics simulations.

    Science.gov (United States)

    Wang, Beibei; Weng, Jingwei; Wang, Wenning

    2014-09-01

    Outer membrane protein TolC serves as an exit duct for exporting substances out of cell. The occluded periplasmic entrance of TolC is required to open for substrate transport, although the opening mechanism remains elusive. In this study, systematic molecular dynamics (MD) simulations for wild type TolC and six mutants were performed to explore the conformational dynamics of TolC. The periplasmic gate was shown to sample multiple conformational states with various degrees of gating opening. The gate opening was facilitated by all mutations except Y362F, which adopts an even more closed state than wild type TolC. The interprotomer salt-bridge R367-D153 is turned out to be crucial for periplasmic gate opening. The mutations that disrupt the interactions at the periplasmic tip may affect the stability of the trimeric assembly of TolC. Structural asymmetry of the periplasmic gate was observed to be opening size dependent. Asymmetric conformations are found in moderately opening states, while the most and the least opening states are often more symmetric. Finally, it is shown that lowering pH can remarkably stabilize the closed state of the periplasmic gate.

  10. The Conformation of Interfacially Adsorbed Ranaspumin-2 Is an Arrested State on the Unfolding Pathway

    Science.gov (United States)

    Morris, Ryan J.; Brandani, Giovanni B.; Desai, Vibhuti; Smith, Brian O.; Schor, Marieke; MacPhee, Cait E.

    2016-08-01

    Ranaspumin-2 (Rsn-2) is a surfactant protein found in the foam nests of the t\\'{u}ngara frog. Previous experimental work has led to a proposed model of adsorption which involves an unusual clam shell-like `unhinging' of the protein at an interface. Interestingly, there is no concomitant denaturation of the secondary structural elements of Rsn-2 with the large scale transformation of its tertiary structure. In this work we use both experiment and simulation to better understand the driving forces underpinning this unusual process. We develop a modified G\\={o}-model approach where we have included explicit representation of the side-chains in order to realistically model the interaction between the secondary structure elements of the protein and the interface. Doing so allows for the study of the underlying energy landscape which governs the mechanism of Rsn-2 interfacial adsorption. Experimentally, we study targeted mutants of Rsn-2, using the Langmuir trough, pendant drop tensiometry and circular dichroism, to demonstrate that the clam-shell model is correct. We find that Rsn-2 adsorption is in fact a two-step process: the hydrophobic N-terminal tail recruits the protein to the interface after which Rsn-2 undergoes an unfolding transition which maintains its secondary structure. Intriguingly, our simulations show that the conformation Rsn-2 adopts at an interface is an arrested state along the denaturation pathway. More generally, our computational model should prove a useful, and computationally efficient, tool in studying the dynamics and energetics of protein-interface interactions.

  11. Alternative sigma factors in the free state are equilibrium mixtures of open and compact conformations.

    Science.gov (United States)

    Raha, Paromita; Chattopadhyay, Suranjana; Mukherjee, Srijata; Chattopadhyay, Ruchira; Roy, Koushik; Roy, Siddhartha

    2010-11-16

    Conformational switching upon core RNA polymerase binding is an integral part of functioning of bacterial sigma factors. Here, we have studied dynamical features of two alternative sigma factors. A study of fluorescence resonance energy transfer and hydrodynamic measurements in Escherichia coli σ(32) suggest a compact shape like those found in complex with anti-sigma factors. On the other hand, the fluorescence anisotropy of probes attached to different regions of the protein and previous hydrogen exchange measurements suggest significant internal flexibility, particularly in the C-terminal half and region 1. In a homologous sigma factor, σ(F) of Mycobacterium tuberculosis, emission spectra and fluorescence resonance energy transfer between the single tryptophan (W112) and probes placed in different regions suggest a compact conformation for a major part of the N-terminal half encompassing region 2 and the flexible C-terminal half. Fluorescence anisotropy measurements suggest significant flexibility in the C-terminal half and region 1, as well. Thus, free alternative sigma factors may be in equilibrium between two conformations: a compact one in which the promoter interacting motifs are trapped in the wrong conformation and another less abundant one with a more open and flexible conformation. Such flexibility may be important for promoter recognition and interaction with many partner proteins.

  12. Distinct states of methionyl-tRNA synthetase indicate inhibitor binding by conformational selection.

    Science.gov (United States)

    Koh, Cho Yeow; Kim, Jessica E; Shibata, Sayaka; Ranade, Ranae M; Yu, Mingyan; Liu, Jiyun; Gillespie, J Robert; Buckner, Frederick S; Verlinde, Christophe L M J; Fan, Erkang; Hol, Wim G J

    2012-10-10

    To guide development of new drugs targeting methionyl-tRNA synthetase (MetRS) for treatment of human African trypanosomiasis, crystal structure determinations of Trypanosoma brucei MetRS in complex with its substrate methionine and its intermediate product methionyl-adenylate were followed by those of the enzyme in complex with high-affinity aminoquinolone inhibitors via soaking experiments. Drastic changes in conformation of one of the two enzymes in the asymmetric unit allowed these inhibitors to occupy an enlarged methionine pocket and a new so-called auxiliary pocket. Interestingly, a small low-affinity compound caused the same conformational changes, removed the methionine without occupying the methionine pocket, and occupied the previously not existing auxiliary pocket. Analysis of these structures indicates that the binding of the inhibitors is the result of conformational selection, not induced fit. Copyright © 2012 Elsevier Ltd. All rights reserved.

  13. THE CONFORMATIONAL STABILITY OF THE REDOX STATES OF LIPOAMIDE DEHYDROGENASE FROM AZOTOBACTER-VINELANDII

    NARCIS (Netherlands)

    VANBERKEL, WJH; REGELINK, AG; BEINTEMA, JJ; KOK, A

    1991-01-01

    The conformational stability of holo-lipoamide and apo-lipoamide dehydrogenase from Azotobacter vinelandii was studied by thermoinactivation, unfolding and limited proteolysis. The oxidized holoenzyme is thermostable, showing a melting temperature, t(m) = 80-degrees-C. The thermal stability of the h

  14. 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....... Compared with existing transposition models, which do not distinguish between different transposition outcomes, we examine the factors influencing each transposition process by means of a competing risk analysis. We find that preference-related factors, in particular the disagreement of a member state...... 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...

  15. Cation ion specifically induces a conformational change in trans-dehydroandrosterone - a solid-state NMR study.

    Science.gov (United States)

    Wang, Darong; Chen, Meiman; Chein, Rong-Jie; Ching, Wei-Min; Hung, Chen-Hsiung; Tzou, Der-Lii M

    2015-04-01

    In this work, we demonstrated that calcium (Ca(+2)) is able to induce a conformational change in trans-dehydroandrosterone (DHEA). To this respect, solid-state NMR spectroscopy was applied to a series of DHEA molecules that were incubated with Ca(+2) under different concentrations. The high-resolution (13)C NMR spectra of the DHEA/Ca(+2) mixtures exhibited two distinct sets of signals; one was attributed to DHEA in the free form, and the second set was due to the DHEA/Ca(+2) complex. Based on chemical shift isotropy and anisotropy analyses, we postulated that Ca(+2) might have associated with the oxygen attached to C17 via a lone-pair of electrons, which induced a conformational change in DHEA. Apart from Ca(+2), we also incubated DHEA with magnesium (Mg(+2)) to determine whether Mg(+2) was able to interact with DHEA in a similar manner to Ca(+2). We found that Mg(+2) was able to induce a conformational change in DHEA deviated from that of Ca(+2). These solid-state NMR observations indicate that DHEA is able to interact with cations, such as Mg(+2) and Ca(+2), with specificity.

  16. Molecular Dynamics Simulation on the Conformational Transition of the Mad2 Protein from the Open to the Closed State

    Directory of Open Access Journals (Sweden)

    Chaoqun Li

    2014-03-01

    Full Text Available The Mad2 protein, with two distinct conformations of open- and closed-states, is a key player in the spindle checkpoint. The closed Mad2 state is more active than the open one. We carried out conventional and targeted molecular dynamics simulations for the two stable Mad2 states and their conformational transition to address the dynamical transition mechanism from the open to the closed state. The intermediate structure in the transition process shows exposure of the β6 strand and an increase of space around the binding sites of β6 strand due to the unfolding of the β7/8 sheet and movement of the β6/4/5 sheet close to the αC helix. Therefore, Mad2 binding to the Cdc20 protein in the spindle checkpoint is made possible. The interconversion between these two states might facilitate the functional activity of the Mad2 protein. Motion correlation analysis revealed the allosteric network between the β1 strand and β7/8 sheet via communication of the β5-αC loop and the β6/4/5 sheet in this transition process.

  17. Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2

    Directory of Open Access Journals (Sweden)

    Gu Jenny

    2007-02-01

    Full Text Available Abstract Background The mechanisms underlying protein function and associated conformational change are dominated by a series of local entropy fluctuations affecting the global structure yet are mediated by only a few key residues. Transitional Dynamic Analysis (TDA is a new method to detect these changes in local protein flexibility between different conformations arising from, for example, ligand binding. Additionally, Positional Impact Vertex for Entropy Transfer (PIVET uses TDA to identify important residue contact changes that have a large impact on global fluctuation. We demonstrate the utility of these methods for Cyclin-dependent kinase 2 (CDK2, a system with crystal structures of this protein in multiple functionally relevant conformations and experimental data revealing the importance of local fluctuation changes for protein function. Results TDA and PIVET successfully identified select residues that are responsible for conformation specific regional fluctuation in the activation cycle of Cyclin Dependent Kinase 2 (CDK2. The detected local changes in protein flexibility have been experimentally confirmed to be essential for the regulation and function of the kinase. The methodologies also highlighted possible errors in previous molecular dynamic simulations that need to be resolved in order to understand this key player in cell cycle regulation. Finally, the use of entropy compensation as a possible allosteric mechanism for protein function is reported for CDK2. Conclusion The methodologies embodied in TDA and PIVET provide a quick approach to identify local fluctuation change important for protein function and residue contacts that contributes to these changes. Further, these approaches can be used to check for possible errors in protein dynamic simulations and have the potential to facilitate a better understanding of the contribution of entropy to protein allostery and function.

  18. Conformational Switching of π-Conjugated Junctions from Merocyanine to Cyanine States by Solvent Polarity.

    Science.gov (United States)

    Arjona-Esteban, Alhama; Stolte, Matthias; Würthner, Frank

    2016-02-12

    Directed by the solvent polarity, the prevalent conformation of a polymethine dye bearing a branched π-conjugated junction can be switched from a heptamethine donor-acceptor (DA) merocyanine-type π-conjugated system to a nonamethine DAD cyanine-type π-conjugated scaffold. Concomitantly the absorption maximum shifts from 585 nm in dichloromethane to 748 nm in methanol solution.

  19. Conformational Analysis, Molecular Structure and Solid State Simulation of the Antiviral Drug Acyclovir (Zovirax Using Density Functional Theory Methods

    Directory of Open Access Journals (Sweden)

    Margarita Clara Alvarez-Ros

    2014-06-01

    Full Text Available The five tautomers of the drug acyclovir (ACV were determined and optimised at the MP2 and B3LYP quantum chemical levels of theory. The stability of the tautomers was correlated with different parameters. On the most stable tautomer N1 was carried out a comprehensive conformational analysis, and the whole conformational parameters (R, β, Φ, φ1, φ2, φ3, φ4, φ5 were studied as well as the NBO Natural atomic charges. The calculations were carried out with full relaxation of all geometrical parameters. The search located at least 78 stable structures within 8.5 kcal/mol electronic energy range of the global minimum, and classified in two groups according to the positive or negative value of the torsional angle j1. In the nitrogen atoms and in the O2' and O5' oxygen atoms of the most stable conformer appear a higher reactivity than in the natural nucleoside deoxyguanosine. The solid state was simulated through a dimer and tetramer forms and the structural parameters were compared with the X-ray crystal data available. Several general conclusions were emphasized.

  20. Solid-state and solution /sup 13/C NMR in the conformational analysis of methadone-hydrochloride and related narcotic analgesics

    Energy Technology Data Exchange (ETDEWEB)

    Sumner, S.C.J.

    1986-01-01

    Solid state and solution /sup 13/C NMR have been used to study the conformations of the racemic mixtures and single enantiomers of methadone hydrochloride, alpha and beta methadol hydrochloride, and alpha and beta acetylmethadol hydrochloride. The NMR spectra acquired for the compounds as solids, and in polar and nonpolar solvents are compared, in order to determine the conformation of the molecules in solution. To determine the reliability of assigning solution conformations by comparing solution and solid state chemical shift data, three bond coupling constants measured in solution are compared with those calculated from X-ray data. The conformations of the racemic mixture and plus enantiomer of methadone hydrochloride have been shown to be very similar in the solid state, where minor differences in conformation can be seen by comparing NMR spectra obtained for the solids. Also shown is that the molecules of methadone hydrochloride have conformations in polar and in nonpolar solvents which are very similar to the conformation of the molecules in the solid state.

  1. Conformational states of a bacterial α2-macroglobulin resemble those of human complement C3.

    Directory of Open Access Journals (Sweden)

    David Neves

    Full Text Available α(2 macroglobulins (α(2Ms are broad-spectrum protease inhibitors that play essential roles in the innate immune system of eukaryotic species. These large, multi-domain proteins are characterized by a broad-spectrum bait region and an internal thioester, which, upon cleavage, becomes covalently associated to the target protease, allowing its entrapment by a large conformational modification. Notably, α(2Ms are part of a larger protein superfamily that includes proteins of the complement system, such as C3, a multi-domain macromolecule which is also characterized by an internal thioester-carrying domain and whose activation represents the pivotal step in the complement cascade. Recently, α(2M/C3-like genes were identified in a large number of bacterial genomes, and the Escherichia coli α(2M homolog (ECAM was shown to be activated by proteases. In this work, we have structurally characterized ECAM by electron microscopy and small angle scattering (SAXS techniques. ECAM is an elongated, flexible molecule with overall similarities to C3 in its inactive form; activation by methylamine, chymotrypsin, or elastase induces a conformational modification reminiscent of the one undergone by the transformation of C3 into its active form, C3b. In addition, the proposed C-terminus of ECAM displays high flexibility and different conformations, and could be the recognition site for partner macromolecules. This work sheds light on a potential bacterial defense mechanism that mimics structural rearrangements essential for activation of the complement cascade in eukaryotes, and represents a possible novel target for the development of antibacterials.

  2. Basis for ligand discrimination between ON and OFF state riboswitch conformations: the case of the SAM-I riboswitch.

    Science.gov (United States)

    Boyapati, Vamsi Krishna; Huang, Wei; Spedale, Jessica; Aboul-Ela, Fareed

    2012-06-01

    Riboswitches are RNA elements that bind to effector ligands and control gene expression. Most consist of two domains. S-Adenosyl Methionine (SAM) binds the aptamer domain of the SAM-I riboswitch and induces conformational changes in the expression domain to form an intrinsic terminator (transcription OFF state). Without SAM the riboswitch forms the transcription ON state, allowing read-through transcription. The mechanistic link between the SAM/aptamer recognition event and subsequent secondary structure rearrangement by the riboswitch is unclear. We probed for those structural features of the Bacillus subtilis yitJ SAM-I riboswitch responsible for discrimination between the ON and OFF states by SAM. We designed SAM-I riboswitch RNA segments forming "hybrid" structures of the ON and OFF states. The choice of segment constrains the formation of a partial P1 helix, characteristic of the OFF state, together with a partial antiterminator (AT) helix, characteristic of the ON state. For most choices of P1 vs. AT helix lengths, SAM binds with micromolar affinity according to equilibrium dialysis. Mutational analysis and in-line probing confirm that the mode of SAM binding by hybrid structures is similar to that of the aptamer. Altogether, binding measurements and in-line probing are consistent with the hypothesis that when SAM is present, stacking interactions with the AT helix stabilize a partially formed P1 helix in the hybrids. Molecular modeling indicates that continuous stacking between the P1 and the AT helices is plausible with SAM bound. Our findings raise the possibility that conformational intermediates may play a role in ligand-induced aptamer folding.

  3. Fifty hertz magnetic fields individually affect chromatin conformation in human lymphocytes: dependence on amplitude, temperature, and initial chromatin state.

    Science.gov (United States)

    Sarimov, Ruslan; Alipov, Eugene D; Belyaev, Igor Y

    2011-10-01

    Effects of magnetic field (MF) at 50 Hz on chromatin conformation were studied by the method of anomalous viscosity time dependence (AVTD) in human lymphocytes from two healthy donors. MF within the peak amplitude range of 5-20 µT affected chromatin conformation. These MF effects differed significantly between studied donors, and depended on magnetic flux density and initial condensation of chromatin. While the initial state of chromatin was rather stable in one donor during one calendar year of measurements, the initial condensation varied significantly in cells from another donor. Both this variation and the MF effect depended on temperature during exposure. Despite these variations, the general rule was that MF condensed the relaxed chromatin and relaxed the condensed chromatin. Thus, in this study we show that individual effects of 50 Hz MF exposure at peak amplitudes within the range of 5-20 µT may be observed in human lymphocytes in dependence on the initial state of chromatin and temperature. Copyright © 2011 Wiley-Liss, Inc.

  4. Protein folding with implicit crowders: a study of conformational states using the Wang-Landau method.

    Science.gov (United States)

    Hoppe, Travis; Yuan, Jian-Min

    2011-03-10

    In this paper we introduce the idea of the implicit crowding method to study the statistical mechanical behaviors of folding of β-sheet peptides. Using a simple bead-lattice model, we are able to consider, separately, the conformational entropy involving the bond angles along the backbone and the orientational entropy associated with the dihedral angles. We use a Ising-like model to partially account for the dihedral angle entropy and, implicitly, the hydrogen-bond formations. We also compare our results to recent experiments and find good quantitative agreement on the predicted folded fraction. On the basis of the predictions from the scaled particle theory, we investigate changes in the melting temperature of the protein, suggesting crowding enhanced stability for a variant of trpzip hairpin and a slight instability for the larger β-sheet designed proteins.

  5. Selection of conformational states in self-assembled surface structures formed from an oligo(naphthylene-ethynylene) 3-bit binary switch

    DEFF Research Database (Denmark)

    Ning, Yanxiao; Cramer, Jacob Roland; Nuermaimaiti, Ajiguli;

    2015-01-01

    ). The conformations result from binary positions of n = 3 naphtalene units on a linear oligo(naphthylene-ethynylene) backbone. On Au(111), inter-molecular interactions involving carboxyl and bulky tert-butyl-phenyl functional groups induce the molecules to form two ordered phases with brick-wall and lamella structure...... the naphthalene units. The present study enhances our understanding of how ordering and selection of molecular conformations is controlled by intermolecular interactions in a complex situation with many distinct conformational states for the participating molecules....

  6. Role of conformation and electronic structure in the chemistry of ground and excited state o-pyrazolylphenylnitrenes.

    Science.gov (United States)

    Carra, Claudio; Bally, Thomas; Albini, Angelo

    2005-04-20

    The chemistry of 2-(1-pyrazolyl)- (2a) and 2-[1-(3,5-dimethylpyrazolyl]phenylnitrene (2b) has been studied in EtOH solution at room temperature, in EtOH glasses at 90 K, and in Ar matrices at 12 K. These nitrenes were chosen as suitable models for clarifying the mechanism of intramolecular reactions because attack at the pyrazole ring can occur according to different modes and the asymmetry of the substituent gives rise to different conformations. Detailed DFT and CASSCF/CASPT2 studies on the conformation and decay paths of both spin states of the nitrenes have been carried out. Ring expansion to dehydroazepines (via benzoazirines) is calculated to be competitive in both nitrenes, but in the dimethyl derivative, 2b, attack onto the N lone pair (which is made more nucleophilic by the methyl groups) is favored. The higher barriers (by 4-8 kcal/mol) in singlet 2a cause 60-70% of this nitrene to decay by intersystem crossing to the triplet. Thus, the seemingly straightforward formation of benzo-fused heterocycles through intramolecular attack of the pyrazoline N lone pair by the singlet phenylnitrene can only overcome ring expansion and intermolecular reactions under favorable circumstances. The comparatively persistent triplet nitrenes are characterized in matrices, and the yields of photocyclization products (mainly pyrazolo[1,5-a]benzimidazole (7) from 2a and 5,6-dihydropyrazolo[1,5-a]quinoxaline (8) from 2b) are shown to depend on the preferred conformation of the starting azide and nitrene.

  7. Conformal, Nanoscale ZnO Surface Modification of Garnet-Based Solid-State Electrolyte for Lithium Metal Anodes.

    Science.gov (United States)

    Wang, Chengwei; Gong, Yunhui; Liu, Boyang; Fu, Kun; Yao, Yonggang; Hitz, Emily; Li, Yiju; Dai, Jiaqi; Xu, Shaomao; Luo, Wei; Wachsman, Eric D; Hu, Liangbing

    2017-01-11

    Solid-state electrolytes are known for nonflammability, dendrite blocking, and stability over large potential windows. Garnet-based solid-state electrolytes have attracted much attention for their high ionic conductivities and stability with lithium metal anodes. However, high-interface resistance with lithium anodes hinders their application to lithium metal batteries. Here, we demonstrate an ultrathin, conformal ZnO surface coating by atomic layer deposition for improved wettability of garnet solid-state electrolytes to molten lithium that significantly decreases the interface resistance to as low as ∼20 Ω·cm(2). The ZnO coating demonstrates a high reactivity with lithium metal, which is systematically characterized. As a proof-of-concept, we successfully infiltrated lithium metal into porous garnet electrolyte, which can potentially serve as a self-supported lithium metal composite anode having both high ionic and electrical conductivity for solid-state lithium metal batteries. The facile surface treatment method offers a simple strategy to solve the interface problem in solid-state lithium metal batteries with garnet solid electrolytes.

  8. Structural studies of Saccharomyces cerevesiae mitochondrial NADP-dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction.

    Science.gov (United States)

    Peng, Yingjie; Zhong, Chen; Huang, Wei; Ding, Jianping

    2008-09-01

    Isocitrate dehydrogenases (IDHs) catalyze oxidative decarboxylation of isocitrate (ICT) into alpha-ketoglutarate (AKG). We report here the crystal structures of Saccharomyces cerevesiae mitochondrial NADP-IDH Idp1p in binary complexes with coenzyme NADP, or substrate ICT, or product AKG, and in a quaternary complex with NADPH, AKG, and Ca(2+), which represent different enzymatic states during the catalytic reaction. Analyses of these structures identify key residues involved in the binding of these ligands. Comparisons among these structures and with the previously reported structures of other NADP-IDHs reveal that eukaryotic NADP-IDHs undergo substantial conformational changes during the catalytic reaction. Binding or release of the ligands can cause significant conformational changes of the structural elements composing the active site, leading to rotation of the large domain relative to the small and clasp domains along two hinge regions (residues 118-124 and residues 284-287) while maintaining the integrity of its secondary structural elements, and thus, formation of at least three distinct overall conformations. Specifically, the enzyme adopts an open conformation when bound to NADP, a quasi-closed conformation when bound to ICT or AKG, and a fully closed conformation when bound to NADP, ICT, and Ca(2+) in the pseudo-Michaelis complex or with NADPH, AKG, and Ca(2+) in the product state. The conformational changes of eukaryotic NADP-IDHs are quite different from those of Escherichia coli NADP-IDH, for which significant conformational changes are observed only between two forms of the apo enzyme, suggesting that the catalytic mechanism of eukaryotic NADP-IDHs is more complex than that of EcIDH, and involves more fine-tuned conformational changes.

  9. Two-state conformational equilibrium in the Par-4 leucine zipper domain.

    Science.gov (United States)

    Schwalbe, Martin; Dutta, Kaushik; Libich, David S; Venugopal, Hariprasad; Claridge, Jolyon K; Gell, David A; Mackay, Joel P; Edwards, Patrick J B; Pascal, Steven M

    2010-08-15

    Prostate apoptosis response factor-4 (Par-4) is a pro-apoptotic and tumor-suppressive protein. A highly conserved heptad repeat sequence at the Par-4 C-terminus suggests the presence of a leucine zipper (LZ). This C-terminal region is essential for Par-4 self-association and interaction with various effector proteins. We have used nuclear magnetic resonance (NMR) spectroscopy to fully assign the chemical shift resonances of a peptide comprising the LZ domain of Par-4 at neutral pH. Further, we have investigated the properties of the Par-4 LZ domain and two point mutants under a variety of conditions using NMR, circular dichroism (CD), light scattering, and bioinformatics. Results indicate an environment-dependent conformational equilibrium between a partially ordered monomer (POM) and a predominantly coiled coil dimer (CCD). The combination of techniques used allows the time scales of the equilibrium to be probed and also helps to identify features of the amino acid sequence that may influence the equilibrium.

  10. Changes of conformation and aggregation state induced by binding of lanthanide ions to insulin

    Institute of Scientific and Technical Information of China (English)

    程驿; 李荣昌; 王夔

    2002-01-01

    To clarify the mechanism of lanthanide ions (Ln3+) on the across-membrane transport of insulin and subsequent reducing blood glucose, the interactions of Ln3+with Zn-insulin and Zn-free insulin are investigated by spectroscopic methods. The results reveal that the binding of Ln3+ to insulin can induce its structure changes from secondary to quaternary structure, depending on the Ln3+ concentration. In the lower concentration, it triggers the conformational changes of insulin monomer in the binding region with insulin receptor (B(24-30)). It would affect insulin-insulin receptor interaction. Moreover, Ln3+ binding promotes the assembly of insulin monomer from dimer to polymer. The potency of Ln3+ in inducing insulin’s aggregation is stronger than that of Zn2+. Furthermore, the aggregation can be reversed partly by EDTA-treatment, indicating that it is not due to denaturation. Similar to Zn2+ effect, Ln3+ can stabilize insulin hexamer in a certain range of concentration, but is stronger than the former.

  11. Changes of conformation and aggregation state induced by binding of lanthanide ions to insulin

    Institute of Scientific and Technical Information of China (English)

    程驿; 李荣昌; 王夔

    2002-01-01

    To clarify the mechanism of lanthanide ions (Ln3+) on the across-membrane transport of insulin and subsequent reducing blood glucose, the interactions of Ln3+ with Zn-insulin and Zn-free insulin are investigated by spectroscopic methods. The results reveal that the binding of Ln3+ to insulin can induce its structure changes from secondary to quaternary structure, depending on the Ln3+ concentration. In the lower concentration, it triggers the conformational changes of insulin monomer in the binding region with insulin receptor (B(24-30)). It would affect insulin-insulin receptor interaction. Moreover, Ln3+ binding promotes the assembly of insulin monomer from dimer to polymer. The potency of Ln3+ in inducing insulin's aggregation is stronger than that of Zn2+. Furthermore, the aggregation can be reversed partly by EDTA-treatment, indicating that it is not due to denaturation. Similar to Zn2+ effect, Ln3+ can stabilize insulin hexamer in a certain range of concentration, but is stronger than the former.

  12. Structure analysis and conformational transitions of the cell penetrating peptide transportan 10 in the membrane-bound state.

    Directory of Open Access Journals (Sweden)

    Susanne Fanghänel

    Full Text Available Structure analysis of the cell-penetrating peptide transportan 10 (TP10 revealed an exemplary range of different conformations in the membrane-bound state. The bipartite peptide (derived N-terminally from galanin and C-terminally from mastoparan was found to exhibit prominent characteristics of (i amphiphilic α-helices, (ii intrinsically disordered peptides, as well as (iii β-pleated amyloid fibrils, and these conformational states become interconverted as a function of concentration. We used a complementary approach of solid-state (19F-NMR and circular dichroism in oriented membrane samples to characterize the structural and dynamical behaviour of TP10 in its monomeric and aggregated forms. Nine different positions in the peptide were selectively substituted with either the L- or D-enantiomer of 3-(trifluoromethyl-bicyclopent-[1.1.1]-1-ylglycine (CF3-Bpg as a reporter group for (19F-NMR. Using the L-epimeric analogs, a comprehensive three-dimensional structure analysis was carried out in lipid bilayers at low peptide concentration, where TP10 is monomeric. While the N-terminal region is flexible and intrinsically unstructured within the plane of the lipid bilayer, the C-terminal α-helix is embedded in the membrane with an oblique tilt angle of ∼ 55° and in accordance with its amphiphilic profile. Incorporation of the sterically obstructive D-CF3-Bpg reporter group into the helical region leads to a local unfolding of the membrane-bound peptide. At high concentration, these helix-destabilizing C-terminal substitutions promote aggregation into immobile β-sheets, which resemble amyloid fibrils. On the other hand, the obstructive D-CF3-Bpg substitutions can be accommodated in the flexible N-terminus of TP10 where they do not promote aggregation at high concentration. The cross-talk between the two regions of TP10 thus exerts a delicate balance on its conformational switch, as the presence of the α-helix counteracts the tendency of the

  13. Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis.

    Directory of Open Access Journals (Sweden)

    Sonia Fieulaine

    2011-05-01

    Full Text Available For several decades, molecular recognition has been considered one of the most fundamental processes in biochemistry. For enzymes, substrate binding is often coupled to conformational changes that alter the local environment of the active site to align the reactive groups for efficient catalysis and to reach the transition state. Adaptive substrate recognition is a well-known concept; however, it has been poorly characterized at a structural level because of its dynamic nature. Here, we provide a detailed mechanism for an induced-fit process at atomic resolution. We take advantage of a slow, tight binding inhibitor-enzyme system, actinonin-peptide deformylase. Crystal structures of the initial open state and final closed state were solved, as well as those of several intermediate mimics captured during the process. Ligand-induced reshaping of a hydrophobic pocket drives closure of the active site, which is finally "zipped up" by additional binding interactions. Together with biochemical analyses, these data allow a coherent reconstruction of the sequence of events leading from the encounter complex to the key-lock binding state of the enzyme. A "movie" that reconstructs this entire process can be further extrapolated to catalysis.

  14. Electron exchange in conformationally restricted donor-spacer-acceptor dyads: angle dependence and involvement of upper-lying excited States.

    Science.gov (United States)

    Benniston, Andrew C; Harriman, Anthony; Li, Peiyi; Patel, Pritesh V; Sams, Craig A

    2008-01-01

    The rate constant for triplet energy transfer (k(TET)) has been measured in fluid solution for a series of mixed-metal Ru-Os bis(2,2':6',2''-terpyridine) complexes built around a tethered biphenyl-based spacer group. The length of the tether controls the central torsion angle for the spacer, which can be varied systematically from 37 to 130 degrees . At low temperature, but still in fluid solution, the spacer adopts the lowest-energy conformation and k(TET) shows a clear correlation with the torsion angle. A similar relationship holds for the inverse quantum yield for emission from the Ru-terpy donor. Triplet energy transfer is more strongly activated at higher temperature and the kinetic data require analysis in terms of two separate processes. The more weakly activated step involves electron exchange from the first-excited triplet state on the Ru-terpy donor and the size of the activation barrier matches well with that calculated from spectroscopic properties. The pre-exponential factor derived for this process correlates remarkably well with the torsion angle and there is a large disparity in electronic coupling through pi and sigma orbitals on the spacer. The more strongly activated step is attributed to electron exchange from an upper-lying triplet state localized on the Ru-terpy donor. Here, the pre-exponential factor is larger but shows the same dependence on the geometry of the spacer. Strangely, the difference in coupling through pi and sigma orbitals is much less pronounced. Despite internal flexibility around the spacer, k(TET) shows a marked dependence on the torsion angle computed for the lowest-energy conformation.

  15. Conformal Nets II: Conformal Blocks

    Science.gov (United States)

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

    2017-03-01

    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.

  16. 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.

  17. Immobilization of the distal hinge in the labile serpin plasminogen activator inhibitor 1: identification of a transition state with distinct conformational and functional properties.

    Science.gov (United States)

    De Taeye, Bart; Compernolle, Griet; Dewilde, Maarten; Biesemans, Wouter; Declerck, Paul J

    2003-06-27

    The serpin plasminogen activator inhibitor-1 (PAI-1) plays an important role in the regulation of the fibrinolytic activity in blood. In plasma, PAI-1 circulates mainly in the active conformation. However, PAI-1 spontaneously converts to a latent conformation. This conversion comprises drastic conformational changes in both the distal and the proximal hinge region of the reactive center loop. To study the functional and conformational rearrangements associated solely with the mobility of the proximal hinge, disulfide bonds were introduced to immobilize the distal hinge region. These mutants exhibited specific activities comparable with that of PAI-1-wt. However, the engineered disulfide bond had a major effect on the conformational and associated functional transitions. Strikingly, in contrast to PAI-1-wt, inactivation of these mutants yielded a virtually complete conversion to a substrate-like conformation. Comparison of the digestion pattern (with trypsin and elastase) of the mutants and PAI-1-wt revealed that the inactivated mutants have a conformation differing from that of latent and active PAI-1-wt. Unique trypsin-susceptible cleavage sites arose upon inactivation of these mutants. The localization of these exposed residues provides evidence that a displacement of alphahF has occurred, indicating that the proximal hinge is partly inserted between s3A and s5A. In conclusion, immobilization of the distal hinge region in PAI-1 allowed the identification of an "intermediate" conformation characterized by a partial insertion of the proximal hinge region. We hypothesize that locking PAI-1 in this transition state between active and latent conformations is associated with a displacement of alphahF, subsequently resulting in substrate behavior.

  18. Parent Hamiltonians for lattice Halperin states from free-boson conformal field theories

    CERN Document Server

    Hackenbroich, Anna

    2016-01-01

    We introduce a family of many-body quantum states that describe interacting spin one-half hard-core particles with bosonic or fermionic statistics on arbitrary one- and two-dimensional lattices. The wave functions at lattice filling fraction $\

  19. Crystal structure of carbonmonoxy sickle hemoglobin in R-state conformation.

    Science.gov (United States)

    Ghatge, Mohini S; Ahmed, Mostafa H; Omar, Abdel Sattar M; Pagare, Piyusha P; Rosef, Susan; Kellogg, Glen E; Abdulmalik, Osheiza; Safo, Martin K

    2016-06-01

    The fundamental pathophysiology of sickle cell disease is predicated by the polymerization of deoxygenated (T-state) sickle hemoglobin (Hb S) into fibers that distort red blood cells into the characteristic sickle shape. The crystal structure of deoxygenated Hb S (DeoxyHb S) and other studies suggest that the polymer is initiated by a primary interaction between the mutation βVal6 from one Hb S molecule, and a hydrophobic acceptor pocket formed by the residues βAla70, βPhe85 and βLeu88 of an adjacent located Hb S molecule. On the contrary, oxygenated or liganded Hb S does not polymerize or incorporate in the polymer. In this paper we present the crystal structure of carbonmonoxy-ligated sickle Hb (COHb S) in the quaternary classical R-state at 1.76Å. The overall structure and the pathological donor and acceptor environments of COHb S are similar to those of the isomorphous CO-ligated R-state normal Hb (COHb A), but differ significantly from DeoxyHb S as expected. More importantly, the packing of COHb S molecules does not show the typical pathological interaction between βVal6 and the βAla70, βPhe85 and βLeu88 hydrophobic acceptor pocket observed in DeoxyHb S crystal. The structural analysis of COHb S, COHb A and DeoxyHb S provides atomic level insight into why liganded hemoglobin does not form a polymer.

  20. 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.

  1. Difference and Influence of Inactive and Active States of Cannabinoid Receptor Subtype CB2: From Conformation to Drug Discovery.

    Science.gov (United States)

    Hu, Jianping; Feng, Zhiwei; Ma, Shifan; Zhang, Yu; Tong, Qin; Alqarni, Mohammed Hamed; Gou, Xiaojun; Xie, Xiang-Qun

    2016-06-27

    antagonist(s) at low concentration. Moreover, the hit from the active CB2 model also behaves as a neutral antagonist at low concentration. Our studies provide new insight leading to a better understanding of the structural and conformational differences between two states of CB2 and illuminate the effects of structure on virtual screening and drug design.

  2. Conformational study and ground state dipole moments of two ketene dithioacetal compounds

    Science.gov (United States)

    Negroni, B.; Botrel, A.; Hérail, M.; Proutière, A.

    1997-03-01

    Dipole moments (μ) of methyl-2-(1,3-dithietan-2-yliden)-3-oxobutanoate ( 1) and methyl-2-(1,3-dithiolan-2-yliden)-3-oxobutanoate ( 2) were measured in benzene solutions. Calculations of μ were performed using both the quantum chemical semiempirical PM3 method and the bond moments additivity model with additional electrostatic interaction calculations in the case of zwitterionic forms. A comparison of calculated values with the experimental ones shows that the electronic delocalization is larger for 2 than for 1 and more pronounced in the solid state than in solution for both molecules, in qualitative agreement with their first nonlinear polarizabilities β(2ω).

  3. 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...

  4. Impact of Interfacial Molecular Conformation and Aggregation State on the Energetic Landscape and Performance in Organic Photovoltaics

    KAUST Repository

    Ngongang Ndjawa, Guy Olivier

    2016-11-25

    In organic photovoltaics (OPVs) the key processes relevant to device operation such as exciton dissociation and free carriers recombination occur at the donor-acceptor (D-A) interface. OPV devices require the bulk heterojunction (BHJ) architecture to function efficiently. In these BHJs, D-A interfaces are arranged in three dimensions, which makes molecular arrangements at these interfaces ill defined and hard to characterize. In addition, molecular materials used in OPVs are inherently disordered and may exhibit variable degrees of structural order in the same BHJ. Yet, D-A molecular arrangements and structure are crucial because they shape the energy landscape and photovoltaic (PV) performance in OPVs. Studies that use well-defined model systems to look in details at the interfacial molecular structure in OPVs and link it to interfacial energy landscape and device operation are critically lacking. We have used in situ photoelectron spectroscopy and ex situ x-ray scattering to study D-A interfaces in tailored bilayers and BHJs based on small molecule donors. We show preferential miscibility at the D-A interface depending on molecular conformation in zinc phthalocyanine (ZnPc)/ C60 bilayers and we derive implications for exciton dissociation. Using sexithiophene (6T), a crystalline donor, we show that the energy landscape at the D-A interface varies markedly depending on the molecular composition of the BHJ. Both the ionization energies of sexithiophene and C60 shift by over ~0.4 eV while the energy of the charge transfer state shifts by ~0.5 eV depending on composition. Such shifts create a downward energy landscape that helps interfacial excitons to overcome their binding energies. Finally, we demonstrate that when both disordered and ordered phases of D coexist at the interface, low-lying energy states form in ordered phases and significantly limit the Voc in devices. Overall our work underlines the importance of the aggregation and conformation states of

  5. Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding.

    Science.gov (United States)

    Gui, Miao; Song, Wenfei; Zhou, Haixia; Xu, Jingwei; Chen, Silian; Xiang, Ye; Wang, Xinquan

    2017-01-01

    The global outbreak of SARS in 2002-2003 was caused by the infection of a new human coronavirus SARS-CoV. The infection of SARS-CoV is mediated mainly through the viral surface glycoproteins, which consist of S1 and S2 subunits and form trimer spikes on the envelope of the virions. Here we report the ectodomain structures of the SARS-CoV surface spike trimer in different conformational states determined by single-particle cryo-electron microscopy. The conformation 1 determined at 4.3 Å resolution is three-fold symmetric and has all the three receptor-binding C-terminal domain 1 (CTD1s) of the S1 subunits in "down" positions. The binding of the "down" CTD1s to the SARS-CoV receptor ACE2 is not possible due to steric clashes, suggesting that the conformation 1 represents a receptor-binding inactive state. Conformations 2-4 determined at 7.3, 5.7 and 6.8 Å resolutions are all asymmetric, in which one RBD rotates away from the "down" position by different angles to an "up" position. The "up" CTD1 exposes the receptor-binding site for ACE2 engagement, suggesting that the conformations 2-4 represent a receptor-binding active state. This conformational change is also required for the binding of SARS-CoV neutralizing antibodies targeting the CTD1. This phenomenon could be extended to other betacoronaviruses utilizing CTD1 of the S1 subunit for receptor binding, which provides new insights into the intermediate states of coronavirus pre-fusion spike trimer during infection.

  6. Conformational changes at the highly reactive cystein and lysine regions of skeletal muscle myosin induced by formation of transition state analogues.

    Science.gov (United States)

    Maruta, S; Homma, K; Ohki, T

    1998-09-01

    Myosin forms stable ternary complexes with Mg2+-ADP and phosphate analogues of aluminum fluoride (AlF4-), beryllium fluoride (BeFn), and scandium fluoride (ScFn). These complexes are distinct from each other and may mimic different transient states in the ATPase cycle [Maruta et al. (1993) J. Biol. Chem. 268, 7093-7100]. Regions of skeletal muscle myosin containing the highly reactive residues Cys 707 (SH1), Cys 697 (SH2), and lysine 83 (RLR) dramatically alter their local conformation when myosin hydrolyzes ATP, and these changes may reflect formation of a series of transient intermediates during ATP hydrolysis. We used the fluorescent probes 4-fluoro-7-sulfamoylbezofurazan, 2-(4'-maleimidylanilino)naphthalene-6-sulfonic acid, and trinitrobenzene-sulfonate, which bind to SH1, SH2, and RLR, respectively, to examine differences in local conformations within myosin.ADP.phosphate analogue (BeFn, Vi, AlF4-, and ScFn) complexes. It was observed that the ternary complexes had SH1 conformations similar to those seen on S-1 in the presence of ATP. In contrast, local conformations in the SH2 and RLR regions of S-1.ADP.BeFn were different from those in corresponding regions of S-1.ADP.AlF4- or ScFn. These results suggest that SH1 and SH2 move distinctly during ATP hydrolysis and that the local conformations of the SH2 and RLR regions more sensitively reflect different transient states.

  7. Local conformational stability of HIV-1 gp120 in unliganded and CD4-bound states as defined by amide hydrogen/deuterium exchange.

    Science.gov (United States)

    Kong, Leopold; Huang, Chih-Chin; Coales, Stephen J; Molnar, Kathleen S; Skinner, Jeff; Hamuro, Yoshitomo; Kwong, Peter D

    2010-10-01

    The binding reaction of the HIV-1 gp120 envelope glycoprotein to the CD4 receptor involves exceptional changes in enthalpy and entropy. Crystal structures of gp120 in unliganded and various ligand-bound states, meanwhile, reveal an inner domain able to fold into diverse conformations, a structurally invariant outer domain, and, in the CD4-bound state, a bridging sheet minidomain. These studies, however, provide only hints as to the flexibility of each state. Here we use amide hydrogen/deuterium exchange coupled to mass spectrometry to provide quantifications of local conformational stability for HIV-1 gp120 in unliganded and CD4-bound states. On average, unliganded core gp120 displayed >10,000-fold slower exchange of backbone-amide hydrogens than a theoretically unstructured protein of the same composition, with binding by CD4 reducing the rate of gp120 amide exchange a further 10-fold. For the structurally constant CD4, alterations in exchange correlated well with alterations in binding surface (P value = 0.0004). For the structurally variable gp120, however, reductions in flexibility extended outside the binding surface, and regions of expected high structural diversity (inner domain/bridging sheet) displayed roughly 20-fold more rapid exchange in the unliganded state than regions of low diversity (outer domain). Thus, despite an extraordinary reduction in entropy, neither unliganded gp120 nor free CD4 was substantially unstructured, suggesting that most of the diverse conformations that make up the gp120 unliganded state are reasonably ordered. The results provide a framework for understanding how local conformational stability influences entropic change, conformational diversity, and structural rearrangements in the gp120-CD4 binding reaction.

  8. 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.)

  9. Trapped Conformational States of Semiquinone (D+•QB−•) Formed by B-Branch Electron Transfer at Low Temperature in Rhodobacter sphaeroides Reaction Centers‡

    Science.gov (United States)

    Paddock, M. L.; Flores, M.; Isaacson, R.; Chang, C.; Abresch, E. C.; Selvaduray, P.; Okamura, M.Y.

    2006-01-01

    The reaction center (RC) from Rhodobacter sphaeroides captures light energy by electron transfer between quinones QA and QB, involving a conformational gating step. In this work, conformational states of D+•QB−• were trapped (80K) and studied using EPR spectroscopy in mutant RCs that lack QA in which QB was reduced by the bacteriopheophytin along the B-branch. In mutant RCs frozen in the dark, a light induced EPR signal due to D+•QB−• formed in 30% of the sample with low quantum yield (0.2%–20%) and decayed in 6 s. A small signal with similar characteristics was also observed in native RCs. In contrast, the EPR signal due to D+QB− in mutant RCs illuminated while freezing formed in ~ 95% of the sample that did not decay (τ >107s) at 80K. In all samples, the observed g-values were the same (g=2.0026) indicating that all active QB−• was located in a proximal conformation coupled with the non-heme Fe2+. We propose that before electron transfer at 80K, the majority (~70%) of QB, structurally located in the distal site, cannot be stably reduced, while the minor (~30%) active configurations are in the proximal site. The large difference in the lifetimes of the un-relaxed and relaxed D+•QB−• states is attributed to relaxation of protein residues and internal water molecules that stabilize D+•QB−•. These results demonstrate energetically significant conformational changes involved in stabilizing the D+•QB−• state. The unrelaxed and relaxed states can be considered to be the initial and final states along the reaction coordinate for conformationally-gated electron transfer. PMID:17115698

  10. Trapped conformational states of semiquinone (D+*QB-*) formed by B-branch electron transfer at low temperature in Rhodobacter sphaeroides reaction centers.

    Science.gov (United States)

    Paddock, M L; Flores, M; Isaacson, R; Chang, C; Abresch, E C; Selvaduray, P; Okamura, M Y

    2006-11-28

    The reaction center (RC) from Rhodobacter sphaeroides captures light energy by electron transfer between quinones QA and QB, involving a conformational gating step. In this work, conformational states of D+*QB-* were trapped (80 K) and studied using EPR spectroscopy in native and mutant RCs that lack QA in which QB was reduced by the bacteriopheophytin along the B-branch. In mutant RCs frozen in the dark, a light induced EPR signal due to D+*QB-* formed in 30% of the sample with low quantum yield (0.2%-20%) and decayed in 6 s. A small signal with similar characteristics was also observed in native RCs. In contrast, the EPR signal due to D+*QB-* in mutant RCs illuminated while freezing formed in approximately 95% of the sample did not decay (tau >107 s) at 80 K (also observed in the native RC). In all samples, the observed g-values were the same (g = 2.0026), indicating that all active QB-*'s were located in a proximal conformation coupled with the nonheme Fe2+. We propose that before electron transfer at 80 K, the majority (approximately 70%) of QB, structurally located in the distal site, was not stably reducible, whereas the minority (approximately 30%) of active configurations was in the proximal site. The large difference in the lifetimes of the unrelaxed and relaxed D+*QB-* states is attributed to the relaxation of protein residues and internal water molecules that stabilize D+*QB-*. These results demonstrate energetically significant conformational changes involved in stabilizing the D+*QB-* state. The unrelaxed and relaxed states can be considered to be the initial and final states along the reaction coordinate for conformationally gated electron transfer.

  11. Electrooptical Absorption Measurements (EOAM) Testify Existence of two Conformers of Prodan and Laurdan with Different Dipole Moments in Equilibrium Ground and Franck-Condon Excited State.

    Science.gov (United States)

    Nemkovich, N A; Detert, H; Roeder, N

    2016-09-01

    The results from the electrooptical absorption measurements (EOAM) on the equilibrium ground and excited Franck-Condon state dipole moments of Prodan and Laurdan in 1,4-dioxane are presented. As follows from experiments Prodan and Laurdan in the equilibrium ground and excited Franck-Condon state have two conformers with considerably different dipole moments. The electrical dipole moments and the transition dipole moment, obtained from the short-wavelength region of the absorption spectrum are parallel. The electrical dipole moments measured at the long-wavelength spectral region are parallel to each other but not parallel to the transition dipole moment m a. The angle θ between the transition dipole moment m a and the dipole moment in the equilibrium ground state μ g of the long-wavelength conformer is about 30(0) for both probes. Obtained results evidence that donor-acceptor pairs of the short-wavelength and long-wavelength conformers are not located on the same axis. Two low-energy conformers of Prodan have been found by density functional theory (DFT) calculations, differing in the orientation of the carbonyl group towards the naphthalene system.

  12. Cavity as a source of conformational fluctuation and high-energy state: High-pressure NMR study of a cavity-enlarged mutant of T4 lysozyme

    CERN Document Server

    Maeno, Akihiro; Hirata, Fumio; Otten, Renee; Dahlquist, Frederick W; Yokoyama, Shigeyuki; Akasaka, Kazuyuki; Mulder, Frans A A; Kitahara, Ryo

    2014-01-01

    Although the structure, function, conformational dynamics, and controlled thermodynamics of proteins are manifested by their corresponding amino acid sequences, the natural rules for molecular design and their corresponding interplay remain obscure. In this study, we focused on the role of internal cavities of proteins in conformational dynamics. We investigated the pressure-induced responses from the cavity-enlarged L99A mutant of T4 lysozyme, using high-pressure NMR spectroscopy. The signal intensities of the methyl groups in the 1H/13C HSQC spectra, particularly those around the enlarged cavity, decreased with the increasing pressure, and disappeared at 200 MPa, without the appearance of new resonances, thus indicating the presence of heterogeneous conformations around the cavity within the ground state ensemble. Above 200 MPa, the signal intensities of more than 20 methyl groups gradually decreased with the increasing pressure, without the appearance of new resonances. Interestingly, these residues closel...

  13. Physicochemical analyses of a bioactive 4-aminoantipyrine analogue - synthesis, crystal structure, solid state interactions, antibacterial, conformational and docking studies.

    Science.gov (United States)

    Alam, Mohammad Sayed; Lee, Dong-Ung

    2016-01-01

    A novel Schiff base derivative of 4-aminoantipyrine, that is, (E)-4-(2-methoxybenzylideneamino)-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H)-one (MBA-dMPP), was synthesized and characterized by FT-IR, (1)H-NMR, and EI-MS. Single-crystal X-ray diffraction data revealed MBA-dMPP adopts a trans configuration around its central C=N double bond, and forms orthorhombic crystals. XRD revealed that MBA-dMPP possess two different planes, in which the pyrazolone and benzylidene groups attached to C9 of the pyrazolone ring are almost coplanar and the phenyl ring connected to the N1 atom of the pyrazolone moiety lies in another plane. The intermolecular, host-guest C-H…O, C-H…N, and C-H…C van der Waals interactions were found to form a 3D network and confer stability to the MBA-dMPP crystal structure. The quantitative and qualitative solid state behaviors of MBA-dMPP were subjected to 3D Hirshfeld surface analysis and 2D fingerprint plotting. Reciprocal H…H contacts contributed most (52.9 %) to the Hirshfeld surface, followed by C…H/H…C contacts (30.2 %), whereas, O…H/H…O and N…H/H…N interactions contributed 15.5 % to the Hirshfeld surface. Electrostatic potentials were mapped over the Hirshfeld surface to analyze electrostatic complementarities within the MBA-dMPP crystal. In addition, geometrical descriptors were also analyzed to the extent of surface interactions. MBA-dMPP was also investigated for in vitro antibacterial activity against Gram-positive and Gram-negative bacterial strains, and showed highest activity against Bacillus cereus (MIC = 12.5 μg mL(-1)) and Salmonellatythimurium (MIC = 50 μg mL(-1)). In silico screening was conducted by docking MBA-dMPP on the active site of S12 bacterial protein (an important therapeutic target of antibacterial agents) and its binding properties were compared with those of ciprofloxacin. Moreover, a field points map of MBA-dMPP ligand was studied to determine electrostatic and van der Waals forces, hydrophobic

  14. Physicochemical analyses of a bioactive 4-aminoantipyrine analogue - synthesis, crystal structure, solid state interactions, antibacterial, conformational and docking studies

    Science.gov (United States)

    Alam, Mohammad Sayed; Lee, Dong-Ung

    2016-01-01

    A novel Schiff base derivative of 4-aminoantipyrine, that is, (E)-4-(2-methoxybenzylideneamino)-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H)-one (MBA-dMPP), was synthesized and characterized by FT-IR, 1H-NMR, and EI-MS. Single-crystal X-ray diffraction data revealed MBA-dMPP adopts a trans configuration around its central C=N double bond, and forms orthorhombic crystals. XRD revealed that MBA-dMPP possess two different planes, in which the pyrazolone and benzylidene groups attached to C9 of the pyrazolone ring are almost coplanar and the phenyl ring connected to the N1 atom of the pyrazolone moiety lies in another plane. The intermolecular, host-guest C-H…O, C-H…N, and C-H…C van der Waals interactions were found to form a 3D network and confer stability to the MBA-dMPP crystal structure. The quantitative and qualitative solid state behaviors of MBA-dMPP were subjected to 3D Hirshfeld surface analysis and 2D fingerprint plotting. Reciprocal H…H contacts contributed most (52.9 %) to the Hirshfeld surface, followed by C…H/H…C contacts (30.2 %), whereas, O…H/H…O and N…H/H…N interactions contributed 15.5 % to the Hirshfeld surface. Electrostatic potentials were mapped over the Hirshfeld surface to analyze electrostatic complementarities within the MBA-dMPP crystal. In addition, geometrical descriptors were also analyzed to the extent of surface interactions. MBA-dMPP was also investigated for in vitro antibacterial activity against Gram-positive and Gram-negative bacterial strains, and showed highest activity against Bacillus cereus (MIC = 12.5 μg mL-1) and Salmonella tythimurium (MIC = 50 μg mL-1). In silico screening was conducted by docking MBA-dMPP on the active site of S12 bacterial protein (an important therapeutic target of antibacterial agents) and its binding properties were compared with those of ciprofloxacin. Moreover, a field points map of MBA-dMPP ligand was studied to determine electrostatic and van der Waals forces, hydrophobic potentials

  15. Structure and Dynamics Study of LeuT Using the Markov State Model and Perturbation Response Scanning Reveals Distinct Ion Induced Conformational States.

    Science.gov (United States)

    Asciutto, Eliana K; Gedeon, Patrick C; General, Ignacio J; Madura, Jeffry D

    2016-08-25

    The bacterial leucine transporter (LeuT), a close homologue of the eukaryote monoamine transporters (MATs), currently serves as a powerful template for computer simulations of MATs. Transport of the amino acid leucine through the membrane is made possible by the sodium electrochemical potential. Recent reports indicate that the substrate transport mechanism is based on structural changes such as hinge movements of key transmembrane domains. In order to further investigate the role of sodium ions in the uptake of leucine, here we present a Markov state model analysis of atomistic simulations of lipid embedded LeuT in different environments, generated by varying the presence of binding pocket sodium ions and substrate. Six metastable conformations are found, and structural differences between them along with transition probabilities are determined. We complete the analysis with the implementation of perturbation response scanning on our system, determining the most sensitive and influential regions of LeuT, in each environment. Our results show that the occupation of sites Na1 and Na2, along with the presence of the substrate, selectively influences the geometry of LeuT. In particular, the occupation of each site Na1/Na2 has strong effects (in terms of changes in influence and/or sensitivity, as compared to the case without ions) in specific regions of LeuT, and the effects are different for simultaneous occupation. Our results strengthen the rationale and provide a conformational mechanism for a putative transport mechanism in which Na2 is necessary, but may not be sufficient, to initiate and stabilize extracellular substrate access to the binding pocket.

  16. 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...

  17. 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

  18. 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.

  19. The Role of TM5 in Na2 Release and the Conformational Transition of Neurotransmitter:Sodium Symporters toward the Inward-Open State.

    Science.gov (United States)

    Stolzenberg, Sebastian; Li, Zheng; Quick, Matthias; Malinauskaite, Lina; Nissen, Poul; Weinstein, Harel; Javitch, Jonathan A; Shi, Lei

    2017-03-20

    Neurotransmitter:sodium symporters (NSS) terminate neurotransmission by the reuptake of released neurotransmitters. This active accumulation of substrate against its concentration gradient is driven by the transmembrane Na+ gradient and requires that the transporter traverses several conformational states. LeuT, a prokaryotic NSS homolog, has been crystallized in outward-open, outward-occluded and inward-open states. Two crystal structures of another prokaryotic NSS homolog, the multi-hydrophobic amino acid transporter (MhsT) from Bacillus halodurans have been resolved in novel inward-occluded states, with the extracellular vestibule closed and the intracellular portion of TM5 (TM5i) in either an unwound or a helical conformation. We have investigated the potential involvement of TM5i in binding and unbinding of Na2, i.e. the Na(+) bound in the Na2 site, by carrying out comparative molecular dynamics simulations of the models derived from the two MhsT structures. We find that the helical TM5i conformation is associated with a higher propensity for Na2 release, which leads to the repositioning of the N terminus (NT) and transition to an inward-open state. By using comparative interaction network analysis, we also identify allosteric pathways connecting TM5i and the Na2 binding site to the extracellular and intracellular regions. Based on our combined computational and mutagenesis studies of MhsT and LeuT, we propose that TM5i plays a key role in Na2 binding and release associated with the conformational transition toward the inward-open state, a role that is likely to be shared across the NSS family.

  20. Conformism and Wealth Distribution

    OpenAIRE

    Mino, Kazuo; Nakamoto, Yasuhiro

    2014-01-01

    This paper explores the role of consumption externalities in a neoclassical growth model in which households have heterogeneous preferences. We fi?nd that the degree of conformism in consumption held by each household signifi?cantly affects the speed of convergence of the aggregate economy as well as the patterns of wealth distribution in the steady state equilibrium. In particular, a higher degree of consumption conformism accelerates the convergence speed of the economy towards the steady s...

  1. Using attenuated total reflection Fourier transform infrared spectroscopy (ATR FT-IR) to study the molecular conformation of parchment artifacts in different macroscopic states.

    Science.gov (United States)

    Gonzalez, Lee; Wade, Matthew; Bell, Nancy; Thomas, Kate; Wess, Tim

    2013-02-01

    Maintaining appropriate temperatures and relative humidity is considered essential to extending the useful life of parchment artifacts. Although the relationship between environmental factors and changes to the physical state of artifacts is reasonably understood, an improved understanding of the relationship between the molecular conformation and changes to the macroscopic condition of parchment is needed to optimize environmental conditions. Using Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR FT-IR) analysis, the conformation of the molecular structure in selected parchment samples with specific macroscopic conditions, typically discoloration and planar deformations (e.g., cockling and tearing), have been made. The results of this investigation showed that the Fourier transform infrared signal differs for parchment samples exhibiting different macroscopic conditions. In areas exhibiting planar deformation, a change in the Fourier Transform Infrared signal was observed that indicates unfolding of the molecular conformation. In comparison, the discolored samples showed a change in molecular conformation that indicates a chemical change within the collagen molecular structure. This paper discusses the possible causal associations and implications of these findings for the conservation and preservation of parchment artifacts.

  2. Conformational states of syntaxin-1 govern the necessity of N-peptide binding in exocytosis of PC12 cells and Caenorhabditis elegans.

    Science.gov (United States)

    Park, Seungmee; Bin, Na-Ryum; Michael Rajah, Maaran; Kim, Byungjin; Chou, Ting-Chieh; Kang, Soo-Young Ann; Sugita, Kyoko; Parsaud, Leon; Smith, Matthew; Monnier, Philippe P; Ikura, Mitsuhiko; Zhen, Mei; Sugita, Shuzo

    2016-02-15

    Syntaxin-1 is the central SNARE protein for neuronal exocytosis. It interacts with Munc18-1 through its cytoplasmic domains, including the N-terminal peptide (N-peptide). Here we examine the role of the N-peptide binding in two conformational states ("closed" vs. "open") of syntaxin-1 using PC12 cells and Caenorhabditis elegans. We show that expression of "closed" syntaxin-1A carrying N-terminal single point mutations (D3R, L8A) that perturb interaction with the hydrophobic pocket of Munc18-1 rescues impaired secretion in syntaxin-1-depleted PC12 cells and the lethality and lethargy of unc-64 (C. elegans orthologue of syntaxin-1)-null mutants. Conversely, expression of the "open" syntaxin-1A harboring the same mutations fails to rescue the impairments. Biochemically, the L8A mutation alone slightly weakens the binding between "closed" syntaxin-1A and Munc18-1, whereas the same mutation in the "open" syntaxin-1A disrupts it. Our results reveal a striking interplay between the syntaxin-1 N-peptide and the conformational state of the protein. We propose that the N-peptide plays a critical role in intracellular trafficking of syntaxin-1, which is dependent on the conformational state of this protein. Surprisingly, however, the N-peptide binding mode seems dispensable for SNARE-mediated exocytosis per se, as long as the protein is trafficked to the plasma membrane.

  3. Multiple conformational states of a new hematopoietic cytokine (megakaryocyte growth and development factor): pH- and urea-induced denaturation.

    Science.gov (United States)

    Hamburger, J B; Chen, E; Narhi, L O; Wu, G M; Brems, D N

    1998-09-01

    The effect of pH and urea on the conformation of recombinant human megakaryocyte growth and development factor (rHuMGDF) was determined by circular dichroism, intrinsic fluorescence spectroscopy, and equilibrium ultracentrifugation. The conformation of rHuMGDF was dependent on pH and urea concentration. Multiple folding forms were evidenced by multiple pH-induced transitions and urea-induced equilibrium transitions that deviated from a simple two-state process. In neutral to alkaline pH, rHuMGDF exists as a monomer, but an acid-induced conformational state self-associates to form a soluble aggregate. A folding intermediate(s) was observed with a more stable secondary structure than tertiary structure and was dependent on the pH of the urea-induced denaturation. The differences in the stabilities of the folding states were most distinct in the pH range of 4.5 to 6.5. The presence of intermediates in the folding pathway of rHuMGDF are similar to findings of previous studies of related growth factors that share a common three-dimensional structure.

  4. 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.

  5. Conformal Infinity

    Science.gov (United States)

    Frauendiener, Jörg

    2004-12-01

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

  6. 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.

  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. Conformational states of Ras complexed with the GTP analogue GppNHp or GppCH2p: implications for the interaction with effector proteins.

    Science.gov (United States)

    Spoerner, Michael; Nuehs, Andrea; Ganser, Petra; Herrmann, Christian; Wittinghofer, Alfred; Kalbitzer, Hans Robert

    2005-02-15

    The guanine nucleotide-binding protein Ras occurs in solution in two different states, state 1 and state 2, when the GTP analogue GppNHp is bound to the active center as detected by (31)P NMR spectroscopy. Here we show that Ras(wt).Mg(2+).GppCH(2)p also exists in two conformational states in dynamic equilibrium. The activation enthalpy DeltaH(++)(12) and the activation entropy DeltaS(++)(12) for the transition from state 1 to state 2 are 70 kJ mol(-1) and 102 J mol(-1) K(-1), within the limits of error identical to those determined for the Ras(wt).Mg(2+).GppNHp complex. The same is true for the equilibrium constants K(12) = [2]/[1] of 2.0 and the corresponding DeltaG(12) of -1.7 kJ mol(-1) at 278 K. This excludes a suggested specific effect of the NH group of GppNHp on the equilibrium. The assignment of the phosphorus resonance lines of the bound analogues has been done by two-dimensional (31)P-(31)P NOESY experiments which lead to a correction of the already reported assignments of bound GppNHp. Mutation of Thr35 in Ras.Mg(2+).GppCH(2)p to serine leads to a shift of the conformational equilibrium toward state 1. Interaction of the Ras binding domain (RBD) of Raf kinase or RalGDS with Ras(wt) or Ras(T35S) shifts the equilibrium completely to state 2. The (31)P NMR experiments suggest that, besides the type of the side chain of residue 35, a main contribution to the conformational equilibrium in Ras complexes with GTP and GTP analogues is the effective acidity of the gamma-phosphate group of the bound nucleotide. A reaction scheme for the Ras-effector interaction is presented which includes the existence of two conformations of the effector loop and a weak binding state.

  9. Structure of the HIV-1 Full-Length Capsid Protein in a Conformationally Trapped Unassembled State Induced by Small-Molecule Binding

    Energy Technology Data Exchange (ETDEWEB)

    Du, Shoucheng; Betts, Laurie; Yang, Ruifeng; Shi, Haibin; Concel, Jason; Ahn, Jinwoo; Aiken, Christopher; Zhang, Peijun; Yeh, Joanne I. (Pitt); (Vanderbilt); (UNC)

    2012-11-26

    The capsid (CA) protein plays crucial roles in HIV infection and replication, essential to viral maturation. The absence of high-resolution structural data on unassembled CA hinders the development of antivirals effective in inhibiting assembly. Unlike enzymes that have targetable, functional substrate-binding sites, the CA does not have a known site that affects catalytic or other innate activity, which can be more readily targeted in drug development efforts. We report the crystal structure of the HIV-1 CA, revealing the domain organization in the context of the wild-type full-length (FL) unassembled CA. The FL CA adopts an antiparallel dimer configuration, exhibiting a domain organization sterically incompatible with capsid assembly. A small compound, generated in situ during crystallization, is bound tightly at a hinge site ('H site'), indicating that binding at this interdomain region stabilizes the ADP conformation. Electron microscopy studies on nascent crystals reveal both dimeric and hexameric lattices coexisting within a single condition, in agreement with the interconvertibility of oligomeric forms and supporting the feasibility of promoting assembly-incompetent dimeric states. Solution characterization in the presence of the H-site ligand shows predominantly unassembled dimeric CA, even under conditions that promote assembly. Our structure elucidation of the HIV-1 FL CA and characterization of a potential allosteric binding site provides three-dimensional views of an assembly-defective conformation, a state targeted in, and thus directly relevant to, inhibitor development. Based on our findings, we propose an unprecedented means of preventing CA assembly, by 'conformationally trapping' CA in assembly-incompetent conformational states induced by H-site binding.

  10. Xanthan Exopolysaccharide: Cu(2+) Complexes Affected from the pH-Dependent Conformational State; Implications for Environmentally Relevant Biopolymers.

    Science.gov (United States)

    Causse, Benjamin; Spadini, Lorenzo; Sarret, Géraldine; Faure, Adeline; Travelet, Christophe; Madern, Dominique; Delolme, Cécile

    2016-04-05

    The conformational impact of environmental biopolymers on metal sorption was studied through Cu sorption on xanthan. The apparent Cu(2+) complexation constant (logK; Cu(2+) + L(-) ↔ CuL(+)) decreased from 2.9 ± 0.1 at pH 3.5 to 2.5 ± 0.1 at pH 5.5 (ionic strength I = 0.1). This behavior is in apparent contradiction with basic thermodynamics, as usually the higher the pH the more cations bind. Our combined titration, circular dichroism and dynamic light scattering study indicated that the change observed in Cu bond strength relates to a conformational change of the structure of xanthan, which generates more chelating sites at pH 3.5 than at pH 5.5. This hypothesis was validated by the fact that the Cu sorption constants on xanthan were always higher than those measured on a mixture of pyruvic and glucuronic acids (logK = 2.2), which are the two constitutive ligands present in the xanthan monomer. This study shows the role of the structural conformation of natural biopolymers in metal bond strength. This finding may help to better predict the fate of Cu and other metals in acidic environmental settings such as aquatic media affected by acid mine drainage, as well as peats and acidic soils, and to better define optimal conditions for bioremediation processes.

  11. Conformational Plasticity of the Cell-Penetrating Peptide SAP As Revealed by Solid-State (19)F-NMR and Circular Dichroism Spectroscopies.

    Science.gov (United States)

    Afonin, Sergii; Kubyshkin, Vladimir; Mykhailiuk, Pavel K; Komarov, Igor V; Ulrich, Anne S

    2017-07-13

    The cell-penetrating peptide SAP, which was designed as an amphipathic poly-l-proline helix II (PPII), was suggested to self-assemble into regular fibrils that are relevant for its internalization. Herein we have analyzed the structure of SAP in the membrane-bound state by solid-state (19)F-NMR, which revealed other structural states, in addition to the expected surface-aligned PPII. Trifluoromethyl-bicyclopentyl-glycine (CF3-Bpg) and two rigid isomers of trifluoromethyl-4,5-methanoprolines (CF3-MePro) were used as labels for (19)F-NMR analysis. The equilibria between different conformations of SAP were studied and were found to be shifted by the substituents at Pro-11. Synchrotron-CD results suggested that substituting Pro-11 by CF3-MePro governed the coil-to-PPII equilibrium in solution and in the presence of a lipid bilayer. Using CD and (19)F-NMR, we examined the slow kinetics of the association of SAP with membranes and the dependence of the SAP conformational dynamics on the lipid composition. The peptide did not bind to lipids in the solid ordered phase and aggregated only in the liquid ordered "raft"-like bilayers. Self-association could not be detected in solution or in the presence of liquid disordered membranes. Surface-bound amphipathic SAP in a nonaggregated state was structured as a mixture of nonideal extended conformations reflecting the equilibrium already present in solution, i.e., before binding to the membrane.

  12. Computational Replication of the Primary Isotope Dependence of Secondary Kinetic Isotope Effects in Solution Hydride Transfer Reactions: Supporting the Isotopically Different Tunneling Ready State Conformations

    OpenAIRE

    2016-01-01

    We recently reported a study of the steric effect on the 1° isotope dependence of 2° KIEs for several hydride transfer reactions in solution (J. Am. Chem. Soc. 2015, 137, 6653). The unusual 2° KIEs decrease as the 1° isotope changes from H to D, and more in the sterically hindered systems. These were explained in terms of a more crowded tunneling ready state (TRS) conformation in D-tunneling, which has a shorter donor-acceptor distance (DAD), than in H-tunneling. In order to examine the isoto...

  13. An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase

    Science.gov (United States)

    Matthes, Dirk; Gapsys, Vytautas; Brennecke, Julian T.; de Groot, Bert L.

    2016-09-01

    The formation of well-defined filamentous amyloid structures involves a polydisperse collection of oligomeric states for which relatively little is known in terms of structural organization. Here we use extensive, unbiased explicit solvent molecular dynamics (MD) simulations to investigate the structural and dynamical features of oligomeric aggregates formed by a number of highly amyloidogenic peptides at atomistic resolution on the μs time scale. A consensus approach has been adopted to analyse the simulations in multiple force fields, yielding an in-depth characterization of pre-fibrillar oligomers and their global and local structure properties. A collision cross section analysis revealed structurally heterogeneous aggregate ensembles for the individual oligomeric states that lack a single defined quaternary structure during the pre-nucleation phase. To gain insight into the conformational space sampled in early aggregates, we probed their substructure and found emerging β-sheet subunit layers and a multitude of ordered intermolecular β-structure motifs with growing aggregate size. Among those, anti-parallel out-of-register β-strands compatible with toxic β-barrel oligomers were particularly prevalent already in smaller aggregates and formed prior to ordered fibrillar structure elements. Notably, also distinct fibril-like conformations emerged in the oligomeric state and underscore the notion that pre-nucleated oligomers serve as a critical intermediate step on-pathway to fibrils.

  14. Characterization of cerebral glucose dynamics in vivo with a four-state conformational model of transport at the blood-brain barrier.

    Science.gov (United States)

    Duarte, João M N; Gruetter, Rolf

    2012-05-01

    Determination of brain glucose transport kinetics in vivo at steady-state typically does not allow distinguishing apparent maximum transport rate (T(max)) from cerebral consumption rate. Using a four-state conformational model of glucose transport, we show that simultaneous dynamic measurement of brain and plasma glucose concentrations provide enough information for independent and reliable determination of the two rates. In addition, although dynamic glucose homeostasis can be described with a reversible Michaelis-Menten model, which is implicit to the large iso-inhibition constant (K(ii)) relative to physiological brain glucose content, we found that the apparent affinity constant (K(t)) was better determined with the four-state conformational model of glucose transport than with any of the other models tested. Furthermore, we confirmed the utility of the present method to determine glucose transport and consumption by analysing the modulation of both glucose transport and consumption by anaesthesia conditions that modify cerebral activity. In particular, deep thiopental anaesthesia caused a significant reduction of both T(max) and cerebral metabolic rate for glucose consumption. In conclusion, dynamic measurement of brain glucose in vivo in function of plasma glucose allows robust determination of both glucose uptake and consumption kinetics.

  15. A CONFORMATIONAL ELASTICITY THEORY

    Institute of Scientific and Technical Information of China (English)

    1998-01-01

    A new statistical theory based on the rotational isomeric state model describing the chain conformational free energy has been proposed. This theory can be used to predict different tensions of rubber elongation for chemically different polymers, and the energy term during the elongation of natural rubber coincides with the experimental one.

  16. Conformational Transitions

    Science.gov (United States)

    Czerminski, Ryszard; Roitberg, Adrian; Choi, Chyung; Ulitsky, Alexander; Elber, Ron

    1991-10-01

    Two computational approaches to study plausible conformations of biological molecules and the transitions between them are presented and discussed. The first approach is a new search algorithm which enhances the sampling of alternative conformers using a mean field approximation. It is argued and demonstrated that the mean field approximation has a small effect on the location of the minima. The method is a combination of the LES protocol (Locally Enhanced Sampling) and simulated annealing. The LES method was used in the past to study the diffusion pathways of ligands from buried active sites in myoglobin and leghemoglobin to the exterior of the protein. The present formulation of LES and its implementation in a Molecular Dynamics program is described. An application for side chain placement in a tetrapeptide is presented. The computational effort associated with conformational searches using LES grows only linearly with the number of degrees of freedom, whereas in the exact case the computational effort grows exponentially. Such saving is of course associated with a mean field approximation. The second branch of studies pertains to the calculation of reaction paths in large and flexible biological systems. An extensive mapping of minima and barriers for two different tetrapeptides is calculated from the known minima and barriers of alanine tetrapeptide which we calculated recently.1 The tetrapeptides are useful models for the formation of secondary structure elements since they are the shortest possible polymers of this type which can still form a complete helical turn. The tetrapeptides are isobutyryl-val(χ1=60)-ala-ala and isobutyryl-val(χ1=-60)-ala-ala. Properties of the hundreds of minima and of the hundreds intervening barriers are discussed. Estimates for thermal transition times between the many conformers (and times to explore the complete phase space) are calculated and compared. It is suggested that the most significant effect of the side chain size is

  17. 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.

  18. A mutational mimic analysis of histone H3 post-translational modifications: specific sites influence the conformational state of H3/H4, causing either positive or negative supercoiling of DNA.

    Science.gov (United States)

    White, Rachel H; Keberlein, Melissa; Jackson, Vaughn

    2012-10-16

    Histone H3 has specific sites of post-translational modifications that serve as epigenetic signals to cellular machinery to direct various processes. Mutational mimics of these modifications (glutamine for acetylation, methionine and leucine for methylation, and glutamic acid for phosphorylation) were constructed at the relevant sites of the major histone variant, H3.2, and their effects on the conformational equilibrium of the H3/H4 tetramer at physiological ionic strength were determined when bound to or free of DNA. The deposition vehicle used for this analysis was NAP1, nucleosome assembly protein 1. Acetylation mimics in the N-terminus preferentially stabilized the left-handed conformer (DNA negatively supercoiled), and mutations within the globular region preferred the right-handed conformer (DNA positively supercoiled). The methylation mimics in the N-terminus tended to maintain characteristics similar to those of wild-type H3/H4; i.e., the conformational equilibrium maintains similar levels of both left- and right-handed conformers. Phosphorylation mimics facilitated a mixed effect, i.e., when at serines, the left-handed conformer, and at threonines, a mixture of both conformers. When double mutations were present, the conformational equilibrium was shifted dramatically, either leftward or rightward depending on the specific sites. In contrast, these mutations tended not to affect the direction and extent of supercoiling for variants H3.1 and H3.3. Variant H3.3 promoted only the left-handed conformer, and H3.1 tended to maintain both conformers. Additional experiments indicate the importance of a propagation mechanism for ensuring the formation of a particular superhelical state over an extended region of the DNA. The potential relevance of these results to the maintenance of epigenetic information on a gene is discussed.

  19. Ultrafast laser control of vibrational dynamics for a two-dimensional model of HONO 2 in the ground electronic state: separation of conformers, control of the bond length, selective preparation of the discrete and the continuum states

    Science.gov (United States)

    Oppel, M.; Paramonov, G. K.

    1998-06-01

    Selective excitation of the vibrational bound and the continuum states, controlled by subpicosecond infrared (IR) laser pulses, is simulated within the Schrödinger wave function formalism for a two-dimensional model of the HONO 2 molecule in the ground electronic state. State-selective excitation of the OH bond is achieved by single optimal laser pulses, with the probability being 97% for the bound states and more than 91% for the resonances. Stable, long-living continuum states are prepared with more than 96% probability by two optimal laser pulses, with the expectation energy of the molecule being well above the dissociation threshold of the ON single bond, and its life-time being at least 100 ps. The length of the ON single bond can be controlled selectively: stretching and contraction by about 45% of its equilibrium length are demonstrated. Laser separation of spatial conformers of HONO 2 in inhomogeneous conditions occurring on an anisotropic surface or created by a direct current (DC) electric field is analysed. The relative yields of target conformers may be very high, ranging from 10 to 10 8, and the absolute yields of up to 40% and more are calculated.

  20. 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...

  1. 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...

  2. Printable Solid-State Lithium-Ion Batteries: A New Route toward Shape-Conformable Power Sources with Aesthetic Versatility for Flexible Electronics.

    Science.gov (United States)

    Kim, Se-Hee; Choi, Keun-Ho; Cho, Sung-Ju; Choi, Sinho; Park, Soojin; Lee, Sang-Young

    2015-08-12

    Forthcoming flexible/wearable electronic devices with shape diversity and mobile usability garner a great deal of attention as an innovative technology to bring unprecedented changes in our daily lives. From the power source point of view, conventional rechargeable batteries (one representative example is a lithium-ion battery) with fixed shapes and sizes have intrinsic limitations in fulfilling design/performance requirements for the flexible/wearable electronics. Here, as a facile and efficient strategy to address this formidable challenge, we demonstrate a new class of printable solid-state batteries (referred to as "PRISS batteries"). Through simple stencil printing process (followed by ultraviolet (UV) cross-linking), solid-state composite electrolyte (SCE) layer and SCE matrix-embedded electrodes are consecutively printed on arbitrary objects of complex geometries, eventually leading to fully integrated, multilayer-structured PRISS batteries with various form factors far beyond those achievable by conventional battery technologies. Tuning rheological properties of SCE paste and electrode slurry toward thixotropic fluid characteristics, along with well-tailored core elements including UV-cured triacrylate polymer and high boiling point electrolyte, is a key-enabling technology for the realization of PRISS batteries. This process/material uniqueness allows us to remove extra processing steps (related to solvent drying and liquid-electrolyte injection) and also conventional microporous separator membranes, thereupon enabling the seamless integration of shape-conformable PRISS batteries (including letters-shaped ones) into complex-shaped objects. Electrochemical behavior of PRISS batteries is elucidated via an in-depth analysis of cell impedance, which provides a theoretical basis to enable sustainable improvement of cell performance. We envision that PRISS batteries hold great promise as a reliable and scalable platform technology to open a new concept of cell

  3. Conformational instability of the lowest triplet state of the benzene nucleus: II. p-Xylene, the influence of substituents

    NARCIS (Netherlands)

    J.H. van der Waals; M.C. van Hemert; W.J. Buma

    1990-01-01

    A calculation of the potential-energy surface of the lowest triplet state of p-xylene as a function of the S8(,) distortion coordinate of the benzene skeleton has been made to learn more about the influence of substituents on the vibronically induced distortion of benzene in its metastable triplet s

  4. Conformational changes in biopolymers

    Science.gov (United States)

    Ivanov, Vassili

    2005-12-01

    Biopolymer conformational changes are involved in many biological processes. This thesis summarizes some theoretical and experimental approaches which I have taken at UCLA to explore conformational changes in biopolymers. The reversible thermal denaturation of the DNA double helix is, perhaps, the simplest example of biopolymer conformational change. I have developed a statistical mechanics model of DNA melting with reduced degrees of freedom, which allows base stacking interaction to be taken into account and treat base pairing and stacking separately. Unlike previous models, this model describes both the unpairing and unstacking parts of the experimental melting curves and explains the observed temperature dependence of the effective thermodynamic parameters used in models of the nearest neighbor type. I developed a basic kinetic model for irreversible thermal denaturation of F-actin, which incorporates depolymerization of F-actin from the ends and breaking of F-actin fiber in the middle. The model explains the cooperativity of F-actin thermal denaturation observed by D. Pavlov et al. in differential calorimetry measurements. CG-rich DNA sequences form left-handed Z-DNA at high ionic strength or upon binding of polyvalent ions and some proteins. I studied experimentally the B-to-Z transition of the (CG)6 dodecamer. Improvement of the locally linearized model used to interpret the data gives evidence for an intermediate state in the B-to-Z transition of DNA, contrary to previous research on this subject. In the past 15 years it has become possible to study the conformational changes of biomolecules using single-molecule techniques. In collaboration with other lab members I performed a single-molecule experiment, where we monitored the displacement of a micrometer-size bead tethered to a surface by a DNA probe undergoing the conformational change. This technique allows probing of conformational changes with subnanometer accuracy. We applied the method to detect

  5. Molecular Dynamics Simulation and Experimental Studies on the Visual Pigment Rhodopsin: Multiple Conformational States and Structural Changes

    CERN Document Server

    Kholmurodov, Kh T; Ostrovsky, M A; Biochemical Physics Institute, Russian Academy of Sciences, Moscow, Russia

    2005-01-01

    Based on the MD simulations with a supercomputer and the special-purposes MDGRAPE-2 machine we have performed 3-ns MD calculations on the rhodopsin molecule and presented the structure analysis data for its dark-adapted state. We have fulfilled the RMSD (root-mean-square deviation) and structural analysis for the rhodopsin (with 11-\\textit{cis} retinal), generated the pictures of the atomic-scale processes for the binding pocket, surrounding the chromophore retinal, and compared the helical deviations for the beta-ionone ring and Schiff base linkage regions of the protein. The most remarkable point of our observations is that the rhodopsin helical distortions in the dark state are accompanied with the transformation of the retinal chromophore, viz. with the rotation of the beta-ionone ring inside the protein binding pocket. The low-temperature absorption spectroscopy technique has been used to study the primary stages of rhodopsin photolysis. The structural transformation properties of rhodopsin were discusse...

  6. Conformal Complementarity Maps

    CERN Document Server

    Barbón, José L F

    2013-01-01

    We study quantum cosmological models for certain classes of bang/crunch singularities, using the duality between expanding bubbles in AdS with a FRW interior cosmology and perturbed CFTs on de Sitter space-time. It is pointed out that horizon complementarity in the AdS bulk geometries is realized as a conformal transformation in the dual deformed CFT. The quantum version of this map is described in full detail in a toy model involving conformal quantum mechanics. In this system the complementarity map acts as an exact duality between eternal and apocalyptic Hamiltonian evolutions. We calculate the commutation relation between the Hamiltonians corresponding to the different frames. It vanishes only on scale invariant states.

  7. Conforming the measured lifetimes of the $5d \\ ^2D_{3/2,5/2}$ states in Cs with theory

    CERN Document Server

    Sahoo, B K

    2015-01-01

    We find very good agreement between our theoretically evaluated lifetimes of the $5d \\ ^2D_{3/2}$ and $5d \\ ^2D_{5/2}$ states of Cs with the experimental values reported in [Phys. Rev. A {\\bf 57}, 4204 (1998)], which were earlier evinced to be disagreeing with an earlier rigorous theoretical study [Phys. Rev. A {\\bf 69}, 040501(R) (2004)] and with another precise measurement [Opt. Lett. {\\bf 21}, 74 (1996)]. In this work, we have carried out calculations of the radiative transition matrix elements using many variants of relativistic many-body methods, mainly in the coupled-cluster theory framework, and analyze propagation of the electron correlation effects to elucidate their roles for accurate evaluations of the matrix elements. We also demonstrate contributions explicitly from the Dirac-Coulomb interactions, frequency independent Breit interaction and lower order quantum electrodynamics (QED) effects. Uncertainties to these matrix elements due to different possible sources of errors are estimated. By combin...

  8. Conformal transformations and conformal invariance in gravitation

    CERN Document Server

    Dabrowski, Mariusz P; Blaschke, David B

    2008-01-01

    Conformal transformations are frequently used tools in order to study relations between various theories of gravity and Einstein relativity. Because of that, in this paper we discuss the rules of conformal transformations for geometric quantities in general relativity. In particular, we discuss the conformal transformations of the matter energy-momentum tensor. We thoroughly discuss the latter and show the subtlety of the conservation law (i.e., the geometrical Bianchi identity) imposed in one of the conformal frames in reference to the other. The subtlety refers to the fact that conformal transformation ``creates'' an extra matter term composed of the conformal factor which enters the conservation law. In an extreme case of the flat original spacetime the matter is ``created'' due to work done by the conformal transformation to bend the spacetime which was originally flat. We also discuss how to construct the conformally invariant gravity which, in the simplest version, is a special case of the Brans-Dicke t...

  9. NiCo2O4@TiN Core-shell Electrodes through Conformal Atomic Layer Deposition for All-solid-state Supercapacitors

    KAUST Repository

    Wang, Ruiqi

    2016-03-04

    Ternary transition metal oxides such as NiCo2O4 show great promise as supercapacitor electrode materials. However, the unsatisfactory rate performance of NiCo2O4 may prove to be a major hurdle to its commercial usage. Herein, we report the development of NiCo2O4@TiN core–shell nanostructures for all-solid-state supercapacitors with significantly enhanced rate capability. We demonstrate that a thin layer of TiN conformally grown by atomic layer deposition (ALD) on NiCo2O4 nanofiber arrays plays a key role in improving their electrical conductivity, mechanical stability, and rate performance. Fabricated using the hybrid NiCo2O4@TiN electrodes, the symmetric all-solid-state supercapacitor exhibited an impressive stack power density of 58.205 mW cm−3 at a stack energy density of 0.061 mWh cm−3. To the best of our knowledge, these values are the highest of any NiCo2O4-based all-solid-state supercapacitor reported. Additionally, the resulting NiCo2O4@TiN all-solid-state device displayed outstanding cycling stability by retaining 70% of its original capacitance after 20,000 cycles at a high current density of 10 mA cm−2. These results illustrate the promise of ALD-assisted hybrid NiCo2O4@TiN electrodes for sustainable and integrated energy storage applications.

  10. Rational design and validation of an anti-protein kinase C active-state specific antibody based on conformational changes

    Science.gov (United States)

    Pena, Darlene Aparecida; Andrade, Victor Piana de; Silva, Gabriela Ávila Fernandes; Neves, José Ivanildo; Oliveira, Paulo Sergio Lopes de; Alves, Maria Julia Manso; Devi, Lakshmi A.; Schechtman, Deborah

    2016-01-01

    Protein kinase C (PKC) plays a regulatory role in key pathways in cancer. However, since phosphorylation is a step for classical PKC (cPKC) maturation and does not correlate with activation, there is a lack of tools to detect active PKC in tissue samples. Here, a structure-based rational approach was used to select a peptide to generate an antibody that distinguishes active from inactive cPKC. A peptide conserved in all cPKCs, C2Cat, was chosen since modeling studies based on a crystal structure of PKCβ showed that it is localized at the interface between the C2 and catalytic domains of cPKCs in an inactive kinase. Anti-C2Cat recognizes active cPKCs at least two-fold better than inactive kinase in ELISA and immunoprecipitation assays, and detects the temporal dynamics of cPKC activation upon receptor or phorbol stimulation. Furthermore, the antibody is able to detect active PKC in human tissue. Higher levels of active cPKC were observed in the more aggressive triple negative breast cancer tumors as compared to the less aggressive estrogen receptor positive tumors. Thus, this antibody represents a reliable, hitherto unavailable and a valuable tool to study PKC activation in cells and tissues. Similar structure-based rational design strategies can be broadly applied to obtain active-state specific antibodies for other signal transduction molecules. PMID:26911897

  11. Rational design and validation of an anti-protein kinase C active-state specific antibody based on conformational changes.

    Science.gov (United States)

    Pena, Darlene Aparecida; Andrade, Victor Piana de; Silva, Gabriela Ávila Fernandes; Neves, José Ivanildo; Oliveira, Paulo Sergio Lopes de; Alves, Maria Julia Manso; Devi, Lakshmi A; Schechtman, Deborah

    2016-02-25

    Protein kinase C (PKC) plays a regulatory role in key pathways in cancer. However, since phosphorylation is a step for classical PKC (cPKC) maturation and does not correlate with activation, there is a lack of tools to detect active PKC in tissue samples. Here, a structure-based rational approach was used to select a peptide to generate an antibody that distinguishes active from inactive cPKC. A peptide conserved in all cPKCs, C2Cat, was chosen since modeling studies based on a crystal structure of PKCβ showed that it is localized at the interface between the C2 and catalytic domains of cPKCs in an inactive kinase. Anti-C2Cat recognizes active cPKCs at least two-fold better than inactive kinase in ELISA and immunoprecipitation assays, and detects the temporal dynamics of cPKC activation upon receptor or phorbol stimulation. Furthermore, the antibody is able to detect active PKC in human tissue. Higher levels of active cPKC were observed in the more aggressive triple negative breast cancer tumors as compared to the less aggressive estrogen receptor positive tumors. Thus, this antibody represents a reliable, hitherto unavailable and a valuable tool to study PKC activation in cells and tissues. Similar structure-based rational design strategies can be broadly applied to obtain active-state specific antibodies for other signal transduction molecules.

  12. Conformal isoparametric hypersurfaces with two distinct conformal principal curvatures in conformal space

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The conformal geometry of regular hypersurfaces in the conformal space is studied.We classify all the conformal isoparametric hypersurfaces with two distinct conformal principal curvatures in the conformal space up to conformal equivalence.

  13. Conformational heterogeneity of the SAM-I riboswitch transcriptional ON state: a chaperone-like role for S-adenosyl methionine.

    Science.gov (United States)

    Huang, Wei; Kim, Joohyun; Jha, Shantenu; Aboul-Ela, Fareed

    2012-05-18

    Riboswitches are promising targets for the design of novel antibiotics and engineering of portable genetic regulatory elements. There is evidence that variability in riboswitch properties allows tuning of expression for genes involved in different stages of biosynthetic pathways by mechanisms that are not currently understood. Here, we explore the mechanism for tuning of S-adenosyl methionine (SAM)-I riboswitch folding. Most SAM-I riboswitches function at the transcriptional level by sensing the cognate ligand SAM. SAM-I riboswitches orchestrate the biosynthetic pathways of cysteine, methionine, SAM, and so forth. We use base-pair probability predictions to examine the secondary-structure folding landscape of several SAM-I riboswitch sequences. We predict different folding behaviors for different SAM-I riboswitch sequences. We identify several "decoy" base-pairing interactions involving 5' riboswitch residues that can compete with the formation of a P1 helix, a component of the ligand-bound "transcription OFF" state, in the absence of SAM. We hypothesize that blockage of these interactions through SAM contacts contributes to stabilization of the OFF state in the presence of ligand. We also probe folding patterns for a SAM-I riboswitch RNA using constructs with different 3' truncation points experimentally. Folding was monitored through fluorescence, susceptibility to base-catalyzed cleavage, nuclear magnetic resonance, and indirectly through SAM binding. We identify key decision windows at which SAM can affect the folding pathway towards the OFF state. The presence of decoy conformations and differential sensitivities to SAM at different transcript lengths is crucial for SAM-I riboswitches to modulate gene expression in the context of global cellular metabolism.

  14. Insight into the conformational stability of membrane-embedded BamA using a combined solution and solid-state NMR approach

    Energy Technology Data Exchange (ETDEWEB)

    Sinnige, Tessa; Houben, Klaartje [Utrecht University, NMR Spectroscopy, Department of Chemistry, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands); Pritisanac, Iva [Physical and Theoretical Chemistry Laboratory (United Kingdom); Renault, Marie [Institute of Pharmacology and Structural Biology (France); Boelens, Rolf; Baldus, Marc, E-mail: m.baldus@uu.nl [Utrecht University, NMR Spectroscopy, Department of Chemistry, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands)

    2015-04-15

    The β-barrel assembly machinery (BAM) is involved in folding and insertion of outer membrane proteins in Gram-negative bacteria, a process that is still poorly understood. With its 790 residues, BamA presents a challenge to current NMR methods. We utilized a “divide and conquer” approach in which we first obtained resonance assignments for BamA’s periplasmic POTRA domains 4 and 5 by solution NMR. Comparison of these assignments to solid-state NMR (ssNMR) data obtained on two BamA constructs including the transmembrane domain and one or two soluble POTRA domains suggested that the fold of POTRA domain 5 critically depends on the interface with POTRA 4. Using specific labeling schemes we furthermore obtained ssNMR resonance assignments for residues in the extracellular loop 6 that is known to be crucial for BamA-mediated substrate folding and insertion. Taken together, our data provide novel insights into the conformational stability of membrane-embedded, non-crystalline BamA.

  15. 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.

  16. 40 CFR 93.157 - Frequency of conformity determinations.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Frequency of conformity determinations... PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR FEDERAL IMPLEMENTATION PLANS Determining Conformity of General Federal Actions to State or Federal Implementation Plans § 93.157...

  17. 40 CFR 93.104 - Frequency of conformity determinations.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Frequency of conformity determinations... PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR FEDERAL IMPLEMENTATION PLANS Conformity to State or Federal Implementation Plans of Transportation Plans, Programs, and Projects...

  18. Solid-state conformation of copolymers of ß-benzyl-L-aspartate with L-alanine, L-leucine, L-valine, γ-benzyl-L-glutamate, or ε-carbobenzoxy-L-lysine

    NARCIS (Netherlands)

    Sederel, Willem L.; Bantjes, Adriaan; Feijen, Jan; Anderson, James M.

    1980-01-01

    The solid-state conformation of copolymers of ß-benzyl-L-aspartate [L-Asp(OBzl)] with L-leucine (L-Leu), L-alanine (L-Ala), L-valine (L-Val), γ-benzyl-L-glutamate [L-Glu(OBzl)], or ε-carbobenzoxy-L-lysine (Cbz-L-Lys) has been studied by ir spectroscopy and circular dichroism (CD). The ir spectra in

  19. Solid-state conformation of copolymers of ß-benzyl-L-aspartate with L-alanine, L-leucine, L-valine, γ-benzyl-L-glutamate, or ε-carbobenzoxy-L-lysine

    NARCIS (Netherlands)

    Sederel, Willem L.; Bantjes, Adriaan; Feijen, Jan; Anderson, James M.

    1980-01-01

    The solid-state conformation of copolymers of ß-benzyl-L-aspartate [L-Asp(OBzl)] with L-leucine (L-Leu), L-alanine (L-Ala), L-valine (L-Val), γ-benzyl-L-glutamate [L-Glu(OBzl)], or ε-carbobenzoxy-L-lysine (Cbz-L-Lys) has been studied by ir spectroscopy and circular dichroism (CD). The ir spectra in

  20. Conformal entropy from horizon states: Solodukhin's method for spherical, toroidal, and hyperbolic black holes in D-dimensional anti-de Sitter spacetimes

    CERN Document Server

    Dias, G A S; Dias, Goncalo A. S.; Lemos, Jose' P. S.

    2006-01-01

    A calculation of the entropy of static, electrically charged, black holes with spherical, toroidal, and hyperbolic compact and oriented horizons, in D spacetime dimensions, is performed. These black holes live in an anti-de Sitter spacetime, i.e., a spacetime with negative cosmological constant. To find the entropy, the approach developed by Solodukhin is followed. The method consists in a redefinition of the variables in the metric, by considering the radial coordinate as a scalar field. Then one performs a 2+(D-2) dimensional reduction, where the (D-2) dimensions are in the angular coordinates, obtaining a 2-dimensional effective scalar field theory. This theory is a conformal theory in an infinitesimally small vicinity of the horizon. The corresponding conformal symmetry will then have conserved charges, associated with its infinitesimal conformal generators, which will generate a classical Poisson algebra of the Virasoro type. Shifting the charges and replacing Poisson brackets by commutators, one recover...

  1. Conformal symmetries of FRW accelerating cosmologies

    Energy Technology Data Exchange (ETDEWEB)

    Kehagias, A. [Physics Division, National Technical University of Athens, 15780 Zografou Campus, Athens (Greece); Department of Theoretical Physics and Center for Astroparticle Physics (CAP) 24 quai E. Ansermet, CH-1211 Geneva 4 (Switzerland); Riotto, A. [Department of Theoretical Physics and Center for Astroparticle Physics (CAP) 24 quai E. Ansermet, CH-1211 Geneva 4 (Switzerland)

    2014-07-15

    We show that any accelerating Friedmann–Robertson–Walker (FRW) cosmology with equation of state w<−1/3 (and therefore not only a de Sitter stage with w=−1) exhibits three-dimensional conformal symmetry on future constant-time hypersurfaces if the bulk theory is invariant under bulk conformal Killing vectors. We also offer an alternative derivation of this result in terms of conformal Killing vectors and show that long wavelength comoving curvature perturbations of the perturbed FRW metric are just conformal Killing motions of the FRW background. We then extend the boundary conformal symmetry to the bulk for accelerating cosmologies. Our findings indicate that one can easily generate perturbations of scalar fields which are not only scale invariant, but also fully conformally invariant on super-Hubble scales. Measuring a scale-invariant power spectrum for the cosmological perturbation does not automatically imply that the universe went through a de Sitter stage.

  2. 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....

  3. 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.

  4. 78 FR 78310 - Approval and Promulgation of Implementation Plans; North Carolina; Transportation Conformity...

    Science.gov (United States)

    2013-12-26

    ... Conformity Memorandum of Agreement Update AGENCY: Environmental Protection Agency (EPA). ACTION: Proposed... establishing transportation conformity criteria and procedures related to interagency consultation and... streamlines the conformity process to allow direct consultation among agencies at the Federal, state and...

  5. 76 FR 77150 - Approval and Promulgation of Air Quality Implementation Plans; Virginia; General Conformity...

    Science.gov (United States)

    2011-12-12

    ... Conformity Requirements for Federal Agencies Applicable to Federal Actions AGENCY: Environmental Protection... regulation adopted by Virginia to incorporate revisions to Federal general conformity requirements... state general conformity requirements rule for Federal agencies applicable to Federal actions...

  6. 78 FR 68005 - Approval and Promulgation of Implementation Plans; Mississippi; Transportation Conformity SIP...

    Science.gov (United States)

    2013-11-13

    ... Conformity SIP--Memorandum of Agreement AGENCY: Environmental Protection Agency (EPA). ACTION: Proposed rule... establishing transportation conformity criteria and procedures related to interagency consultation and... streamlines the conformity process to allow direct consultation among agencies at the Federal, state and...

  7. New potentials for conformal mechanics

    CERN Document Server

    Papadopoulos, G

    2012-01-01

    We show that V=\\alpha x^2+\\beta x^{-2} arises as a potential of 1-dimensional conformal theories. This class of conformal models includes the DFF model \\alpha=0 and the harmonic oscillator \\beta=0. The construction is based on a different embedding of the conformal symmetry group into the time re-parameterizations from that of the DFF model and its generalizations. Depending on the range of the couplings $\\alpha, \\beta$, these models can have a ground state and a well-defined energy spectrum, and exhibit either a $SL(2,\\bR)$ or a SO(3) conformal symmetry. The latter group can also be embedded in Diff(S^1). We also present several generalizations of these models which include the Calogero models with harmonic oscillator couplings and non-linear models with suitable metric and potential couplings. In addition, we give the conditions on the couplings for a class of gaugetheories to admit a SL(2,\\bR) or SO(3) conformal symmetry. We present examples of such systems with general gauge groups and global symmetries t...

  8. Evidence of PPII-like helical conformation and glass transition in a self-assembled solid-state polypeptide-surfactant complex: poly(L-histidine)/docylbenzenesulfonic acid.

    Science.gov (United States)

    Ramani, Ramasubbu; Hanski, Sirkku; Laiho, Ari; Tuma, Roman; Kilpeläinen, Simo; Tuomisto, Filip; Ruokolainen, Janne; Ikkala, Olli

    2008-05-01

    We present lamellar self-assembly of cationic poly(L-histidine) (PLH) stoichiometrically complexed with an anionic surfactant, dodecyl benzenesulfonic acid (DBSA), which allows a stabilized conformation reminiscent of polyproline type II (PPII) left-handed helices. Such a conformation has no intrapeptide hydrogen bonds, and it has previously been found to be one source of flexibility, e.g., in collagen and elastin, as well as an intermediate in silk processing. PLH(DBSA)1.0 complexes were characterized by Fourier transform infrared spectroscopy (FTIR), circular dichroism (CD), small-angle X-ray scattering (SAXS), transmission electron microscopy (TEM), and differential scanning calorimetry (DSC). The PPII-like conformation in PLH(DBSA)1.0 is revealed by characteristic CD and FTIR spectra, where the latter indicates absence of intrachain peptide hydrogen bonds. In addition, a glass transition was directly verified by DSC at ca. 135 degrees C for PLH(DBSA)1.0 and indirectly by SAXS and TEM in comparison to pure PLH at 165 degrees C, thus indicating plasticization. Glass transitions have not been observed before in polypeptide-surfactant complexes. The present results show that surfactant binding can be a simple scheme to provide steric crowding to stabilize PPII conformation to tune the polypeptide properties, plasticization and flexibility.

  9. Genetic parameters between feed-intake-related traits and conformation in 2 separate dairy populations-the Netherlands and United States

    NARCIS (Netherlands)

    Manzanilla-Pech, C.I.V.; Veerkamp, R.F.; Tempelman, R.J.; Pelt, van M.L.; Weigel, K.A.; VandeHaar, M.; Lawlor, T.J.; Spurlock, D.M.; Armentano, L.E.; Staples, C.R.; Hanigan, M.; Haas, De Y.

    2016-01-01

    To include feed-intake-related traits in the breeding goal, accurate estimates of genetic parameters of feed intake, and its correlations with other related traits (i.e., production, conformation) are required to compare different options. However, the correlations between feed intake and

  10. ATP and MO25alpha regulate the conformational state of the STRADalpha pseudokinase and activation of the LKB1 tumour suppressor.

    Science.gov (United States)

    Zeqiraj, Elton; Filippi, Beatrice Maria; Goldie, Simon; Navratilova, Iva; Boudeau, Jérôme; Deak, Maria; Alessi, Dario R; van Aalten, Daan M F

    2009-06-09

    Pseudokinases lack essential residues for kinase activity, yet are emerging as important regulators of signal transduction networks. The pseudokinase STRAD activates the LKB1 tumour suppressor by forming a heterotrimeric complex with LKB1 and the scaffolding protein MO25. Here, we describe the structure of STRADalpha in complex with MO25alpha. The structure reveals an intricate web of interactions between STRADalpha and MO25alpha involving the alphaC-helix of STRADalpha, reminiscent of the mechanism by which CDK2 interacts with cyclin A. Surprisingly, STRADalpha binds ATP and displays a closed conformation and an ordered activation loop, typical of active protein kinases. Inactivity is accounted for by nonconservative substitution of almost all essential catalytic residues. We demonstrate that binding of ATP enhances the affinity of STRADalpha for MO25alpha, and conversely, binding of MO25alpha promotes interaction of STRADalpha with ATP. Mutagenesis studies reveal that association of STRADalpha with either ATP or MO25alpha is essential for LKB1 activation. We conclude that ATP and MO25alpha cooperate to maintain STRADalpha in an "active" closed conformation required for LKB1 activation. It has recently been demonstrated that a mutation in human STRADalpha that truncates a C-terminal region of the pseudokinase domain leads to the polyhydramnios, megalencephaly, symptomatic epilepsy (PMSE) syndrome. We demonstrate this mutation destabilizes STRADalpha and prevents association with LKB1. In summary, our findings describe one of the first structures of a genuinely inactive pseudokinase. The ability of STRADalpha to activate LKB1 is dependent on a closed "active" conformation, aided by ATP and MO25alpha binding. Thus, the function of STRADalpha is mediated through an active kinase conformation rather than kinase activity. It is possible that other pseudokinases exert their function through nucleotide binding and active conformations.

  11. ATP and MO25α Regulate the Conformational State of the STRADα Pseudokinase and Activation of the LKB1 Tumour Suppressor

    Science.gov (United States)

    Zeqiraj, Elton; Filippi, Beatrice Maria; Goldie, Simon; Navratilova, Iva; Boudeau, Jérôme; Deak, Maria; Alessi, Dario R.; van Aalten, Daan M. F.

    2009-01-01

    Pseudokinases lack essential residues for kinase activity, yet are emerging as important regulators of signal transduction networks. The pseudokinase STRAD activates the LKB1 tumour suppressor by forming a heterotrimeric complex with LKB1 and the scaffolding protein MO25. Here, we describe the structure of STRADα in complex with MO25α. The structure reveals an intricate web of interactions between STRADα and MO25α involving the αC-helix of STRADα, reminiscent of the mechanism by which CDK2 interacts with cyclin A. Surprisingly, STRADα binds ATP and displays a closed conformation and an ordered activation loop, typical of active protein kinases. Inactivity is accounted for by nonconservative substitution of almost all essential catalytic residues. We demonstrate that binding of ATP enhances the affinity of STRADα for MO25α, and conversely, binding of MO25α promotes interaction of STRADα with ATP. Mutagenesis studies reveal that association of STRADα with either ATP or MO25α is essential for LKB1 activation. We conclude that ATP and MO25α cooperate to maintain STRADα in an “active” closed conformation required for LKB1 activation. It has recently been demonstrated that a mutation in human STRADα that truncates a C-terminal region of the pseudokinase domain leads to the polyhydramnios, megalencephaly, symptomatic epilepsy (PMSE) syndrome. We demonstrate this mutation destabilizes STRADα and prevents association with LKB1. In summary, our findings describe one of the first structures of a genuinely inactive pseudokinase. The ability of STRADα to activate LKB1 is dependent on a closed “active” conformation, aided by ATP and MO25α binding. Thus, the function of STRADα is mediated through an active kinase conformation rather than kinase activity. It is possible that other pseudokinases exert their function through nucleotide binding and active conformations. PMID:19513107

  12. ATP and MO25alpha regulate the conformational state of the STRADalpha pseudokinase and activation of the LKB1 tumour suppressor.

    Directory of Open Access Journals (Sweden)

    Elton Zeqiraj

    2009-06-01

    Full Text Available Pseudokinases lack essential residues for kinase activity, yet are emerging as important regulators of signal transduction networks. The pseudokinase STRAD activates the LKB1 tumour suppressor by forming a heterotrimeric complex with LKB1 and the scaffolding protein MO25. Here, we describe the structure of STRADalpha in complex with MO25alpha. The structure reveals an intricate web of interactions between STRADalpha and MO25alpha involving the alphaC-helix of STRADalpha, reminiscent of the mechanism by which CDK2 interacts with cyclin A. Surprisingly, STRADalpha binds ATP and displays a closed conformation and an ordered activation loop, typical of active protein kinases. Inactivity is accounted for by nonconservative substitution of almost all essential catalytic residues. We demonstrate that binding of ATP enhances the affinity of STRADalpha for MO25alpha, and conversely, binding of MO25alpha promotes interaction of STRADalpha with ATP. Mutagenesis studies reveal that association of STRADalpha with either ATP or MO25alpha is essential for LKB1 activation. We conclude that ATP and MO25alpha cooperate to maintain STRADalpha in an "active" closed conformation required for LKB1 activation. It has recently been demonstrated that a mutation in human STRADalpha that truncates a C-terminal region of the pseudokinase domain leads to the polyhydramnios, megalencephaly, symptomatic epilepsy (PMSE syndrome. We demonstrate this mutation destabilizes STRADalpha and prevents association with LKB1. In summary, our findings describe one of the first structures of a genuinely inactive pseudokinase. The ability of STRADalpha to activate LKB1 is dependent on a closed "active" conformation, aided by ATP and MO25alpha binding. Thus, the function of STRADalpha is mediated through an active kinase conformation rather than kinase activity. It is possible that other pseudokinases exert their function through nucleotide binding and active conformations.

  13. Representation of target-bound drugs by computed conformers: implications for conformational libraries

    Directory of Open Access Journals (Sweden)

    Goede Andrean

    2006-06-01

    Full Text Available Abstract Background The increasing number of known protein structures provides valuable information about pharmaceutical targets. Drug binding sites are identifiable and suitable lead compounds can be proposed. The flexibility of ligands is a critical point for the selection of potential drugs. Since computed 3D structures of millions of compounds are available, the knowledge of their binding conformations would be a great benefit for the development of efficient screening methods. Results Integration of two public databases allowed superposition of conformers for 193 approved drugs with 5507 crystallised target-bound counterparts. The generation of 9600 drug conformers using an atomic force field was carried out to obtain an optimal coverage of the conformational space. Bioactive conformations are best described by a conformational ensemble: half of all drugs exhibit multiple active states, distributed over the entire range of the reachable energy and conformational space. A number of up to 100 conformers per drug enabled us to reproduce the bound states within a similarity threshold of 1.0 Å in 70% of all cases. This fraction rises to about 90% for smaller or average sized drugs. Conclusion Single drugs adopt multiple bioactive conformations if they interact with different target proteins. Due to the structural diversity of binding sites they adopt conformations that are distributed over a broad conformational space and wide energy range. Since the majority of drugs is well represented by a predefined low number of conformers (up to 100 this procedure is a valuable method to compare compounds by three-dimensional features or for fast similarity searches starting with pharmacophores. The underlying 9600 generated drug conformers are downloadable from the Super Drug Web site 1. All superpositions are visualised at the same source. Additional conformers (110,000 of 2400 classified WHO-drugs are also available.

  14. 40 CFR 51.857 - Frequency of conformity determinations.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 2 2010-07-01 2010-07-01 false Frequency of conformity determinations... Conformity of General Federal Actions to State or Federal Implementation Plans § 51.857 Frequency of conformity determinations. Link to an amendment published at 75 FR 17272, April 5, 2010. (a) The...

  15. Transitive conformal holonomy groups

    CERN Document Server

    Alt, Jesse

    2011-01-01

    For $(M,[g])$ a conformal manifold of signature $(p,q)$ and dimension at least three, the conformal holonomy group $\\mathrm{Hol}(M,[g]) \\subset O(p+1,q+1)$ is an invariant induced by the canonical Cartan geometry of $(M,[g])$. We give a description of all possible connected conformal holonomy groups which act transitively on the M\\"obius sphere $S^{p,q}$, the homogeneous model space for conformal structures of signature $(p,q)$. The main part of this description is a list of all such groups which also act irreducibly on $\\R^{p+1,q+1}$. For the rest, we show that they must be compact and act decomposably on $\\R^{p+1,q+1}$, in particular, by known facts about conformal holonomy the conformal class $[g]$ must contain a metric which is locally isometric to a so-called special Einstein product.

  16. 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.

  17. Eikonalization of Conformal Blocks

    CERN Document Server

    Fitzpatrick, A Liam; Walters, Matthew T; Wang, Junpu

    2015-01-01

    Classical field configurations such as the Coulomb potential and Schwarzschild solution are built from the $t$-channel exchange of many light degrees of freedom. We study the CFT analog of this phenomenon, which we term the `eikonalization' of conformal blocks. We show that when an operator $T$ appears in the OPE $\\mathcal{O}(x) \\mathcal{O}(0)$, then the large spin $\\ell$ Fock space states $[TT \\cdots T]_{\\ell}$ also appear in this OPE with a computable coefficient. The sum over the exchange of these Fock space states in an $\\langle \\mathcal{O} \\mathcal{O} \\mathcal{O} \\mathcal{O} \\rangle$ correlator build the classical `$T$ field' in the dual AdS description. In some limits the sum of all Fock space exchanges can be represented as the exponential of a single $T$ exchange in the 4-pt correlator of $\\mathcal{O}$. Our results should be useful for systematizing $1/\\ell$ perturbation theory in general CFTs and simplifying the computation of large spin OPE coefficients. As examples we obtain the leading $\\log \\ell$...

  18. Heterogeneous Conformism and Wealth Distribution in a Neoclassical Growth Model

    OpenAIRE

    Mino, Kazuo; Nakamoto, Yasuhiro

    2015-01-01

    This paper explores the role of consumption externalities in a neoclassical growth model in which households have heterogeneous preferences. We fi nd that a higher degree of average conformism accelerates the convergence speed of the economy towards the steady state as in the case of homogeneous conformism. Furthermore, we reveal that the wealth inequality expands or shrinks in the case of heterogeneous conformism, while it does not expand but shrinks in the case of homogeneous conformism.

  19. Conformant Planning via Symbolic Model Checking

    CERN Document Server

    Cimatti, A; 10.1613/jair.774

    2011-01-01

    We tackle the problem of planning in nondeterministic domains, by presenting a new approach to conformant planning. Conformant planning is the problem of finding a sequence of actions that is guaranteed to achieve the goal despite the nondeterminism of the domain. Our approach is based on the representation of the planning domain as a finite state automaton. We use Symbolic Model Checking techniques, in particular Binary Decision Diagrams, to compactly represent and efficiently search the automaton. In this paper we make the following contributions. First, we present a general planning algorithm for conformant planning, which applies to fully nondeterministic domains, with uncertainty in the initial condition and in action effects. The algorithm is based on a breadth-first, backward search, and returns conformant plans of minimal length, if a solution to the planning problem exists, otherwise it terminates concluding that the problem admits no conformant solution. Second, we provide a symbolic representation ...

  20. Conformal Relativity: Theory and Observations

    CERN Document Server

    Pervushin, V; Zorin, A

    2005-01-01

    Theoretical and observational arguments are listed in favor of a new principle of relativity of units of measurements as the basis of a conformal-invariant unification of General Relativity and Standard Model by replacement of all masses with a scalar (dilaton) field. The relative units mean conformal observables: the coordinate distance, conformal time, running masses, and constant temperature. They reveal to us a motion of a universe along its hypersurface in the field space of events like a motion of a relativistic particle in the Minkowski space, where the postulate of the vacuum as a state with minimal energy leads to arrow of the geometric time. In relative units, the unified theory describes the Cold Universe Scenario, where the role of the conformal dark energy is played by a free minimal coupling scalar field in agreement with the most recent distance-redshift data from type Ia supernovae. In this Scenario, the evolution of the Universe begins with the effect of intensive creation of primordial W-Z-b...

  1. Dynamics and structural changes induced by ATP and/or substrate binding in the inward-facing conformation state of P-glycoprotein

    Science.gov (United States)

    Watanabe, Yurika; Hsu, Wei-Lin; Chiba, Shuntaro; Hayashi, Tomohiko; Furuta, Tadaomi; Sakurai, Minoru

    2013-02-01

    P-glycoprotein (P-gp) is a multidrug transporter that catalyzes the transport of a substrate. To elucidate the underlying mechanism of this type of substrate transport, we performed molecular dynamics (MD) simulations using the X-ray crystal structure of P-gp, which has an inward-facing conformation. Our simulations indicated that the dimerization of the nucleotide binding domains (NBDs) is driven by the binding of ATP to the NBDs and/or the binding of the substrate to a cavity in the transmembrane domains (TMDs). Based on these results, we discuss a role of ATP in the allosteric communication that occurs between the NBDs and the TMDs.

  2. [Dosimetric evaluation of conformal radiotherapy: conformity factor].

    Science.gov (United States)

    Oozeer, R; Chauvet, B; Garcia, R; Berger, C; Felix-Faure, C; Reboul, F

    2000-01-01

    The aim of three-dimensional conformal therapy (3DCRT) is to treat the Planning Target Volume (PTV) to the prescribed dose while reducing doses to normal tissues and critical structures, in order to increase local control and reduce toxicity. The evaluation tools used for optimizing treatment techniques are three-dimensional visualization of dose distributions, dose-volume histograms, tumor control probabilities (TCP) and normal tissue complication probabilities (NTCP). These tools, however, do not fully quantify the conformity of dose distributions to the PTV. Specific tools were introduced to measure this conformity for a given dose level. We have extended those definitions to different dose levels, using a conformity index (CI). CI is based on the relative volumes of PTV and outside the PTV receiving more than a given dose. This parameter has been evaluated by a clinical study including 82 patients treated for lung cancer and 82 patients treated for prostate cancer. The CI was low for lung dosimetric studies (0.35 at the prescribed dose 66 Gy) due to build-up around the GTV and to spinal cord sparing. For prostate dosimetric studies, the CI was higher (0.57 at the prescribed dose 70 Gy). The CI has been used to compare treatment plans for lung 3DCRT (2 vs 3 beams) and prostate 3DCRT (4 vs 7 beams). The variation of CI with dose can be used to optimize dose prescription.

  3. On conformally related -waves

    Indian Academy of Sciences (India)

    Varsha Daftardar-Gejji

    2001-05-01

    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 $g_{ik}$ and $\\overline{g}_{ik}$ ($=^{-2}g_{ik}$, : a scalar function), are distinct metrics having the same Einstein tensor, $G_{ik}=\\overline{G}_{ik}$, then both represent (generalized) $pp$-waves and $_{i}$ is a null convariantly constant vector of $g_{ik}$. Thus $pp$-waves are the only candidates which yield conformally related nontrivial solutions of $G_{ik}=T_{ik}=\\overline{G}_{ik}$, with $T_{ik}$ being conformally invariant source. In this paper the functional form of the conformal factor for the conformally related $pp$-waves/generalized $pp$-waves has been obtained. It has been shown that the most general $pp$-wave, conformally related to ${\\rm d}s^{2}=-2{\\rm d}u[{\\rm d}v-m{\\rm d}y+H{\\rm d}u]+P^{-2}[{\\rm d}y^{2}+{\\rm d}z^{2}]$, turns out to the $(au+b)^{-2}{\\rm d}s^{2}$, where , are constants. Only in the special case when $m=0$, $H=1$, and $P=P(y,z)$, the conformal factor is $(au+b)^{-2}$ or $(a(u+v)+b)^{-2}$.

  4. 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....

  5. Ligand-Stabilized Reduced-Dimensionality Perovskites

    KAUST Repository

    Quan, Li Na

    2016-02-03

    Metal halide perovskites have rapidly advanced thin film photovoltaic performance; as a result, the materials’ observed instabilities urgently require a solution. Using density functional theory (DFT), we show that a low energy of formation, exacerbated in the presence of humidity, explains the propensity of perovskites to decompose back into their precursors. We find, also using DFT, that intercalation of phenylethylammonium between perovskite layers introduces quantitatively appreciable van der Waals interactions; and these drive an increased formation energy and should therefore improve material stability. Here we report the reduced-dimensionality (quasi-2D) perovskite films that exhibit improved stability while retaining the high performance of conventional three-dimensional perovskites. Continuous tuning of the dimensionality, as assessed using photophysical studies, is achieved by the choice of stoichiometry in materials synthesis. We achieved the first certified hysteresis-free solar power conversion in a planar perovskite solar cell, obtaining a 15.3% certified PCE, and observe greatly improved performance longevity.

  6. Ligand-Stabilized Reduced-Dimensionality Perovskites.

    Science.gov (United States)

    Quan, Li Na; Yuan, Mingjian; Comin, Riccardo; Voznyy, Oleksandr; Beauregard, Eric M; Hoogland, Sjoerd; Buin, Andrei; Kirmani, Ahmad R; Zhao, Kui; Amassian, Aram; Kim, Dong Ha; Sargent, Edward H

    2016-03-02

    Metal halide perovskites have rapidly advanced thin-film photovoltaic performance; as a result, the materials' observed instabilities urgently require a solution. Using density functional theory (DFT), we show that a low energy of formation, exacerbated in the presence of humidity, explains the propensity of perovskites to decompose back into their precursors. We find, also using DFT, that intercalation of phenylethylammonium between perovskite layers introduces quantitatively appreciable van der Waals interactions. These drive an increased formation energy and should therefore improve material stability. Here we report reduced-dimensionality (quasi-2D) perovskite films that exhibit improved stability while retaining the high performance of conventional three-dimensional perovskites. Continuous tuning of the dimensionality, as assessed using photophysical studies, is achieved by the choice of stoichiometry in materials synthesis. We achieve the first certified hysteresis-free solar power conversion in a planar perovskite solar cell, obtaining a 15.3% certified PCE, and observe greatly improved performance longevity.

  7. Conformational elasticity theory of chain molecules

    Institute of Scientific and Technical Information of China (English)

    YANG; Xiaozhen

    2001-01-01

    This paper develops a conformational elasticity theory of chain molecules, which is based on three key points: (ⅰ) the molecular model is the rotational isomeric state (RIS) model; (ⅱ) the conformational distribution function of a chain molecule is described by a function of two variables, the end-to-end distance of a chain conformation and the energy of the conformation; (ⅲ) the rule of changes in the chain conformational states during deformation is that a number of chain conformations would vanish. The ideal deformation behavior calculated by the theory shows that the change in chain conformations is physically able to make the upward curvature of the stress-strain curve at the large-scale deformation of natural rubber. With the theory, different deformation behaviors between polymers with different chemical structures can be described, the energy term of the stress in the deformations can be predicted, and for natural rubber the fraction of the energy term is around 13%, coinciding with the experimental results.

  8. On the stochastic dynamics of molecular conformation

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    An important functioning mechanism of biological macromolecules is the transition between different conformed states due to thermal fluctuation. In the present paper, a biological macromolecule is modeled as two strands with side chains facing each other, and its stochastic dynamics including the statistics of stationary motion and the statistics of conformational transition is studied by using the stochastic averaging method for quasi Hamiltonian systems. The theoretical results are confirmed with the results from Monte Carlo simulation.

  9. Implications of conformal symmetry in quantum mechanics

    Science.gov (United States)

    Okazaki, Tadashi

    2017-09-01

    In conformal quantum mechanics with the vacuum of a real scaling dimension and with a complete orthonormal set of energy eigenstates, which is preferable under the unitary evolution, the dilatation expectation value between energy eigenstates monotonically decreases along the flow from the UV to the IR. In such conformal quantum mechanics, there exist bounds on scaling dimensions of the physical states and the gauge operators.

  10. Synthesis, Structure, and Molecular Recognition of S6 - and (SO2 )6 -Corona[6](het)arenes: Control of Macrocyclic Conformation and Properties by the Oxidation State of the Bridging Heteroatoms.

    Science.gov (United States)

    Guo, Qing-Hui; Zhao, Liang; Wang, Mei-Xiang

    2016-05-10

    We report herein the synthesis, structure, and molecular recognition of S6 - and (SO2 )6 -corona[6](het)arenes, and demonstrate a unique and efficient strategy of regulating macrocyclic conformation and properties by adjusting the oxidation state of the heteroatom linkages. The one-pot nucleophilic aromatic substitution reaction of 1,4-benzenedithiol derivatives, biphenyl-4,4'-dithiol and 9,9-dipropyl-9H-fluorene-2,7-dithiol with 3,6-dichlorotetrazine afforded S6 -corona[3]arene[3]tetrazines. These compounds underwent inverse-electron-demand Diels-Alder reaction with enamines and norbornadiene to produce S6 -corona[3]arene[3]pyridazines. Facile oxidation of sulfide linkages yielded (SO2 )6 -corona[3]arene[3]pyridazines. All corona[6](het)arenes adopted generally hexagonal macrocyclic ring structures; however, their electronic properties and conformation could be fine-tuned by altering the oxidation state of the sulfur linkages. Whereas (SO2 )6 -corona[3]arene[3]pyridazines were electron-deficient, S6 -corona[3]arene[3]pyridazines acted as electron-rich macrocyclic hosts that recognized various organic cations in both aqueous and organic solutions.

  11. Conformational state of the MscS mechanosensitive channel in solution revealed by pulsed electron-electron double resonance (PELDOR) spectroscopy.

    Science.gov (United States)

    Pliotas, Christos; Ward, Richard; Branigan, Emma; Rasmussen, Akiko; Hagelueken, Gregor; Huang, Hexian; Black, Susan S; Booth, Ian R; Schiemann, Olav; Naismith, James H

    2012-10-02

    The heptameric mechanosensitive channel of small conductance (MscS) provides a critical function in Escherichia coli where it opens in response to increased bilayer tension. Three approaches have defined different closed and open structures of the channel, resulting in mutually incompatible models of gating. We have attached spin labels to cysteine mutants on key secondary structural elements specifically chosen to discriminate between the competing models. The resulting pulsed electron-electron double resonance (PELDOR) spectra matched predicted distance distributions for the open crystal structure of MscS. The fit for the predictions by structural models of MscS derived by other techniques was not convincing. The assignment of MscS as open in detergent by PELDOR was unexpected but is supported by two crystal structures of spin-labeled MscS. PELDOR is therefore shown to be a powerful experimental tool to interrogate the conformation of transmembrane regions of integral membrane proteins.

  12. EC declaration of conformity.

    Science.gov (United States)

    Donawa, M E

    1996-05-01

    The CE-marking procedure requires that manufacturers draw up a written declaration of conformity before placing their products on the market. However, some companies do not realize that this is a requirement for all devices. Also, there is no detailed information concerning the contents and format of the EC declaration of conformity in the medical device Directives or in EC guidance documentation. This article will discuss some important aspects of the EC declaration of conformity and some of the guidance that is available on its contents and format.

  13. Mutual Recognition of the Food and Drug Administration and European Community Member State Conformity Assessment Procedures; pharmaceutical GMP inspection reports, medical device quality system evaluation reports, and certain medical device premarket evaluation reports--FDA. Proposed rule.

    Science.gov (United States)

    1998-04-10

    The Food and Drug Administration (FDA) is proposing to amend its regulations pursuant to an international agreement that is expected to be concluded between the United States and the European Community (EC) (Ref. 1). Under the terms of that agreement, FDA may normally endorse good manufacturing practice (GMP) inspection reports for pharmaceuticals provided by equivalent EC Member State regulatory authorities and medical device quality system evaluation reports and certain medical device premarket evaluation reports provided by equivalent conformity assessment bodies. FDA is taking this action to enhance its ability to ensure the safety and efficacy of pharmaceuticals and medical devices through more efficient and effective utilization of its regulatory resources. The agency is requesting comments on the proposed rule.

  14. 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.

  15. Animal culture: chimpanzee conformity?

    Science.gov (United States)

    van Schaik, Carel P

    2012-05-22

    Culture-like phenomena in wild animals have received much attention, but how good is the evidence and how similar are they to human culture? New data on chimpanzees suggest their culture may even have an element of conformity.

  16. Solid-state structure and solution conformation of the nootropic agent N[2-( N,N-Diisopropylamino)ethyl]-2-oxo-1-pyrrolidinacetamide sulphate. X-ray and homonuclear two-dimensional 1H NMR studies

    Science.gov (United States)

    Bandoli, Giuliano; Nicolini, Marino; Pappalardo, Giuseppe C.; Grassi, Antonio; Perly, Bruno

    1987-04-01

    The crystal and molecular structure of the nootropic agent N-[2-( N,N-diisopropyl-amino)ethyl]-2-oxo-1-pyrrolidinacetamide sulphate was determined by X-ray analysis. The conformational properties in the solution state were deduced from the 1H-NMR spectrum run in 2H 2O at 500 MHz. Spectral assignments were made with the aid of the COSY 45 shift correlation experiment. Crystals were triclinic with unit cell dimensions a = 13.410(10), b = 11.382(8), c = 6.697(4) », α = 83.80(3), β = 88.61(3)and γ = 72.25(6)° ; space group Poverline1. The structure was determined from 1047 three-dimensional counter data and refined to a value of 7.5% for the conventional discrepancy factor R. One molecule of the solvent acetonitrile is incorporated per two of the (C 14H 28N 3O 2) +-(HSO 4) -. The five-membered heterocyclic ring is in an envelope ( Cs) conformation and the "flap" atom deviates by 0.31 » from the plane of the other four. This plane forms a dihedral angle of 71.4° with the amide group, with the CO fragment directed toward the ring. All bond angles and distances are in good agreement with expected standard values. A strong OH⋯O intermolecular bond (2.61 ») links the cation of the hydrogen-sulphate anion, while the loosely held MeCN molecule is trapped in the polar pockets. The molecular conformation in the solid was compared with results from 1H NMR spectral analysis which showed that in solution wide torsional oscillations can occur about the bonds of the chain bonded to the N(1) atom.

  17. Screen-printed graphite macroelectrodes for the direct electron transfer of cytochrome c: a deeper study of the effect of pH on the conformational states, immobilization and peroxidase activity.

    Science.gov (United States)

    Gómez-Mingot, Maria; Montiel, Vicente; Banks, Craig E; Iniesta, Jesús

    2014-03-21

    The direct electron transfer of cytochrome c has been studied at screen-printed graphite macroelectrodes without recourse to mediators or the need for any electrode pre-treatment as is commonly employed within the literature. A wide range of pH values from 2.0 to 11.0 have been explored upon the electrochemical response of cytochrome c and different voltammetric signatures have been observed. The direct electron transfer of the alkaline transition of cytochrome c was found impeded within alkaline media leading to either an irreversible redox process or even no voltammetric responses. In acidic aqueous media the electrochemical process is observed to undergo a mixed diffusion and adsorption controlled process rather than a purely diffusional process of the native conformation as observed at pH 7.0. Interestingly, at pH 3.5 a new conformational state is revealed in cooperation with the native conformation. The immobilization of the protein was satisfactorily obtained using a simple method by cycling the protein at specific solution pH values allowing amperometric responses to be obtained and gives rise to useful pseudo-peroxidase activity for sensing H2O2. Apparent Michaelis-Menten constant values (Km) were calculated via the Lineweaver-Burk method with deduced values of 25 ± 4, 98 ± 12 and 230 ± 30 mM, respectively for pH values of 2.0, 3.0 and 7.0. Such work is important for those utilising cytochrome c in bio-electrochemical and related applications.

  18. 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....

  19. Conformally coupled inflation

    CERN Document Server

    Faraoni, Valerio

    2013-01-01

    A massive scalar field in a curved spacetime can propagate along the light cone, a causal pathology, which can, in principle, be eliminated only if the scalar couples conformally to the Ricci curvature of spacetime. This property mandates conformal coupling for the field driving inflation in the early universe. During slow-roll inflation, this coupling can cause super-acceleration and, as a signature, a blue spectrum of primordial gravitational waves.

  20. 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...

  1. Conformally Coupled Inflation

    Directory of Open Access Journals (Sweden)

    Valerio Faraoni

    2013-07-01

    Full Text Available A massive scalar field in a curved spacetime can propagate along the light cone, a causal pathology, which can, in principle, be eliminated only if the scalar couples conformally to the Ricci curvature of spacetime. This property mandates conformal coupling for the field driving inflation in the early universe. During slow-roll inflation, this coupling can cause super-acceleration and, as a signature, a blue spectrum of primordial gravitational waves.

  2. Conformational sampling techniques.

    Science.gov (United States)

    Hatfield, Marcus P D; Lovas, Sándor

    2014-01-01

    The potential energy hyper-surface of a protein relates the potential energy of the protein to its conformational space. This surface is useful in determining the native conformation of a protein or in examining a statistical-mechanical ensemble of structures (canonical ensemble). In determining the potential energy hyper-surface of a protein three aspects must be considered; reducing the degrees of freedom, a method to determine the energy of each conformation and a method to sample the conformational space. For reducing the degrees of freedom the choice of solvent, coarse graining, constraining degrees of freedom and periodic boundary conditions are discussed. The use of quantum mechanics versus molecular mechanics and the choice of force fields are also discussed, as well as the sampling of the conformational space through deterministic and heuristic approaches. Deterministic methods include knowledge-based statistical methods, rotamer libraries, homology modeling, the build-up method, self-consistent electrostatic field, deformation methods, tree-based elimination and eigenvector following routines. The heuristic methods include Monte Carlo chain growing, energy minimizations, metropolis monte carlo and molecular dynamics. In addition, various methods to enhance the conformational search including the deformation or smoothing of the surface, scaling of system parameters, and multi copy searching are also discussed.

  3. A conformal block Farey tail

    Science.gov (United States)

    Maloney, Alexander; Maxfield, Henry; Ng, Gim Seng

    2017-06-01

    We investigate the constraints of crossing symmetry on CFT correlation functions. Four point conformal blocks are naturally viewed as functions on the upper-half plane, on which crossing symmetry acts by PSL(2, Z ) modular transformations. This allows us to construct a unique, crossing symmetric function out of a given conformal block by averaging over PSL(2, Z ). In some two dimensional CFTs the correlation functions are precisely equal to the modular average of the contributions of a finite number of light states. For example, in the two dimensional Ising and tri-critical Ising model CFTs, the correlation functions of identical operators are equal to the PSL(2, Z ) average of the Virasoro vacuum block; this determines the 3 point function coefficients uniquely in terms of the central charge. The sum over PSL(2, Z ) in CFT2 has a natural AdS3 interpretation as a sum over semi-classical saddle points, which describe particles propagating along rational tangles in the bulk. We demonstrate this explicitly for the correlation function of certain heavy operators, where we compute holographically the semi-classical conformal block with a heavy internal operator.

  4. Solution- and solid-state conformations of C(α)-alkyl analogues of methylphenidate (Ritalin) salts: avoidance of gauche(+)gauche(-) interactions.

    Science.gov (United States)

    Steinberg, Avital; Froimowitz, Mark; Parrish, Damon A; Deschamps, Jeffrey R; Glaser, Robert

    2011-11-18

    Alkyl analogues of methylphenidate (Ritalin) salts are slow onset, long duration dopamine reuptake inhibitors with a potential use as a cocaine abuse pharmacotherapy. X-ray crystallographic studies and nuclear magnetic resonance (NMR) investigations strongly suggest that avoidance of sterically unfavorable gauche(-)gauche(+) orientations effectively influences both the C(α)-alkyl side chain conformation and the formation of a predominant rotamer about the CH-CH bond ligating piperidine and C(Ar)R moieties. The favored CH-CH rotamer in D(2)O and in CD(2)Cl(2) of the pharmacologically interesting i-Bu and CH(2)-cyc-Pnt (RS,RS)-salts has the same antiperiplanar arrangement that was found in the crystal structures, although there clearly is a fast equilibrium involving smaller amounts of synclinal partners. While the rotamer in the (RS,SR)-i-Bu HCl crystal structure exhibits a synclinal orientation for the vicinal pair of adjacent methine protons, the weighted time-averaged arrangement for these protons becomes almost completely antiperiplanar when the crystals are dissolved in D(2)O. Increased steric congestion around the CH-CH bond in the analogous N-methyl tertiary ammonium salts seems to augment the quantity of the preferred rotamer within the mixture. The stereochemistry of the species observed via NMR seems to arise from specific combinations of N-methyl orientation and avoidance of sterically unfavorable gauche(-)gauche(+) arrangements.

  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. 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.

  7. New T6 heat treatments for AlSi alloys conformed in semi-solid state; Nuevos tratamientos T6 para aleaciones de AlSi obtenidas por conformacion en estado semisolido

    Energy Technology Data Exchange (ETDEWEB)

    Menargues, S.; Baile, M. T.; Forn, A.

    2013-07-01

    In this work the microstructural changes that occurs during the solution and aging steps of heat treated of AlSi alloys, conformed in semi-solid state, were analysed. The study allowed developing a new T6 heat treatment, with solution times down to 30 min. With this new short heat treatment, the alloy showed better mechanical properties in comparison with the same alloy heat treated in standard conditions (solution times between 6 h and 8 h). This new heat treatment, carried out at 540 degree centigrade, allowed complete magnesium dissolution and, at the same time, minimizes the grain and eutectic silicon growth. Although this experimentation was carried out with A356 and A357 aluminum alloys, conformed by Sub-Liquidus-Casting process, these results may be applicable to components produced with other semi-solid technologies and with others AlSi hard enable alloys that form coherent magnesium precipitates. The characterization of samples was carried out by micrographic analysis, by hardness and ultramicrohardnes tests. (Author)

  8. Conformal Window and Correlation Functions in Lattice Conformal QCD

    Science.gov (United States)

    Iwasaki, Y.

    We discuss various aspects of Conformal Field Theories on the Lattice. We mainly investigate the SU(3) gauge theory with Nf degenerate fermions in the fundamental representation, employing the one-plaquette gauge action and the Wilson fermion action. 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 ≤ Nf ≤ 16. Secondly, we introduce a new concept, "conformal theories with IR cutof" and point out that any numerical simulation on a lattice is bounded by an IR cutoff ∧IR. Then we make predictions that when Nf is within the conformal window, the propagator of a meson G(t) behaves at large t, as G(t) = c exp (-mHt)/tα, that is, a modified Yukawa-type decay form, instead of the usual exponential decay form exp (-mHt), in the small quark mass region. This holds on an any lattice for any coupling constant g, as far as g is between 0 and g*, where g* is the IR fixed point. We verify that numerical results really satisfy the predictions for the Nf = 7 case and the Nf = 16 case. Thirdly, we discuss small number of flavors (Nf = 2 ˜ 6) QCD at finite temperatures. We point out theoretically and verify numerically that the correlation functions at T/Tc > 1 exhibit the characteristics of the conformal function with IR cutoff, an exponential decay with power correction. Investigating our numerical data by a new method which we call the "local-analysis" of propagators, we observe that the Nf = 7 case and the Nf = 2 at T ˜ 2Tc case are similar to each other, while the Nf = 16 case and the Nf = 2 at T = 102 ˜ 105Tc cases are similar to each other. Further, we observe 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 = 102 ˜ 105Tc cases are close to

  9. Boundary Conformal Field Theory

    CERN Document Server

    Cardy, J L

    2004-01-01

    Boundary conformal field theory (BCFT) is simply the study of conformal field theory (CFT) in domains with a boundary. It gains its significance because, in some ways, it is mathematically simpler: the algebraic and geometric structures of CFT appear in a more straightforward manner; and because it has important applications: in string theory in the physics of open strings and D-branes, and in condensed matter physics in boundary critical behavior and quantum impurity models. In this article, however, I describe the basic ideas from the point of view of quantum field theory, without regard to particular applications nor to any deeper mathematical formulations.

  10. Conformal field theory

    CERN Document Server

    Ketov, Sergei V

    1995-01-01

    Conformal field theory is an elegant and powerful theory in the field of high energy physics and statistics. In fact, it can be said to be one of the greatest achievements in the development of this field. Presented in two dimensions, this book is designed for students who already have a basic knowledge of quantum mechanics, field theory and general relativity. The main idea used throughout the book is that conformal symmetry causes both classical and quantum integrability. Instead of concentrating on the numerous applications of the theory, the author puts forward a discussion of the general

  11. 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.

  12. Conformational properties of oxazoline-amino acids

    Science.gov (United States)

    Staś, Monika; Broda, Małgorzata A.; Siodłak, Dawid

    2016-04-01

    Oxazoline-amino acids (Xaa-Ozn) occur in natural peptides of potentially important bioactivity. The conformations of the model compounds: Ac-(S)-Ala-Ozn(4R-Me), Ac-(S)-Ala-Ozn(4S-Me), and (gauche+, gauche-, anti) Ac-(S)-Val-Ozn(4R-Me) were studied at meta-hybrid M06-2X/6-311++G(d,p) method including solvent effect. Boc-L-Ala-L-Ozn-4-COOMe and Boc-L-Val-L-Ozn-4-COOMe were synthesized and studied by FT-IR and NMR-NOE methods. The conformations in crystal state were gathered from the Cambridge Structural Data Base. The main conformational feature of the oxazoline amino acids is the conformation β2 (ϕ,ψ ∼ -161°, -6°), which predominates in weakly polar environment and still is accessible in polar surrounding. The changes of the conformational preferences towards the conformations αR (ϕ,ψ ∼ -70°, -15°) and then β (ϕ,ψ ∼ -57°, -155°) are observed with increase of the environment polarity.

  13. Photosystem I light-harvesting complex Lhca4 adopts multiple conformations : Red forms and excited-state quenching are mutually exclusive

    NARCIS (Netherlands)

    Passarini, Francesca; Wientjes, Emilie; van Amerongen, Herbert; Croce, Roberta

    2010-01-01

    In this work we have investigated the origin of the multi-exponential fluorescence decay and of the short excited-state lifetime of Lhca4. Lhca4 is the antenna complex of Photosystem I which accommodates the red-most chlorophyll forms and it has been proposed that these chlorophylls can play a role

  14. Photosystem I light-harvesting complex Lhca4 adopts multiple conformations: red forms and excited-state quenching are mutually exclusive

    NARCIS (Netherlands)

    Passarini, F.; Wientjes, E.; Amerongen, van H.; Croce, R.

    2010-01-01

    In this work we have investigated the origin of the multi-exponential fluorescence decay and of the short excited-state lifetime of Lhca4. Lhca4 is the antenna complex of Photosystem I which accommodates the red-most chlorophyll forms and it has been proposed that these chlorophylls can play a role

  15. Structural and magnetic conformation of a cerocene [Ce(COT'')2]- exhibiting a uniconfigurational f1 ground state and slow-magnetic relaxation.

    Science.gov (United States)

    Le Roy, Jennifer J; Korobkov, Ilia; Kim, Jee Eon; Schelter, Eric J; Murugesu, Muralee

    2014-02-21

    Magnet-like behaviour, in the form of slow relaxation of the magnetization, was observed for a monometallic cerium(III) sandwich complex. The use of trimethylsilyl substituted COT ligands (COT'') led to the formation of a staggered COT'' arrangement in the cerocene-type sandwich complex with a well-defined oxidation state of +3 for the Ce ion.

  16. Helical Conformation in the CA-SP1 Junction of the Immature HIV-1 Lattice Determined from Solid-State NMR of Virus-like Particles.

    Science.gov (United States)

    Bayro, Marvin J; Ganser-Pornillos, Barbie K; Zadrozny, Kaneil K; Yeager, Mark; Tycko, Robert

    2016-09-21

    Maturation of HIV-1 requires disassembly of the Gag polyprotein lattice, which lines the viral membrane in the immature state, and subsequent assembly of the mature capsid protein lattice, which encloses viral RNA in the mature state. Metastability of the immature lattice has been proposed to depend on the existence of a structurally ordered, α-helical segment spanning the junction between capsid (CA) and spacer peptide 1 (SP1) subunits of Gag, a segment that is dynamically disordered in the mature capsid lattice. We report solid state nuclear magnetic resonance (ssNMR) measurements on the immature lattice in noncrystalline, spherical virus-like particles (VLPs) derived from Gag. The ssNMR data provide definitive evidence for this critical α-helical segment in the VLPs. Differences in ssNMR chemical shifts and signal intensities between immature and mature lattice assemblies also support a major rearrangement of intermolecular interactions in the maturation process, consistent with recent models from electron cryomicroscopy and X-ray crystallography.

  17. 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-...

  18. Conformal cloak for waves

    CERN Document Server

    Chen, Huanyang; Tyc, Tomas

    2011-01-01

    Conformal invisibility devices are only supposed to work within the validity range of geometrical optics. Here we show by numerical simulations and analytical arguments that for certain quantized frequencies they are nearly perfect even in a regime that clearly violates geometrical optics. The quantization condition follows from the analogy between the Helmholtz equation and the stationary Schrodinger equation.

  19. Conformal supermultiplets without superpartners

    CERN Document Server

    Jarvis, Peter

    2011-01-01

    We consider polynomial deformations of Lie superalgebras and their representations. For the class A(n-1,0) ~ sl(n/1), we identify families of superalgebras of quadratic and cubic type, consistent with Jacobi identities. For such deformed superalgebras we point out the possibility of zero step supermultiplets, carried on a single, irreducible representation of the even (Lie) subalgebra. For the conformal group SU(2,2) in 1+3-dimensional spacetime, such irreducible (unitary) representations correspond to standard conformal fields (j_1,j_2;d), where (j_1,j_2) is the spin and d the conformal dimension; in the massless class j_1 j_2=0, and d=j_1+j_2+1. We show that these repesentations are zero step supermultiplets for the superalgebra SU_(2)(2,2/1), the quadratic deformation of conformal supersymmetry SU(2,2/1). We propose to elevate SU_(2)(2,2/1) to a symmetry of the S-matrix. Under this scenario, low-energy standard model matter fields (leptons, quarks, Higgs scalars and gauge fields) descended from such confor...

  20. Conformal General Relativity

    CERN Document Server

    Pervushin, V

    2001-01-01

    The inflation-free solution of problems of the modern cosmology (horizon, cosmic initial data, Planck era, arrow of time, singularity,homogeneity, and so on) is considered in the conformal-invariant unified theory given in the space with geometry of similarity where we can measure only the conformal-invariant ratio of all quantities. Conformal General Relativity is defined as the $SU_c(3)\\times SU(2)\\times U(1)$-Standard Model where the dimensional parameter in the Higgs potential is replaced by a dilaton scalar field described by the negative Penrose-Chernikov-Tagirov action. Spontaneous SU(2) symmetry breaking is made on the level of the conformal-invariant angle of the dilaton-Higgs mixing, and it allows us to keep the structure of Einstein's theory with the equivalence principle. We show that the lowest order of the linearized equations of motion solves the problems mentioned above and describes the Cold Universe Scenario with the constant temperature T and z-history of all masses with respect to an obser...

  1. Excited-State Conformational/Electronic Responses of Saddle-Shaped N,N'-Disubstituted-Dihydrodibenzo[a,c]phenazines: Wide-Tuning Emission from Red to Deep Blue and White Light Combination.

    Science.gov (United States)

    Zhang, Zhiyun; Wu, Yu-Sin; Tang, Kuo-Chun; Chen, Chi-Lin; Ho, Jr-Wei; Su, Jianhua; Tian, He; Chou, Pi-Tai

    2015-07-08

    A tailored strategy is utilized to modify 5,10-dimethylphenazine (DMP) to donor-acceptor type N,N'-disubstituted-dihydrodibenzo[a,c]phenazines. The representative compounds DMAC (N,N'-dimethyl), DPAC (N,N'-diphenyl), and FlPAC (N-phenyl-N'-fluorenyl) reveal significant nonplanar distortions (i.e., a saddle shape) and remarkably large Stokes-shifted emission independent of the solvent polarity. For DPAC and FlPAC with higher steric hindrance on the N,N'-substituents, normal Stokes-shifted emission also appears, for which the peak wavelength reveals solvent-polarity dependence. These unique photophysical behaviors are rationalized by electronic configuration coupled conformation changes en route to the geometry planarization in the excited state. This proposed mechanism is different from the symmetry rule imposed to explain the anomalously long-wavelength emission for DMP and is firmly supported by polarity-, viscosity-, and temperature-dependent steady-state and nanosecond time-resolved spectroscopy. Together with femtosecond early dynamics and computational simulation of the reaction energy surfaces, the results lead us to establish a sequential, three-step kinetics. Upon electronic excitation of N,N'-disubstituted-dihydrodibenzo[a,c]phenazines, intramolecular charge-transfer takes place, followed by the combination of polarization stabilization and skeletal motion toward the planarization, i.e., elongation of the π-delocalization over the benzo[a,c]phenazines moiety. Along the planarization, DPAC and FlPAC encounter steric hindrance raised by the N,N'-disubstitutes, resulting in a local minimum state, i.e., the intermediate. The combination of initial charge-transfer state, intermediate, and the final planarization state renders the full spectrum of interest and significance in their anomalous photophysics. Depending on rigidity, the N,N'-disubstituted-dihydrodibenzo[a,c]phenazines exhibit multiple emissions, which can be widely tuned from red to deep blue and

  2. 40 CFR 93.161 - Conformity evaluation for Federal installations with facility-wide emission budgets.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Conformity evaluation for Federal... PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR FEDERAL IMPLEMENTATION PLANS Determining Conformity of General Federal Actions to State or...

  3. 40 CFR 93.158 - Criteria for determining conformity of general Federal actions.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Criteria for determining conformity of... (CONTINUED) AIR PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR FEDERAL IMPLEMENTATION PLANS Determining Conformity of General Federal Actions to State or Federal Implementation...

  4. 40 CFR 93.159 - Procedures for conformity determinations of general Federal actions.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Procedures for conformity... PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR FEDERAL IMPLEMENTATION PLANS Determining Conformity of General Federal Actions to State or...

  5. Conformational Dynamics on the Extracellular Side of LeuT Controlled by Na+ and K+ Ions and the Protonation State of Glu(290)

    DEFF Research Database (Denmark)

    Khelashvili, George; Schmidt, Solveig Gaarde; Shi, Lei

    2016-01-01

    the unoccupied Na2 site of dopamine transporter following the release of the Na2-bound Na+. Here we evaluate with computational simulations and experimental measurements of ion affinities under corresponding conditions, the consequences of K+ binding in the Na2 site of LeuT, a bacterial homolog of NSS, when both......, point to the Glu290 protonation state as a main determinant in the structural reconfiguration of the extracellular vestibule of LeuT in which a “water gate” opens through coordinated motions of residues Leu25, Tyr108, and Phe253. The resulting water channel enables the binding/dissociation of the Na...

  6. 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

  7. A Conformal Extension Theorem based on Null Conformal Geodesics

    CERN Document Server

    Lübbe, Christian

    2008-01-01

    In this article we describe the formulation of null geodesics as null conformal geodesics and their description in the tractor formalism. A conformal extension theorem through an isotropic singularity is proven by requiring the boundedness of the tractor curvature and its derivatives to sufficient order along a congruence of null conformal geodesic. This article extends earlier work by Tod and Luebbe.

  8. 20 CFR 640.4 - Standard for conformity.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 3 2010-04-01 2010-04-01 false Standard for conformity. 640.4 Section 640.4 Employees' Benefits EMPLOYMENT AND TRAINING ADMINISTRATION, DEPARTMENT OF LABOR STANDARD FOR BENEFIT PAYMENT PROMPTNESS-UNEMPLOYMENT COMPENSATION § 640.4 Standard for conformity. A State law will satisfy...

  9. Conformation of some carboxylic acids and their derivatives

    NARCIS (Netherlands)

    Kanters, J.A.; Kroon, Jan; Peerdeman, A.F.; Schoone, J.C.

    1967-01-01

    The conformation in the crystalline state of some aliphatic carboxylic acids and their derivatives has been analysed. This analysis, based upon the results of structure determinations by means of X-ray diffraction, seems to support the concept that the conformation of a molecule is governed chiefly

  10. Jet-cooled fluorescence excitation spectra, conformation, and carbonyl wagging potential energy function of cyclopentanone and its deuterated isotopomers in the S1 (n,π*) electronic excited states

    Science.gov (United States)

    Zhang, Jian; Chiang, Whe-Yi; Laane, Jaan

    1993-04-01

    The jet-cooled fluorescence excitation spectra of cyclopentanone and its 2,2,5,5-d4 isotopomer have been recorded in the 305-335 nm region. In addition, the spectra of d1, d2, and d3 species were obtained from isotopic mixtures. The electronic band origin of the d0 molecule for the S1 (n,π*) state of A2 symmetry occurs at 30 276 cm-1, while that of the d4 molecule is at 30 265 cm-1. More than 100 fluorescence bands were assigned for each species. These arise from combinations of ν3 (C=O stretch), ν11 (ring-angle bending), ν18 (ring twisting), ν25 (C=O out-of-plane wag), ν26 (ring bending), and ν36 (C=O in-plane wag) and their vibrational excited states. The vibrational frequencies for ν3, ν11, and ν36 are significantly lower in the S1 state than the S0 ground state. However, the out-of-plane ring modes ν18 and ν26 are only slightly shifted. A progression observed for ν26 does indicate that in the S1 state, the bent ring conformation lies about 500 cm-1 above the ring-twisting minimum and corresponds to a saddle point in the two-dimensional ring-twisting/ring-bending potential energy surface. Band progressions for ν18 can be used to calculate the ring-twisting barriers (the barriers to planarity) for the d0 and d4 isotopomers to be 1433 and 1240 cm-1, respectively. Because of limited data, however, these values may be as much as several hundred cm-1 too high. The energies for the C=O out-of-plane wagging states up to v25=9 for each isotopomer were determined for the S1 state and these were used to calculate the C=O wagging potential energy functions for each. In the S1 state, the barrier to inversion of the C=O group is 672±10 cm-1 and the wagging angle is 22°±1°.

  11. CONFORMATIONAL PROPERTIES OF STRETCHED POLYETHYLENE CHAIN

    Institute of Scientific and Technical Information of China (English)

    Lin-xi Zhang; De-lu Zhao

    2000-01-01

    When polyethylene chains are stretched, the chains are regarded as being confined in an infinite cylinder with decreasing diameter. The conformational properties of polyethylene chains confined in an infinite cylinder are investigated by using rotational isomeric state model. Using the average conformational energy and entropy and the average length, we can determine the elastic force f, or the fraction of the energy term to the total force fe/f, where fe=(б)/(б)/(б). Comparisons with experimental data are also made. The results of these microscopic calculations are discussed in terms of the macroscopic phenomena of rubber elasticity.

  12. Ubiquitin chain conformation regulates recognition and activity of interacting proteins.

    Science.gov (United States)

    Ye, Yu; Blaser, Georg; Horrocks, Mathew H; Ruedas-Rama, Maria J; Ibrahim, Shehu; Zhukov, Alexander A; Orte, Angel; Klenerman, David; Jackson, Sophie E; Komander, David

    2012-12-13

    Mechanisms of protein recognition have been extensively studied for single-domain proteins, but are less well characterized for dynamic multidomain systems. Ubiquitin chains represent a biologically important multidomain system that requires recognition by structurally diverse ubiquitin-interacting proteins. Ubiquitin chain conformations in isolation are often different from conformations observed in ubiquitin-interacting protein complexes, indicating either great dynamic flexibility or extensive chain remodelling upon binding. Using single-molecule fluorescence resonance energy transfer, we show that Lys 63-, Lys 48- and Met 1-linked diubiquitin exist in several distinct conformational states in solution. Lys 63- and Met 1-linked diubiquitin adopt extended 'open' and more compact 'closed' conformations, and ubiquitin-binding domains and deubiquitinases (DUBs) select pre-existing conformations. By contrast, Lys 48-linked diubiquitin adopts predominantly compact conformations. DUBs directly recognize existing conformations, but may also remodel ubiquitin chains to hydrolyse the isopeptide bond. Disruption of the Lys 48-diubiquitin interface changes conformational dynamics and affects DUB activity. Hence, conformational equilibria in ubiquitin chains provide an additional layer of regulation in the ubiquitin system, and distinct conformations observed in differently linked polyubiquitin may contribute to the specificity of ubiquitin-interacting proteins.

  13. From integrable to conformal theory

    Energy Technology Data Exchange (ETDEWEB)

    Babelon, O. (Paris-6 Univ., 75 (France). Lab. de Physique Theorique et Hautes Energies)

    1990-12-01

    Working in the context of Toda field theory, we establish the relationship between their integrability properties and their conformal structure, thereby clarifying the role of the Yang-Baxter equation in conformal field theory. (orig.).

  14. A conformal block Farey tail

    CERN Document Server

    Maloney, Alexander; Ng, Gim Seng

    2016-01-01

    We investigate the constraints of crossing symmetry on CFT correlation functions. Four point conformal blocks are naturally viewed as functions on the upper-half plane, on which crossing symmetry acts by PSL(2,Z) modular transformations. This allows us to construct a unique, crossing symmetric function out of a given conformal block by averaging over PSL(2,Z). In some two dimensional CFTs the correlation functions are precisely equal to the modular average of the contributions of a finite number of light states. For example, in the two dimensional Ising and tri-critical Ising model CFTs, the correlation functions of identical operators are equal to the PSL(2,Z) average of the Virasoro vacuum block; this determines the 3 point function coefficients uniquely in terms of the central charge. The sum over PSL(2,Z) in CFT2 has a natural AdS3 interpretation as a sum over semi-classical saddle points, which describe particles propagating along rational tangles in the bulk. We demonstrate this explicitly for the corre...

  15. Conformation of 1,2-Dimethoxyethane in Water

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    To understand the conformation of 1,2-dimethoxyethane (DME) in water, a system of two kinds of molecules, DME and H2O, was focused. The interaction of various conformers of DME with water was studied by means of ab initio molecular orbital calculation with 6-31G(d)basis set. It is shown that there are two forms of interactions between the two molecules in the sys tem, the close touched (H2O attaches to the two oxygen atoms of DME) and the open touched (H2O attaches to one oxygen atom of DME) structures. The conformation of DME is remark ably influenced by the interactions. Instead the ttt conformer is preferred in the gas state, with a close touched H2O the tgt conformer becomes the most stable one. The obtained hydration ener gies show that the stabilized order of DME conformers by water is tgt>tgg'>ttt.

  16. On conformal lenses

    CERN Document Server

    Chen, Huanyang; Li, Hui

    2011-01-01

    Plane mirror can make one object into two for observers on the object's side. Yet, there seems no way to achieve the same effect for observers from all directions. In this letter, we will design a new class of gradient index lenses from multivalued optical conformal mapping. We shall call them the conformal lenses. Such lenses can transform one source into two (or even many) omnidirectionally. Like the overlapped illusion optics does, they can even transform multiple sources into one. Rather than using negative index materials, implementation here only needs isotropic positive index materials like other gradient index lenses. One obvious drawback however, is that they have singular permittivity values which restrict them to functioning at one single frequency. This however, needs not be the case when applying transmutation methods, which enable the lenses to work in a broadband frequency range.

  17. 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.

  18. Conformational flexibility of aspartame.

    Science.gov (United States)

    Toniolo, Claudio; Temussi, Pierandrea

    2016-05-01

    L-Aspartyl-L-phenylalanine methyl ester, better known as aspartame, is not only one of the most used artificial sweeteners, but also a very interesting molecule with respect to the correlation between molecular structure and taste. The extreme conformational flexibility of this dipeptide posed a huge difficulty when researchers tried to use it as a lead compound to design new sweeteners. In particular, it was difficult to take advantage of its molecular model as a mold to infer the shape of the, then unknown, active site of the sweet taste receptor. Here, we follow the story of the 3D structural aspects of aspartame from early conformational studies to recent docking into homology models of the receptor. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 376-384, 2016.

  19. A profissão de músico conforme apresentada em jornais paraibanos The profession of musician in the paraíba state newspapers

    Directory of Open Access Journals (Sweden)

    Sandra Souza

    2010-04-01

    Full Text Available O artigo relata estudo sobre a profissão dos músicos na Paraíba, realizado por meio da aplicação da análise de conteúdo de dois jornais diários do Estado. A referida análise foi desenvolvida com uma amostra de números referentes aos anos de 2001 e 2003. Identificaram-se quatro categorias (papel social da música; incentivo à música; profissão e organização político-associativas. Tal estudo empírico resultou na identificação de aspectos centrais e importantes na construção da identidade profissional, como: o profissionalismo versus amadorismo; o mito da fama versus o anonimato; desvalorização da chamada prata da casa versus valorização do estrangeiro, etc. Embora não esgotem o tema, situam o lugar que a profissão ocupa na sociedade e pode se constituir em fonte para a elaboração de novas questões e hipóteses para os pesquisadores que se interessarem pela temática.The article reports study on the profession of musicians in the State of Paraíba, conducted by applying the analysis of contents of two daily newspapers of the State. The analysis itself was developed with a sample of issues of the years 2001 and 2003. Four categories were identified (social role of the music; encouraging the music; profession and associative political organization. Such empirical study resulted in the identification of key and important aspects, in the construction of a professional identity, as, professionalism versus amateurism; the myth of fame versus the anonymity; the depreciation of the so-called home talent versus the value of the foreign ones, and so on. Even though this type of media does not exhaust the subject, it establishes the position that the profession occupies in the society and may constitute itself a source for the development of new questions and hypotheses for the researchers interested in the topic.

  20. 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....

  1. Conformational Dynamics on the Extracellular Side of LeuT Controlled by Na+ and K+ Ions and the Protonation State of Glu290.

    Science.gov (United States)

    Khelashvili, George; Schmidt, Solveig Gaarde; Shi, Lei; Javitch, Jonathan A; Gether, Ulrik; Loland, Claus J; Weinstein, Harel

    2016-09-16

    Ions play key mechanistic roles in the gating dynamics of neurotransmitter:sodium symporters (NSSs). In recent microsecond scale molecular dynamics simulations of a complete model of the dopamine transporter, a NSS protein, we observed a partitioning of K(+) ions from the intracellular side toward the unoccupied Na2 site of dopamine transporter following the release of the Na2-bound Na(+) Here we evaluate with computational simulations and experimental measurements of ion affinities under corresponding conditions, the consequences of K(+) binding in the Na2 site of LeuT, a bacterial homolog of NSS, when both Na(+) ions and substrate have left, and the transporter prepares for a new cycle. We compare the results with the consequences of binding Na(+) in the same apo system. Analysis of >50-μs atomistic molecular dynamics and enhanced sampling trajectories of constructs with Glu(290), either charged or neutral, point to the Glu(290) protonation state as a main determinant in the structural reconfiguration of the extracellular vestibule of LeuT in which a "water gate" opens through coordinated motions of residues Leu(25), Tyr(108), and Phe(253) The resulting water channel enables the binding/dissociation of the Na(+) and K(+) ions that are prevalent, respectively, in the extracellular and intracellular environments.

  2. Enhanced conformational sampling technique provides an energy landscape view of large-scale protein conformational transitions.

    Science.gov (United States)

    Shao, Qiang

    2016-10-26

    Large-scale conformational changes in proteins are important for their functions. Tracking the conformational change in real time at the level of a single protein molecule, however, remains a great challenge. In this article, we present a novel in silico approach with the combination of normal mode analysis and integrated-tempering-sampling molecular simulation (NMA-ITS) to give quantitative data for exploring the conformational transition pathway in multi-dimensional energy landscapes starting only from the knowledge of the two endpoint structures of the protein. The open-to-closed transitions of three proteins, including nCaM, AdK, and HIV-1 PR, were investigated using NMA-ITS simulations. The three proteins have varied structural flexibilities and domain communications in their respective conformational changes. The transition state structure in the conformational change of nCaM and the associated free-energy barrier are in agreement with those measured in a standard explicit-solvent REMD simulation. The experimentally measured transition intermediate structures of the intrinsically flexible AdK are captured by the conformational transition pathway measured here. The dominant transition pathways between the closed and fully open states of HIV-1 PR are very similar to those observed in recent REMD simulations. Finally, the evaluated relaxation times of the conformational transitions of three proteins are roughly at the same level as reported experimental data. Therefore, the NMA-ITS method is applicable for a variety of cases, providing both qualitative and quantitative insights into the conformational changes associated with the real functions of proteins.

  3. Computation of conformational coupling in allosteric proteins.

    Directory of Open Access Journals (Sweden)

    Brian A Kidd

    2009-08-01

    Full Text Available In allosteric regulation, an effector molecule binding a protein at one site induces conformational changes, which alter structure and function at a distant active site. Two key challenges in the computational modeling of allostery are the prediction of the structure of one allosteric state starting from the structure of the other, and elucidating the mechanisms underlying the conformational coupling of the effector and active sites. Here we approach these two challenges using the Rosetta high-resolution structure prediction methodology. We find that the method can recapitulate the relaxation of effector-bound forms of single domain allosteric proteins into the corresponding ligand-free states, particularly when sampling is focused on regions known to change conformation most significantly. Analysis of the coupling between contacting pairs of residues in large ensembles of conformations spread throughout the landscape between and around the two allosteric states suggests that the transitions are built up from blocks of tightly coupled interacting sets of residues that are more loosely coupled to one another.

  4. Two Additional Remarks on Conformism

    OpenAIRE

    Schlicht, Ekkehart

    2014-01-01

    Abstract This note offers two comments on the article “Social Influences towards Conformism in Economic Experiments” by Hargreaves Heap that is to appear in the Economics e-Journal. One relates to the concept of conformism, the other lines out some phenomena where an explicit recognition of group processes, such as conformism, may be analytically helpful.

  5. Conformational stability and self-association equilibrium in biologics.

    Science.gov (United States)

    Clarkson, Benjamin R; Schön, Arne; Freire, Ernesto

    2016-02-01

    Biologics exist in equilibrium between native, partially denatured, and denatured conformational states. The population of any of these states is dictated by their Gibbs energy and can be altered by changes in physical and solution conditions. Some conformations have a tendency to self-associate and aggregate, an undesirable phenomenon in protein therapeutics. Conformational equilibrium and self-association are linked thermodynamic functions. Given that any associative reaction is concentration dependent, conformational stability studies performed at different protein concentrations can provide early clues to future aggregation problems. This analysis can be applied to the selection of protein variants or the identification of better formulation solutions. In this review, we discuss three different aggregation situations and their manifestation in the observed conformational equilibrium of a protein.

  6. 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.

  7. Project-Level Conformity and Hot-Spot Analyses

    Science.gov (United States)

    This page contains policy guidance issued by EPA and/or the U.S. Department of Transportation to assist state and local transportation and air quality agencies implement the transportation conformity program.

  8. OSI Conformance Testing for Bibliographic Applications.

    Science.gov (United States)

    Arbez, Gilbert; Swain, Leigh

    1990-01-01

    Describes the development of Open Systems Interconnection (OSI) conformance testing sites, conformance testing tools, and conformance testing services. Discusses related topics such as interoperability testing, arbitration testing, and international harmonization of conformance testing. A glossary is included. (24 references) (SD)

  9. Leaf growth is conformal

    CERN Document Server

    Alim, Karen; Shraiman, Boris I; Boudaoud, Arezki

    2016-01-01

    Growth pattern dynamics lie at the heart of morphogenesis. Here, we investigate the growth of plant leaves. We compute the conformal transformation that maps the contour of a leaf at a given stage onto the contour of the same leaf at a later stage. Based on the mapping we predict the local displacement field in the leaf blade and find it to agree with the experimentally measured displacement field to 92%. This approach is applicable to any two-dimensional system with locally isotropic growth, enabling the deduction of the whole growth field just from observation of the tissue contour.

  10. 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....

  11. Leaf growth is conformal

    Science.gov (United States)

    Alim, Karen; Armon, Shahaf; Shraiman, Boris I.; Boudaoud, Arezki

    2016-10-01

    Growth pattern dynamics lie at the heart of morphogenesis. Here, we investigate the growth of plant leaves. We compute the conformal transformation that maps the contour of a leaf at a given stage onto the contour of the same leaf at a later stage. Based on the mapping we predict the local displacement field in the leaf blade and find it to agree with the experimentally measured displacement field to 92%. This approach is applicable to any two-dimensional system with locally isotropic growth, enabling the deduction of the whole growth field just from observation of the tissue contour.

  12. Conformal fluid dynamics

    CERN Document Server

    Jarvis, P D

    2006-01-01

    We present a conformal theory of a dissipationless relativistic fluid in 2 space-time dimensions. The theory carries with it a representation of the algebra of 2-$D$ area-preserving diffeomorphisms in the target space of the complex scalar potentials. A complete canonical description is given, and the central charge of the current algebra is calculated. The passage to the quantum theory is discussed in some detail; as a result of operator ordering problems, full quantization at the level of the fields is as yet an open problem.

  13. Conformational Transition of Poly (Acrylic Acid) Detected by Microcantilever Sensing

    Institute of Scientific and Technical Information of China (English)

    LI Kai; LIU Hong; ZHANG Qing-Chuan; XUE Chang-Guo; WU Xiao-Ping

    2007-01-01

    Poly (acrylic acid) (PAA) chains are grafted on one side of a microcantilever by the self-assembled method and the deflections of the microcantilever are detected as a function of medium pH from 3 to 11. It is found that when the pH varies, the microcantilever deflects because of the changing surface stress. By analysing the electrostatic repulsive effect, the surface stress change is related to the conformation transition of PAA from a collapse state to a swelling state. This method offers the interaction information among the polymer chains during the conformational transition and affords an alternative way to study conformational change of polymers.

  14. Relating conformation to function in integrin α5β1.

    Science.gov (United States)

    Su, Yang; Xia, Wei; Li, Jing; Walz, Thomas; Humphries, Martin J; Vestweber, Dietmar; Cabañas, Carlos; Lu, Chafen; Springer, Timothy A

    2016-07-05

    Whether β1 integrin ectodomains visit conformational states similarly to β2 and β3 integrins has not been characterized. Furthermore, despite a wealth of activating and inhibitory antibodies to β1 integrins, the conformational states that these antibodies stabilize, and the relation of these conformations to function, remain incompletely characterized. Using negative-stain electron microscopy, we show that the integrin α5β1 ectodomain adopts extended-closed and extended-open conformations as well as a bent conformation. Antibodies SNAKA51, 8E3, N29, and 9EG7 bind to different domains in the α5 or β1 legs, activate, and stabilize extended ectodomain conformations. Antibodies 12G10 and HUTS-4 bind to the β1 βI domain and hybrid domains, respectively, activate, and stabilize the open headpiece conformation. Antibody TS2/16 binds a similar epitope as 12G10, activates, and appears to stabilize an open βI domain conformation without requiring extension or hybrid domain swing-out. mAb13 and SG/19 bind to the βI domain and βI-hybrid domain interface, respectively, inhibit, and stabilize the closed conformation of the headpiece. The effects of the antibodies on cell adhesion to fibronectin substrates suggest that the extended-open conformation of α5β1 is adhesive and that the extended-closed and bent-closed conformations are nonadhesive. The functional effects and binding sites of antibodies and fibronectin were consistent with their ability in binding to α5β1 on cell surfaces to cross-enhance or inhibit one another by competitive or noncompetitive (allosteric) mechanisms.

  15. 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

  16. Conformal invariant saturation

    CERN Document Server

    Navelet, H

    2002-01-01

    We show that, in onium-onium scattering at (very) high energy, a transition to saturation happens due to quantum fluctuations of QCD dipoles. This transition starts when the order alpha^2 correction of the dipole loop is compensated by its faster energy evolution, leading to a negative interference with the tree level amplitude. After a derivation of the the one-loop dipole contribution using conformal invariance of the elastic 4-gluon amplitude in high energy QCD, we obtain an exact expression of the saturation line in the plane (Y,L) where Y is the total rapidity and L, the logarithm of the onium scale ratio. It shows universal features implying the Balitskyi - Fadin - Kuraev - Lipatov (BFKL) evolution kernel and the square of the QCD triple Pomeron vertex. For large L, only the higher BFKL Eigenvalue contributes, leading to a saturation depending on leading log perturbative QCD characteristics. For initial onium scales of same order, however, it involves an unlimited summation over all conformal BFKL Eigen...

  17. Hot Conformal Gauge Theories

    CERN Document Server

    Mojaza, Matin; Sannino, Francesco

    2010-01-01

    We compute the nonzero temperature free energy up to the order g^6 \\ln(1/g) in the coupling constant for vector like SU(N) gauge theories featuring matter transforming according to different representations of the underlying gauge group. The number of matter fields, i.e. flavors, is arranged 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 o...

  18. Spacetime Conformal Fluctuations and Quantum Dephasing

    Science.gov (United States)

    Bonifacio, Paolo M.

    2009-06-01

    Any quantum system interacting with a complex environment undergoes decoherence. Empty space is filled with vacuum energy due to matter fields in their ground state and represents an underlying environment that any quantum particle has to cope with. In particular quantum gravity vacuum fluctuations should represent a universal source of decoherence. To study this problem we employ a stochastic approach that models spacetime fluctuations close to the Planck scale by means of a classical, randomly fluctuating metric (random gravity framework). We enrich the classical scheme for metric perturbations over a curved background by also including matter fields and metric conformal fluctuations. We show in general that a conformally modulated metric induces dephasing as a result of an effective nonlinear newtonian potential obtained in the appropriate nonrelativistic limit of a minimally coupled Klein-Gordon field. The special case of vacuum fluctuations is considered and a quantitative estimate of the expected effect deduced. Secondly we address the question of how conformal fluctuations could physically arise. By applying the random gravity framework we first show that standard GR seems to forbid spontaneous conformal metric modulations. Finally we argue that a different result follows within scalar-tensor theories of gravity such as e.g. Brans-Dicke theory. In this case a conformal modulation of the metric arises naturally as a result of the fluctuations in the Brans-Dicke field and quantum dephasing of a test particle is expected to occur. For large negative values of the coupling parameter the conformal fluctuations may also contribute to alleviate the well known problem of the large zero point energy due to quantum matter fields.

  19. Determination of conformational entropy of fully and partially folded conformations of holo- and apomyoglobin.

    Science.gov (United States)

    Stadler, Andreas M; Koza, Michael Marek; Fitter, Jörg

    2015-01-08

    Holo- and apomyoglobin can be stabilized in native folded, partially folded molten globules (MGs) and denatured states depending on the solvent composition. Although the protein has been studied as a model system in the field of protein folding, little is known about the internal dynamics of the different structural conformations on the picosecond time scale. In a comparative experimental study we investigated the correlation between protein folding and dynamics on the picosecond time scale using incoherent quasielastic neutron scattering (QENS). The measured mean square displacements (MSDs) of conformational motions depend significantly on the secondary structure content of the protein, whereas the correlation times of the observed internal dynamics were found to be similar irrespective of the degree of folding. The conformational entropy difference ΔSconf between the folded conformations and the acid denatured state could be determined from the measured MSDs and was compared to the entropy difference ΔS obtained from thermodynamic parameters reported in the literature. The observed difference between ΔS and ΔSconf was attributed to the entropy difference ΔShydr of dynamically disordered water molecules of the hydration shell. The entropy content of the hydration water is significantly larger in the native folded proteins than in the partially folded MGs. We demonstrate the potential of incoherent neutron scattering for the investigation of the role of conformational dynamics in protein folding.

  20. 15 CFR 758.5 - Conformity of documents and unloading of items.

    Science.gov (United States)

    2010-01-01

    ... 15 Commerce and Foreign Trade 2 2010-01-01 2010-01-01 false Conformity of documents and unloading... REGULATIONS EXPORT CLEARANCE REQUIREMENTS § 758.5 Conformity of documents and unloading of items. (a) Purpose... country other than that of the ultimate consignee as stated on the export license. (b) Conformity...

  1. 40 CFR 51.858 - Criteria for determining conformity of general Federal actions.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 2 2010-07-01 2010-07-01 false Criteria for determining conformity of... Determining Conformity of General Federal Actions to State or Federal Implementation Plans § 51.858 Criteria for determining conformity of general Federal actions. Link to an amendment published at 75 FR...

  2. 40 CFR 51.859 - Procedures for conformity determinations of general Federal actions.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 2 2010-07-01 2010-07-01 false Procedures for conformity... IMPLEMENTATION PLANS Determining Conformity of General Federal Actions to State or Federal Implementation Plans § 51.859 Procedures for conformity determinations of general Federal actions. Link to an...

  3. Subtleties Concerning Conformal Tractor Bundles

    CERN Document Server

    Graham, C Robin

    2012-01-01

    The realization of tractor bundles as associated bundles in conformal geometry is studied. It is shown that different natural choices of principal bundle with normal Cartan connection corresponding to a given conformal manifold can give rise to topologically distinct associated tractor bundles for the same inducing representation. Consequences for homogeneous models and conformal holonomy are described. A careful presentation is made of background material concerning standard tractor bundles and equivalence between parabolic geometries and underlying structures.

  4. Dimensional Reduction for Conformal Blocks

    CERN Document Server

    Hogervorst, Matthijs

    2016-01-01

    We consider the dimensional reduction of a CFT, breaking multiplets of the d-dimensional conformal group SO(d+1,1) up into multiplets of SO(d,1). This leads to an expansion of d-dimensional conformal blocks in terms of blocks in d-1 dimensions. In particular, we obtain a formula for 3d conformal blocks as an infinite sum over 2F1 hypergeometric functions with closed-form coefficients.

  5. Loop Virasoro Lie conformal algebra

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Henan, E-mail: wuhenanby@163.com; Chen, Qiufan; Yue, Xiaoqing [Department of Mathematics, Tongji University, Shanghai 200092 (China)

    2014-01-15

    The Lie conformal algebra of loop Virasoro algebra, denoted by CW, is introduced in this paper. Explicitly, CW is a Lie conformal algebra with C[∂]-basis (L{sub i} | i∈Z) and λ-brackets [L{sub i} {sub λ} L{sub j}] = (−∂−2λ)L{sub i+j}. Then conformal derivations of CW are determined. Finally, rank one conformal modules and Z-graded free intermediate series modules over CW are classified.

  6. Conformal frames in cosmology

    CERN Document Server

    Domènech, Guillem

    2016-01-01

    From higher dimensional theories, e.g. string theory, one expects the presence of non-minimally coupled scalar fields. We review the notion of conformal frames in cosmology and emphasize their physical equivalence, which holds at least at a classical level. Furthermore, if there is a field, or fields, which dominates the universe, as it is often the case in cosmology, we can use such notion of frames to treat our system, matter and gravity, as two different sectors. On one hand, the gravity sector which describes the dynamics of the geometry and on the other hand the matter sector which has such geometry as a playground. We use this interpretation to build a model where the fact that a curvaton couples to a particular frame metric could leave an imprint in the CMB.

  7. Reflections on Conformal Spectra

    CERN Document Server

    Kim, Hyungrok; Ooguri, Hirosi

    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 $\\Delta_0$ 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 $\\Delta_0$ as well as for large $\\Delta_0$. 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.

  8. Reflections on Conformal Spectra

    CERN Document Server

    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

  9. Conformational Memory of a Protein Revealed by Single-Molecule Spectroscopy.

    Science.gov (United States)

    Schörner, Mario; Beyer, Sebastian Reinhardt; Southall, June; Cogdell, Richard J; Köhler, Jürgen

    2015-11-01

    Proteins are supramolecular machines that carry out a wide range of different functions, many of which require flexibility. Up until now spontaneous conformational fluctuations of proteins have always been assumed to reflect a stochastic random process. However, if changing between different conformational states was random, then it would be difficult to understand how conformational control of protein function could have evolved. Here we demonstrate that a single protein can show conformational memory. This is exactly the process that can facilitate the evolution of control of switching between two conformational states that can then be used to regulate protein function.

  10. Enhancing Moral Conformity and Enhancing Moral Worth.

    Science.gov (United States)

    Douglas, Thomas

    2014-01-01

    It is plausible that we have moral reasons to become better at conforming to our moral reasons. However, it is not always clear what means to greater moral conformity we should adopt. John Harris has recently argued that we have reason to adopt traditional, deliberative means in preference to means that alter our affective or conative states directly-that is, without engaging our deliberative faculties. One of Harris' concerns about direct means is that they would produce only a superficial kind of moral improvement. Though they might increase our moral conformity, there is some deeper kind of moral improvement that they would fail to produce, or would produce to a lesser degree than more traditional means. I consider whether this concern might be justified by appeal to the concept of moral worth. I assess three attempts to show that, even where they were equally effective at increasing one's moral conformity, direct interventions would be less conducive to moral worth than typical deliberative alternatives. Each of these attempts is inspired by Kant's views on moral worth. Each, I argue, fails.

  11. 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.

  12. Water drives peptide conformational transitions

    CERN Document Server

    Nerukh, Dmitry

    2011-01-01

    Transitions between metastable conformations of a dipeptide are investigated using classical molecular dynamics simulation with explicit water molecules. The distribution of the surrounding water at different moments before the transitions and the dynamical correlations of water with the peptide's configurational motions indicate that water is the main driving force of the conformational changes.

  13. 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.

  14. 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.

  15. 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.

  16. Generally covariant vs. gauge structure for conformal field theories

    Energy Technology Data Exchange (ETDEWEB)

    Campigotto, M., E-mail: martacostanza.campigotto@to.infn.it [Dipartimento di Fisica, University of Torino, Via P. Giuria 1, 10125, Torino (Italy); Istituto Nazionale di Fisica Nucleare (INFN), Via P. Giuria 1, 10125, Torino (Italy); Fatibene, L. [Dipartimento di Matematica, University of Torino, Via C. Alberto 10, 10123, Torino (Italy); Istituto Nazionale di Fisica Nucleare (INFN), Via P. Giuria 1, 10125, Torino (Italy)

    2015-11-15

    We introduce the natural lift of spacetime diffeomorphisms for conformal gravity and discuss the physical equivalence between the natural and gauge natural structure of the theory. Accordingly, we argue that conformal transformations must be introduced as gauge transformations (affecting fields but not spacetime point) and then discuss special structures implied by the splitting of the conformal group. -- Highlights: •Both a natural and a gauge natural structure for conformal gravity are defined. •Global properties and natural lift of spacetime transformations are described. •The possible definitions of physical state are considered and discussed. •The gauge natural theory has less physical states than the corresponding natural one. •The dynamics forces to prefer the gauge natural structure over the natural one.

  17. The conformational dynamics of the mitochondrial Hsp70 chaperone.

    Science.gov (United States)

    Mapa, Koyeli; Sikor, Martin; Kudryavtsev, Volodymyr; Waegemann, Karin; Kalinin, Stanislav; Seidel, Claus A M; Neupert, Walter; Lamb, Don C; Mokranjac, Dejana

    2010-04-09

    Heat shock proteins 70 (Hsp70) represent a ubiquitous and conserved family of molecular chaperones involved in a plethora of cellular processes. The dynamics of their ATP hydrolysis-driven and cochaperone-regulated conformational cycle are poorly understood. We used fluorescence spectroscopy to analyze, in real time and at single-molecule resolution, the effects of nucleotides and cochaperones on the conformation of Ssc1, a mitochondrial member of the family. We report that the conformation of its ADP state is unexpectedly heterogeneous, in contrast to a uniform ATP state. Substrates are actively involved in determining the conformation of Ssc1. The J protein Mdj1 does not interact transiently with the chaperone, as generally believed, but rather is released slowly upon ATP hydrolysis. Analysis of the major bacterial Hsp70 revealed important differences between highly homologous members of the family, possibly explaining tuning of Hsp70 chaperones to meet specific functions in different organisms and cellular compartments.

  18. Hot Conformal Gauge Theories

    DEFF Research Database (Denmark)

    Mojaza, Matin; Pica, Claudio; Sannino, Francesco

    2010-01-01

    We compute the nonzero temperature free energy up to the order g^6 \\ln(1/g) in the coupling constant for vector like SU(N) gauge theories featuring matter transforming according to different representations of the underlying gauge group. The number of matter fields, i.e. flavors, is arranged in s.......e. they are independent on the specific matter representation.......We compute the nonzero temperature free energy up to the order g^6 \\ln(1/g) in the coupling constant for vector like SU(N) gauge theories featuring matter transforming according to different representations of the underlying gauge group. The number of matter fields, i.e. flavors, is arranged...... 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...

  19. The Conformal Standard Model

    CERN Document Server

    Latosinski, Adam; Meissner, Krzysztof A; Nicolai, Hermann

    2015-01-01

    We present an extended version of the Conformal Standard Model (characterized by the absence of any new intermediate scales between the electroweak scale and the Planck scale) with an enlarged scalar sector coupling to right-chiral neutrinos in such a way that the scalar potential and the Yukawa couplings involving only right-chiral neutrinos are invariant under a new global symmetry SU(3)$_N$ which is broken explicitly only by the Yukawa interaction coupling right-chiral neutrinos and the electroweak lepton doublets. We point out four main advantages of such an enlargement, namely: (1) the economy of the (non-supersymmetric) Standard Model, and thus its observational success, is preserved; (2) thanks to the enlarged scalar sector the RG improved one-loop effective potential is everywhere positive with a stable global minimum, thereby avoiding the notorious instability of the Standard Model vacuum; (3) the pseudo-Goldstone bosons resulting from spontaneous breaking of the SU(3)$_N$ symmetry are natural Dark M...

  20. Regular Submanifolds in Conformal Space Qnp

    Institute of Scientific and Technical Information of China (English)

    Changxiong NIE; Chuanxi WU

    2012-01-01

    The authors study the regular submanifolds in the conformal space Qnp and introduce the submanifold theory in the conformal space Qnp.The first variation formula of the Willmore volume functional of pseudo-Riemannian submanifolds in the conformal space Qnp is given.Finally,the conformal isotropic submanifolds in the conformal space Qnp are classified.

  1. Conformal collider physics: Energy and charge correlations

    CERN Document Server

    Hofman, Diego M

    2008-01-01

    We study observables in a conformal field theory which are very closely related to the ones used to describe hadronic events at colliders. We focus on the correlation functions of the energies deposited on calorimeters placed at a large distance from the collision. We consider initial states produced by an operator insertion and we study some general properties of the energy correlation functions for conformal field theories. We argue that the small angle singularities of energy correlation functions are controlled by the twist of non-local light-ray operators with a definite spin. We relate the charge two point function to a particular moment of the parton distribution functions appearing in deep inelastic scattering. The one point energy correlation functions are characterized by a few numbers. For ${\\cal N}=1$ superconformal theories the one point function for states created by the R-current or the stress tensor are determined by the two parameters $a$ and $c$ characterizing the conformal anomaly. Demandin...

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

    Science.gov (United States)

    Kamachi, Takashi; Yoshizawa, Kazunari

    2016-02-22

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

  3. Generalized Wilson-Fisher critical points from the conformal OPE

    CERN Document Server

    Gliozzi, Ferdinando; Petkou, Anastasios C; Wen, Congkao

    2016-01-01

    We study possible smooth deformations of Generalized Free Conformal Field Theories in arbitrary dimensions by exploiting the singularity structure of the conformal blocks dictated by the null states. We derive in this way, at the first non trivial order in the $\\epsilon$-expansion, the anomalous dimensions of an infinite class of scalar local operators, without using the equations of motion. In the cases where other computational methods apply, the results agree.

  4. Conformal anomaly around the sudden singularity

    CERN Document Server

    Houndjo, S J M

    2010-01-01

    Quantum effects due to particle creation on a classical sudden singularity have been investigated in a previous work. The conclusion was that quantum effects do not lead to the avoidance nor the modification of the sudden future singularity. In this paper, we investigate quantum corrections coming from conformal anomaly near the sudden future singularity. We conclude that when the equation of state is chosen to be $p=-\\rho-A\\rho^\\alpha$, the conformal anomaly can transform the sudden singularity in the singularity of type III for any $\\alpha> 1/2$ and in the singularity of the type I (the big rip) or the big crunch for $1/2<\\alpha<3/2$.

  5. Conformal anomaly around the sudden singularity

    Science.gov (United States)

    Houndjo, S. J. M.

    2010-10-01

    Quantum effects due to particle creation on a classical sudden singularity have been investigated in a previous work. The conclusion was that quantum effects do not lead to the avoidance nor the modification of the sudden future singularity. In this paper, we investigate quantum corrections coming from conformal anomaly near the sudden future singularity. We conclude that when the equation of state is chosen to be p=-ρ-Aρα, the conformal anomaly can transform the sudden singularity into the singularity of type III for any α>1/2 and into the singularity of the type I (the big rip) or the big crunch for 1/2<α<3/2.

  6. Spacetime Conformal Fluctuations and Quantum Dephasing

    CERN Document Server

    Bonifacio, Paolo M

    Any quantum system interacting with a complex environment undergoes decoherence. Empty space is filled with vacuum energy due to matter fields in their ground state and represents an underlying environment that any quantum particle has to cope with. In particular quantum gravity vacuum fluctuations should represent a universal source of decoherence. To study this problem we employ a stochastic approach that models spacetime fluctuations close to the Planck scale by means of a classical, randomly fluctuating metric (random gravity framework). We enrich the classical scheme for metric perturbations over a curved background by also including matter fields and metric conformal fluctuations. We show in general that a conformally modulated metric induces dephasing as a result of an effective nonlinear newtonian potential obtained in the appropriate nonrelativistic limit of a minimally coupled Klein-Gordon field. The special case of vacuum fluctuations is considered and a quantitative estimate of the expected effect...

  7. Conformal Patterson-Walker metrics

    CERN Document Server

    Hammerl, Matthias; Šilhan, Josef; Taghavi-Chabert, Arman; Žádník, Vojtěch

    2016-01-01

    The classical Patterson-Walker construction of a split-signature (pseudo-)Riemannian structure from a given torsion-free affine connection is generalized to a construction of a split-signature conformal structure from a given projective class of connections. A characterization of the induced structures is obtained. We achieve a complete description of Einstein metrics in the conformal class formed by the Patterson-Walker metric. Finally, we describe all symmetries of the conformal Patterson-Walker metric. In both cases we obtain descriptions in terms of geometric data on the original structure.

  8. Spatially separated polar samples of the cis and trans conformers of 3-fluorophenol

    CERN Document Server

    Kierspel, Thomas; Chang, Yuan-Pin; Küpper, Jochen

    2013-01-01

    We demonstrate the spatial separation of the cis- and trans-conformers of 3-fluorophenol in the gas phase based on their distinct electric dipole moments. For both conformers we create very polar samples of their lowest-energy rotational quantum states. A >95 % pure beam of trans-3-fluorophenol and a >90 % pure beam of the lowest-energy rotational states of the less polar cis-3-fluorophenol were obtained for helium and neon supersonic expansions, respectively. This is the first demonstration of the spatial separation of the lowest-energy rotational states of the least polar conformer, which is necessary for strong alignment and orientation of all individual conformers.

  9. New open conformation of SMYD3 implicates conformational selection and allostery

    Directory of Open Access Journals (Sweden)

    Nicholas Spellmon

    2016-12-01

    Full Text Available SMYD3 plays a key role in cancer cell viability, adhesion, migration and invasion. SMYD3 promotes formation of inducible regulatory T cells and is involved in reducing autoimmunity. However, the nearly “closed” substrate-binding site and poor in vitro H3K4 methyltransferase activity have obscured further understanding of this oncogenically related protein. Here we reveal that SMYD3 can adopt an “open” conformation using molecular dynamics simulation and small-angle X-ray scattering. This ligand-binding-capable open state is related to the crystal structure-like closed state by a striking clamshell-like inter-lobe dynamics. The two states are characterized by many distinct structural and dynamical differences and the conformational transition pathway is mediated by a reversible twisting motion of the C-terminal domain (CTD. The spontaneous transition from the closed to open states suggests two possible, mutually non-exclusive models for SMYD3 functional regulation and the conformational selection mechanism and allostery may regulate the catalytic or ligand binding competence of SMYD3. This study provides an immediate clue to the puzzling role of SMYD3 in epigenetic gene regulation.

  10. Entanglement Entropy from the Truncated Conformal Space

    CERN Document Server

    Palmai, T

    2016-01-01

    A new numerical approach to entanglement entropies of the Renyi 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 Renyi entropies of low-lying states in the transverse field Ising model.

  11. 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.

  12. Conformational Nonequilibrium Enzyme Kinetics: Generalized Michaelis-Menten Equation.

    Science.gov (United States)

    Piephoff, D Evan; Wu, Jianlan; Cao, Jianshu

    2017-08-03

    In a conformational nonequilibrium steady state (cNESS), enzyme turnover is modulated by the underlying conformational dynamics. On the basis of a discrete kinetic network model, we use an integrated probability flux balance method to derive the cNESS turnover rate for a conformation-modulated enzymatic reaction. The traditional Michaelis-Menten (MM) rate equation is extended to a generalized form, which includes non-MM corrections induced by conformational population currents within combined cyclic kinetic loops. When conformational detailed balance is satisfied, the turnover rate reduces to the MM functional form, explaining its general validity. For the first time, a one-to-one correspondence is established between non-MM terms and combined cyclic loops with unbalanced conformational currents. Cooperativity resulting from nonequilibrium conformational dynamics can be achieved in enzymatic reactions, and we provide a novel, rigorous means of predicting and characterizing such behavior. Our generalized MM equation affords a systematic approach for exploring cNESS enzyme kinetics.

  13. National Automated Conformity Inspection Process -

    Data.gov (United States)

    Department of Transportation — The National Automated Conformity Inspection Process (NACIP) Application is intended to expedite the workflow process as it pertains to the FAA Form 81 0-10 Request...

  14. Graphene-based conformal devices.

    Science.gov (United States)

    Park, Yong Ju; Lee, Seoung-Ki; Kim, Min-Seok; Kim, Hyunmin; Ahn, Jong-Hyun

    2014-08-26

    Despite recent progress in bendable and stretchable thin-film transistors using novel designs and materials, the development of conformal devices remains limited by the insufficient flexibility of devices. Here, we demonstrate the fabrication of graphene-based conformal and stretchable devices such as transistor and tactile sensor on a substrate with a convoluted surface by scaling down the device thickness. The 70 nm thick graphene-based conformal devices displayed a much lower bending stiffness than reported previously. The demonstrated devices provided excellent conformal coverage over an uneven animal hide surface without the need for an adhesive. In addition, the ultrathin graphene devices formed on the three-dimensionally curved animal hide exhibited stable electrical characteristics, even under repetitive bending and twisting. The advanced performance and flexibility demonstrated here show promise for the development and adoption of wearable electronics in a wide range of future applications.

  15. 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.

  16. Conformal anomalies and gravitational waves

    Science.gov (United States)

    Meissner, Krzysztof A.; Nicolai, Hermann

    2017-09-01

    We argue that the presence of conformal anomalies in gravitational theories can lead to observable modifications to Einstein's equations via the induced anomalous effective actions, whose non-localities can overwhelm the smallness of the Planck scale. The fact that no such effects have been seen in recent cosmological or gravitational wave observations therefore imposes strong restrictions on the field content of possible extensions of Einstein's theory: all viable theories should have vanishing conformal anomalies. We then show that a complete cancellation of conformal anomalies in D = 4 for both the C2 invariant and the Euler (Gauss-Bonnet) invariant E4 can only be achieved for N-extended supergravity multiplets with N ⩾ 5, as well as for M theory compactified to four dimensions. Although there remain open questions, in particular concerning the true significance of conformal anomalies in non-conformal theories, as well as their possible gauge dependence for spin s ⩾3/2, these cancellations suggest a hidden conformal structure of unknown type in these theories.

  17. Initial conformation of kinesin's neck linker

    CERN Document Server

    Geng, Yi-Zhao; Liu, Shu-Xia; Yan, Shiwei

    2013-01-01

    How ATP binding initiates the docking process of kinesin's neck linker is a key question in understanding kinesin mechanism. It is believed that the formation of an extra turn structure by the first three amino acids of neck linker (LYS325, THR326, ILE327 in 2KIN) is crucial for initiating the docking process. But the initial conformation of neck linker (specially the three amino acids of the extra turn) and the neck linker docking initiation mechanism remain unclear. By using molecular dynamics method, we investigate the initial conformation of kinesin's neck linker in the docking process. We find that, in the initial state of NL docking process, NL still has interactions with {\\beta}0 and forms a conformation similar to the "cover-neck bundle" structure proposed by Hwang et al. [Structure 2008, 16(1): 62-71]. From this initial structure, the docking of the "cover-neck bundle" structure can be achieved. The motor head provides a forward force on the initial cover-neck bundle structure through ATP-induced rot...

  18. Conformal Anomaly and Counterterms in Designer Gravity

    CERN Document Server

    Anabalon, Andres; Choque, David; Martinez, Cristian

    2015-01-01

    We construct concrete counterterms of the Balasubramanian-Kraus type for Einstein-scalar theories with designer gravity boundary conditions in AdS$_{4}$, so that the total action is finite on-shell and satisfy a well defined variational principle for an arbitrary scalar field potential. We focus on scalar fields with the conformal mass, $m^{2}=-2l^{-2}$, and show that the holographic mass matches the Hamiltonian mass for any boundary conditions. We compute the conformal anomaly of the dual field theory in the generic case, as well as when there exist logarithmic branches of non-linear origin. As expected, the conformal anomaly vanishes for the boundary conditions that are AdS invariant. When the anomaly does not vanish, the dual stress tensor describes a thermal gas with an equation of state related to the boundary conditions of the scalar field. When the anomaly vanishes, we recover the dual theory of a massless thermal gas. As an application of the formalism, we consider a general family of exact hairy blac...

  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. Salmon calcitonin: conformational changes and stabilizer effects

    Directory of Open Access Journals (Sweden)

    Shan-Yang Lin

    2015-11-01

    Full Text Available The therapeutic activity of peptides or protein drugs is highly dependent on their conformational structure. The protein structure is flexible and responds to external conditions, which may compromise the protein's native conformation and influence its physical and chemical stability. The physical and chemical stability of peptides or protein drugs are important characteristics of biopharmaceutical products. Calcitonin (CT is a polypeptide hormone that participates in diverse physiological functions in humans; therefore, it is a potentially useful protein for investigations of different aspects of pharmacology and drug delivery systems. Of the different types of CT available for clinical use, salmon CT (sCT is one of the most potent. In this review article, the commercially available sCT was selected as a suitable peptide candidate for the discussion of its stability and conformational changes in the aqueous and solid states using Fourier transform infrared (FTIR spectroscopic analysis under different external conditions, including pH, temperature, drying method, and added excipients. Particularly, excipients that have been optimized as stabilizers of sCT in aqueous solution and as lyophilized and spray-dried drug formulations are also discussed.

  1. Spatial separation of molecular conformers and clusters.

    Science.gov (United States)

    Horke, Daniel; Trippel, Sebastian; Chang, Yuan-Pin; Stern, Stephan; Mullins, Terry; Kierspel, Thomas; Küpper, Jochen

    2014-01-09

    Gas-phase molecular physics and physical chemistry experiments commonly use supersonic expansions through pulsed valves for the production of cold molecular beams. However, these beams often contain multiple conformers and clusters, even at low rotational temperatures. We present an experimental methodology that allows the spatial separation of these constituent parts of a molecular beam expansion. Using an electric deflector the beam is separated by its mass-to-dipole moment ratio, analogous to a bender or an electric sector mass spectrometer spatially dispersing charged molecules on the basis of their mass-to-charge ratio. This deflector exploits the Stark effect in an inhomogeneous electric field and allows the separation of individual species of polar neutral molecules and clusters. It furthermore allows the selection of the coldest part of a molecular beam, as low-energy rotational quantum states generally experience the largest deflection. Different structural isomers (conformers) of a species can be separated due to the different arrangement of functional groups, which leads to distinct dipole moments. These are exploited by the electrostatic deflector for the production of a conformationally pure sample from a molecular beam. Similarly, specific cluster stoichiometries can be selected, as the mass and dipole moment of a given cluster depends on the degree of solvation around the parent molecule. This allows experiments on specific cluster sizes and structures, enabling the systematic study of solvation of neutral molecules.

  2. 7 CFR 22.305 - Conformance with OMB Circular No. A-95.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 1 2010-01-01 2010-01-01 false Conformance with OMB Circular No. A-95. 22.305 Section 22.305 Agriculture Office of the Secretary of Agriculture RURAL DEVELOPMENT COORDINATION Roles and Responsibilities of State Governments § 22.305 Conformance with OMB Circular No. A-95. The State and multicounty...

  3. Reply to "Comment on `Quantum massive conformal gravity' by F. F. Faria"

    Science.gov (United States)

    Faria, F. F.

    2017-01-01

    Recently in (Eur Phys J C 76:341, 2016), Myung has suggested that the renormalizability of massive conformal gravity is meaningless unless the massive ghost states of the theory are stable. Here we show that massive conformal gravity can be renormalizable having unstable ghost states.

  4. Conformational dynamics of a ligand-free adenylate kinase.

    Directory of Open Access Journals (Sweden)

    Hyun Deok Song

    Full Text Available Adenylate kinase (AdK is a phosphoryl-transfer enzyme with important physiological functions. Based on a ligand-free open structure and a ligand-bound closed structure solved by crystallography, here we use molecular dynamics simulations to examine the stability and dynamics of AdK conformations in the absence of ligands. We first perform multiple simulations starting from the open or the closed structure, and observe their free evolutions during a simulation time of 100 or 200 nanoseconds. In all seven simulations starting from the open structure, AdK remained stable near the initial conformation. The eight simulations initiated from the closed structure, in contrast, exhibited large variation in the subsequent evolutions, with most (seven undergoing large-scale spontaneous conformational changes and approaching or reaching the open state. To characterize the thermodynamics of the transition, we propose and apply a new sampling method that employs a series of restrained simulations to calculate a one-dimensional free energy along a curved pathway in the high-dimensional conformational space. Our calculated free energy profile features a single minimum at the open conformation, and indicates that the closed state, with a high (∼13 kcal/mol free energy, is not metastable, consistent with the observed behaviors of the unrestrained simulations. Collectively, our simulations suggest that it is energetically unfavorable for the ligand-free AdK to access the closed conformation, and imply that ligand binding may precede the closure of the enzyme.

  5. Conformation-dependent DNA attraction

    Science.gov (United States)

    Li, Weifeng; Nordenskiöld, Lars; Zhou, Ruhong; Mu, Yuguang

    2014-05-01

    Understanding how DNA molecules interact with other biomolecules is related to how they utilize their functions and is therefore critical for understanding their structure-function relationships. For a long time, the existence of Z-form DNA (a left-handed double helical version of DNA, instead of the common right-handed B-form) has puzzled the scientists, and the definitive biological significance of Z-DNA has not yet been clarified. In this study, the effects of DNA conformation in DNA-DNA interactions are explored by molecular dynamics simulations. Using umbrella sampling, we find that for both B- and Z-form DNA, surrounding Mg2+ ions always exert themselves to screen the Coulomb repulsion between DNA phosphates, resulting in very weak attractive force. On the contrary, a tight and stable bound state is discovered for Z-DNA in the presence of Mg2+ or Na+, benefiting from their hydrophobic nature. Based on the contact surface and a dewetting process analysis, a two-stage binding process of Z-DNA is outlined: two Z-DNA first attract each other through charge screening and Mg2+ bridges to phosphate groups in the same way as that of B-DNA, after which hydrophobic contacts of the deoxyribose groups are formed via a dewetting effect, resulting in stable attraction between two Z-DNA molecules. The highlighted hydrophobic nature of Z-DNA interaction from the current study may help to understand the biological functions of Z-DNA in gene transcription.Understanding how DNA molecules interact with other biomolecules is related to how they utilize their functions and is therefore critical for understanding their structure-function relationships. For a long time, the existence of Z-form DNA (a left-handed double helical version of DNA, instead of the common right-handed B-form) has puzzled the scientists, and the definitive biological significance of Z-DNA has not yet been clarified. In this study, the effects of DNA conformation in DNA-DNA interactions are explored by

  6. Mutual information after a local quench in conformal field theory

    CERN Document Server

    Asplund, Curtis T

    2013-01-01

    We compute the entanglement entropy and mutual information for two disjoint intervals in two-dimensional conformal field theories as a function of time after a local quench, using the replica trick and boundary conformal field theory. We obtain explicit formulae for the universal contributions, which are leading in the regimes of, for example, close or well-separated intervals of fixed length. The results are largely consistent with the quasiparticle picture, in which entanglement above that present in the ground state is carried by pairs of entangled, freely propagating excitations. We also calculate the mutual information for two disjoint intervals in a proposed holographic local quench, whose holographic energy-momentum tensor matches the conformal field theory one. We find that the holographic mutual information shows qualitative differences from the conformal field theory results and we discuss possible interpretations of this.

  7. Conformal anomaly of generalized form factors and finite loop integrals

    CERN Document Server

    Chicherin, Dmitry

    2017-01-01

    We reveal a new mechanism of conformal symmetry breaking at Born level. It occurs in generalized form factors with several local operators and an on-shell state of massless particles. The effect is due to hidden singularities on collinear configurations of the momenta. This conformal anomaly is different from the holomorphic anomaly of amplitudes. We present a number of examples in four and six dimensions. We find an application of the new conformal anomaly to finite loop momentum integrals with one or more massless legs. The collinear region around a massless leg creates a contact anomaly, made visible by the loop integration. The anomalous conformal Ward identity for an $\\ell-$loop integral is a 2nd-order differential equation whose right-hand side is an $(\\ell-1)-$loop integral. We show several examples, in particular the four-dimensional scalar double box.

  8. 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

  9. 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

  10. Multiple Conformations of E. Coli Hsp90 in Solution: Insights Into the Conformational Dynamics of Hsp90

    Energy Technology Data Exchange (ETDEWEB)

    Krukenberg, K.A.; Forster, F.; Rice, L.M.; Sali, A.; Agard, D.A.

    2009-05-20

    Hsp90, an essential eukaryotic chaperone, depends upon its intrinsic ATPase activity for function. Crystal structures of the bacterial Hsp90 homolog, HtpG, and the yeast Hsp90 reveal large domain rearrangements between the nucleotide-free and the nucleotide-bound forms. We used small-angle X-ray scattering and recently developed molecular modeling methods to characterize the solution structure of HtpG and demonstrate how it differs from known Hsp90 conformations. In addition to this HtpG conformation, we demonstrate that under physiologically relevant conditions, multiple conformations coexist in equilibrium. In solution, nucleotide-free HtpG adopts a more extended conformation than observed in the crystal, and upon the addition of AMPPNP, HtpG is in equilibrium between this open state and a closed state that is in good agreement with the yeast AMPPNP crystal structure. These studies provide a unique view of Hsp90 conformational dynamics and provide a model for the role of nucleotide in effecting conformational change.

  11. Eigenstate Thermalization Hypothesis in Conformal Field Theory

    CERN Document Server

    Lashkari, Nima; Liu, Hong

    2016-01-01

    We investigate the eigenstate thermalization hypothesis (ETH) in d+1 dimensional conformal field theories by studying reduced density matrices in energy eigenstates. We show that if local probes of high energy primary eigenstates satisfy ETH, then any finite energy observable with support on a subsystem of finite size satisfies ETH. In two dimensions, we discover that if ETH holds locally, the finite size reduced density matrix of states created by heavy primary operators is well-approximated by a projection to the Virasoro identity block.

  12. [Dynamics of electron-conformational transitions in proteins and physical mechanisms of biomacromolecule function].

    Science.gov (United States)

    Shaĭtan, K V

    1992-01-01

    The proteins can be considered as a microheterogeneous structured media possessing memory and feedback properties. The conformational energy surface depends on the chemical states of protein groups. Conformational motions are local diffusion with relaxation times much longer than vibrational relaxation times in condensed media. Owing to the hierarchy of relaxation times chemical reaction rates depend on conformation parametrically. Regulation of functional activity by conformational mobility is accomplished via transmission of information in the form of changes in the distribution functions of separate groups along the conformational substates. The interpretation of drastic effects on conformational mobility needs super-stochastic approaches. A possible mechanism of sharp conformational change are discussed in terms of the catastrophe theory.

  13. Conformity Behavior During a Fire Disaster

    National Research Council Canada - National Science Library

    Duo, Qi; Shen, Huizhang; Zhao, Jidi; Gong, Xiaomin

    2016-01-01

    ..., the number of choices offered for making an escape was negatively related to conformity behavior, and decision-making performance was found to be a dual mediator both between the level of fear activation and conformity behavior and between the number of choices and conformity behavior. Keywords: conformity behavior, fire disaster, fear activation, number...

  14. Group Cohesiveness, Deviation, Stress, and Conformity

    Science.gov (United States)

    1993-08-11

    Yuke1son, Weinberg & Jackson , 1984; Carron & Chelladurai, 1981). The classical studies of jury dynamics began to appear within the field of...1987), individuation was negatively correlated with conformity (Santee & Maslach , 1982). Conformity Paradi&ms Host studies of conformity have...appear to affect conformity rates independently of attraction . However, later ~tudies by Dittes and Kelley (1956) and Jackson and Saltzstein (1958

  15. Black Holes as Conformal Field Theories on Horizons

    CERN Document Server

    Halyo, Edi

    2015-01-01

    We show that any nonextreme black hole can be described by a state with $L_0=E_R$ in a $D=2$ chiral conformal field theory with central charge $c=12E_R$ where $E_R$ is the dimensionless Rindler energy of the black hole. The theory lives in the very near horizon region, i.e. around the origin of Rindler space. Black hole hair is the momentum along the Euclidean dimensionless Rindler time direction. As evidence, we show that $D$--dimensional Schwarzschild black holes and $D=2$ dilatonic ones that are obtained from them by spherical reduction are described by the same conformal field theory states.

  16. Conformal Gravity Rotation Curves with a Conformal Higgs Halo

    CERN Document Server

    Horne, Keith

    2016-01-01

    We discuss the effect of a conformally coupled Higgs field on conformal gravity (CG) predictions for the rotation curves of galaxies. The Mannheim-Kazanas (MK) metric is a valid vacuum solution of CG's 4-th order Poisson equation only if the Higgs field has a particular radial profile, S(r)=S_0 a/(r+a), decreasing from S_0 at r=0 with radial scale length a. Since particle rest masses scale with S(r)/S_0, their world lines do not follow time-like geodesics of the MK metric g_{\\mu\

  17. Unbiased simulations reveal the inward-facing conformation of the human serotonin transporter and Na+ ion release

    DEFF Research Database (Denmark)

    Koldsø, Heidi; Noer, Pernille Rimmer; Grouleff, Julie;

    2011-01-01

    . The simulations reveal a transition of hSERT from an outward-facing occluded conformation to an inward-facing conformation in a one-substrate-bound state. Simulations with a second substrate in the proposed symport effector site did not lead to conformational changes associated with translocation. The central...

  18. 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

  19. 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.

  20. Conformal Mapping for Multiple Terminals

    CERN Document Server

    Wang, Weimin; Wang, Qiang; Ren, Hao

    2015-01-01

    Conformal mapping is an important mathematical tool in many physical and engineering fields, especially in electrostatics, fluid mechanics, classical mechanics, and transformation optics. However in the existing textbooks and literatures, it is only adopted to solve the problems which have only two terminals. Two terminals with electric potential differences, pressure difference, optical path difference, etc., can be mapped conformally onto a solvable structure, e.g., a rectangle, where the two terminals are mapped onto two opposite edges of the rectangle. Here we show a conformal mapping method for multiple terminals, which is more common in practical applications. Through accurate analysis of the boundary conditions, additional terminals or boundaries are folded in the inner of the mapped rectangle. Then the solution will not be influenced. The method is described in several typical situations and two application examples are detailed. The first example is an electrostatic actuator with three electrodes. A ...

  1. Conformal Anomalies and Gravitational Waves

    CERN Document Server

    Meissner, Krzysztof A

    2016-01-01

    We argue that the presence of conformal anomalies in gravitational theories can lead to observable modifications to Einstein's equations via the induced anomalous effective actions, whose non-localities can overwhelm the smallness of the Planck scale. The fact that no such effects have been seen in recent cosmological or gravitational wave observations therefore imposes strong restrictions on the field content of possible extensions of Einstein's theory: all viable theories should have vanishing conformal anomalies. We then show that, among presently known theories, a complete cancellation of conformal anomalies in $D=4$ for both the $C^2$ invariant and the Euler (Gauss-Bonnet) invariant $E_4$ can only be achieved for $N$-extended supergravities with $N\\geq 5$, as well as for M theory compactified to four dimensions.

  2. Lectures on Conformal Field Theory

    CERN Document Server

    Qualls, Joshua D

    2015-01-01

    These lectures notes are based on courses given at National Taiwan University, National Chiao-Tung University, and National Tsing Hua University in the spring term of 2015. Although the course was offered primarily for graduate students, these lecture notes have been prepared for a more general audience. They are intended as an introduction to conformal field theories in various dimensions, with applications related to topics of particular interest: topics include the conformal bootstrap program, boundary conformal field theory, and applications related to the AdS/CFT correspondence. We assume the reader to be familiar with quantum mechanics at the graduate level and to have some basic knowledge of quantum field theory. Familiarity with string theory is not a prerequisite for this lectures, although it can only help.

  3. Renyi entropy and conformal defects

    Energy Technology Data Exchange (ETDEWEB)

    Bianchi, Lorenzo [Humboldt-Univ. Berlin (Germany). Inst. fuer Physik; Hamburg Univ. (Germany). II. Inst. fuer Theoretische Physik; Meineri, Marco [Scuola Normale Superiore, Pisa (Italy); Perimeter Institute for Theoretical Physics, Waterloo, ON (Canada); Istituto Nazionale di Fisica Nucleare, Pisa (Italy); Myers, Robert C. [Perimeter Institute for Theoretical Physics, Waterloo, ON (Canada); Smolkin, Michael [California Univ., Berkely, CA (United States). Center for Theoretical Physics and Department of Physics

    2016-04-18

    We propose a field theoretic framework for calculating the dependence of Renyi entropies on the shape of the entangling surface in a conformal field theory. Our approach rests on regarding the corresponding twist operator as a conformal defect and in particular, we define the displacement operator which implements small local deformations of the entangling surface. We identify a simple constraint between the coefficient defining the two-point function of the displacement operator and the conformal weight of the twist operator, which consolidates a number of distinct conjectures on the shape dependence of the Renyi entropy. As an example, using this approach, we examine a conjecture regarding the universal coefficient associated with a conical singularity in the entangling surface for CFTs in any number of spacetime dimensions. We also provide a general formula for the second order variation of the Renyi entropy arising from small deformations of a spherical entangling surface, extending Mezei's results for the entanglement entropy.

  4. Ligand-driven conformational changes of MurD visualized by paramagnetic NMR.

    Science.gov (United States)

    Saio, Tomohide; Ogura, Kenji; Kumeta, Hiroyuki; Kobashigawa, Yoshihiro; Shimizu, Kazumi; Yokochi, Masashi; Kodama, Kota; Yamaguchi, Hiroto; Tsujishita, Hideki; Inagaki, Fuyuhiko

    2015-11-19

    Proteins, especially multi-domain proteins, often undergo drastic conformational changes upon binding to ligands or by post-translational modifications, which is a key step to regulate their function. However, the detailed mechanisms of such dynamic regulation of the functional processes are poorly understood because of the lack of an efficient tool. We here demonstrate detailed characterization of conformational changes of MurD, a 47 kDa protein enzyme consisting of three domains, by the use of solution NMR equipped with paramagnetic lanthanide probe. Quantitative analysis of pseudocontact shifts has identified a novel conformational state of MurD, named semi-closed conformation, which is found to be the key to understand how MurD regulates the binding of the ligands. The modulation of the affinity coupled with conformational changes accentuates the importance of conformational state to be evaluated in drug design.

  5. 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.

  6. 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

  7. Nonlocal gravity: Conformally flat spacetimes

    CERN Document Server

    Bini, Donato

    2016-01-01

    The field equations of the recent nonlocal generalization of Einstein's theory of gravitation are presented in a form that is reminiscent of general relativity. The implications of the nonlocal field equations are studied in the case of conformally flat spacetimes. Even in this simple case, the field equations are intractable. Therefore, to gain insight into the nature of these equations, we investigate the structure of nonlocal gravity in two-dimensional spacetimes. While any smooth 2D spacetime is conformally flat and satisfies Einstein's field equations, only a subset containing either a Killing vector or a homothetic Killing vector can satisfy the field equations of nonlocal gravity.

  8. Manifestation of Conformal Symmetry in the Light Flavor Baryon Sector

    CERN Document Server

    Kirchbach, M

    2010-01-01

    On the AdS_5 cone, conformally compactified to R^1xS^3, a quark-diquark model of light flavor baryons is developed. The system on this manifold is decribed in terms of a scalar conformal equation, gauged by the field of a D3 brane whose transversal dimensions have been conformally warpped over R^1xS^3. Such a system does not result exactly conformally invariant because the gauge potential slightly modifies the conformal centrifugal barrier of the free geodesic motion. Thanks to this, the model describes the correct mass ordering in the P11-S11 pairs through the N spectrum as a combined effect of conformal symmetry breaking, on the one side, and a parity change of the diquark from a scalar at low masses, to a pseudoscalar at higher masses, on the other. We calculate the number of resonances with masses below 2500 MeV needed for the completeness of the above scheme and find a total of 32 "missing" nucleon and Delta states. Their absence or presence in the respective spectra relates to the degree to which confor...

  9. The discodermolide hairpin structure flows from conformationally stable modular motifs.

    Science.gov (United States)

    Jogalekar, Ashutosh S; Kriel, Frederik H; Shi, Qi; Cornett, Ben; Cicero, Daniel; Snyder, James P

    2010-01-14

    (+)-Discodermolide (DDM), a polyketide macrolide from marine sponge, is a potent microtubule assembly promoter. Reported solid-state, solution, and protein-bound DDM conformations reveal the unusual result that a common hairpin conformational motif exists in all three microenvironments. No other flexible microtubule binding agent exhibits such constancy of conformation. In the present study, we combine force-field conformational searches with NMR deconvolution in different solvents to compare DDM conformers with those observed in other environments. While several conformational families are perceived, the hairpin form dominates. The stability of this motif is dictated primarily by steric factors arising from repeated modular segments in DDM composed of the C(Me)-CHX-C(Me) fragment. Furthermore, docking protocols were utilized to probe the DDM binding mode in beta-tubulin. A previously suggested pose is substantiated (Pose-1), while an alternative (Pose-2) has been identified. SAR analysis for DDM analogues differentiates the two poses and suggests that Pose-2 is better able to accommodate the biodata.

  10. An SIS model for cultural trait transmission with conformity bias.

    Science.gov (United States)

    Walters, Caroline E; Kendal, Jeremy R

    2013-12-01

    Epidemiological models have been applied to human health-related behaviors that are affected by social interaction. Typically these models have not considered conformity bias, that is, the exaggerated propensity to adopt commonly observed behaviors or opinions, or content biases, where the content of the learned trait affects the probability of adoption. Here we consider an interaction of these two effects, presenting an SIS-type model for the spread and persistence of a behavior which is transmitted via social learning. Uptake is controlled by a nonlinear dependence on the proportion of individuals demonstrating the behavior in a population. Three equilibrium solutions are found, their linear stability is analyzed and the results are compared with a model for unbiased social learning. Our analysis focuses on the effects of the strength of conformity bias and the effects of content biases which alter a conformity threshold frequency of the behavior, above which there is an exaggerated propensity for adoption. The strength of the conformity bias is found to qualitatively alter the predictions regarding whether the trait becomes endemic within the population and the proportion of individuals who display the trait when it is endemic. As the conformity strength increases, the number of feasible equilibrium solutions increases from two to three, leading to a situation where the stable equilibrium attained is dependent upon the initial state. Varying the conformity threshold frequency directionally alters the behavior invasion threshold. Finally we discuss the possible application of this model to binge drinking behavior.

  11. Conformational changes in hemoglobin triggered by changing the iron charge

    Energy Technology Data Exchange (ETDEWEB)

    Croci, S., E-mail: simo@unipr.it [University of Parma, Departments of Public Health, INBB Parma (Italy); Achterhold, K. [Physik-Department E17 (Germany); Ortalli, I. [University of Parma, Departments of Public Health, INBB Parma (Italy); Parak, F. G. [Physik-Department E17 (Germany)

    2008-07-15

    In this work the hemoglobin conformational changes induced by changing the iron charge have been studied and compared with Myoglobin. Moessbauer spectroscopy was used to follow the change of the iron conformation. In order to compare the conformational relaxation of hemoglobin and myoglobin, and to study a possible influence of the quaternary structure, an intermediate metastable state of hemoglobin has been created by low temperature X-ray irradiation of methemoglobin. The irradiation reduces the Fe(III) of the heme groups to Fe(II) Low Spin, where the water is still bound on the sixth coordination. Heating cycles performed at temperatures from 140 K to 200 K allow the molecules to overcome an activation energy barrier and to relax into a stable conformation such as deoxy-hemoglobin or carboxy-hemoglobin, if CO is present. Slightly different structures (conformational substates) reveal themselves as a distribution of energy barriers ({Delta}G). The distribution of the activation energy, for the decay of the Fe(II) Low Spin intermediate, has been fitted with a Gaussian. For comparison, published myoglobin data were re-analysed in the same way. The average energy value at characteristic temperature is very similar in case of myoglobin and hemoglobin. The larger Gaussian energy distribution for myoglobin with respect to hemoglobin shows that more conformational substates are available. This may be caused by a larger area exposed to water. In hemoglobin, part of the surface of the chains is not water accessible due to the quaternary structure.

  12. Conformational analysis of a flexible oligosaccharide using residual dipolar couplings.

    Science.gov (United States)

    Tian, F; Al-Hashimi, H M; Craighead, J L; Prestegard, J H

    2001-01-24

    We present a new approach to the analysis of the conformational and the motional properties of an oligosaccharide, methyl 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside. The approach relies on an order matrix analysis of residual dipolar couplings in the solution state. By combining a number of different types of couplings, (1)D(CH), (2)D(CH), and D(HH), an order matrix is solved for each ring of the trimannoside. The resulting order parameters indicate the internal motion at the alpha (1,3) linkage to be limited, while significant motion is suggested at the alpha (1,6) linkage. Two structures for the trimannoside were determined by aligning the order tensor principal axes obtained from two different orienting media, bicelles and phage. The very similar conformations at the alpha (1,3) linkage of these two structures confirm that the internal motion at the alpha (1,3) linkage is small and the conformation is a good representation of a single preferred structure. The different conformations at the alpha (1,6) linkage suggest that the motional amplitudes are large and the conformations must be viewed as virtual conformers. Compared with traditional NMR methods, data acquisition is easy and data analysis is straightforward.

  13. Non-conformally flat initial data for binary compact objects

    CERN Document Server

    Uryu, Koji; Friedman, John L; Gourgoulhon, Eric; Shibata, Masaru

    2009-01-01

    A new method is described for constructing initial data for a binary neutron-star (BNS) system in quasi-equilibrium circular orbit. Two formulations for non-conformally flat data, waveless (WL) and near-zone helically symmetric (NHS), are introduced; in each formulation, the Einstein-Euler system, written in 3+1 form on an asymptotically flat spacelike hypersurface, is exactly solved for all the metric components including the spatially non-conformally flat part, and for irrotational flow. A numerical method applicable to both formulations is explained with an emphasis on the imposition of a spatial gauge condition. Results are shown for solution sequences of irrotational BNSs with matter approximated by a parametrized equations of state that uses a few segments of polytropic equations of state. WL/NHS formulations correct the results from the conformally flat -- Isenberg-Wilson-Mathews (IWM) -- formulation. Binding energy or total angular momentum of solution sequences computed within the IWM formulation are...

  14. Ground- and excited-state stability of the conformers of 3,5-dinitrocatechol and its complexes with W(VI) and V(V): combined theoretical and experimental study.

    Science.gov (United States)

    Delchev, V B; Gavazov, K B; Shterev, I G

    2014-12-01

    We performed a theoretical and experimental study of the (photo)stability of 3,5-dinitrocatechol (DNC) and its complexes with W(VI) and V(V). The investigation showed that irradiation of DNC is accompanied by a parallel proton migration from the hydroxy group to the neighboring NO2 group, which results in a large Stokes shift of the absorption and emission bands. It was found that W(VI) forms a more stable 1:2 complex than V(V). The complex is stable even under UV irradiation. The most stable W(VI)(DNC)2 conformer is comprised of two mutually perpendicular DNC molecules as ligands.

  15. Helical conformations of hexapeptides containing N-terminus diproline segments.

    Science.gov (United States)

    Raghothama, Srinivasarao; Aravinda, Subrayashastry; Shamala, Narayanaswamy; Balaram, Padmanabhan

    2010-01-01

    The role of N-terminus diproline segments in facilitating helical folding in short peptides has been investigated in a set of model hexapeptides of the type Piv-Xxx-Yyy-Aib-Leu-Aib-Phe-OMe (Piv, pivaloyl). Nine sequences have been investigated with the following N-terminus dipeptide segments: (D)Pro-Ala (4) and Pro-PsiPro (5, Psi, pseudoproline), Ala-Ala (6), Ala-Pro (7), Pro-Ala (8), Aib-Ala (9), Ala-Aib (10). The analog sequences Piv-Pro-Pro-Ala-Leu-Aib-Phe-OMe (2) and Piv-Pro-Pro-Ala-Aib-Ala-Aib-OMe (3) have also been studied. Solid state conformations have been determined by X-ray crystallography for peptides 4, 6, and 8 and compared with the previously determined crystal structure of peptide 1 (Boc-Pro-Pro-Aib-Leu-Aib-Val-OMe); (Rai et al., JACS 2006, 128, 7916-7928). Peptides 1 and 6 adopt almost identical helical conformations with unfolding of the helix at the N-terminus Pro (1) residue. Peptide 4 reveals the anticipated (D)Pro-Ala type II' beta-turn, followed by a stretch of 3(10)-helix. Peptide 8 adopts a folded conformation stabilized by four successive 4-->1 intramolecular hydrogen bonds. Ala (2) adopts an alpha(L) conformation, resulting in a type II beta-turn conformation followed by a stretch of 3(10)-helix. Conformational properties in solution were probed using solvent perturbation of NH chemical shifts which permit delineation of hydrogen bonded NH groups and nuclear Overhauser effects (NOEs) between backbone protons, which are diagnostic of local residue conformations. The results suggest that, continuous helical conformations are indeed significantly populated for peptides 2 and 3. Comparison of the results for peptides 1 and 2, suggest that there is a significant influence of the residue that follows diproline segments in influencing backbone folding.

  16. Current Reflection and Transmission at Conformal Defects: Applying BCFT to Transport Process

    CERN Document Server

    Kimura, Taro

    2014-01-01

    We study reflection/transmission process at conformal defects by introducing new transport coefficients for conserved currents. These coefficients are defined by using BCFT techniques thanks to the folding trick, which turns the conformal defect into the boundary. With this definition, exact computations are demonstrated to describe reflection/transmission process for a class of conformal defects. We also compute the boundary entropy based on the boundary state.

  17. Stochastic ensembles, conformationally adaptive teamwork, and enzymatic detoxification.

    Science.gov (United States)

    Atkins, William M; Qian, Hong

    2011-05-17

    It has been appreciated for a long time that enzymes exist as conformational ensembles throughout multiple stages of the reactions they catalyze, but there is renewed interest in the functional implications. The energy landscape that results from conformationlly diverse poteins is a complex surface with an energetic topography in multiple dimensions, even at the transition state(s) leading to product formation, and this represents a new paradigm. At the same time there has been renewed interest in conformational ensembles, a new paradigm concerning enzyme function has emerged, wherein catalytic promiscuity has clear biological advantages in some cases. "Useful", or biologically functional, promiscuity or the related behavior of "multifunctionality" can be found in the immune system, enzymatic detoxification, signal transduction, and the evolution of new function from an existing pool of folded protein scaffolds. Experimental evidence supports the widely held assumption that conformational heterogeneity promotes functional promiscuity. The common link between these coevolving paradigms is the inherent structural plasticity and conformational dynamics of proteins that, on one hand, lead to complex but evolutionarily selected energy landscapes and, on the other hand, promote functional promiscuity. Here we consider a logical extension of the overlap between these two nascent paradigms: functionally promiscuous and multifunctional enzymes such as detoxification enzymes are expected to have an ensemble landscape with more states accessible on multiple time scales than substrate specific enzymes. Two attributes of detoxification enzymes become important in the context of conformational ensembles: these enzymes metabolize multiple substrates, often in substrate mixtures, and they can form multiple products from a single substrate. These properties, combined with complex conformational landscapes, lead to the possibility of interesting time-dependent, or emergent

  18. Molecular mechanics conformational analysis of tylosin

    Science.gov (United States)

    Ivanov, Petko M.

    1998-01-01

    The conformations of the 16-membered macrolide antibiotic tylosin were studied with molecular mechanics (AMBER∗ force field) including modelling of the effect of the solvent on the conformational preferences (GB/SA). A Monte Carlo conformational search procedure was used for finding the most probable low-energy conformations. The present study provides complementary data to recently reported analysis of the conformations of tylosin based on NMR techniques. A search for the low-energy conformations of protynolide, a 16-membered lactone containing the same aglycone as tylosin, was also carried out, and the results were compared with the observed conformation in the crystal as well as with the most probable conformations of the macrocyclic ring of tylosin. The dependence of the results on force field was also studied by utilizing the MM3 force field. Some particular conformations were computed with the semiempirical molecular orbital methods AM1 and PM3.

  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. Conformal Data from Finite Entanglement Scaling

    CERN Document Server

    Stojevic, Vid; McCulloch, I P; Tagliacozzo, L; Verstraete, Frank

    2014-01-01

    In this paper we apply the formalism of translation invariant (continuous) matrix product states in the thermodynamic limit to $(1+1)$ dimensional critical models. Finite bond dimension bounds the entanglement entropy and introduces an effective finite correlation length, so that the state is perturbed away from criticality. The assumption that the scaling hypothesis holds for this kind of perturbation is known in the literature as finite entanglement scaling. We provide further evidence for the validity of finite entanglement scaling and based on this formulate a scaling algorithm to estimate the central charge and critical exponents of the conformally invariant field theories describing the critical models under investigation. The algorithm is applied to three exemplary models; the cMPS version to the non-relativistic Lieb-Liniger model and the relativistic massless boson, and MPS version to the one-dimensional quantum Ising model at the critical point. Another new aspect to our approach is that we directly...

  1. Quasilocal rotating conformal Killing horizons

    CERN Document Server

    Chatterjee, Ayan

    2015-01-01

    The formulation of quasi-local conformal Killling horizons(CKH) is extended to include rotation. This necessitates that the horizon be foliated by 2-spheres which may be distorted. Matter degrees of freedom which fall through the horizon is taken to be a real scalar field. We show that these rotating CKHs also admit a first law in differential form.

  2. Conformal mapping for multiple terminals

    Science.gov (United States)

    Wang, Weimin; Ma, Wenying; Wang, Qiang; Ren, Hao

    2016-11-01

    Conformal mapping is an important mathematical tool that can be used to solve various physical and engineering problems in many fields, including electrostatics, fluid mechanics, classical mechanics, and transformation optics. It is an accurate and convenient way to solve problems involving two terminals. However, when faced with problems involving three or more terminals, which are more common in practical applications, existing conformal mapping methods apply assumptions or approximations. A general exact method does not exist for a structure with an arbitrary number of terminals. This study presents a conformal mapping method for multiple terminals. Through an accurate analysis of boundary conditions, additional terminals or boundaries are folded into the inner part of a mapped region. The method is applied to several typical situations, and the calculation process is described for two examples of an electrostatic actuator with three electrodes and of a light beam splitter with three ports. Compared with previously reported results, the solutions for the two examples based on our method are more precise and general. The proposed method is helpful in promoting the application of conformal mapping in analysis of practical problems.

  3. 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...

  4. 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...

  5. Temperature: Human Regulating, Ants Conforming

    Science.gov (United States)

    Clopton, Joe R.

    2007-01-01

    Biological processes speed up as temperature rises. Procedures for demonstrating this with ants traveling on trails, and data gathered by students on the Argentine ant ("Linepithema humile") are presented. The concepts of temperature regulation and conformity are detailed with a focus on the processes rather than on terms that label the organisms.

  6. A tutorial on conformal prediction

    CERN Document Server

    Shafer, Glenn

    2007-01-01

    Conformal prediction uses past experience to determine precise levels of confidence in new predictions. Given an error probability $\\epsilon$, together with a method that makes a prediction $\\hat{y}$ of a label $y$, it produces a set of labels, typically containing $\\hat{y}$, that also contains $y$ with probability $1-\\epsilon$. Conformal prediction can be applied to any method for producing $\\hat{y}$: a nearest-neighbor method, a support-vector machine, ridge regression, etc. Conformal prediction is designed for an on-line setting in which labels are predicted successively, each one being revealed before the next is predicted. The most novel and valuable feature of conformal prediction is that if the successive examples are sampled independently from the same distribution, then the successive predictions will be right $1-\\epsilon$ of the time, even though they are based on an accumulating dataset rather than on independent datasets. In addition to the model under which successive examples are sampled indepen...

  7. Correct Representation of Conformational Equilibria.

    Science.gov (United States)

    Fulop, F.; And Others

    1983-01-01

    In representing conformational equilibria of compounds having only one chiral center, erroneous formulas showing different antipodes on the two sides of the equilibrium are rare. In contrast, with compounds having two or more chiral centers especially with saturated heterocycles, this erroneous representation occurs frequently in the chemical…

  8. 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 the $...

  9. Temperature: Human Regulating, Ants Conforming

    Science.gov (United States)

    Clopton, Joe R.

    2007-01-01

    Biological processes speed up as temperature rises. Procedures for demonstrating this with ants traveling on trails, and data gathered by students on the Argentine ant ("Linepithema humile") are presented. The concepts of temperature regulation and conformity are detailed with a focus on the processes rather than on terms that label the organisms.

  10. Src kinase conformational activation: thermodynamics, pathways, and mechanisms.

    Directory of Open Access Journals (Sweden)

    Sichun Yang

    2008-03-01

    Full Text Available Tyrosine kinases of the Src-family are large allosteric enzymes that play a key role in cellular signaling. Conversion of the kinase from an inactive to an active state is accompanied by substantial structural changes. Here, we construct a coarse-grained model of the catalytic domain incorporating experimental structures for the two stable states, and simulate the dynamics of conformational transitions in kinase activation. We explore the transition energy landscapes by constructing a structural network among clusters of conformations from the simulations. From the structural network, two major ensembles of pathways for the activation are identified. In the first transition pathway, we find a coordinated switching mechanism of interactions among the alphaC helix, the activation-loop, and the beta strands in the N-lobe of the catalytic domain. In a second pathway, the conformational change is coupled to a partial unfolding of the N-lobe region of the catalytic domain. We also characterize the switching mechanism for the alphaC helix and the activation-loop in detail. Finally, we test the performance of a Markov model and its ability to account for the structural kinetics in the context of Src conformational changes. Taken together, these results provide a broad framework for understanding the main features of the conformational transition taking place upon Src activation.

  11. Fake Conformal Symmetry in Unimodular Gravity

    CERN Document Server

    Oda, Ichiro

    2016-01-01

    We study Weyl symmetry (local conformal symmetry) in unimodular gravity. It is shown that the Noether currents for both Weyl symmetry and global scale symmetry, identically vanish as in the conformally invariant scalar-tensor gravity. We clearly explain why in the class of conformally invariant gravitational theories, the Noether currents vanish by starting with the conformally invariant scalar-tensor gravity. Moreover, we comment on both classical and quantum-mechanical equivalences among Einstein's general relativity, the conformally invariant scalar-tensor gravity and the Weyl-transverse (WTDiff) gravity. Finally, we discuss the Weyl current in the conformally invariant scalar action and see that it is also vanishing.

  12. Fake conformal symmetry in unimodular gravity

    Science.gov (United States)

    Oda, Ichiro

    2016-08-01

    We study Weyl symmetry (local conformal symmetry) in unimodular gravity. It is shown that the Noether currents for both Weyl symmetry and global scale symmetry vanish exactly as in conformally invariant scalar-tensor gravity. We clearly explain why in the class of conformally invariant gravitational theories, the Noether currents vanish by starting with conformally invariant scalar-tensor gravity. Moreover, we comment on both classical and quantum-mechanical equivalences in Einstein's general relativity, conformally invariant scalar-tensor gravity, and the Weyl-transverse gravity. Finally, we discuss the Weyl current in the conformally invariant scalar action and see that it is also vanishing.

  13. Genetic analyses for conformation traits in South African Jersey and ...

    African Journals Online (AJOL)

    JACO

    Genetic trends for conformation traits of the South African Holstein show that ... African Holstein and Jersey cattle, in order to estimate breeding values for the .... life and type traits from the United States and diseases other than mastitis from ...

  14. Cyclic AMP analog blocks kinase activation by stabilizing inactive conformation: conformational selection highlights a new concept in allosteric inhibitor design.

    Science.gov (United States)

    Badireddy, Suguna; Yunfeng, Gao; Ritchie, Mark; Akamine, Pearl; Wu, Jian; Kim, Choel W; Taylor, Susan S; Qingsong, Lin; Swaminathan, Kunchithapadam; Anand, Ganesh S

    2011-03-01

    The regulatory (R) subunit of protein kinase A serves to modulate the activity of protein kinase A in a cAMP-dependent manner and exists in two distinct and structurally dissimilar, end point cAMP-bound "B" and C-subunit-bound "H"-conformations. Here we report mechanistic details of cAMP action as yet unknown through a unique approach combining x-ray crystallography with structural proteomics approaches, amide hydrogen/deuterium exchange and ion mobility mass spectrometry, applied to the study of a stereospecific cAMP phosphorothioate analog and antagonist((Rp)-cAMPS). X-ray crystallography shows cAMP-bound R-subunit in the B form but surprisingly the antagonist Rp-cAMPS-bound R-subunit crystallized in the H conformation, which was previously assumed to be induced only by C-subunit-binding. Apo R-subunit crystallized in the B form as well but amide exchange mass spectrometry showed large differences between apo, agonist and antagonist-bound states of the R-subunit. Further ion mobility reveals the apo R-subunit as an ensemble of multiple conformations with collisional cross-sectional areas spanning both the agonist and antagonist-bound states. Thus contrary to earlier studies that explained the basis for cAMP action through "induced fit" alone, we report evidence for conformational selection, where the ligand-free apo form of the R-subunit exists as an ensemble of both B and H conformations. Although cAMP preferentially binds the B conformation, Rp-cAMPS interestingly binds the H conformation. This reveals the unique importance of the equatorial oxygen of the cyclic phosphate in mediating conformational transitions from H to B forms highlighting a novel approach for rational structure-based drug design. Ideal inhibitors such as Rp-cAMPS are those that preferentially "select" inactive conformations of target proteins by satisfying all "binding" constraints alone without inducing conformational changes necessary for activation.

  15. Conformers, infrared spectrum, UV-induced photochemistry, and near-IR-induced generation of two rare conformers of matrix-isolated phenylglycine

    Science.gov (United States)

    Borba, Ana; Gómez-Zavaglia, Andrea; Fausto, Rui

    2014-10-01

    The conformational space of α-phenylglycine (PG) have been investigated theoretically at both the DFT/B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) levels of approximation. Seventeen different minima were found on the investigated potential energy surfaces, which are characterized by different dominant intramolecular interactions: type I conformers are stabilized by hydrogen bonds of the type N-H...O=C, type II by a strong O-H...N hydrogen bond, type III by weak N-H...O-H hydrogen bonds, and type IV by a C=O...H-C contact. The calculations indicate also that entropic effects are relevant in determining the equilibrium populations of the conformers of PG in the gas phase, in particular in the case of conformers of type II, where the strong intramolecular O-H...N hydrogen bond considerably diminishes entropy by reducing the conformational mobility of the molecule. In consonance with the relative energies of the conformers and barriers for conformational interconversion, only 3 conformers of PG were observed for the compound isolated in cryogenic Ar, Xe, and N2 matrices: the conformational ground state (ICa), and forms ICc and IITa. All other significantly populated conformers existing in the gas phase prior to deposition convert either to conformer ICa or to conformer ICc during matrix deposition. The experimental observation of ICc had never been achieved hitherto. Narrowband near-IR irradiation of the first overtone of νOH vibrational mode of ICa and ICc in nitrogen matrices (at 6910 and 6930 cm-1, respectively) led to selective generation of two additional conformers of high-energy, ITc and ITa, respectively, which were also observed experimentally for the first time. In addition, these experiments also provided the key information for the detailed vibrational characterization of the 3 conformers initially present in the matrices. On the other hand, UV irradiation (λ = 255 nm) of PG isolated in a xenon matrix revealed that PG undergoes facile photofragmentation

  16. Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis

    KAUST Repository

    Feng, Yitao

    2016-10-13

    The glutamine binding protein (GlnBP) binds l-glutamine and cooperates with its cognate transporters during glutamine uptake. Crystal structure analysis has revealed an open and a closed conformation for apo- and holo-GlnBP, respectively. However, the detailed conformational dynamics have remained unclear. Herein, we combined NMR spectroscopy, MD simulations, and single-molecule FRET techniques to decipher the conformational dynamics of apo-GlnBP. The NMR residual dipolar couplings of apo-GlnBP were in good agreement with a MD-derived structure ensemble consisting of four metastable states. The open and closed conformations are the two major states. This four-state model was further validated by smFRET experiments and suggests the conformational selection mechanism in ligand recognition of GlnBP. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

  17. Structural studies of conformational changes of proteins upon phosphorylation: Structures of activated CheY, CheY-N16-FliM complex, and AAA {sup +} ATPase domain of NtrC1 in both inactive and active states

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Seok-Yong

    2003-04-10

    Protein phosphorylation is a general mechanism for signal transduction as well as regulation of cellular function. Unlike phosphorylation in eukaryotic systems that uses Ser/Thr for the sites of modification, two-component signal transduction systems, which are prevalent in bacteria, archea, and lower eukaryotes, use an aspartate as the site of phosphorylation. Two-component systems comprise a histidine kinase and a receiver domain. The conformational change of the receiver domain upon phosphorylation leads to signal transfer to the downstream target, a process that had not been understood well at the molecular level. The transient nature of the phospho-Asp bond had made structural studies difficult. The discovery of an excellent analogue for acylphosphate, BeF{sub 3}{sup -}, enabled structural study of activated receiver domains. The structure of activated Chemotaxis protein Y (CheY) was determined both by NMR spectroscopy and X-ray crystallography. These structures revealed the molecular basis of the conformational change that is coupled to phosphorylation. Phosphorylation of the conserved Asp residue in the active site allows hydrogen bonding of the T87 O{gamma} to phospho-aspartate, which in turn leads to the rotation of Y106 into the ''in'' position (termed Y-T coupling). The structure of activated CheY complexed with the 16 N-terminal residues of FliM (N16-FliM), its target, was also determined by X-ray crystallography and confirmed the proposed mechanism of activation (Y-T coupling). First, N16-FliM binds to the region on CheY that undergoes a significant conformational change. Second, the ''in'' position of Y106 presents a better binding surface for FliM because the sidechain of Y106 in the inactive form of CheY (''out'' position) sterically interferes with binding of N16-FliM. In addition to confirmation of Y-T coupling, the structure of the activated CheY-N16-FliM complex suggested that the N16

  18. Conformational control of benzophenone-sensitized charge transfer in dinucleotides.

    Science.gov (United States)

    Merz, Thomas; Wenninger, Matthias; Weinberger, Michael; Riedle, Eberhard; Wagenknecht, Hans-Achim; Schütz, Martin

    2013-11-14

    Charge transfer in DNA cannot be understood without addressing the complex conformational flexibility, which occurs on a wide range of timescales. In order to reduce this complexity four dinucleotide models 1X consisting of benzophenone linked by a phosphodiester to one of the natural nucleosides X = A, G, T, C were studied in water and methanol. The theoretical work focuses on the dynamics and electronic structure of 1G. Predominant conformations in the two solvents were obtained by molecular dynamics simulations. 1G in MeOH adopts mainly an open geometry with a distance of 12–16 Å between the two aromatic parts. In H2O the two parts of 1G form primarily a stacked conformation yielding a distance of 5–6 Å. The low-lying excited states were investigated by electronic structure theory in a QM/MM environment for representative snapshots of the trajectories. Photo-induced intramolecular charge transfer in the S1 state occurs exclusively in the stacked conformation. Ultrafast transient absorption spectroscopy with 1X reveals fast charge transfer from S1 in both solvents with varying yields. Significant charge transfer from the T1 state is only found for the nucleobases with the lowest oxidation potential: in H2O, charge transfer occurs with 3.2 × 10(9) s(-1) for 1A and 6.0 × 10(9) s(-1) for 1G. The reorganization energy remains nearly unchanged going from MeOH to the more polar H2O. The electronic coupling is rather low even for the stacked conformation with H(AB) = 3 meV and explains the moderate charge transfer rates. The solvent controls the conformational distribution and therefore gates the charge transfer due to differences in distance and stacking.

  19. Conformal Gravity rotation curves with a conformal Higgs halo

    Science.gov (United States)

    Horne, Keith

    2016-06-01

    We discuss the effect of a conformally coupled Higgs field on conformal gravity (CG) predictions for the rotation curves of galaxies. The Mannheim-Kazanas (MK) metric is a valid vacuum solution of CG's fourth-order Poisson equation if and only if the Higgs field has a particular radial profile, S(r) = S0 a/(r + a), decreasing from S0 at r = 0 with radial scalelength a. Since particle rest masses scale with S(r)/S0, their world lines do not follow time-like geodesics of the MK metric gμν, as previously assumed, but rather those of the Higgs-frame MK metric tilde{g}_{μ ν }=Ω ^2 g_{μ ν }, with the conformal factor Ω(r) = S(r)/S0. We show that the required stretching of the MK metric exactly cancels the linear potential that has been invoked to fit galaxy rotation curves without dark matter. We also formulate, for spherical structures with a Higgs halo S(r), the CG equations that must be solved for viable astrophysical tests of CG using galaxy and cluster dynamics and lensing.

  20. Modeling conformational ensembles of slow functional motions in Pin1-WW.

    Directory of Open Access Journals (Sweden)

    Faruck Morcos

    Full Text Available Protein-protein interactions are often mediated by flexible loops that experience conformational dynamics on the microsecond to millisecond time scales. NMR relaxation studies can map these dynamics. However, defining the network of inter-converting conformers that underlie the relaxation data remains generally challenging. Here, we combine NMR relaxation experiments with simulation to visualize networks of inter-converting conformers. We demonstrate our approach with the apo Pin1-WW domain, for which NMR has revealed conformational dynamics of a flexible loop in the millisecond range. We sample and cluster the free energy landscape using Markov State Models (MSM with major and minor exchange states with high correlation with the NMR relaxation data and low NOE violations. These MSM are hierarchical ensembles of slowly interconverting, metastable macrostates and rapidly interconverting microstates. We found a low population state that consists primarily of holo-like conformations and is a "hub" visited by most pathways between macrostates. These results suggest that conformational equilibria between holo-like and alternative conformers pre-exist in the intrinsic dynamics of apo Pin1-WW. Analysis using MutInf, a mutual information method for quantifying correlated motions, reveals that WW dynamics not only play a role in substrate recognition, but also may help couple the substrate binding site on the WW domain to the one on the catalytic domain. Our work represents an important step towards building networks of inter-converting conformational states and is generally applicable.

  1. Geometric modular action for disjoint intervals and boundary conformal field theory

    Energy Technology Data Exchange (ETDEWEB)

    Longo, Roberto [Universita di Roma (Italy); Martinetti, Pierre; Rehren, Karl-Henning [Universitaet Goettingen (Germany). Courant Centre

    2010-07-01

    In suitable states, the modular group of local algebras associated with unions of disjoint intervals in chiral conformal quantum field theory acts geometrically. We translate this result into the setting of boundary conformal quantum field theory and interpret it as a relation between temperature and acceleration.

  2. 46 CFR 386.5 - Conformity with signs and posted regulations.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 8 2010-10-01 2010-10-01 false Conformity with signs and posted regulations. 386.5 Section 386.5 Shipping MARITIME ADMINISTRATION, DEPARTMENT OF TRANSPORTATION MISCELLANEOUS REGULATIONS GOVERNING PUBLIC BUILDINGS AND GROUNDS AT THE UNITED STATES MERCHANT MARINE ACADEMY § 386.5 Conformity...

  3. N=2 Conformal Supergravity from Twistor-String Theory

    CERN Document Server

    Ahn, C

    2004-01-01

    A chiral superfield strength in N=2 conformal supergravity at linearized level is obtained by acting two superspace derivatives on N=4 chiral superfield strength which can be described in terms of N=4 twistor superfields. By decomposing SU(4)_R representation of N=4 twistor superfields into the SU(2)_R representation with an invariant U(1)_R charge, the surviving N=2 twistor superfields contain the physical states of N=2 conformal supergravity. These N=2 twistor superfields are functions of homogeneous coordinates of weighted complex projective space WCP^{3|4} where the two weighted fermionic coordinates have weight -1 and 3.

  4. Conformally symmetric traversable wormholes in f( G) gravity

    Science.gov (United States)

    Sharif, M.; Fatima, H. Ismat

    2016-11-01

    We discuss non-static conformally symmetric traversable wormholes for spherically symmetric spacetime using the model f(G)=α Gn, where n>0 and α is an arbitrary constant. We investigate wormhole solutions by taking two types of shape function and found that physically realistic wormholes exist only for even values of n. We also check the validity of flare-out condition, required for wormhole construction, for the shape functions deduced from two types of equation of state. It is found that this condition is satisfied by these functions in all cases except phantom case with non-static conformal symmetry.

  5. GMOR-like relation in IR-conformal gauge theories

    CERN Document Server

    Patella, Agostino

    2011-01-01

    A generalization of the GMOR relation to the case of infrared-conformal gauge theories is discussed. The starting point is the chiral Ward identity connecting the isovector pseudoscalar susceptibility to the chiral condensate, in a mass-deformed theory. A renormalization-group analysis shows that the pseudoscalar susceptibility is not saturated by the lightest state, but a contribution from the continuum part of the spectrum survives in the chiral limit. The computation also shows how infrared-conformal gauge theories behave differently, depending on whether the anomalous dimension of the chiral condensate be smaller or larger than 1.

  6. Conformational Asymmetry and Quasicrystal Approximants in Linear Diblock Copolymers

    Science.gov (United States)

    Schulze, Morgan W.; Lewis, Ronald M.; Lettow, James H.; Hickey, Robert J.; Gillard, Timothy M.; Hillmyer, Marc A.; Bates, Frank S.

    2017-05-01

    Small angle x-ray scattering experiments on three model low molar mass diblock copolymer systems containing minority polylactide and majority hydrocarbon blocks demonstrate that conformational asymmetry stabilizes the Frank-Kasper σ phase. Differences in block flexibility compete with space filling at constant density inducing the formation of polyhedral shaped particles that assemble into this low symmetry ordered state with local tetrahedral coordination. These results confirm predictions from self-consistent field theory that establish the origins of symmetry breaking in the ordering of block polymer melts subjected to compositional and conformational asymmetry.

  7. Modelling proteins' hidden conformations to predict antibiotic resistance

    Science.gov (United States)

    Hart, Kathryn M.; Ho, Chris M. W.; Dutta, Supratik; Gross, Michael L.; Bowman, Gregory R.

    2016-10-01

    TEM β-lactamase confers bacteria with resistance to many antibiotics and rapidly evolves activity against new drugs. However, functional changes are not easily explained by differences in crystal structures. We employ Markov state models to identify hidden conformations and explore their role in determining TEM's specificity. We integrate these models with existing drug-design tools to create a new technique, called Boltzmann docking, which better predicts TEM specificity by accounting for conformational heterogeneity. Using our MSMs, we identify hidden states whose populations correlate with activity against cefotaxime. To experimentally detect our predicted hidden states, we use rapid mass spectrometric footprinting and confirm our models' prediction that increased cefotaxime activity correlates with reduced Ω-loop flexibility. Finally, we design novel variants to stabilize the hidden cefotaximase states, and find their populations predict activity against cefotaxime in vitro and in vivo. Therefore, we expect this framework to have numerous applications in drug and protein design.

  8. Affine conformal vectors in space-time

    Science.gov (United States)

    Coley, A. A.; Tupper, B. O. J.

    1992-05-01

    All space-times admitting a proper affine conformal vector (ACV) are found. By using a theorem of Hall and da Costa, it is shown that such space-times either (i) admit a covariantly constant vector (timelike, spacelike, or null) and the ACV is the sum of a proper affine vector and a conformal Killing vector or (ii) the space-time is 2+2 decomposable, in which case it is shown that no ACV can exist (unless the space-time decomposes further). Furthermore, it is proved that all space-times admitting an ACV and a null covariantly constant vector (which are necessarily generalized pp-wave space-times) must have Ricci tensor of Segré type {2,(1,1)}. It follows that, among space-times admitting proper ACV, the Einstein static universe is the only perfect fluid space-time, there are no non-null Einstein-Maxwell space-times, and only the pp-wave space-times are representative of null Einstein-Maxwell solutions. Otherwise, the space-times can represent anisotropic fluids and viscous heat-conducting fluids, but only with restricted equations of state in each case.

  9. Conformational transitions of a weak polyampholyte

    KAUST Repository

    Narayanan Nair, Arun Kumar

    2014-10-07

    Using grand canonical Monte Carlo simulations of a flexible polyelectrolyte where the charges are in contact with a reservoir of constant chemical potential given by the solution pH, we study the behavior of weak polyelectrolytes in poor and good solvent conditions for polymer backbone. We address the titration behavior and conformational properties of a flexible diblock polyampholyte chain formed of two oppositely charged weak polyelectrolyte blocks, each containing equal number of identical monomers. The change of solution pH induces charge asymmetry in a diblock polyampholyte. For diblock polyampholyte chains in poor solvents, we demonstrate that a discontinuous transition between extended (tadpole) and collapsed (globular) conformational states is attainable by varying the solution pH. The double-minima structure in the probability distribution of the free energy provides direct evidence for the first-order like nature of this transition. At the isoelectric point electrostatically driven coil-globule transition of diblock polyampholytes in good solvents is found to consist of different regimes identified with increasing electrostatic interaction strength. At pH values above or below the isoelectric point diblock chains are found to have polyelectrolyte-like behavior due to repulsion between uncompensated charges along the chain.

  10. 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...

  11. Conformal invariance in conditioned stochastic particle systems

    Science.gov (United States)

    Schütz, Gunter M.

    2017-08-01

    We consider space-time correlations in generic one-dimensional stochastic interacting particle systems with short-range interactions that undergo a fluctuation with an atypically activity of particle jumps or reactions or spin flips. We briefly review the approach in the framework of the quantum Hamiltonian formalism and present examples where the dynamics during such large fluctuations is governed not by the typical stationary dynamics, but by ballistic universality classes with dynamical exponent z=1 that are described unitary conformally invariant field theories with central charge c. For reaction-diffusion and spin flip dynamics we identify critical points (a) in the Ising universality class with c=1/2 , and (b) in the universality class of the three-states Potts model with c=4/5 . For the Ising universality class we obtain a universal scaling form for the generating function of cumulants of the jump activity. For repulsive driven diffusive systems with one conservation law the regime of an atypically high current or hopping activity is generically conformally invariant with central charge c=1 .

  12. Specific chemical reactivities of spatially separated 3-aminophenol conformers with cold Ca$^+$ ions

    CERN Document Server

    Chang, Yuan-Pin; Küpper, Jochen; Rösch, Daniel; Wild, Dieter; Willitsch, Stefan

    2013-01-01

    Many molecules exhibit multiple rotational isomers (conformers) that interconvert thermally and are difficult to isolate. Consequently, a precise characterization of their role in chemical reactions has proven challenging. We have probed the reactivity of specific conformers using an experimental technique based on their spatial separation in a molecular beam by electrostatic deflection. The separated conformers react with a target of Coulomb-crystallized ions in a trap. In the reaction of Ca$^+$ with 3-aminophenol, we find a twofold larger rate constant for the \\textit{cis}- compared to the \\textit{trans}-conformer (differentiated by the O-H bond orientation). This result is explained by conformer-specific differences in the long-range ion-molecule interaction potentials. Our approach demonstrates the possibility of controlling reactivity through selection of conformational states.

  13. Smart Conformists: Children and Adolescents Associate Conformity With Intelligence Across Cultures.

    Science.gov (United States)

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

    2017-08-24

    The current study used a novel methodology based on multivocal ethnography to assess the relations between conformity and evaluations of intelligence and good behavior among Western (U.S.) and non-Western (Ni-Vanuatu) children (6- to 11-year-olds) and adolescents (13- to 17-year-olds; N = 256). Previous research has shown that U.S. adults were less likely to endorse high-conformity children as intelligent than Ni-Vanuatu adults. The current data demonstrate that in contrast to prior studies documenting cultural differences between adults' evaluations of conformity, children and adolescents in the United States and Vanuatu have a conformity bias when evaluating peers' intelligence and behavior. Conformity bias for good behavior increases with age. The results have implications for understanding the interplay of conformity bias and trait psychology across cultures and development. © 2017 The Authors. Child Development © 2017 Society for Research in Child Development, Inc.

  14. Boundary terms of conformal anomaly

    Directory of Open Access Journals (Sweden)

    Sergey N. Solodukhin

    2016-01-01

    Full Text Available We analyze the structure of the boundary terms in the conformal anomaly integrated over a manifold with boundaries. We suggest that the anomalies of type B, polynomial in the Weyl tensor, are accompanied with the respective boundary terms of the Gibbons–Hawking type. Their form is dictated by the requirement that they produce a variation which compensates the normal derivatives of the metric variation on the boundary in order to have a well-defined variational procedure. This suggestion agrees with recent findings in four dimensions for free fields of various spins. We generalize this consideration to six dimensions and derive explicitly the respective boundary terms. We point out that the integrated conformal anomaly in odd dimensions is non-vanishing due to the boundary terms. These terms are specified in three and five dimensions.

  15. Conformal Bootstrap in Mellin Space

    CERN Document Server

    Gopakumar, Rajesh; Sen, Kallol; Sinha, Aninda

    2016-01-01

    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 epsilon expansion of the Wilson-Fisher fixed point by computing operator dimensions and, strikingly, OPE coefficients to higher orders in epsilon than currently available using other analytic techniques (including Feynman diagram calculations). Our results enable us to get a somewhat better agreement of certain observables in the 3d Ising model, with the precise numerical values that...

  16. 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.

  17. The Conformational Behaviour of Glucosamine

    Science.gov (United States)

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

    2014-06-01

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

  18. Boundary terms of conformal anomaly

    Energy Technology Data Exchange (ETDEWEB)

    Solodukhin, Sergey N., E-mail: Sergey.Solodukhin@lmpt.univ-tours.fr

    2016-01-10

    We analyze the structure of the boundary terms in the conformal anomaly integrated over a manifold with boundaries. We suggest that the anomalies of type B, polynomial in the Weyl tensor, are accompanied with the respective boundary terms of the Gibbons–Hawking type. Their form is dictated by the requirement that they produce a variation which compensates the normal derivatives of the metric variation on the boundary in order to have a well-defined variational procedure. This suggestion agrees with recent findings in four dimensions for free fields of various spins. We generalize this consideration to six dimensions and derive explicitly the respective boundary terms. We point out that the integrated conformal anomaly in odd dimensions is non-vanishing due to the boundary terms. These terms are specified in three and five dimensions.

  19. 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)

  20. Generative models of conformational dynamics.

    Science.gov (United States)

    Langmead, Christopher James

    2014-01-01

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

  1. 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.

  2. 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...

  3. Ligand induced conformational changes of the human serotonin transporter revealed by molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Heidi Koldsø

    Full Text Available The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design.

  4. Ligand induced conformational changes of the human serotonin transporter revealed by molecular dynamics simulations.

    Science.gov (United States)

    Koldsø, Heidi; Autzen, Henriette Elisabeth; Grouleff, Julie; Schiøtt, Birgit

    2013-01-01

    The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design.

  5. Characterizing Protein Structure, Dynamics and Conformation in Lyophilized Solids

    OpenAIRE

    Moorthy, Balakrishnan S.; Iyer, Lavanya K.; Topp, Elizabeth M.

    2015-01-01

    The long-term stability of protein therapeutics in the solid-state depends on the preservation of native structure during lyophilization and in the lyophilized powder. Proteins can reversibly or irreversibly unfold upon lyophilization, acquiring conformations susceptible to degradation during storage. Therefore, characterizing proteins in the dried state is crucial for the design of safe and efficacious formulations. This review summarizes the basic principles and applications of the analytic...

  6. SIMS: a hybrid method for rapid conformational analysis.

    Directory of Open Access Journals (Sweden)

    Bryant Gipson

    Full Text Available Proteins are at the root of many biological functions, often performing complex tasks as the result of large changes in their structure. Describing the exact details of these conformational changes, however, remains a central challenge for computational biology due the enormous computational requirements of the problem. This has engendered the development of a rich variety of useful methods designed to answer specific questions at different levels of spatial, temporal, and energetic resolution. These methods fall largely into two classes: physically accurate, but computationally demanding methods and fast, approximate methods. We introduce here a new hybrid modeling tool, the Structured Intuitive Move Selector (sims, designed to bridge the divide between these two classes, while allowing the benefits of both to be seamlessly integrated into a single framework. This is achieved by applying a modern motion planning algorithm, borrowed from the field of robotics, in tandem with a well-established protein modeling library. sims can combine precise energy calculations with approximate or specialized conformational sampling routines to produce rapid, yet accurate, analysis of the large-scale conformational variability of protein systems. Several key advancements are shown, including the abstract use of generically defined moves (conformational sampling methods and an expansive probabilistic conformational exploration. We present three example problems that sims is applied to and demonstrate a rapid solution for each. These include the automatic determination of "active" residues for the hinge-based system Cyanovirin-N, exploring conformational changes involving long-range coordinated motion between non-sequential residues in Ribose-Binding Protein, and the rapid discovery of a transient conformational state of Maltose-Binding Protein, previously only determined by Molecular Dynamics. For all cases we provide energetic validations using well

  7. Octonionic geometry and conformal transformations

    CERN Document Server

    Gogberashvili, Merab

    2016-01-01

    We describe space-time using split octonions over the reals and use their group of automorphisms, the non-compact form of Cartan's exceptional Lie group G2, as the main geometrical group of the model. It is studied connections of the G2-rotations of octonionic 8D space with the conformal transformations in 4D Minkowski space-time. It is shown that the dimensional constant needed in these analysis naturally gives the observed value of the cosmological constant.

  8. 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...... the $\\delta$-expansion, for a wide range of number of flavours. We also find that this is always smaller than the anomalous dimension of the fermion mass operator. These findings challenge the partial compositeness paradigm....

  9. Holographic multiverse and conformal invariance

    Energy Technology Data Exchange (ETDEWEB)

    Garriga, Jaume [Departament de Física Fonamental i Institut de Ciències del Cosmos, Universitat de Barcelona, Martí i Franquès 1, 08193 Barcelona (Spain); Vilenkin, Alexander, E-mail: jaume.garriga@ub.edu, E-mail: vilenkin@cosmos.phy.tufts.edu [Institute of Cosmology, Department of Physics and Astronomy, Tufts University, 212 College Ave., Medford, MA 02155 (United States)

    2009-11-01

    We consider a holographic description of the inflationary multiverse, according to which the wave function of the universe is interpreted as the generating functional for a lower dimensional Euclidean theory. We analyze a simple model where transitions between inflationary vacua occur through bubble nucleation, and the inflating part of spacetime consists of de Sitter regions separated by thin bubble walls. In this model, we present some evidence that the dual theory is conformally invariant in the UV.

  10. Monogenic Functions in Conformal Geometry

    Directory of Open Access Journals (Sweden)

    Michael Eastwood

    2007-08-01

    Full Text Available Monogenic functions are basic to Clifford analysis. On Euclidean space they are defined as smooth functions with values in the corresponding Clifford algebra satisfying a certain system of first order differential equations, usually referred to as the Dirac equation. There are two equally natural extensions of these equations to a Riemannian spin manifold only one of which is conformally invariant. We present a straightforward exposition.

  11. Conformal theory of galactic halos

    CERN Document Server

    Nesbet, R K

    2011-01-01

    Current cosmological theory describes an isolated galaxy as an observable central galaxy, surrounded by a large spherical halo attributed to dark matter. Galaxy formation by condensation of mass-energy out of a primordial uniform background is shown here to leave a scar, observed as a centripetal gravitational field halo in anomalous galactic rotation and in gravitational lensing. Conformal theory accounts for the otherwise counterintuitive centripetal effect.

  12. All N=4 Conformal Supergravities

    CERN Document Server

    Butter, Daniel; de Wit, Bernard; Sahoo, Bindusar

    2016-01-01

    All N=4 conformal supergravities in four space-time dimensions are constructed. These are the only N=4 supergravity theories whose actions are invariant under off-shell supersymmetry. They are encoded in terms of a holomorphic function that is homogeneous of zeroth degree in scalar fields that parametrize an SU(1,1)/U(1) coset space. When this function equals a constant the Lagrangian is invariant under continuous SU(1,1) transformations.

  13. Anomalous Dimensions of Conformal Baryons

    CERN Document Server

    Pica, Claudio

    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 for a wide range of number of flavours. We also find that this is always smaller than the anomalous dimension of the fermion mass operator. These findings challenge the partial compositeness paradigm.

  14. Exceptional and Spinorial Conformal Windows

    CERN Document Server

    Mojaza, Matin; Ryttov, Thomas A; Sannino, Francesco

    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 to a spinorial representation. We investigate the phase diagram using a purely perturbative four loop analysis, the all-orders beta function and the ladder approximation.

  15. Conformal window and Landau singularities

    CERN Document Server

    Grunberg, G

    2001-01-01

    A physical characterization of Landau singularities is emphasized, which should trace the lower boundary N_f^* of the conformal window in QCD and supersymmetric QCD. A natural way to disentangle ``perturbative'' from ``non-perturbative'' contributions below N_f^* is suggested. Assuming an infrared fixed point is present in the perturbative part of the QCD coupling even in some range below N_f^* leads to the condition gamma(N_f^*)=1, where gamma is the critical exponent. Using the Banks-Zaks expansion, one gets 4conformal window. Some evidence for such a fixed point in QCD is provided through a modified Banks-Zaks expansion. Conformal window amplitudes, which contain power contributions, are show...

  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. 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.

  18. Conformity of nurse prescribing to care needs: nurses' understanding

    Directory of Open Access Journals (Sweden)

    Marília Silveira Faeda

    Full Text Available 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: a descriptive study, with a quantitative approach, was conducted at 20 in-patient units of a teaching hospital in the state of São Paulo. The participants (N=139 answered a semi-structured questionnaire. Results: For 43 (30.9% nurses, nurse prescribing is always in line with patients' care needs. The fields of body care and elimination, skin and mucosa care and investigation and monitoring were the most frequently addressed. Conclusion: in the perception of most nurses, nurse prescribing does not conform with patients' health heeds. The establishment of strategies to improve prescribing quality is recommended, as well as the development of permanent qualification programs and the systematic use of instruments for assessment of patients' care demands regarding nursing.

  19. Sampling Realistic Protein Conformations Using Local Structural Bias

    DEFF Research Database (Denmark)

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

    2006-01-01

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

  20. Two different molecular conformations found in chitosan type II salts.

    Science.gov (United States)

    Lertworasirikul, Amornrat; Tsue, Shin-ichiro; Noguchi, Keiichi; Okuyama, Kenji; Ogawa, Kozo

    2003-05-23

    The type II structure of chitosan acidic salts prepared from crab tendon in solid state was studied using an X-ray fiber diffraction technique together with the linked-atom least-squares (LALS) technique. The cylindrical Patterson method was applied to confirm the molecular conformation of the chitosan. It was shown that there are two different helical conformations for type II salts. One is the relaxed twofold helix having a tetrasaccharide as an asymmetric unit as found in chitosan.HCl salt, which was previously reported as a conformation of chitosan.HCOOH salt. The other is the fourfold helix having a disaccharide as an asymmetric unit newly found in chitosan.HI salt.

  1. Conformal couplings and "azimuthal matching" of QCD Pomerons

    CERN Document Server

    Marchal, N

    2000-01-01

    Using the asymptotic conformal invariance of perturbative QCD we derive the expression of the coupling of external states to all conformal spin-p components of the forward elastic amplitude. Using the wave-function formalism for structure functions at small x, we derive the perturbative coupling of the virtual photon for p= 1, which is maximal for linear transverse polarization. The non-perturbative coupling to the proton is discussed in terms of ``azimuthal matching'' between the proton color dipoles and the quark- antiquark configurations of the photon. As an application, the recent conjecture of a second QCD Pomeron related to the conformal spin-1 component is shown to rely upon a strong azimuthal matching of the p= 1 component in gamma* -proton scattering.

  2. Conformity of nurse prescribing to care needs: nurses' understanding.

    Science.gov (United States)

    Faeda, Marília Silveira; Perroca, Márcia Galan

    2017-04-01

    investigate the understanding of nurses on nurse prescribing conformity to the care needs of hospitalized patients and factors associated with that conformity. a descriptive study, with a quantitative approach, was conducted at 20 in-patient units of a teaching hospital in the state of São Paulo. The participants (N=139) answered a semi-structured questionnaire. For 43 (30.9%) nurses, nurse prescribing is always in line with patients' care needs. The fields of body care and elimination, skin and mucosa care and investigation and monitoring were the most frequently addressed. in the perception of most nurses, nurse prescribing does not conform with patients' health heeds. The establishment of strategies to improve prescribing quality is recommended, as well as the development of permanent qualification programs and the systematic use of instruments for assessment of patients' care demands regarding nursing.

  3. MIXED SELF-CONFORMAL MULTIFRACTAL MEASURES

    Institute of Scientific and Technical Information of China (English)

    Meifeng Dai

    2009-01-01

    Mixed multifractal analysis studies the simultaneous scaling behavior of finitely many measures. A self-conformal measure is a measure invariant under a set of conformal mappings. In this paper, we provide a description of the mixed multifractal theory of finitely many self-conformal measures.

  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...

  5. On the cohomology of Leibniz conformal algebras

    Science.gov (United States)

    Zhang, Jiao

    2015-04-01

    We construct a new cohomology complex of Leibniz conformal algebras with coefficients in a representation instead of a module. The low-dimensional cohomology groups of this complex are computed. Meanwhile, we construct a Leibniz algebra from a Leibniz conformal algebra and prove that the category of Leibniz conformal algebras is equivalent to the category of equivalence classes of formal distribution Leibniz algebras.

  6. Recent Advances in Computational Conformal Geometry

    OpenAIRE

    Gu, Xianfeng David; Luo, Feng; Yau, Shing-Tung

    2009-01-01

    Computational conformal geometry focuses on developing the computational methodologies on discrete surfaces to discover conformal geometric invariants. In this work, we briefly summarize the recent developments for methods and related applications in computational conformal geometry. There are two major approaches, holomorphic differentials and curvature flow. Holomorphic differential method is a linear method, which is more efficient and robust to triangulations with lower qua...

  7. Fragment-based identification of determinants of conformational and spectroscopic change at the ricin active site

    Directory of Open Access Journals (Sweden)

    Soares Alexei S

    2007-11-01

    Full Text Available Abstract Background Ricin is a potent toxin and known bioterrorism threat with no available antidote. The ricin A-chain (RTA acts enzymatically to cleave a specific adenine base from ribosomal RNA, thereby blocking translation. To understand better the relationship between ligand binding and RTA active site conformational change, we used a fragment-based approach to find a minimal set of bonding interactions able to induce rearrangements in critical side-chain positions. Results We found that the smallest ligand stabilizing an open conformer of the RTA active site pocket was an amide group, bound weakly by only a few hydrogen bonds to the protein. Complexes with small amide-containing molecules also revealed a switch in geometry from a parallel towards a splayed arrangement of an arginine-tryptophan cation-pi interaction that was associated with an increase and red-shift in tryptophan fluorescence upon ligand binding. Using the observed fluorescence signal, we determined the thermodynamic changes of adenine binding to the RTA active site, as well as the site-specific binding of urea. Urea binding had a favorable enthalpy change and unfavorable entropy change, with a ΔH of -13 ± 2 kJ/mol and a ΔS of -0.04 ± 0.01 kJ/(K*mol. The side-chain position of residue Tyr80 in a complex with adenine was found not to involve as large an overlap of rings with the purine as previously considered, suggesting a smaller role for aromatic stacking at the RTA active site. Conclusion We found that amide ligands can bind weakly but specifically to the ricin active site, producing significant shifts in positions of the critical active site residues Arg180 and Tyr80. These results indicate that fragment-based drug discovery methods are capable of identifying minimal bonding determinants of active-site side-chain rearrangements and the mechanistic origins of spectroscopic shifts. Our results suggest that tryptophan fluorescence provides a sensitive probe for the

  8. Inflation and conformal invariance: the perspective from radial quantization

    Energy Technology Data Exchange (ETDEWEB)

    Kehagias, Alex [Physics Division, National Technical University of Athens, 15780 Zografou Campus, Athens (Greece); Theoretical Physics Department, CERN, CH-1211 Geneva 23 (Switzerland); Riotto, Antonio [Department of Theoretical Physics and Center for Astroparticle Physics (CAP) 24 quai E. Ansermet, CH-1211 Geneva 4 (Switzerland)

    2017-05-15

    According to the dS/CFT correspondence, correlators of fields generated during a primordial de Sitter phase are constrained by three-dimensional conformal invariance. Using the properties of radially quantized conformal field theories and the operator-state correspondence, we glean information on some points. The Higuchi bound on the masses of spin-s states in de Sitter is a direct consequence of reflection positivity in radially quantized CFT{sub 3} and the fact that scaling dimensions of operators are energies of states. The partial massless states appearing in de Sitter correspond from the boundary CFT{sub 3} perspective to boundary states with highest weight for the conformal group. Finally, we discuss the inflationary consistency relations and the role of asymptotic symmetries which transform asymptotic vacua to new physically inequivalent vacua by generating long perturbation modes. We show that on the CFT{sub 3} side, asymptotic symmetries have a nice quantum mechanics interpretation. For instance, acting with the asymptotic dilation symmetry corresponds to evolving states forward (or backward) in ''time'' and the charge generating the asymptotic symmetry transformation is the Hamiltonian itself. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  9. Conformation and interactions of dopamine hydrochloride in solution

    Energy Technology Data Exchange (ETDEWEB)

    Callear, Samantha K.; Imberti, Silvia [ISIS Facility, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX (United Kingdom); Johnston, Andrew; McLain, Sylvia E. [Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU (United Kingdom)

    2015-01-07

    The aqueous solution of dopamine hydrochloride has been investigated using neutron and X-ray total scattering data together with Monte-Carlo based modelling using Empirical Potential Structure Refinement. The conformation of the protonated dopamine molecule is presented and the results compared to the conformations found in crystal structures, dopamine-complexed protein crystal structures and predicted from theoretical calculations and pharmacophoric models. It is found that protonated dopamine adopts a range of conformations in solution, highlighting the low rotational energy barrier between different conformations, with the preferred conformation being trans-perpendicular. The interactions between each of the species present (protonated dopamine molecules, water molecules, and chloride anions) have been determined and are discussed with reference to interactions observed in similar systems both in the liquid and crystalline state, and predicted from theoretical calculations. The expected strong hydrogen bonds between the strong hydrogen bond donors and acceptors are observed, together with evidence of weaker CH hydrogen bonds and π interactions also playing a significant role in determining the arrangement of adjacent molecules.

  10. Entanglement Temperature in Non-conformal Cases

    CERN Document Server

    He, Song; Wu, Jun-Bao

    2013-01-01

    Potential reconstruction can be used to find various analytical asymptotical AdS solutions in Einstein dilation system generally. We have generated two simple solutions without physical singularity called zero temperature solutions. We also proposed a numerical way to obtain black hole solution in Einstein dilaton system with special dilaton potential. By using this method, we obtain the corresponding black hole solutions numerically and investigate the thermal stability of the black hole by comparing the free energy of thermal gas and the corresponding black hole. In two groups of non-conformal gravity solutions obtained in this paper, we find that the two thermal gas solutions are more unstable than black hole solutions respectively. Finally, we consider black hole solutions as a thermal state of zero temperature solutions to check that the first thermal dynamical law exists in entanglement system from holographic point of view.

  11. Conformal bootstrap, universality and gravitational scattering

    Directory of Open Access Journals (Sweden)

    Steven Jackson

    2015-12-01

    Full Text Available We use the conformal bootstrap equations to study the non-perturbative gravitational scattering between infalling and outgoing particles in the vicinity of a black hole horizon in AdS. We focus on irrational 2D CFTs with large c and only Virasoro symmetry. The scattering process is described by the matrix element of two light operators (particles between two heavy states (BTZ black holes. We find that the operator algebra in this regime is (i universal and identical to that of Liouville CFT, and (ii takes the form of an exchange algebra, specified by an R-matrix that exactly matches the scattering amplitude of 2+1 gravity. The R-matrix is given by a quantum 6j-symbol and the scattering phase by the volume of a hyperbolic tetrahedron. We comment on the relevance of our results to scrambling and the holographic reconstruction of the bulk physics near black hole horizons.

  12. Conformal Bootstrap, Universality and Gravitational Scattering

    CERN Document Server

    Jackson, Steven; Verlinde, Herman

    2014-01-01

    We use the conformal bootstrap equations to study the non-perturbative gravitational scattering between infalling and outgoing particles in the vicinity of a black hole horizon in AdS. We focus on irrational 2D CFTs with large $c$, a sparse light spectrum and only Virasoro symmetry. The scattering process is described by the matrix element of two light operators (particles) between two heavy states (BTZ black holes). We find that the operator algebra in this regime is (i) universal and identical to that of Liouville CFT, and (ii) takes the form of an exchange algebra, specified by an R-matrix that exactly matches with the scattering amplitude of 2+1 gravity. The R-matrix is given by a quantum 6j-symbol and the scattering phase by the volume of a hyperbolic tetrahedron. We comment on the relevance of our results to scrambling and the holographic reconstruction of the bulk physics near black hole horizons.

  13. Quantum entanglement of local operators in conformal field theories.

    Science.gov (United States)

    Nozaki, Masahiro; Numasawa, Tokiro; Takayanagi, Tadashi

    2014-03-21

    We introduce a series of quantities which characterize a given local operator in any conformal field theory from the viewpoint of quantum entanglement. It is defined by the increased amount of (Rényi) entanglement entropy at late time for an excited state defined by acting the local operator on the vacuum. We consider a conformal field theory on an infinite space and take the subsystem in the definition of the entanglement entropy to be its half. We calculate these quantities for a free massless scalar field theory in two, four and six dimensions. We find that these results are interpreted in terms of quantum entanglement of a finite number of states, including Einstein-Podolsky-Rosen states. They agree with a heuristic picture of propagations of entangled particles.

  14. 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.)

  15. Probabilistic sampling of protein conformations: new hope for brute force?

    Science.gov (United States)

    Feldman, Howard J; Hogue, Christopher W V

    2002-01-01

    Protein structure prediction from sequence alone by "brute force" random methods is a computationally expensive problem. Estimates have suggested that it could take all the computers in the world longer than the age of the universe to compute the structure of a single 200-residue protein. Here we investigate the use of a faster version of our FOLDTRAJ probabilistic all-atom protein-structure-sampling algorithm. We have improved the method so that it is now over twenty times faster than originally reported, and capable of rapidly sampling conformational space without lattices. It uses geometrical constraints and a Leonard-Jones type potential for self-avoidance. We have also implemented a novel method to add secondary structure-prediction information to make protein-like amounts of secondary structure in sampled structures. In a set of 100,000 probabilistic conformers of 1VII, 1ENH, and 1PMC generated, the structures with smallest Calpha RMSD from native are 3.95, 5.12, and 5.95A, respectively. Expanding this test to a set of 17 distinct protein folds, we find that all-helical structures are "hit" by brute force more frequently than beta or mixed structures. For small helical proteins or very small non-helical ones, this approach should have a "hit" close enough to detect with a good scoring function in a pool of several million conformers. By fitting the distribution of RMSDs from the native state of each of the 17 sets of conformers to the extreme value distribution, we are able to estimate the size of conformational space for each. With a 0.5A RMSD cutoff, the number of conformers is roughly 2N where N is the number of residues in the protein. This is smaller than previous estimates, indicating an average of only two possible conformations per residue when sterics are accounted for. Our method reduces the effective number of conformations available at each residue by probabilistic bias, without requiring any particular discretization of residue conformational

  16. Conformational plasticity and dynamics in the generic protein folding catalyst SlyD unraveled by single-molecule FRET.

    Science.gov (United States)

    Kahra, Dana; Kovermann, Michael; Löw, Christian; Hirschfeld, Verena; Haupt, Caroline; Balbach, Jochen; Hübner, Christian Gerhard

    2011-08-26

    The relation between conformational dynamics and chemistry in enzyme catalysis recently has received increasing attention. While, in the past, the mechanochemical coupling was mainly attributed to molecular motors, nowadays, it seems that this linkage is far more general. Single-molecule fluorescence methods are perfectly suited to directly evidence conformational flexibility and dynamics. By labeling the enzyme SlyD, a member of peptidyl-prolyl cis-trans isomerases of the FK506 binding protein type with an inserted chaperone domain, with donor and acceptor fluorophores for single-molecule fluorescence resonance energy transfer, we directly monitor conformational flexibility and conformational dynamics between the chaperone domain and the FK506 binding protein domain. We find a broad distribution of distances between the labels with two main maxima, which we attribute to an open conformation and to a closed conformation of the enzyme. Correlation analysis demonstrates that the conformations exchange on a rate in the 100 Hz range. With the aid from Monte Carlo simulations, we show that there must be conformational flexibility beyond the two main conformational states. Interestingly, neither the conformational distribution nor the dynamics is significantly altered upon binding of substrates or other known binding partners. Based on these experimental findings, we propose a model where the conformational dynamics is used to search the conformation enabling the chemical step, which also explains the remarkable substrate promiscuity connected with a high efficiency of this class of peptidyl-prolyl cis-trans isomerases.

  17. 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

  18. Gauge Choice in Conformal Gravity

    Science.gov (United States)

    Sultana, Joseph; Kazanas, Demosthenes

    2017-01-01

    In a recent paper (MNRAS 458, 4122 (2016)) 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 (CG), 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.

  19. 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.

  20. Conformance Testing: Measurement Decision Rules

    Science.gov (United States)

    Mimbs, Scott M.

    2010-01-01

    The goal of a Quality Management System (QMS) as specified in ISO 9001 and AS9100 is to provide assurance to the customer that end products meet specifications. Measuring devices, often called measuring and test equipment (MTE), are used to provide the evidence of product conformity to specified requirements. Unfortunately, processes that employ MTE can become a weak link to the overall QMS if proper attention is not given to the measurement process design, capability, and implementation. Documented "decision rules" establish the requirements to ensure measurement processes provide the measurement data that supports the needs of the QMS. Measurement data are used to make the decisions that impact all areas of technology. Whether measurements support research, design, production, or maintenance, ensuring the data supports the decision is crucial. Measurement data quality can be critical to the resulting consequences of measurement-based decisions. Historically, most industries required simplistic, one-size-fits-all decision rules for measurements. One-size-fits-all rules in some cases are not rigorous enough to provide adequate measurement results, while in other cases are overly conservative and too costly to implement. Ideally, decision rules should be rigorous enough to match the criticality of the parameter being measured, while being flexible enough to be cost effective. The goal of a decision rule is to ensure that measurement processes provide data with a sufficient level of quality to support the decisions being made - no more, no less. This paper discusses the basic concepts of providing measurement-based evidence that end products meet specifications. Although relevant to all measurement-based conformance tests, the target audience is the MTE end-user, which is anyone using MTE other than calibration service providers. Topics include measurement fundamentals, the associated decision risks, verifying conformance to specifications, and basic measurement

  1. From conformal to Einstein gravity

    Science.gov (United States)

    Anastasiou, Giorgos; Olea, Rodrigo

    2016-10-01

    We provide a simple derivation of the equivalence between Einstein and conformal gravity (CG) with Neumann boundary conditions given by Maldacena. As Einstein spacetimes are Bach flat, a generic solution to CG would contain both Einstein and non-Einstein parts. Using this decomposition of the spacetime curvature in the Weyl tensor makes manifest the equivalence between the two theories, both at the level of the action and the variation of it. As a consequence, we show that the on-shell action for critical gravity in four dimensions is given uniquely in terms of the Bach tensor.

  2. From Conformal to Einstein Gravity

    CERN Document Server

    Anastasiou, Giorgos

    2016-01-01

    We provide a simple derivation of the equivalence between Einstein and Conformal Gravity (CG) with Neumann boundary conditions given by Maldacena. As Einstein spacetimes are Bach flat, a generic solution to CG would contain both Einstein and non-Einstein part. Using this decomposition of the spacetime curvature in the Weyl tensor, makes manifest the equivalence between the two theories, both at the level of the action and the variation of it. As a consequence, we show that the on-shell action for Critical Gravity in four dimensions is given uniquely in terms of the Bach tensor.

  3. Toward TeV Conformality

    Energy Technology Data Exchange (ETDEWEB)

    Appelquist, T; Avakian, A; Babich, R; Brower, R C; Cheng, M; Clark, M A; Cohen, S D; Fleming, G T; Kiskis, J; Neil, E T; Osborn, J C; Rebbi, C; Schaich, D; Soltz, R; Vranas, P

    2009-11-30

    We study the chiral condensate <{bar {psi}}{psi}> for an SU(3) gauge theory with N{sub f} massless Dirac fermions in the fundamental representation when N{sub f} is increased from 2 to 6. For N{sub f} = 2, our lattice simulations of <{bar {psi}}{psi}>/F{sup 3}, where F is the Nambu-Goldstone-boson decay constant, agree with the measured QCD value. For N{sub f} = 6, this ratio shows significant enhancement, presaging an even larger enhancement anticipated as N{sub f} increases further, toward the critical value for transition from confinement to infrared conformality.

  4. A chemical chaperone induces inhomogeneous conformational changes in flexible proteins.

    Science.gov (United States)

    Hamdane, Djemel; Velours, Christophe; Cornu, David; Nicaise, Magali; Lombard, Murielle; Fontecave, Marc

    2016-07-27

    Organic osmolytes also known as chemical chaperones are major cellular compounds that favor, by an unclear mechanism, protein's compaction and stabilization of the native state. Here, we have examined the chaperone effect of the naturally occurring trimethylamine N-oxide (TMAO) osmolyte on a loosely packed protein (LPP), known to be a highly flexible form, using an apoprotein mutant of the flavin-dependent RNA methyltransferase as a model. Thermal and chemical denaturation experiments showed that TMAO stabilizes the structural integrity of the apoprotein dramatically. The denaturation reaction is irreversible indicating that the stability of the apoprotein is under kinetic control. This result implies that the stabilization is due to a TMAO-induced reconfiguration of the flexible LPP state, which leads to conformational limitations of the apoprotein likely driven by favorable entropic contribution. Evidence for the conformational perturbation of the apoprotein had been obtained through several biophysical approaches notably analytical ultracentrifugation, circular dichroism, fluorescence spectroscopy, labelling experiments and proteolysis coupled to mass spectrometry. Unexpectedly, TMAO promotes an overall elongation or asymmetrical changes of the hydrodynamic shape of the apoprotein without alteration of the secondary structure. The modulation of the hydrodynamic properties of the protein is associated with diverse inhomogenous conformational changes: loss of the solvent accessible cavities resulting in a dried protein matrix; some side-chain residues initially buried become solvent exposed while some others become hidden. Consequently, the TMAO-induced protein state exhibits impaired capability in the flavin binding process. Our study suggests that the nature of protein conformational changes induced by the chemical chaperones may be specific to protein packing and plasticity. This could be an efficient mechanism by which the cell controls and finely tunes the

  5. Information content of long-range NMR data for the characterization of conformational heterogeneity

    Energy Technology Data Exchange (ETDEWEB)

    Andrałojć, Witold [University of Florence, Center for Magnetic Resonance (CERM) (Italy); Berlin, Konstantin; Fushman, David, E-mail: fushman@umd.edu [University of Maryland, Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization (United States); Luchinat, Claudio, E-mail: luchinat@cerm.unifi.it; Parigi, Giacomo; Ravera, Enrico [University of Florence, Center for Magnetic Resonance (CERM) (Italy); Sgheri, Luca [CNR, Istituto per le Applicazioni del Calcolo, Sezione di Firenze (Italy)

    2015-07-15

    Long-range NMR data, namely residual dipolar couplings (RDCs) from external alignment and paramagnetic data, are becoming increasingly popular for the characterization of conformational heterogeneity of multidomain biomacromolecules and protein complexes. The question addressed here is how much information is contained in these averaged data. We have analyzed and compared the information content of conformationally averaged RDCs caused by steric alignment and of both RDCs and pseudocontact shifts caused by paramagnetic alignment, and found that, despite the substantial differences, they contain a similar amount of information. Furthermore, using several synthetic tests we find that both sets of data are equally good towards recovering the major state(s) in conformational distributions.

  6. Assessing Energy-Dependent Protein Conformational Changes in the TonB System.

    Science.gov (United States)

    Larsen, Ray A

    2017-01-01

    Changes in conformation can alter a protein's vulnerability to proteolysis. Thus, in vivo differential proteinase sensitivity provides a means for identifying conformational changes that mark discrete states in the activity cycle of a protein. The ability to detect a specific conformational state allows for experiments to address specific protein-protein interactions and other physiological components that potentially contribute to the function of the protein. This chapter presents the application of this technique to the TonB-dependent energy transduction system of Gram-negative bacteria, a strategy that has refined our understanding of how the TonB protein is coupled to the ion electrochemical gradient of the cytoplasmic membrane.

  7. Study of conformation and dynamic of surfactant molecules in graphite oxide via NMR

    Energy Technology Data Exchange (ETDEWEB)

    Ai, X.Q. [Jiangsu Second Normal University, College of Physics and Electronic Engineering, Nanjing (China); Ma, L.G. [Nanjing Xiaozhuang University, School of Electronic Engineering, Nanjing (China)

    2016-08-15

    The conformation and dynamic of surfactant in graphite oxide (GO) was investigated by solid-state {sup 13}C magic-angle-spinning NMR and {sup 1}H-{sup 13}C cross-polarization/magic-angle-spinning NMR spectra. The conformation ordering of the alkyl chains in the confined system shows strong dependence on its orientation. While the alkyl chains parallel to the GO layer in lateral monolayer arrangement are in gauche conformation in addition to a small amount of all-trans conformation, those with orientation radiating away from the GO in paraffin bilayer arrangement is in all-trans conformation in addition to some gauche conformation even though high-order diffraction peaks appears. NMR results suggest that the least mobile segment is located at the GO-surfactant interface corresponding to the N-methylene group. Further from it, the mobility of the alkyl chain increases. The terminal methyl and N-methyl carbon groups have the highest mobile. The chains in all-trans conformational state are characterized as more rigid than chains with gauche conformation; each segment of the confined alkyl chains with the lateral monolayer arrangement exhibits less mobility as compared to that with the paraffin bilayer arrangement. (orig.)

  8. Conformal ALON® and spinel windows

    Science.gov (United States)

    Goldman, Lee M.; Smith, Mark; Ramisetty, Mohan; Jha, Santosh; Sastri, Suri

    2017-05-01

    The requirements for modern aircraft based reconnaissance systems are driving the need for conformal windows for future sensor systems. However, limitations on optical systems and the ability to produce windows in complex geometries currently limit the geometry of existing windows and window assemblies to faceted assemblies of flat windows. ALON consists primarily of aluminum and oxygen, similar to that of alumina, with a small amount of nitrogen added to help stabilize the cubic gamma-AlON phase. ALON's chemical similarity to alumina, translates into a robust manufacturing process. This ease of processing has allowed Surmet to produce ALON windows and domes in a wide variety of geometries and sizes. Spinel (MgAl2O4) contains equal molar amounts of MgO and Al2O3, and is a cubic material, that transmits further into the Infrared than ALON. Spinel is produced via powder processing techniques similar to those used to produce ALON. Surmet is now applying the lessons learned with ALON to produce conformal spinel windows and domes as well.

  9. Holography and Conformal Anomaly Matching

    CERN Document Server

    Cabo-Bizet, Alejandro; Narain, K S

    2013-01-01

    We discuss various issues related to the understanding of the conformal anomaly matching in CFT from the dual holographic viewpoint. First, we act with a PBH diffeomorphism on a generic 5D RG flow geometry and show that the corresponding on-shell bulk action reproduces the Wess-Zumino term for the dilaton of broken conformal symmetry, with the expected coefficient aUV-aIR. Then we consider a specific 3D example of RG flow whose UV asymptotics is normalizable and admits a 6D lifting. We promote a modulus \\rho appearing in the geometry to a function of boundary coordinates. In a 6D description {\\rho} is the scale of an SU(2) instanton. We determine the smooth deformed background up to second order in the space-time derivatives of \\rho and find that the 3D on-shell action reproduces a boundary kinetic term for the massless field \\tau= log(\\rho) with the correct coefficient \\delta c=cUV-cIR. We further analyze the linearized fluctuations around the deformed background geometry and compute the one-point functions ...

  10. Conformational equilibria and intrinsic affinities define integrin activation.

    Science.gov (United States)

    Li, Jing; Su, Yang; Xia, Wei; Qin, Yan; Humphries, Martin J; Vestweber, Dietmar; Cabañas, Carlos; Lu, Chafen; Springer, Timothy A

    2017-03-01

    We show that the three conformational states of integrin α5β1 have discrete free energies and define activation by measuring intrinsic affinities for ligand of each state and the equilibria linking them. The 5,000-fold higher affinity of the extended-open state than the bent-closed and extended-closed states demonstrates profound regulation of affinity. Free energy requirements for activation are defined with protein fragments and intact α5β1 On the surface of K562 cells, α5β1 is 99.8% bent-closed. Stabilization of the bent conformation by integrin transmembrane and cytoplasmic domains must be overcome by cellular energy input to stabilize extension. Following extension, headpiece opening is energetically favored. N-glycans and leg domains in each subunit that connect the ligand-binding head to the membrane repel or crowd one another and regulate conformational equilibria in favor of headpiece opening. The results suggest new principles for regulating signaling in the large class of receptors built from extracellular domains in tandem with single-span transmembrane domains.

  11. Axial symmetry and conformal Killing vectors

    CERN Document Server

    Mars, M; Mars, Marc; Senovilla, Jose M.M.

    1993-01-01

    Axisymmetric spacetimes with a conformal symmetry are studied and it is shown that, if there is no further conformal symmetry, the axial Killing vector and the conformal Killing vector must commute. As a direct consequence, in conformally stationary and axisymmetric spacetimes, no restriction is made by assuming that the axial symmetry and the conformal timelike symmetry commute. Furthermore, we prove that in axisymmetric spacetimes with another symmetry (such as stationary and axisymmetric or cylindrically symmetric spacetimes) and a conformal symmetry, the commutator of the axial Killing vector with the two others mush vanish or else the symmetry is larger than that originally considered. The results are completely general and do not depend on Einstein's equations or any particular matter content.

  12. Simulating Protein Conformations through Global Optimization

    CERN Document Server

    Mucherino, A; Pardalos, P M

    2008-01-01

    Many researches have been working on the protein folding problem from more than half century. Protein folding is indeed one of the major unsolved problems in science. In this work, we discuss a model for the simulation of protein conformations. This simple model is based on the idea of imposing few geometric requirements on chains of atoms representing the backbone of a protein conformation. The model leads to the formulation of a global optimization problem, whose solutions correspond to conformations satisfying the desired requirements. The global optimization problem is solved by the recently proposed Monkey Search algorithm. The simplicity of the optimization problem and the effectiveness of the used meta-heuristic search allowed the simulation of a large set of high-quality conformations. We show that, even though only few geometric requirements are imposed, some of the simulated conformation results to be similar (in terms of RMSD) to conformations real proteins actually have in nature.

  13. Measuring the mechanical properties of molecular conformers

    Science.gov (United States)

    Jarvis, S. P.; Taylor, S.; Baran, J. D.; Champness, N. R.; Larsson, J. A.; Moriarty, P.

    2015-09-01

    Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules.

  14. Conformal submanifold geometry I-III

    CERN Document Server

    Burstall, Francis E

    2010-01-01

    In Part I, we develop the notions of a Moebius structure and a conformal Cartan geometry, establish an equivalence between them; we use them in Part II to study submanifolds of conformal manifolds in arbitrary dimension and codimension. We obtain Gauss-Codazzi-Ricci equations and a conformal Bonnet theorem characterizing immersed submanifolds of the conformal n-sphere. These methods are applied in Part III to study constrained Willmore surfaces, isothermic surfaces, Guichard surfaces and conformally-flat submanifolds with flat normal bundle, and their spectral deformations, in arbitrary codimension. The high point of these applications is a unified theory of Moebius-flat submanifolds, which include Guichard surfaces and conformally flat hypersurfaces.

  15. Conformational Switching in the Fungal Light Sensor Vivid

    Energy Technology Data Exchange (ETDEWEB)

    Zoltowski,B.; Schwerdtgeger, C.; Widom, J.; Loros, J.; Bilwes, A.; Dunlap, J.; Crane, B.

    2007-01-01

    The Neurospora crassa photoreceptor Vivid tunes blue-light responses and modulates gating of the circadian clock. Crystal structures of dark-state and light-state Vivid reveal a light, oxygen, or voltage Per-Arnt-Sim domain with an unusual N-terminal cap region and a loop insertion that accommodates the flavin cofactor. Photoinduced formation of a cystein-flavin adduct drives flavin protonation to induce an N-terminal conformational change. A cysteine-to-serine substitution remote from the flavin adenine dinucleotide binding site decouples conformational switching from the flavin photocycle and prevents Vivid from sending signals in Neurospora. Key elements of this activation mechanism are conserved by other photosensors such as White Collar-1, ZEITLUPE, ENVOY, and flavin-binding, kelch repeat, F-BOX 1 (FKF1).

  16. Conformational Heterogeneity in the Activation Mechanism of Bax.

    Science.gov (United States)

    Barnes, C Ashley; Mishra, Pushpa; Baber, James L; Strub, Marie-Paule; Tjandra, Nico

    2017-08-01

    Bax is known for its pro-apoptotic role within the mitochondrial pathway of apoptosis. However, the mechanism for transitioning Bax from cytosolic to membrane-bound oligomer remains elusive. Previous nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) studies defined monomeric Bax as conformationally homogeneous. Yet it has recently been proposed that monomeric Bax exists in equilibrium with a minor state that is distinctly different from its NMR structure. Here, we revisited the structural analysis of Bax using methods uniquely suited for unveiling "invisible" states of proteins, namely, NMR paramagnetic relaxation enhancements and EPR double electron-electron resonance (DEER). Additionally we examined the effect of glycerol, the co-solvent of choice in DEER studies, on the structure of Bax using NMR chemical-shift perturbations and residual dipolar couplings. Based on our combined NMR and EPR results, Bax is a conformationally homogeneous protein prior to its activation. Published by Elsevier Ltd.

  17. TASI Lectures on the Conformal Bootstrap

    CERN Document Server

    Simmons-Duffin, David

    2016-01-01

    These notes are from courses given at TASI and the Advanced Strings School in summer 2015. Starting from principles of quantum field theory and the assumption of a traceless stress tensor, we develop the basics of conformal field theory, including conformal Ward identities, radial quantization, reflection positivity, the operator product expansion, and conformal blocks. We end with an introduction to numerical bootstrap methods, focusing on the 2d and 3d Ising models.

  18. Conformal Invariance and Quantum Nature of Particles

    CERN Document Server

    Salehi, H; Salehi, Hadi; Bisabr, Yousef

    2003-01-01

    We investigate a gravitational model whose vacuum sector is invariant under conformal transformations. In this model, matter is taken to be coupled with a metric which is different but conformally related to the metric appearing explicitly in the vacuum sector. It is then show that the effect of a conformal symmetry breaking would lead to a particle concept. In particular, a correspondence between quantum nature of the particles and the gravitational interaction of matter is established.

  19. 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....

  20. Enzymatic detoxication, conformational selection, and the role of molten globule active sites.

    Science.gov (United States)

    Honaker, Matthew T; Acchione, Mauro; Zhang, Wei; Mannervik, Bengt; Atkins, William M

    2013-06-21

    The role of conformational ensembles in enzymatic reactions remains unclear. Discussion concerning "induced fit" versus "conformational selection" has, however, ignored detoxication enzymes, which exhibit catalytic promiscuity. These enzymes dominate drug metabolism and determine drug-drug interactions. The detoxication enzyme glutathione transferase A1-1 (GSTA1-1), exploits a molten globule-like active site to achieve remarkable catalytic promiscuity wherein the substrate-free conformational ensemble is broad with barrierless transitions between states. A quantitative index of catalytic promiscuity is used to compare engineered variants of GSTA1-1 and the catalytic promiscuity correlates strongly with characteristics of the thermodynamic partition function, for the substrate-free enzymes. Access to chemically disparate transition states is encoded by the substrate-free conformational ensemble. Pre-steady state catalytic data confirm an extension of the conformational selection model, wherein different substrates select different starting conformations. The kinetic liability of the conformational breadth is minimized by a smooth landscape. We propose that "local" molten globule behavior optimizes detoxication enzymes.

  1. 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.

  2. Conformal Anomaly and Large Scale Gravitational Coupling

    CERN Document Server

    Salehi, H

    2000-01-01

    We present a model in which the breackdown of conformal symmetry of a quantum stress-tensor due to the trace anomaly is related to a cosmological effect in a gravitational model. This is done by characterizing the traceless part of the quantum stress-tensor in terms of the stress-tensor of a conformal invariant classical scalar field. We introduce a conformal frame in which the anomalous trace is identified with a cosmological constant. In this conformal frame we establish the Einstein field equations by connecting the quantum stress-tensor with the large scale distribution of matter in the universe.

  3. Conformal invariance conserved quantity of Hamilton systems

    Institute of Scientific and Technical Information of China (English)

    Cai Jian-Le; Luo Shao-Kai; Mei Feng-Xiang

    2008-01-01

    This paper studies conformal invariance and comserved quantRies of Hamilton system.The definition and the determining equation of conformal invariance for Hamilton system are provided.The relationship between the conformal invariance and the Lie symmetry are discussed,and the necessary and sufficient condition that the conformal invariance would be the Lie symmetry of the system under the infinitesimal one-parameter transformation group is deduced.It gives the conserved quantities of the system and an example for illustration.

  4. Conformational heterogeneity of the calmodulin binding interface

    Science.gov (United States)

    Shukla, Diwakar; Peck, Ariana; Pande, Vijay S.

    2016-04-01

    Calmodulin (CaM) is a ubiquitous Ca2+ sensor and a crucial signalling hub in many pathways aberrantly activated in disease. However, the mechanistic basis of its ability to bind diverse signalling molecules including G-protein-coupled receptors, ion channels and kinases remains poorly understood. Here we harness the high resolution of molecular dynamics simulations and the analytical power of Markov state models to dissect the molecular underpinnings of CaM binding diversity. Our computational model indicates that in the absence of Ca2+, sub-states in the folded ensemble of CaM's C-terminal domain present chemically and sterically distinct topologies that may facilitate conformational selection. Furthermore, we find that local unfolding is off-pathway for the exchange process relevant for peptide binding, in contrast to prior hypotheses that unfolding might account for binding diversity. Finally, our model predicts a novel binding interface that is well-populated in the Ca2+-bound regime and, thus, a candidate for pharmacological intervention.

  5. 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.

  6. Approaching Conformality with Ten Flavors

    CERN Document Server

    Appelquist, Thomas; Buchoff, Michael I; Cheng, Michael; Cohen, Saul D; Fleming, George T; Kiskis, Joe; Lin, Meifeng; Na, Heechang; Neil, Ethan T; Osborn, James C; Rebbi, Claudio; Schaich, David; Schroeder, Chris; Voronov, Gennady; Vranas, Pavlos

    2012-01-01

    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 ten 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 approximately equal to 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.

  7. A conformal model of gravitons

    CERN Document Server

    Donoghue, John F

    2016-01-01

    In the description of general covariance, the vierbein and the Lorentz connection can be treated as independent fundamental fields. With the usual gauge Lagrangian, the Lorentz connection is characterized by an asymptotically free running coupling. When running from high energy, the coupling gets large at a scale which can be called the Planck mass. If the Lorentz connection is confined at that scale, the low energy theory can have the Einstein Lagrangian induced at low energy through dimensional transmutation. However, in general there will be new divergences in such a theory and the Lagrangian basis should be expanded. I construct a conformally invariant model with a larger basis size which potentially may have the same property.

  8. Charged gravastars admitting conformal motion

    CERN Document Server

    Usmani, A A; Ray, Saibal; Nandi, K K; Kuhfittig, Peter K F; Rakib, Sk A; Hasan, Z

    2010-01-01

    We propose a new model of a {\\it gravastar} admitting conformal motion. While retaining the framework of the Mazur-Mottola model, the gravastar is assumed to be internally charged, with an exterior defined by a Reissner-Nordstr{\\"o}m rather than a Schwarzschild line element. The solutions obtained involve (i) the interior region, (ii) the shell, and (iii) the exterior region of the sphere. Of these three cases the first case is of primary interest since the total gravitational mass vanishes for vanishing charge and turns the total gravitational mass into an {\\it electromagnetic mass} under certain conditions. This suggests that the interior de Sitter vacuum of a charged gravastar is essentially an electromagnetic mass model that must generate the gravitational mass. We have also analyzed various other aspects such as the stress energy tensor in the thin shell and the entropy of the system.

  9. 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.

  10. 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.

  11. Electromagnetic characterization of conformal antennas

    Science.gov (United States)

    Volakis, John L.; Kempel, Leo C.; Alexanian, Angelos; Jin, J. M.; Yu, C. L.; Woo, Alex C.

    1992-01-01

    The ultimate objective of this project is to develop a new technique which permits an accurate simulation of microstrip patch antennas or arrays with various feed, superstrate and/or substrate configurations residing in a recessed cavity whose aperture is planar, cylindrical or otherwise conformed to the substructure. The technique combines the finite element and boundary integral methods to formulate a system suitable for solution via the conjugate gradient method in conjunction with the fast Fourier transform. The final code is intended to compute both scattering and radiation patterns of the structure with an affordable memory demand. With upgraded capabilities, the four included papers examined the radar cross section (RCS), input impedance, gain, and resonant frequency of several rectangular configurations using different loading and substrate/superstrate configurations.

  12. Conformal invariance on orbifolds and excitations of singularity

    CERN Document Server

    Yin, Z

    2007-01-01

    We study conformal field theory on two-dimensional orbifolds and show this to be an effective way to analyze physical effects of geometric singularities with angular deficits. They are closely related to boundaries and cross caps. Representatives classes of singularities can be described exactly using generalizations of boundary states. From this we compute correlation functions and derive the spectra of excitations localized at the singularities.

  13. Non-Equilibrium Thermodynamics in Conformal Field Theory

    CERN Document Server

    Hollands, Stephan

    2016-01-01

    We present a model independent, operator algebraic approach to non-equilibrium quantum thermodynamics within the framework of two-dimensional Conformal Field Theory. Two infinite reservoirs in equilibrium at their own temperatures and chemical potentials are put in contact through a defect line, possibly by inserting a probe. As time evolves, the composite system then approaches a non-equilibrium steady state that we describe. In particular, we re-obtain recent formulas of Bernard and Doyon.

  14. Side chain conformational averaging in human dihydrofolate reductase.

    Science.gov (United States)

    Tuttle, Lisa M; Dyson, H Jane; Wright, Peter E

    2014-02-25

    The three-dimensional structures of the dihydrofolate reductase enzymes from Escherichia coli (ecDHFR or ecE) and Homo sapiens (hDHFR or hE) are very similar, despite a rather low level of sequence identity. Whereas the active site loops of ecDHFR undergo major conformational rearrangements during progression through the reaction cycle, hDHFR remains fixed in a closed loop conformation in all of its catalytic intermediates. To elucidate the structural and dynamic differences between the human and E. coli enzymes, we conducted a comprehensive analysis of side chain flexibility and dynamics in complexes of hDHFR that represent intermediates in the major catalytic cycle. Nuclear magnetic resonance relaxation dispersion experiments show that, in marked contrast to the functionally important motions that feature prominently in the catalytic intermediates of ecDHFR, millisecond time scale fluctuations cannot be detected for hDHFR side chains. Ligand flux in hDHFR is thought to be mediated by conformational changes between a hinge-open state when the substrate/product-binding pocket is vacant and a hinge-closed state when this pocket is occupied. Comparison of X-ray structures of hinge-open and hinge-closed states shows that helix αF changes position by sliding between the two states. Analysis of χ1 rotamer populations derived from measurements of (3)JCγCO and (3)JCγN couplings indicates that many of the side chains that contact helix αF exhibit rotamer averaging that may facilitate the conformational change. The χ1 rotamer adopted by the Phe31 side chain depends upon whether the active site contains the substrate or product. In the holoenzyme (the binary complex of hDHFR with reduced nicotinamide adenine dinucleotide phosphate), a combination of hinge opening and a change in the Phe31 χ1 rotamer opens the active site to facilitate entry of the substrate. Overall, the data suggest that, unlike ecDHFR, hDHFR requires minimal backbone conformational rearrangement as

  15. [An examination of self-monitoring as a determinant of compliant conforming behaviour].

    Science.gov (United States)

    Mizuno, K; Hashimoto, T

    1992-12-01

    The present study investigated the determinant of compliant conforming behaviour from the view-point of the self-monitoring. Subjects, who were classified into High Self-Monitors (HSM) and Low Self-Monitors (LSM), participated in the experiment in which they had a task to distinguish the size of two circles. About the half of subjects performed the task with confederates. In eight of 13 trials, confederates had mistaken distinctions intentionally. The results showed HSM were more conformable to confederates than LSM for male subjects. HSM seemed to conform themselves to confederates easily, because their behaviour was guided by external cues. By contrast, LSM would conform themselves with difficulty, because their behaviour was guided by their internal states. But there were no significant differences for female subjects, and the ability of self-monitoring was considered as the less explanatory determinant for conformity in this experiment.

  16. Conformational transformations of sulfur-containing rings: 2-methyltetrahydrothiophene gas-phase structures.

    Science.gov (United States)

    Van, Vinh; Dindic, Christina; Nguyen, Ha Vinh Lam; Stahl, Wolfgang

    2015-02-02

    Stable conformations of five-member rings with the prototype cyclopentane are well-known to exist as twist or envelope structures and are of general interest in chemistry. Here, we report on the conformational analysis of the sulfur-containing ring 2-methyltetrahydrothiophene studied by a combination of molecular beam Fourier transform microwave (MB-FTMW) spectroscopy and quantum chemistry. Two twist conformers were observed, whereby highly accurate molecular parameters could be determined. In addition, the (34) S-isotopologue of the most stable conformer was assigned in natural abundances. Geometry optimizations were performed at different levels of theory and the calculated rotational constants were compared with experimental values. Two transition states optimized at the MP2/6-311++G(d,p) level using the Berny algorithm could illustrate the intramolecular conversion between both conformers.

  17. Alternative Conformations of Cytochrome c: Structure, Function, and Detection.

    Science.gov (United States)

    Hannibal, Luciana; Tomasina, Florencia; Capdevila, Daiana A; Demicheli, Verónica; Tórtora, Verónica; Alvarez-Paggi, Damián; Jemmerson, Ronald; Murgida, Daniel H; Radi, Rafael

    2016-01-26

    Cytochrome c (cyt c) is a cationic hemoprotein of ∼100 amino acid residues that exhibits exceptional functional versatility. While its primary function is electron transfer in the respiratory chain, cyt c is also recognized as a key component of the intrinsic apoptotic pathway, the mitochondrial oxidative protein folding machinery, and presumably as a redox sensor in the cytosol, along with other reported functions. Transition to alternative conformations and gain-of-peroxidase activity are thought to further enable the multiple functions of cyt c and its translocation across cellular compartments. In vitro, direct interactions of cyt c with cardiolipin, post-translational modifications such as tyrosine nitration, phosphorylation, methionine sulfoxidation, mutations, and even fine changes in electrical fields lead to a variety of conformational states that may be of biological relevance. The identification of these alternative conformations and the elucidation of their functions in vivo continue to be a major challenge. Here, we unify the knowledge of the structural flexibility of cyt c that supports functional moonlighting and review biochemical and immunochemical evidence confirming that cyt c undergoes conformational changes during normal and altered cellular homeostasis.

  18. Partner's stake in conformity and abused wives' psychological trauma.

    Science.gov (United States)

    Demaris, Alfred; Kaukinen, Catherine

    2008-10-01

    This study investigates the potential buffering effect of help-seeking in the association between intimate partner assault and women's psychological trauma, and how this, in turn, may depend on the partner's stake in conformity. The sample consists of 374 women reporting the experience of domestic violence from a current intimate partner, drawn from the larger survey Violence and Threats of Violence Against Women and Men in the United States, 1994-1996. Help-seeking did not appear to buffer the impact of assault severity, contrary to expectation. However, the partner's stake in conformity did condition the effect of his or her having been arrested. Victims had higher levels of posttraumatic stress disorder (PTSD) when police arrested partners of average or below-average stake in conformity. But victims of partners characterized by higher than average stake in conformity did not show elevated PTSD due to their partners having been arrested. On the other hand, PTSD was higher among women experiencing more emotional abuse from the partner.

  19. Exploring the BTZ bulk with boundary conformal blocks

    CERN Document Server

    da Cunha, Bruno Carneiro

    2016-01-01

    We point out a simple relation between the bulk field at an arbitrary radial position and the boundary OPE, by placing some old work by Ferrara, Gatto, Grillo and Parisi in the AdS/CFT context. This gives us, in principle, a prescription for extracting the classical bulk field from the boundary conformal block, and also clarifies why the latter is computed by a geodesic Witten diagram. We apply this prescription to the BTZ black hole - viewed as a pure state created by the insertion of a heavy operator in the boundary CFT_2 - and use it to relate a classical field in the bulk to a heavy-light Virasoro conformal block in the boundary. In particular, we obtain a relation between the radial bulk position and the conformal ratios in the boundary CFT. We use this to show that the singular points of the radial bulk equation occur when the dual boundary operators approach each other and that the associated bulk monodromies map to monodromies of the (appropriately transformed) conformal block, thus providing a CFT in...

  20. Conformational study of a putative HLTV-1 retroviral protease inhibitor.

    Science.gov (United States)

    Llido, S; d'Estaintot, B L; Dautant, A; Geoffre, S; Picard, P; Precigoux, G

    1993-05-01

    The crystal structure of prolyl-glutaminyl-valyl-statyl-alanyl-leucine (Pro-Gln-Val-Sta-Ala-Leu, C(32)H(57)N(7)0(9).5H(2)0, M(r) = 683.9 + 90.1), a putative HTLV-1 protease inhibitor based on one of the consensus retroviral protease cleavage sequences, and containing the statine residue [(4S,3S)-4-amino-3-hydroxy-6-methylheptanoic acid], has been determined by X-ray diffraction. The same molecule has been modelled in the active site of the HTLV-1 protease and both conformations have been compared. The peptide crystallizes as a pentahydrate in space group P2(1) with a = 10.874(2), b = 9.501(2), c = 21.062(5) A, beta = 103.68 (1) degrees, Z = 2, V= 2114.3 A(3), D(x) = 1.21 g cm(-3), micro = 8.02 cm(-1), T= 293 K, lambda(Cu Kalpha) = 1.5418 A. The structure has been refined to an R value of 0.070 for 2152 observed reflections. The peptide main chain can be described as extended and adopts the usual zigzag conformation from the prolyl to the statyl residue. The main difference in conformation between the individual observed and modelled molecules is located on the Sta, Ala and Leu residues with the main chain of the modelled molecule rotated by about 180 degrees as compared to the observed conformation in the crystal state.

  1. TOWARDS UNDERSTANDING OF HELIX B BASED CONFORMATIONAL DISEASES IN SERPIN

    Directory of Open Access Journals (Sweden)

    Mohamad Aman Jairajpuri

    2012-12-01

    Full Text Available Serine protease inhibitors (serpins are a unique family of protease inhibitors that are prone to polymer formation due to their metastable nature and a complex inhibition mechanism that involves large scale conformational change. Helix B is in the shutter region near the strand 2A and strand 3A of �-sheet A, where reactive centre loop inserts during the serpin inhibition mechanism. Helix B region in serpins is a mutation hotspot for naturally occurring variants that result in pathological conditions due to polymerization. Helix B residues are completely buried in the native state and loop inserted latent state but not in the inhibitory loop inserted cleaved conformation. Native to cleaved transition during inhibition forms a large cavity in the shutter region, which invariably is the largest cavity in most serpins in native state. In a recent paper we had for the first time hypothesized that exposure of helix B at the N-terminal end is important for smooth insertion of the reactive center loop during serpin inhibition mechanism. It is therefore possible that natural variant that induces conformational deformation of helix B probably alter the cavity size which increases the rate of loop-sheet interaction between the monomers resulting in increased polymerization.

  2. Conformational Dynamics of o-Fluoro-Substituted Z-Azobenzene.

    Science.gov (United States)

    Rastogi, S K; Rogers, R A; Shi, J; Gao, C; Rinaldi, P L; Brittain, W J

    2015-11-20

    A conformational analysis of o-fluoro Z-azobenzene reveals a slight preference for aromatic C-F/π interaction. Density functional theory (DFT) indicates that the conformation with a C-F/π interaction is preferred by approximately 0.3-0.5 kcal/mol. Ground-state conformations were corroborated with X-ray crystallography. (Z)-Azobenzene (Z-AB) with at least one o-fluoro per ring displays (19)F-(19)F through-space (TS) coupling. 2D J-resolved NMR was used to distinguish through-bond from TS coupling ((TS)JFF). (TS)JFF decreases as the temperature is lowered and the multiplets coalesce into broad singlets. We hypothesize that the coalescence temperature (Tc) corresponds to the barrier for phenyl rotation. The experimentally determined barrier of 8-10 kcal/mol has been qualitatively verified by DFT where transition states with a bisected geometry were identified with zero-point energies of 6-9 kcal/mol relative to ground state. These values are significantly higher that values estimated from previous theoretical studies but lie within a reasonable range for phenyl rotation in hydrocarbon systems.

  3. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Keedy, Daniel A.; Kenner, Lillian R.; Warkentin, Matthew; Woldeyes, Rahel A.; Hopkins, Jesse B.; Thompson, Michael C.; Brewster, Aaron S.; Van Benschoten, Andrew H.; Baxter, Elizabeth L.; Uervirojnangkoorn, Monarin; McPhillips, Scott E.; Song, Jinhu; Alonso-Mori, Roberto; Holton, James M.; Weis, William I.; Brunger, Axel T.; Soltis, S. Michael; Lemke, Henrik; Gonzalez, Ana; Sauter, Nicholas K.; Cohen, Aina E.; van den Bedem, Henry; Thorne, Robert E.; Fraser, James S.

    2015-09-30

    Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. Here we compare the conformational ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography. The diffraction-before-destruction nature of XFEL experiments provides a radiation-damage-free view of the functionally important alternative conformations of CypA, confirming earlier synchrotron-based results. We monitored the temperature dependences of these alternative conformations with eight synchrotron datasets spanning 100-310 K. Multiconformer models show that many alternative conformations in CypA are populated only at 240 K and above, yet others remain populated or become populated at 180 K and below. These results point to a complex evolution of conformational heterogeneity between 180-–240 K that involves both thermal deactivation and solvent-driven arrest of protein motions in the crystal. The lack of a single shared conformational response to temperature within the dynamic active-site network provides evidence for a conformation shuffling model, in which exchange between rotamer states of a large aromatic ring in the middle of the network shifts the conformational ensemble for the other residues in the network. Together, our multitemperature analyses and XFEL data motivate a new generation of temperature- and time-resolved experiments to structurally characterize the dynamic underpinnings of protein function.

  4. Mg(2+)-induced conformational changes in the btuB riboswitch from E. coli.

    Science.gov (United States)

    Choudhary, Pallavi K; Sigel, Roland K O

    2014-01-01

    Mg(2+) has been shown to modulate the function of riboswitches by facilitating the ligand-riboswitch interactions. The btuB riboswitch from Escherichia coli undergoes a conformational change upon binding to its ligand, coenzyme B12 (adenosyl-cobalamine, AdoCbl), and down-regulates the expression of the B12 transporter protein BtuB in order to control the cellular levels of AdoCbl. Here, we discuss the structural folding attained by the btuB riboswitch from E. coli in response to Mg(2+) and how it affects the ligand binding competent conformation of the RNA. The btuB riboswitch notably adopts different conformational states depending upon the concentration of Mg(2+). With the help of in-line probing, we show the existence of at least two specific conformations, one being achieved in the complete absence of Mg(2+) (or low Mg(2+) concentration) and the other appearing above ∼0.5 mM Mg(2+). Distinct regions of the riboswitch exhibit different dissociation constants toward Mg(2+), indicating a stepwise folding of the btuB RNA. Increasing the Mg(2+) concentration drives the transition from one conformation toward the other. The conformational state existing above 0.5 mM Mg(2+) defines the binding competent conformation of the btuB riboswitch which can productively interact with the ligand, coenzyme B12, and switch the RNA conformation. Moreover, raising the Mg(2+) concentration enhances the ratio of switched RNA in the presence of AdoCbl. The lack of a AdoCbl-induced conformational switch experienced by the btuB riboswitch in the absence of Mg(2+) indicates a crucial role played by Mg(2+) for defining an active conformation of the riboswitch.

  5. Conformational re-analysis of (+)-meptazinol: an opioid with mixed analgesic pharmacophores

    Institute of Scientific and Technical Information of China (English)

    Wei LI; Xing-hai WANG; Choi-wan LAU; Yun TANG; Qiong XIE; Zhui-bai QIU

    2006-01-01

    Aim: To further investigate the analgesic pharmacophore of (+)-meptazinol. Methods: Two different opioid pharmacophores, Pharm-Ⅰ and Pharm-Ⅱ, were established from structures of nine typical opiates and meperidine by using molecular modeling approaches according to their different structure activity relationship properties. They were further validated by a set of conformationally constrained arylpiperidines. Two conformers of (+)-meptazinol (Conformer-Ⅰ and Con-former-Ⅱ) detected in solution were then fitted into the pharmacophores, respectively, by Fit Atoms facilities available in SYBYL, a computational modeling tool kit for molecular design and analysis. Results: Conformer-Ⅰ fit Pharm-Ⅰ from typical opiates well. However, Conformer-Ⅱ fit none of these pharmacophores. Instead, it was found to be similar to another potent analgesic, benzofuro[2,3-c] pyridin-6-ol, whose pharmacophore was suggested to hold the transitional state between the two established pharmacophores. Unlike typical analgesics derived from 4-aryl piperidine (eg, meperidine) with one conformer absolutely overwhelming, the (+)-meptazinol exists in two conformers with similar amounts in solution. Furthermore, both conformers can not transform to each other freely in ordinary conditions based on our NMR results. Conclusion: (+)-meptazinol was suggested to be an opioid with mixed analgesic pharmacophores, which may account for the complicated pharmacological properties of meptazinol.

  6. Conformal Higgs, or techni-dilaton- composite Higgs near conformality

    CERN Document Server

    Yamawaki, Koichi

    2010-01-01

    In contrast to the folklore that Technicolor (TC) is a "Higgsless theory", we shall discuss existence of a composite Higgs boson, Techni-Dilaton (TD), a pseudo-Nambu-Goldstone boson of the scale invariance in the Scale-invariant/Walking/Conformal TC (SWC TC) which generates a large anomalous dimension $\\gamma_m \\simeq 1$ in a wide region from the dynamical mass $m$ $= {\\cal O}$ (TeV) of the techni-fermion all the way up to the intrinsic scale $\\Lambda_{\\rm TC}$ of the SWC TC (analogue of $\\Lambda_{\\rm QCD}$), where $\\Lambda_{\\rm TC} $ is taken typically as the scale of the Extended TC scale $\\Lambda_{\\rm ETC}$: $\\Lambda_{\\rm TC} \\simeq \\Lambda_{\\rm ETC}\\sim10^3$ TeV $ (\\gg m)$. All the techni-hadrons have mass on the same order ${\\cal O} (m)$, which in SWC TC is extremely smaller than the intrinsic scale $\\Lambda_{\\rm TC} \\simeq \\Lambda_{\\rm ETC} $, in sharp contrast to QCD where both are of the same order. The mass of TD arises from the {\\it non-perturbative scale anomaly} associated with the techni-fermion ...

  7. Potential Energy Surface-Based Automatic Deduction of Conformational Transition Networks and Its Application on Quantum Mechanical Landscapes of d-Glucose Conformers.

    Science.gov (United States)

    Satoh, Hiroko; Oda, Tomohiro; Nakakoji, Kumiyo; Uno, Takeaki; Tanaka, Hiroaki; Iwata, Satoru; Ohno, Koichi

    2016-11-08

    This paper describes our approach that is built upon the potential energy surface (PES)-based conformational analysis. This approach automatically deduces a conformational transition network, called a conformational reaction route map (r-map), by using the Scaled Hypersphere Search of the Anharmonic Downward Distortion Following method (SHS-ADDF). The PES-based conformational search has been achieved by using large ADDF, which makes it possible to trace only low transition state (TS) barriers while restraining bond lengths and structures with high free energy. It automatically performs sampling the minima and TS structures by simply taking into account the mathematical feature of PES without requiring any a priori specification of variable internal coordinates. An obtained r-map is composed of equilibrium (EQ) conformers connected by reaction routes via TS conformers, where all of the reaction routes are already confirmed during the process of the deduction using the intrinsic reaction coordinate (IRC) method. The postcalculation analysis of the deduced r-map is interactively carried out using the RMapViewer software we have developed. This paper presents computational details of the PES-based conformational analysis and its application to d-glucose. The calculations have been performed for an isolated glucose molecule in the gas phase at the RHF/6-31G level. The obtained conformational r-map for α-d-glucose is composed of 201 EQ and 435 TS conformers and that for β-d-glucose is composed of 202 EQ and 371 TS conformers. For the postcalculation analysis of the conformational r-maps by using the RMapViewer software program we have found multiple minimum energy paths (MEPs) between global minima of (1)C4 and (4)C1 chair conformations. The analysis using RMapViewer allows us to confirm the thermodynamic and kinetic predominance of (4)C1 conformations; that is, the potential energy of the global minimum of (4)C1 is lower than that of (1)C4 (thermodynamic predominance

  8. The conformal approach to asymptotic analysis

    CERN Document Server

    Nicolas, Jean-Philippe

    2015-01-01

    This essay was written as an extended version of a talk given at a conference in Strasbourg on "Riemann, Einstein and geometry", organized by Athanase Papadopoulos in September 2014. Its aim is to present Roger Penrose's approach to asymptotic analysis in general relativity, which is based on conformal geometric techniques, focusing on historical and recent aspects of two specialized topics~: conformal scattering and peeling.

  9. Regular conformal system for Einstein equations

    Energy Technology Data Exchange (ETDEWEB)

    Choquet-Bruhat, Y.; Novello, M.

    1987-06-21

    We give a system of partial differential equations satisfied by a metric g conformal to an Einstein metric and by the conformal factor ..omega.., regular system in the sense that it does not contain negative powers of ..omega... We use the ideas of Friedrich but we obtain here a hyperbolic system in the sense of Leray, by a different method.

  10. Asymptotic symmetry algebra of conformal gravity

    CERN Document Server

    Irakleidou, M

    2016-01-01

    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 non-trivial boundary conditions is five dimensional and it leads to global geon solution with non-vanishing charges.

  11. 40 CFR 52.138 - Conformity procedures.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 3 2010-07-01 2010-07-01 false Conformity procedures. 52.138 Section...) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS Arizona § 52.138 Conformity procedures. (a) Purpose. The... plans for metropolitan transportation planning organizations (MPOs) to use when determining...

  12. 14 CFR 17.45 - Conforming amendments.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false Conforming amendments. 17.45 Section 17.45 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF TRANSPORTATION PROCEDURAL RULES PROCEDURES FOR PROTESTS AND CONTRACTS DISPUTES Finality and Review § 17.45 Conforming amendments. The...

  13. 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…

  14. An extension theorem for conformal gauge singularities

    CERN Document Server

    Tod, Paul

    2007-01-01

    We analyse conformal gauge, or isotropic, singularities in cosmological models in general relativity. Using the calculus of tractors, we find conditions in terms of tractor curvature for a local extension of the conformal structure through a cosmological singularity and prove a local extension theorem.

  15. 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…

  16. DIMENSIONS FOR RANDOM SELF-CONFORMAL SETS

    Institute of Scientific and Technical Information of China (English)

    Liu Yanyan; Wu Jun

    2003-01-01

    A set is called regular if its Hausdorff dimension and upper box-counting dimension coincide.In this paper,we prove that the random self-conformal set is regular almost surely.Also we determine the dimensions for a class of random self-conformal sets.

  17. Double resonance spectroscopy of different conformers of the neurotransmitter amphetamine and its clusters with water

    Science.gov (United States)

    Brause, R.; Fricke, H.; Gerhards, M.; Weinkauf, R.; Kleinermanns, K.

    2006-08-01

    In this paper the conformational landscape of amphetamine in the neutral ground state is examined by both spectroscopy and theory. Several spectroscopic methods are used: laser-induced fluorescence (LIF), resonance-enhanced two-photon ionization (R2PI), dispersed fluorescence and IR/R2PI hole burning spectroscopy. The latter two methods provide for the first time vibrationally resolved spectra of the neutral ground state of dl-amphetamine and the amphetamine-(H 2O) 1,2 complexes. Nine stable conformers of the monomer were found by DFT (B3LYP/6-311++G(d,p)) and ab initio (MP2/6-311++G(d,p)) calculations. For conformer analysis the vibrations observed in the IR/R2PI hole burning and dispersed fluorescence spectra obtained from single vibronic levels (SVLF) of a selected conformer were compared with the results of an ab initio normal mode analysis. By this procedure three S 0 → S 1 transitions in the R2PI spectrum were assigned to three different conformer structures. Another weak transition earlier attributed to another conformer could be assigned to a vibronic band of one of the three conformers. Furthermore spectra of amphetamine-(H 2O) 1,2 are tentatively assigned.

  18. Double resonance spectroscopy of different conformers of the neurotransmitter amphetamine and its clusters with water

    Energy Technology Data Exchange (ETDEWEB)

    Brause, R. [Institut fuer Physikalische Chemie, Heinrich-Heine-Universitaet, Universitaetsstrasse 1, D-40225 Duesseldorf (Germany); Fricke, H. [Institut fuer Physikalische Chemie, Heinrich-Heine-Universitaet, Universitaetsstrasse 1, D-40225 Duesseldorf (Germany); Gerhards, M. [Institut fuer Physikalische Chemie, Heinrich-Heine-Universitaet, Universitaetsstrasse 1, D-40225 Duesseldorf (Germany); Weinkauf, R. [Institut fuer Physikalische Chemie, Heinrich-Heine-Universitaet, Universitaetsstrasse 1, D-40225 Duesseldorf (Germany); Kleinermanns, K. [Institut fuer Physikalische Chemie, Heinrich-Heine-Universitaet, Universitaetsstrasse 1, D-40225 Duesseldorf (Germany)], E-mail: kleinermanns@uni-duesseldorf.de

    2006-08-21

    In this paper the conformational landscape of amphetamine in the neutral ground state is examined by both spectroscopy and theory. Several spectroscopic methods are used: laser-induced fluorescence (LIF), resonance-enhanced two-photon ionization (R2PI), dispersed fluorescence and IR/R2PI hole burning spectroscopy. The latter two methods provide for the first time vibrationally resolved spectra of the neutral ground state of dl-amphetamine and the amphetamine-(H{sub 2}O){sub 1,2} complexes. Nine stable conformers of the monomer were found by DFT (B3LYP/6-311++G(d,p)) and ab initio (MP2/6-311++G(d,p)) calculations. For conformer analysis the vibrations observed in the IR/R2PI hole burning and dispersed fluorescence spectra obtained from single vibronic levels (SVLF) of a selected conformer were compared with the results of an ab initio normal mode analysis. By this procedure three S{sub 0} {sup {yields}} S{sub 1} transitions in the R2PI spectrum were assigned to three different conformer structures. Another weak transition earlier attributed to another conformer could be assigned to a vibronic band of one of the three conformers. Furthermore spectra of amphetamine-(H{sub 2}O){sub 1,2} are tentatively assigned.

  19. A geodesic model in conformal superspace

    CERN Document Server

    Gomes, Henrique de A

    2016-01-01

    In this paper, I look for the most general geometrodynamical symmetries compatible with spatial relational principles. I argue that they lead either to a completely static Universe, or one embodying spatial conformal diffeomorphisms. Demanding locality for an action compatible with these principles severely limits its form, both for the gravitational part as well as all matter couplings. The simplest and most natural choice for pure gravity has two propagating physical degrees of freedom (and no refoliation-invariance). The system has a geometric interpretation as a geodesic model in infinite dimensional conformal superspace. Conformal superspace is a stratified manifold, with different strata corresponding to different isometry groups. Choosing space to be (homeomorphic to) $S^3$, conformal superspace has a preferred stratum with maximal stabilizer group. This stratum consists of a single point -- corresponding to the conformal geometry of the round 3-sphere. This is the most homogeneous non-degenerate geome...

  20. On Combinatorial Expansions of Conformal Blocks

    CERN Document Server

    Marshakov, A; Morozov, A

    2009-01-01

    In a recent paper (arXiv:0906.3219) the representation of Nekrasov partition function in terms of nontrivial two-dimensional conformal field theory has been suggested. For non-vanishing value of the deformation parameter \\epsilon=\\epsilon_1+\\epsilon_2 the instanton partition function is identified with a conformal block of Liouville theory with the central charge c = 1+ 6\\epsilon^2/\\epsilon_1\\epsilon_2. If reversed, this observation means that the universal part of conformal blocks, which is the same for all two-dimensional conformal theories with non-degenerate Virasoro representations, possesses a non-trivial decomposition into sum over sets of the Young diagrams, different from the natural decomposition studied in conformal field theory. We provide some details about this intriguing new development in the simplest case of the four-point correlation functions.