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Sample records for conformational transition intermediates

  1. HIV-1 Env trimer opens through an asymmetric intermediate in which individual protomers adopt distinct conformations.

    Science.gov (United States)

    Ma, Xiaochu; Lu, Maolin; Gorman, Jason; Terry, Daniel S; Hong, Xinyu; Zhou, Zhou; Zhao, Hong; Altman, Roger B; Arthos, James; Blanchard, Scott C; Kwong, Peter D; Munro, James B; Mothes, Walther

    2018-03-21

    HIV-1 entry into cells requires binding of the viral envelope glycoprotein (Env) to receptor CD4 and coreceptor. Imaging of individual Env molecules on native virions shows Env trimers to be dynamic, spontaneously transitioning between three distinct well-populated conformational states: a pre-triggered Env (State 1), a default intermediate (State 2) and a three-CD4-bound conformation (State 3), which can be stabilized by binding of CD4 and coreceptor-surrogate antibody 17b. Here, using single-molecule Fluorescence Resonance Energy Transfer (smFRET), we show the default intermediate configuration to be asymmetric, with individual protomers adopting distinct conformations. During entry, this asymmetric intermediate forms when a single CD4 molecule engages the trimer. The trimer can then transition to State 3 by binding additional CD4 molecules and coreceptor.

  2. Unconventional actin conformations localize on intermediate filaments in mitosis

    International Nuclear Information System (INIS)

    Hubert, Thomas; Vandekerckhove, Joel; Gettemans, Jan

    2011-01-01

    Research highlights: → Unconventional actin conformations colocalize with vimentin on a cage-like structure in metaphase HEK 293T cells. → These conformations are detected with the anti-actin antibodies 1C7 ('lower dimer') and 2G2 ('nuclear actin'), but not C4 (monomeric actin). → Mitotic unconventional actin cables are independent of filamentous actin or microtubules. → Unconventional actin colocalizes with vimentin on a nocodazole-induced perinuclear dense mass of cables. -- Abstract: Different structural conformations of actin have been identified in cells and shown to reside in distinct subcellular locations of cells. In this report, we describe the localization of actin on a cage-like structure in metaphase HEK 293T cells. Actin was detected with the anti-actin antibodies 1C7 and 2G2, but not with the anti-actin antibody C4. Actin contained in this structure is independent of microtubules and actin filaments, and colocalizes with vimentin. Taking advantage of intermediate filament collapse into a perinuclear dense mass of cables when microtubules are depolymerized, we were able to relocalize actin to such structures. We hypothesize that phosphorylation of intermediate filaments at mitosis entry triggers the recruitment of different actin conformations to mitotic intermediate filaments. Storage and partition of the nuclear actin and antiparallel 'lower dimer' actin conformations between daughter cells possibly contribute to gene transcription and transient actin filament dynamics at G1 entry.

  3. Characterization of monomeric intermediates during VSV glycoprotein structural transition.

    Directory of Open Access Journals (Sweden)

    Aurélie A Albertini

    2012-02-01

    Full Text Available Entry of enveloped viruses requires fusion of viral and cellular membranes, driven by conformational changes of viral glycoproteins. Crystal structures provide static pictures of pre- and post-fusion conformations of these proteins but the transition pathway remains elusive. Here, using several biophysical techniques, including analytical ultracentrifugation, circular dichroïsm, electron microscopy and small angle X-ray scattering, we have characterized the low-pH-induced fusogenic structural transition of a soluble form of vesicular stomatitis virus (VSV glycoprotein G ectodomain (G(th, aa residues 1-422, the fragment that was previously crystallized. While the post-fusion trimer is the major species detected at low pH, the pre-fusion trimer is not detected in solution. Rather, at high pH, G(th is a flexible monomer that explores a large conformational space. The monomeric population exhibits a marked pH-dependence and adopts more elongated conformations when pH decreases. Furthermore, large relative movements of domains are detected in absence of significant secondary structure modification. Solution studies are complemented by electron micrographs of negatively stained viral particles in which monomeric ectodomains of G are observed at the viral surface at both pH 7.5 and pH 6.7. We propose that the monomers are intermediates during the conformational change and thus that VSV G trimers dissociate at the viral surface during the structural transition.

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

    Directory of Open Access Journals (Sweden)

    Barry J Grant

    2009-03-01

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

  5. Evidence for an intermediate conformational state of LacY.

    Science.gov (United States)

    Jiang, Xiaoxu; Guan, Lan; Zhou, Yonggang; Hong, Wen-Xu; Zhang, Qinghai; Kaback, H Ronald

    2012-03-20

    LacY mutant Cys154 → Gly exhibits a periplasmic-closed crystal structure identical to the WT, but is periplasmic-open in the membrane. The mutant hardly catalyzes transport, but binds galactosides from either side of the membrane with the same affinity and is resistant to site-directed proteolysis relative to the pseudo-WT. Site-directed alkylation was also applied to 11 single-Cys mutants in Cys154 → Gly LacY in right-side-out membrane vesicles or after solubilization and purification in dodecyl-β-D-maltopyranoside (DDM). Unlike the pseudo-WT, Cys replacements on the periplasmic side of the Cys154 → Gly mutant label rapidly in the membrane without sugar, but labeling decreases markedly after the mutant proteins are purified. Thus, Cys154 → Gly LacY likely favors a higher-energy intermediate periplasmic-open conformation in situ, but collapses to a lower-energy periplasmic-closed conformation in DDM after purification. Notably, branched-chain or neopentyl glycol maltoside detergents stabilize Cys154 → Gly LacY in the membrane-embedded form.

  6. Conformational transitions of a weak polyampholyte

    KAUST Repository

    Nair, Arun Kumar Narayanan

    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.

  7. Conformational transitions of a weak polyampholyte

    KAUST Repository

    Nair, Arun Kumar Narayanan; Uyaver, Sahin; Sun, Shuyu

    2014-01-01

    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.

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

    Science.gov (United States)

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

    2011-01-01

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

  9. Excited state conformational dynamics in carotenoids: dark intermediates and excitation energy transfer.

    Science.gov (United States)

    Beck, Warren F; Bishop, Michael M; Roscioli, Jerome D; Ghosh, Soumen; Frank, Harry A

    2015-04-15

    A consideration of the excited state potential energy surfaces of carotenoids develops a new hypothesis for the nature of the conformational motions that follow optical preparation of the S2 (1(1)Bu(+)) state. After an initial displacement from the Franck-Condon geometry along bond length alternation coordinates, it is suggested that carotenoids pass over a transition-state barrier leading to twisted conformations. This hypothesis leads to assignments for several dark intermediate states encountered in femtosecond spectroscopic studies. The Sx state is assigned to the structure reached upon the onset of torsional motions near the transition state barrier that divides planar and twisted structures on the S2 state potential energy surface. The X state, detected recently in two-dimensional electronic spectra, corresponds to a twisted structure well past the barrier and approaching the S2 state torsional minimum. Lastly, the S(∗) state is assigned to a low lying S1 state structure with intramolecular charge transfer character (ICT) and a pyramidal conformation. It follows that the bent and twisted structures of carotenoids that are found in photosynthetic light-harvesting proteins yield excited-state structures that favor the development of an ICT character and optimized energy transfer yields to (bacterio)chlorophyll acceptors. Copyright © 2015 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    Harada, Ryuhei; Takano, Yu; Shigeta, Yasuteru

    2014-03-01

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

  11. Line broadening in multiphoton processes with a resonant intermediate transition

    International Nuclear Information System (INIS)

    Wang, C.C.; James, J.V.; Xia, J.

    1983-01-01

    The linewidth of the excitation spectrum for multiphoton ionization is found to be broadened much more severely than the cascade fluorescence originating from the resonant intermediate level. These results are due to the mutual effects of the ionizing and resonating transitions, which are not properly accounted for in perturbative treatments

  12. Frustration-guided motion planning reveals conformational transitions in proteins.

    Science.gov (United States)

    Budday, Dominik; Fonseca, Rasmus; Leyendecker, Sigrid; van den Bedem, Henry

    2017-10-01

    Proteins exist as conformational ensembles, exchanging between substates to perform their function. Advances in experimental techniques yield unprecedented access to structural snapshots of their conformational landscape. However, computationally modeling how proteins use collective motions to transition between substates is challenging owing to a rugged landscape and large energy barriers. Here, we present a new, robotics-inspired motion planning procedure called dCC-RRT that navigates the rugged landscape between substates by introducing dynamic, interatomic constraints to modulate frustration. The constraints balance non-native contacts and flexibility, and instantaneously redirect the motion towards sterically favorable conformations. On a test set of eight proteins determined in two conformations separated by, on average, 7.5 Å root mean square deviation (RMSD), our pathways reduced the Cα atom RMSD to the goal conformation by 78%, outperforming peer methods. We then applied dCC-RRT to examine how collective, small-scale motions of four side-chains in the active site of cyclophilin A propagate through the protein. dCC-RRT uncovered a spatially contiguous network of residues linked by steric interactions and collective motion connecting the active site to a recently proposed, non-canonical capsid binding site 25 Å away, rationalizing NMR and multi-temperature crystallography experiments. In all, dCC-RRT can reveal detailed, all-atom molecular mechanisms for small and large amplitude motions. Source code and binaries are freely available at https://github.com/ExcitedStates/KGS/. © 2017 Wiley Periodicals, Inc.

  13. Laser induced popcornlike conformational transition of nanodiamond as a nanoknife

    International Nuclear Information System (INIS)

    Chang, C.-C.; Chen, P.-H.; Chu, H.-L.; Lee, T.-C.; Chou, C.-C.; Chao, J.-I; Su, C.-Y.; Chen, J.S.; Tsai, J.-S.; Tsai, C.-M.; Ho, Y.-P.; Sun, K.W.; Cheng, C.-L.; Chen, F.-R.

    2008-01-01

    Nanodiamond (ND) is surrounded by layers of graphite on its surface. This unique structure feature creates unusual fluorescence spectra, which can be used as an indicator to monitor its surface modification. Meanwhile, the impurity, nitroso (C-N=O) inside the ND can be photolyzed by two-photon absorption, releasing NO to facilitate the formation of a sp 3 diamond structure in the core of ND and transforming it into a sp 2 graphite structure. Such a conformational transition enlarges the size of ND from 8 to 90 nm, resulting in a popcornlike structure. This transition reaction may be useful as nanoknives in biomedical application

  14. Intermediate conformation between native β-sheet and non-native α-helix is a precursor of trifluoroethanol-induced aggregation of Human Carbonic Anhydrase-II

    International Nuclear Information System (INIS)

    Gupta, Preeti; Deep, Shashank

    2014-01-01

    Highlights: • HCAII forms amyloid-like aggregates at moderate concentration of trifluoroethanol. • Protein adopts a state between β-sheet and α-helix at moderate % of TFE. • Hydrophobic surface(s) of partially structured conformation forms amyloid. • High % of TFE induces stable α-helical state preventing aggregation. - Abstract: In the present work, we examined the correlation between 2,2,2-trifluoroethanol (TFE)-induced conformational transitions of human carbonic anhydrase II (HCAII) and its aggregation propensity. Circular dichroism data indicates that protein undergoes a transition from β-sheet to α-helix on addition of TFE. The protein was found to aggregate maximally at moderate concentration of TFE at which it exists somewhere between β-sheet and α-helix, probably in extended non-native β-sheet conformation. Thioflavin-T (ThT) and Congo-Red (CR) assays along with fluorescence microscopy and transmission electron microscopy (TEM) data suggest that the protein aggregates induced by TFE possess amyloid-like features. Anilino-8-naphthalene sulfonate (ANS) binding studies reveal that the exposure of hydrophobic surface(s) was maximum in intermediate conformation. Our study suggests that the exposed hydrophobic surface and/or the disruption of the structural features protecting a β-sheet protein might be the major reason(s) for the high aggregation propensity of non-native intermediate conformation of HCAII

  15. The Role of Conserved Waters in Conformational Transitions of Q61H K-ras

    Science.gov (United States)

    Prakash, Priyanka; Sayyed-Ahmad, Abdallah; Gorfe, Alemayehu A.

    2012-01-01

    To investigate the stability and functional role of long-residence water molecules in the Q61H variant of the signaling protein K-ras, we analyzed all available Ras crystal structures and conformers derived from a series of independent explicit solvent molecular dynamics (MD) simulations totaling 1.76 µs. We show that the protein samples a different region of phase space in the presence and absence of several crystallographically conserved and buried water molecules. The dynamics of these waters is coupled with the local as well as the global motions of the protein, in contrast to less buried waters whose exchange with bulk is only loosely coupled with the motion of loops in their vicinity. Aided by two novel reaction coordinates involving the distance (d) between the Cα atoms of G60 at switch 2 and G10 at the P-loop and the N-Cα-C-O dihedral (ξ) of G60, we further show that three water molecules located in lobe1, at the interface between the lobes and at lobe2, are involved in the relative motion of residues at the two lobes of Q61H K-ras. Moreover, a d/ξ plot classifies the available Ras x-ray structures and MD-derived K-ras conformers into active GTP-, intermediate GTP-, inactive GDP-bound, and nucleotide-free conformational states. The population of these states and the transition between them is modulated by water-mediated correlated motions involving the functionally critical switch 2, P-loop and helix 3. These results suggest that water molecules act as allosteric ligands to induce a population shift among distinct switch 2 conformations that differ in effector recognition. PMID:22359497

  16. Conformational intermediate of the amyloidogenic protein beta 2-microglobulin at neutral pH

    DEFF Research Database (Denmark)

    Heegaard, N H; Sen, J W; Kaarsholm, N C

    2001-01-01

    electrophoresis that two conformers spontaneously exist in aqueous buffers at neutral pH. Upon treatment of wild-type beta(2)-microglobulin with acetonitrile or trifluoroethanol, two conformations were also observed. These conformations were in equilibrium dependent on the sample temperature and the percentage...

  17. Conformal invariance at a deconfinement phase transition in (2+1) dimensions

    International Nuclear Information System (INIS)

    Christensen, J.; Damgaard, P.H.

    1990-08-01

    The conformal dimension of the Polyakov line at the deconfinement phase transition of (2+1)-dimensional SU(2) lattice gauge theory is determined numerically using two-dimensional finite size conformal field theory. Excellent agreement with two-dimensional Ising model values is found for both the renormalized coupling on a spatially toroidal geometry and the conformal dimensions on a finite-width strip geometry. (orig.)

  18. First Order Electroweak Phase Transition from (Non)Conformal Extensions of the Standard Model

    DEFF Research Database (Denmark)

    Sannino, Francesco; Virkajärvi, Jussi

    2015-01-01

    We analyse and compare the finite-temperature electroweak phase transition properties of classically (non)conformal extensions of the Standard Model. In the classically conformal scenarios the breaking of the electroweak symmetry is generated radiatively. The models feature new scalars coupled co...... the associated models are testable at the upcoming Large Hadron Collider run two experiments....

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

    Science.gov (United States)

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

    2011-11-07

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

  20. Monovalent cation induced structural transitions in telomeric DNAs: G-DNA folding intermediates

    International Nuclear Information System (INIS)

    Hardin, C.C.; Watson, T.; Henderson, E.; Prosser, J.K.

    1991-01-01

    Telomeric DNA consists of G- and C-rich strands that are always polarized such that the G-rich strand extends past the 3' end of the duplex to form a 12-16-base overhang. These overhanging strands can self-associate in vitro to form intramolecular structures that have several unusual physical properties and at least one common feature, the presence of non-Watson-Crick G·G base pairs. The term G-DNA was coined for this class of structures. On the basis of gel electrophoresis, imino proton NMR, and circular dichroism (CD) results, the authors find that changing the counterions from sodium to potassium specifically induces conformational transitions in the G-rich telomeric DNA from Tetrahymena, d(T 2 G 4 ) 4 (TET4), which results in a change from the intramolecular species to an apparent multistranded structure, accompanied by an increase in the melting temperature of the base pairs of >25 degree, as monitored by loss of the imino proton NMR signals. They infer that the multistranded structure is a quadruplex. The results indicate that specific differences in ionic interactions can result in a switch in telomeric DNAs between intramolecular hairpin-like or quadruplex-containing species and intermolecular quadruplex structures, all of which involve G·G base pairing interaction. They propose a model in which duplex or hairpin forms of G-DNA are folding intermediates in the formation of either 1-, 2-, or 4-stranded quadruplex structures

  1. Conformational Analysis of DNA Repair Intermediates by Time-Resolved Fluorescence Spectroscopy

    OpenAIRE

    Lin, Su; Horning, David P.; Szostak, Jack W.; Chaput, John C.

    2009-01-01

    DNA repair enzymes are essential for maintaining the integrity of the DNA sequence. Unfortunately, very little is known about how these enzymes recognize damaged regions along the helix. Structural analysis of cellular repair enzymes bound to DNA reveals that these enzymes are able to recognize DNA in a variety of conformations. However, the prevalence of these deformations in the absence of enzymes remains unclear, as small populations of DNA conformations are often difficult to detect by NM...

  2. Phase Transitions, Geometrothermodynamics, and Critical Exponents of Black Holes with Conformal Anomaly

    Directory of Open Access Journals (Sweden)

    Jie-Xiong Mo

    2014-01-01

    Full Text Available We investigate the phase transitions of black holes with conformal anomaly in canonical ensemble. Some interesting and novel phase transition phenomena have been discovered. It is shown that there are striking differences in both Hawking temperature and phase structure between black holes with conformal anomaly and those without it. Moreover, we probe in detail the dependence of phase transitions on the choice of parameters. The results show that black holes with conformal anomaly have much richer phase structure than those without it. There would be two, only one, or no phase transition points depending on the parameters. The corresponding parameter regions are derived both numerically and graphically. Geometrothermodynamics are built up to examine the phase structure we have discovered. It is shown that Legendre invariant thermodynamic scalar curvature diverges exactly where the specific heat diverges. Furthermore, critical behaviors are investigated by calculating the relevant critical exponents. And we prove that these critical exponents satisfy the thermodynamic scaling laws.

  3. Phase transition and gravitational wave phenomenology of scalar conformal extensions of the Standard Model

    Energy Technology Data Exchange (ETDEWEB)

    Marzola, Luca; Racioppi, Antonio; Vaskonen, Ville [National Institute of Chemical Physics and Biophysics, Tallinn (Estonia)

    2017-07-15

    Thermal corrections in classically conformal models typically induce a strong first-order electroweak phase transition, thereby resulting in a stochastic gravitational background that could be detectable at gravitational wave observatories. After reviewing the basics of classically conformal scenarios, in this paper we investigate the phase transition dynamics in a thermal environment and the related gravitational wave phenomenology within the framework of scalar conformal extensions of the Standard Model. We find that minimal extensions involving only one additional scalar field struggle to reproduce the correct phase transition dynamics once thermal corrections are accounted for. Next-to-minimal models, instead, yield the desired electroweak symmetry breaking and typically result in a very strong gravitational wave signal. (orig.)

  4. Conformational transition of κ-casein in micellar environment: Insight from the tryptophan fluorescence

    Science.gov (United States)

    Mishra, Smruti; Meher, Geetanjali; Chakraborty, Hirak

    2017-11-01

    Intrinsically disordered proteins (IDPs) are under intense analysis due to their structural flexibility and importance in biological functions. Minuscule modulation in the microenvironment induces significant conformational changes in IDPs, and these non-native conformations of the IDPs often induce aggregation and cause cell death. Changes in the membrane composition often change the microenvironment, which promote conformational change and aggregation of IDPs. κ-Casein, an important milk protein, belongs to the class of IDPs containing net negative charges. In this present work, we have studied the interaction of κ-casein with cetyltrimethyl ammonium bromide (CTAB), a positively charged surfactant, utilizing various steady state fluorescence, time-resolved fluorescence and circular dichroism spectroscopy. Our results clearly indicate that κ-casein undergoes at least two conformational transitions in presence of various concentrations of CTAB. The intrinsically disordered κ-casein assumes a partially folded conformation at lower concentration of CTAB, which adopts an unstructured conformation at higher concentration of CTAB. The partially folded conformation of κ-casein at a lower CTAB concentration might be induced by the favorable electrostatic interaction between the positively charged surfactant headgroup and net negative charges of the protein, whereas surfactant nature of CTAB is being pronounced at higher concentration of CTAB.

  5. H/L transition time estimation in JET using conformal predictors

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, S., E-mail: sergio.gonzalez@ciemat.es [Asociacion EURATOM/CIEMAT para Fusion, Madrid 28040 (Spain); Vega, J. [Asociacion EURATOM/CIEMAT para Fusion, Madrid 28040 (Spain); Murari, A. [Consorzio RFX, Associazione EURATOM/ENEA per la Fusione, Padova 4-25127 (Italy); Pereira, A. [Asociacion EURATOM/CIEMAT para Fusion, Madrid 28040 (Spain); Dormido-Canto, S.; Ramirez, J.M. [Departamento de Informatica y Automatica, UNED, Madrid 28040 (Spain)

    2012-12-15

    Highlights: Black-Right-Pointing-Pointer H/L transitions have been predicted using H/L and L/H models. Black-Right-Pointing-Pointer Models have been built using conformal predictors to hedge the prediction with confidence and credibility measures. Black-Right-Pointing-Pointer Models have been trained using linear and radial basis function kernels. Black-Right-Pointing-Pointer Conformal measures have proven their usefulness to validate data-driven models. - Abstract: Recent advances in data mining allow the automatic recognition of physical phenomena in the databases of fusion devices without human intervention. This is important to create large databases of physical events (thereby increasing the statistical relevance) in an unattended manner. Important examples are the L/H and H/L transitions. In this contribution, a novel technique is introduced to automatically locate H/L transitions in JET by using conformal predictors. The focus is on H/L transitions because typically there is not a clear signature in the time series of the most widely available signals to recognize the change of confinement. Conformal predictors hedge their prediction by means of two parameters: confidence and credibility. The technique has been based on binary supervised classifiers to separate the samples of the respective confinement modes. Results with several underlying classifiers are presented.

  6. pH-Driven Ordering Transitions in Liquid Crystal Induced by Conformational Changes of Cardiolipin.

    Science.gov (United States)

    Sidiq, Sumyra; Verma, Indu; Pal, Santanu Kumar

    2015-04-28

    We report an investigation of interfacial phenomena occurring at aqueous-liquid crystal (LC) interfaces that triggers an orientational ordering transition of the LC in the presence of cardiolipin (CL) by varying pH, salt concentration and valence. In particular, the effects of three different conformational isomeric forms of the CL are observed to cause the response of the LC ordering to vary significantly from one to another at those interfaces. An ordering transition of the LC was observed when the CL is mostly in undissociated (at pH 2) and/or in bicyclic (at pH 4) conformation in which LC shows changes in the optical appearance from bright to dark. By contrast, no change in the optical appearance of the LC was observed when the pH of the system increases to 8 or higher in which the CL mostly exists in the open conformation. Fluorescence microscopy measurements further suggest that pH-dependent conformational forms of the CL have different ability to self-assemble (thus different packing efficiency) at aqueous-LC interfaces leading to dissimilar orientational behavior of the LC. Specifically, we found that change in headgroup-headgroup repulsion of the central phosphatidyl groups of the CL plays a key role in tuning the lipid packing efficiency and thus responses to interfacial phenomena. Orientational ordering transition of the LC was also observed as a function of increasing the ionic strength (buffer capacity) and strongly influenced in the presence of mono and divalent cations. Langmuir-Blodgett (LB) and polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) measurements provide further insight in modulation of the lipid packing efficiency and alkyl chain conformation of the CL at different pH and ionic conditions. Overall, the results presented in this paper establish that LCs offer a promising approach to differentiate different conformations (label free detection) of the CL through ordering transition of the LC at aqueous

  7. Substrate binding accelerates the conformational transitions and substrate dissociation in multidrug efflux transporter AcrB

    Directory of Open Access Journals (Sweden)

    Beibei eWang

    2015-04-01

    Full Text Available The tripartite efflux pump assembly AcrAB-TolC is the major multidrug resistance transporter in E. coli. The inner membrane transporter AcrB is a homotrimer, energized by the proton movement down the transmembrane electrochemical gradient. The asymmetric crystal structures of AcrB with three monomers in distinct conformational states (access (A, binding (B and extrusion (E support a functional rotating mechanism, in which each monomer of AcrB cycles among the three states in a concerted way. However, the relationship between the conformational changes during functional rotation and drug translocation has not been totally understood. Here, we explored the conformational changes of the AcrB homotrimer during the ABE→BEA transition in different substrate-binding states using targeted MD simulations. It was found that the dissociation of substrate from the distal binding pocket of B monomer is closely related to the concerted conformational changes in the translocation pathway, especially the side chain reorientation of Phe628 and Tyr327. A second substrate binding at the proximal binding pocket of A monomer evidently accelerates the conformational transitions as well as substrate dissociation in B monomer. The acceleration effect of the multi-substrate binding mode provides a molecular explanation for the positive cooperativity observed in the kinetic studies of substrate efflux and deepens our understanding of the functional rotating mechanism of AcrB.

  8. Conformational transition paths harbor structures useful for aiding drug discovery and understanding enzymatic mechanisms in protein kinases.

    Science.gov (United States)

    Wong, Chung F

    2016-01-01

    This short article examines the usefulness of fast simulations of conformational transition paths in elucidating enzymatic mechanisms and guiding drug discovery for protein kinases. It applies the transition path method in the MOIL software package to simulate the paths of conformational transitions between six pairs of structures from the Protein Data Bank. The structures along the transition paths were found to resemble experimental structures that mimic transient structures believed to form during enzymatic catalysis or conformational transitions, or structures that have drug candidates bound. These findings suggest that such simulations could provide quick initial insights into the enzymatic mechanisms or pathways of conformational transitions of proteins kinases, or could provide structures useful for aiding structure-based drug design. © 2015 The Protein Society.

  9. A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

    Science.gov (United States)

    Dalgicdir, Cahit; Sensoy, Ozge; Peter, Christine; Sayar, Mehmet

    2013-12-01

    One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.

  10. A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

    International Nuclear Information System (INIS)

    Dalgicdir, Cahit; Sensoy, Ozge; Sayar, Mehmet; Peter, Christine

    2013-01-01

    One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties

  11. A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

    Energy Technology Data Exchange (ETDEWEB)

    Dalgicdir, Cahit; Sensoy, Ozge; Sayar, Mehmet, E-mail: msayar@ku.edu.tr [College of Engineering, Koç University, 34450 Istanbul (Turkey); Peter, Christine [Max Planck Institute for Polymer Research, 55128 Mainz (Germany); Department of Chemistry, University of Konstanz, 78547 Konstanz (Germany)

    2013-12-21

    One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.

  12. Solid-to-hybrid transitioning armature railgun with non-conforming-to-prejudice bore profile

    Science.gov (United States)

    Solberg, Jerome Michael

    2012-12-04

    An improved railgun, railgun barrel, railgun projectile, and railgun system for accelerating a solid-to-hybrid transitioning armature projectile using a barrel having a bore that does not conform to a cross-sectional profile of the projectile, to contact and guide the projectile only by the rails in a low pressure bore volume so as to minimize damage, failure, and/or underperformance caused by plasma armatures, insulator ablation, and/or restrikes.

  13. An intracellular interaction network regulates conformational transitions in the dopamine transporter

    DEFF Research Database (Denmark)

    Kniazeff, Julie; Shi, Lei; Løland, Claus Juul

    2008-01-01

    Neurotransmitter:sodium symporters (NSS)(1) mediate sodium-dependent reuptake of neurotransmitters from the synaptic cleft and are targets for many psychoactive drugs. The crystal structure of the prokaryotic NSS protein, LeuT, was recently solved at high resolution; however, the mechanistic...... and the intracellular milieu. The mechanism that emerges from these findings may be unique to the NSS family, where the local disruption of ionic interactions modulates the transition of the transporter between the outward- and inward-facing conformations....

  14. Detection of Intermediate-Period Transiting Planets with a Network of Small Telescopes: transitsearch.org

    Science.gov (United States)

    Seagroves, Scott; Harker, Justin; Laughlin, Gregory; Lacy, Justin; Castellano, Tim

    2003-12-01

    We describe a project (transitsearch.org) currently attempting to discover transiting intermediate-period planets orbiting bright parent stars, and we simulate that project's performance. The discovery of such a transit would be an important astronomical advance, bridging the critical gap in understanding between HD 209458b and Jupiter. However, the task is made difficult by intrinsically low transit probabilities and small transit duty cycles. This project's efficient and economical strategy is to photometrically monitor stars that are known (from radial velocity surveys) to bear planets, using a network of widely spaced observers with small telescopes. These observers, each individually capable of precision (1%) differential photometry, monitor candidates during the time windows in which the radial velocity solution predicts a transit if the orbital inclination is close to 90°. We use Monte Carlo techniques to simulate the performance of this network, performing simulations with different configurations of observers in order to optimize coordination of an actual campaign. Our results indicate that transitsearch.org can reliably rule out or detect planetary transits within the current catalog of known planet-bearing stars. A distributed network of skilled amateur astronomers and small college observatories is a cost-effective method for discovering the small number of transiting planets with periods in the range 10 days

  15. Distribution, transition and thermodynamic stability of protein conformations in the denaturant-induced unfolding of proteins.

    Science.gov (United States)

    Bian, Liujiao; Ji, Xu

    2014-01-01

    Extensive and intensive studies on the unfolding of proteins require appropriate theoretical model and parameter to clearly illustrate the feature and characteristic of the unfolding system. Over the past several decades, four approaches have been proposed to describe the interaction between proteins and denaturants, but some ambiguity and deviations usually occur in the explanation of the experimental data. In this work, a theoretical model was presented to show the dependency of the residual activity ratio of the proteins on the molar denaturant concentration. Through the characteristic unfolding parameters ki and Δmi in this model, the distribution, transition and thermodynamic stability of protein conformations during the unfolding process can be quantitatively described. This model was tested with the two-state unfolding of bovine heart cytochrome c and the three-state unfolding of hen egg white lysozyme induced by both guanidine hydrochloride and urea, the four-state unfolding of bovine carbonic anhydrase b induced by guanidine hydrochloride and the unfolding of some other proteins induced by denaturants. The results illustrated that this model could be used accurately to reveal the distribution and transition of protein conformations in the presence of different concentrations of denaturants and to evaluate the unfolding tendency and thermodynamic stability of different conformations. In most denaturant-induced unfolding of proteins, the unfolding became increasingly hard in next transition step and the proteins became more unstable as they attained next successive stable conformation. This work presents a useful method for people to study the unfolding of proteins and may be used to describe the unfolding and refolding of other biopolymers induced by denaturants, inducers, etc.

  16. Transitional Disks Associated with Intermediate-Mass Stars: Results of the SEEDS YSO Survey

    Science.gov (United States)

    Grady, C.; Fukagawa, M.; Maruta, Y.; Ohta, Y.; Wisniewski, J.; Hashimoto, J.; Okamoto, Y.; Momose, M.; Currie, T.; McElwain, M.; hide

    2014-01-01

    Protoplanetary disks are where planets form, grow, and migrate to produce the diversity of exoplanet systems we observe in mature systems. Disks where this process has advanced to the stage of gap opening, and in some cases central cavity formation, have been termed pre-transitional and transitional disks in the hope that they represent intermediate steps toward planetary system formation. Recent reviews have focussed on disks where the star is of solar or sub-solar mass. In contrast to the sub-millimeter where cleared central cavities predominate, at H-band some T Tauri star transitional disks resemble primordial disks in having no indication of clearing, some show a break in the radial surface brightness profile at the inner edge of the outer disk, while others have partially to fully cleared gaps or central cavities. Recently, the Meeus Group I Herbig stars, intermediate-mass PMS stars with IR spectral energy distributions often interpreted as flared disks, have been proposed to have transitional and pre-transitional disks similar to those associated with solar-mass PMS stars, based on thermal-IR imaging, and sub-millimeter interferometry. We have investigated their appearance in scattered light as part of the Strategic Exploration of Exoplanets and Disks with Subaru (SEEDS), obtaining H-band polarimetric imagery of 10 intermediate-mass stars with Meeus Group I disks. Augmented by other disks with imagery in the literature, the sample is now sufficiently large to explore how these disks are similar to and differ from T Tauri star disks. The disk morphologies seen in the Tauri disks are also found for the intermediate-mass star disks, but additional phenomena are found; a hallmark of these disks is remarkable individuality and diversity which does not simply correlate with disk mass or stellar properties, including age, including spiral arms in remnant envelopes, arms in the disk, asymmetrically and potentially variably shadowed outer disks, gaps, and one disk

  17. Optical properties of chalcopyrite-type intermediate transition metal band materials from first principles

    International Nuclear Information System (INIS)

    Aguilera, I.; Palacios, P.; Wahnon, P.

    2008-01-01

    The optical properties of a novel potential high-efficiency photovoltaic material have been studied. This material is based on a chalcopyrite-type semiconductor (CuGaS 2 ) with some Ga atom substituted by Ti and is characterized by the formation of an isolated transition-metal band between the valence band and the conduction band. We present a study in which ab-initio density functional theory calculations within the generalized gradient approximation are carried out to determine the optical reflectivity and absorption coefficient of the materials of interest. Calculations for the host semiconductor are in good agreement with experimental results within the limitations of the approach. We find, as desired, that because of the intermediate band, the new Ti-substituted material would be able to absorb photons of energy lower than the band-gap of the host chalcopyrite. We also analyze the partial contributions to the main peaks of its spectrum

  18. Hydrogen-bonded intermediates and transition states during spontaneous and acid-catalyzed hydrolysis of the carcinogen (+)-anti-BPDE.

    Science.gov (United States)

    Palenik, Mark C; Rodriguez, Jorge H

    2014-07-07

    Understanding mechanisms of (+)-anti-BPDE detoxification is crucial for combating its mutagenic and potent carcinogenic action. However, energetic-structural correlations of reaction intermediates and transition states during detoxification via hydrolysis are poorly understood. To gain mechanistic insight we have computationally characterized intermediate and transition species associated with spontaneous and general-acid catalyzed hydrolysis of (+)-anti-BPDE. We studied the role of cacodylic acid as a proton donor in the rate limiting step. The computed activation energy (ΔG‡) is in agreement with the experimental value for hydrolysis in a sodium cacodylate buffer. Both types of, spontaneous and acid catalyzed, BPDE hydrolysis can proceed through low-entropy hydrogen bonded intermediates prior to formation of transition states whose energies determine reaction activation barriers and rates.

  19. Transition from 2-D radiotherapy to 3-D conformal and intensity modulated radiotherapy

    International Nuclear Information System (INIS)

    2008-05-01

    Cancer is one of the leading causes of death globally and radiotherapy is currently an essential component in the management of cancer patients, either alone or in combination with surgery or chemotherapy, both for cure or palliation. It is now recognized that safe and effective radiotherapy service needs not only substantial capital investment in radiotherapy equipment and specially designed facilities but also continuous investment in maintenance and upgrading of the equipment to comply with the technical progress, but also in training the staff. The recent IAEA-TECDOC publication 'Setting up a Radiotherapy Programme: Clinical, Medical Physics, Radiation Protection and Safety Aspects' provides general guidelines for designing and implementing radiotherapy services in Member States. Advances in computer technology have enabled the possibility of transitioning from basic 2- dimensional treatment planning and delivery (2-D radiotherapy) to a more sophisticated approach with 3-dimensional conformal radiotherapy (3-D CRT). Whereas 2-D radiotherapy can be applied with simple equipment, infrastructure and training, transfer to 3-D conformal treatments requires more resources in technology, equipment, staff and training. A novel radiation treatment approach using Intensity Modulated Radiation Therapy (IMRT) that optimizes the delivery of radiation to irregularly shaped tumour volumes demands even more sophisticated equipment and seamless teamwork, and consequentially more resources, advanced training and more time for treatment planning and verification of dose delivery than 3-D CRT. Whereas 3-D CRT can be considered as a standard, IMRT is still evolving. Due to the increased interest of Member States to the modern application of radiotherapy the IAEA has received a number of requests for guidance coming from radiotherapy departments that wish to upgrade their facilities to 3-D CRT and IMRT through Technical Cooperation programme. These requests are expected to increase

  20. High-pressure behavior of intermediate scapolite: compressibility, structure deformation and phase transition

    Science.gov (United States)

    Lotti, Paolo; Comboni, Davide; Merlini, Marco; Hanfland, Michael

    2018-05-01

    Scapolites are common volatile-bearing minerals in metamorphic rocks. In this study, the high-pressure behavior of an intermediate member of the scapolite solid solution series (Me47), chemical formula (Na1.86Ca1.86K0.23Fe0.01)(Al4.36Si7.64)O24[Cl0.48(CO3)0.48(SO4)0.01], has been investigated up to 17.79 GPa, by means of in situ single-crystal synchrotron X-ray diffraction. The isothermal elastic behavior of the studied scapolite has been described by a III-order Birch-Murnaghan equation of state, which provided the following refined parameters: V 0 = 1110.6(7) Å3, {K_{{V_0}}} = 70(2) GPa ({β _{{V_0}}} = 0.0143(4) GPa-1) and {K_{{V}}^' = 4.8(7). The refined bulk modulus is intermediate between those previously reported for Me17 and Me68 scapolite samples, confirming that the bulk compressibility among the solid solution increases with the Na content. A discussion on the P-induced structure deformation mechanisms of tetragonal scapolite at the atomic scale is provided, along with the implications of the reported results for the modeling of scapolite stability. In addition, a single-crystal to single-crystal phase transition, which is displacive in character, has been observed toward a triclinic polymorph at 9.87 GPa. The high-pressure triclinic polymorph was found to be stable up to the highest pressure investigated.

  1. The effect of conformational transition of gelatin-polysaccharide polyelectrolyte complex on its functional properties

    Directory of Open Access Journals (Sweden)

    Tomáš Valenta

    2017-01-01

    Full Text Available The blends of gelatin and shear-thinning hydrocolloids (guar gum, kappa-carrageenan and xanthan gum were examined to determine the effect of the conformational change on the functional properties of the solutions. The polyelectrolyte complexes of 0.5% gelatin/0.5% polysaccharide in 70 mM KCl or 70 mM NaCl were investigated by the laboratory rheometer and conductivity meter in the temperature range 25 - 45 °C. The rheological data were fitted by the power-law and Herschel-Bulkley model to obtain the flow parameters. The functional properties of the samples were substantially affected by the conformational change of the polysaccharide, as well as by the type of the hydrocolloid and salt solution. There was an evident change of viscosity and conductivity of the solutions upon heating, corresponding to the helix-coil transition of the polysaccharide at temperature about 35 °C. The type of the salt solvent had an effect on the gelation properties of the samples. Gelatin/kappa-carrageenan blend in NaCl provided a gel of high consistency at ambient temperature (20 - 25 °C, whereas the blend in KCl did not gel in the studied temperature range. The potential stability of the blends was determined by zeta-potential analysis. The low values of ζ-potential indicate that the gelatin/polysaccharide blends are electrically unstable systems which tend to coagulate. The mixtures of gelatin/polysaccharide electrostatic complexes may have a great potential in many food applications.

  2. Carrier behavior in special multilayer device composed of different transition metal oxide-based intermediate connectors

    International Nuclear Information System (INIS)

    Deng, Yan-Hong; Chen, Xiang-Yu; Ou, Qing-Dong; Wang, Qian-Kun; Jiang, Xiao-Cheng; Zhang, Dan-Dan; Li, Yan-Qing

    2014-01-01

    The impact of illumination on the connection part of the tandem organic light-emitting diodes was studied by using a special organic multilayer sample consisted of two organic active layers coupled with different transition metal oxide (TMO)-based intermediate connectors (ICs). Through measuring the current density-voltage characteristic, interfacial electronic structures, and capacitance-voltage characteristic, we observe an unsymmetrical phenomenon in current density-voltage and capacitance-voltage curves of Mg:Alq 3 /MoO 3 and MoO 3 composed devices, which was induced by the charge spouting zone near the ICs region and the recombination state in the MoO 3 layer. Moreover, Mg:Alq 3 /MoO 3 composed device displays a photovoltaic effect and the V oc shifts to forward bias under illumination. Our results demonstrate that the TMO-based IC structure coupled with photovoltaic effect can be a good approach for the study of photodetector, light sensor, and so on.

  3. Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states

    Science.gov (United States)

    Qiao, Qin; Zhang, Hou-Dao; Huang, Xuhui

    2016-04-01

    Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kinetics are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.

  4. Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states

    International Nuclear Information System (INIS)

    Qiao, Qin; Zhang, Hou-Dao; Huang, Xuhui

    2016-01-01

    Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kinetics are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.

  5. Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states

    Energy Technology Data Exchange (ETDEWEB)

    Qiao, Qin, E-mail: qqiao@ust.hk; Zhang, Hou-Dao [Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); Huang, Xuhui, E-mail: xuhuihuang@ust.hk [Department of Chemistry, Division of Biomedical Engineering, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); The HKUST Shenzhen Research Institute, Shenzhen (China)

    2016-04-21

    Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kinetics are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.

  6. Conformational transitions and interactions underlying the function of membrane embedded receptor protein kinases.

    Science.gov (United States)

    Bocharov, Eduard V; Sharonov, Georgy V; Bocharova, Olga V; Pavlov, Konstantin V

    2017-09-01

    Among membrane receptors, the single-span receptor protein kinases occupy a broad but specific functional niche determined by distinctive features of the underlying transmembrane signaling mechanisms that are briefly overviewed on the basis of some of the most representative examples, followed by a more detailed discussion of several hierarchical levels of organization and interactions involved. All these levels, including single-molecule interactions (e.g., dimerization, liganding, chemical modifications), local processes (e.g. lipid membrane perturbations, cytoskeletal interactions), and larger scale phenomena (e.g., effects of membrane surface shape or electrochemical potential gradients) appear to be closely integrated to achieve the observed diversity of the receptor functioning. Different species of receptor protein kinases meet their specific functional demands through different structural features defining their responses to stimulation, but certain common patterns exist. Signaling by receptor protein kinases is typically associated with the receptor dimerization and clustering, ligand-induced rearrangements of receptor domains through allosteric conformational transitions with involvement of lipids, release of the sequestered lipids, restriction of receptor diffusion, cytoskeleton and membrane shape remodeling. Understanding of complexity and continuity of the signaling processes can help identifying currently neglected opportunities for influencing the receptor signaling with potential therapeutic implications. This article is part of a Special Issue entitled: Interactions between membrane receptors in cellular membranes edited by Kalina Hristova. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Analysis of an ATP-induced conformational transition of ABC transporter MsbA using a coarse-grained model.

    Science.gov (United States)

    Arai, Naoki; Furuta, Tadaomi; Sakurai, Minoru

    2017-01-01

    Upon the binding of ATP molecules to nucleotide binding domains (NBDs), ATP-binding cassette (ABC) exporters undergo a conformational transition from an inward-facing (IF) to an outward-facing (OF) state. This molecular event is a typical example of chemo-mechanical coupling. However, the underlying mechanism remains unclear. In this study, we analyzed the IF→OF transition of a representative ABC exporter, MsbA, by solving the equation of motion under an elastic network model (ENM). ATP was represented as a single node in ENM or replaced by external forces. When two ATP nodes were added to the ENM of the IF state protein, the two NBDs dimerized; subsequently, the two transmembrane domains opened toward the extracellular side, resulting in the formation of the OF structure. Such a conformational transition was also reproduced by applying external forces, which caused the rotational motion of the NBDs instead of the addition of ATP nodes. The process of the conformational transition was analyzed in detail using cross-correlation maps for node-node interactions. More importantly, it was revealed that the ATP binding energy is converted into distortion energy of several transmembrane helices. These results are useful for understanding the chemo-mechanical coupling in ABC transporters.

  8. Reversible conformational transition gives rise to 'zig-zag' temperature dependence of the rate constant of irreversible thermoinactivation of enzymes.

    Science.gov (United States)

    Levitsky VYu; Melik-Nubarov, N S; Siksnis, V A; Grinberg VYa; Burova, T V; Levashov, A V; Mozhaev, V V

    1994-01-15

    We have obtained unusual 'zig-zag' temperature dependencies of the rate constant of irreversible thermoinactivation (k(in)) of enzymes (alpha-chymotrypsin, covalently modified alpha-chymotrypsin, and ribonuclease) in a plot of log k(in) versus reciprocal temperature (Arrhenius plot). These dependencies are characterized by the presence of both ascending and descending linear portions which have positive and negative values of the effective activation energy (Ea), respectively. A kinetic scheme has been suggested that fits best for a description of these zig-zag dependencies. A key element of this scheme is the temperature-dependent reversible conformational transition of enzyme from the 'low-temperature' native state to a 'high-temperature' denatured form; the latter form is significantly more stable against irreversible thermoinactivation than the native enzyme. A possible explanation for a difference in thermal stabilities is that low-temperature and high-temperature forms are inactivated according to different mechanisms. Existence of the suggested conformational transition was proved by the methods of fluorescence spectroscopy and differential scanning calorimetry. The values of delta H and delta S for this transition, determined from calorimetric experiments, are highly positive; this fact underlies a conclusion that this heat-induced transition is caused by an unfolding of the protein molecule. Surprisingly, in the unfolded high-temperature conformation, alpha-chymotrypsin has a pronounced proteolytic activity, although this activity is much smaller than that of the native enzyme.

  9. 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.

  10. 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.

    2011-01-01

    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[CH2N]–Pro–2-(indol-3-yl)-ethylamine, 1 (R = fluorenylmethoxycarbonyl, Fmoc), and 2 (R = Ac), of Pin1 were synthesized and bioassayed. Inhibitor 1 had an IC50 value of 6.3 μM, which is 4.5-fold better inhibition 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 IC50 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. PMID:21980916

  11. Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Yuqi; Wang, Jinan; Shao, Qiang, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn; Zhu, Weiliang, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn [ACS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203 (China); Shi, Jiye, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn [UCB Pharma, 216 Bath Road, Slough SL1 4EN (United Kingdom)

    2015-03-28

    The application of temperature replica exchange molecular dynamics (REMD) simulation on protein motion is limited by its huge requirement of computational resource, particularly when explicit solvent model is implemented. In the previous study, we developed a velocity-scaling optimized hybrid explicit/implicit solvent REMD method with the hope to reduce the temperature (replica) number on the premise of maintaining high sampling efficiency. In this study, we utilized this method to characterize and energetically identify the conformational transition pathway of a protein model, the N-terminal domain of calmodulin. In comparison to the standard explicit solvent REMD simulation, the hybrid REMD is much less computationally expensive but, meanwhile, gives accurate evaluation of the structural and thermodynamic properties of the conformational transition which are in well agreement with the standard REMD simulation. Therefore, the hybrid REMD could highly increase the computational efficiency and thus expand the application of REMD simulation to larger-size protein systems.

  12. DNA minor groove electrostatic potential: influence of sequence-specific transitions of the torsion angle gamma and deoxyribose conformations.

    Science.gov (United States)

    Zhitnikova, M Y; Shestopalova, A V

    2017-11-01

    The structural adjustments of the sugar-phosphate DNA backbone (switching of the γ angle (O5'-C5'-C4'-C3') from canonical to alternative conformations and/or C2'-endo → C3'-endo transition of deoxyribose) lead to the sequence-specific changes in accessible surface area of both polar and non-polar atoms of the grooves and the polar/hydrophobic profile of the latter ones. The distribution of the minor groove electrostatic potential is likely to be changing as a result of such conformational rearrangements in sugar-phosphate DNA backbone. Our analysis of the crystal structures of the short free DNA fragments and calculation of their electrostatic potentials allowed us to determine: (1) the number of classical and alternative γ angle conformations in the free B-DNA; (2) changes in the minor groove electrostatic potential, depending on the conformation of the sugar-phosphate DNA backbone; (3) the effect of the DNA sequence on the minor groove electrostatic potential. We have demonstrated that the structural adjustments of the DNA double helix (the conformations of the sugar-phosphate backbone and the minor groove dimensions) induce changes in the distribution of the minor groove electrostatic potential and are sequence-specific. Therefore, these features of the minor groove sizes and distribution of minor groove electrostatic potential can be used as a signal for recognition of the target DNA sequence by protein in the implementation of the indirect readout mechanism.

  13. Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions

    Directory of Open Access Journals (Sweden)

    Qing Wang

    2016-05-01

    Full Text Available Free energy calculations of the potential of mean force (PMF based on the combination of targeted molecular dynamics (TMD simulations and umbrella samplings as a function of physical coordinates have been applied to explore the detailed pathways and the corresponding free energy profiles for the conformational transition processes of the butane molecule and the 35-residue villin headpiece subdomain (HP35. The accurate PMF profiles for describing the dihedral rotation of butane under both coordinates of dihedral rotation and root mean square deviation (RMSD variation were obtained based on the different umbrella samplings from the same TMD simulations. The initial structures for the umbrella samplings can be conveniently selected from the TMD trajectories. For the application of this computational method in the unfolding process of the HP35 protein, the PMF calculation along with the coordinate of the radius of gyration (Rg presents the gradual increase of free energies by about 1 kcal/mol with the energy fluctuations. The feature of conformational transition for the unfolding process of the HP35 protein shows that the spherical structure extends and the middle α-helix unfolds firstly, followed by the unfolding of other α-helices. The computational method for the PMF calculations based on the combination of TMD simulations and umbrella samplings provided a valuable strategy in investigating detailed conformational transition pathways for other allosteric processes.

  14. Ab-initio vibrational properties of transition metal chalcopyrite alloys determined as high-efficiency intermediate-band photovoltaic materials

    International Nuclear Information System (INIS)

    Palacios, P.; Aguilera, I.; Wahnon, P.

    2008-01-01

    In this work, we present frozen phonon and linear response ab-initio research into the vibrational properties of the CuGaS 2 chalcopyrite and transition metal substituted (CuGaS 2 )M alloys. These systems are potential candidates for developing a novel solar-cell material with enhanced optoelectronic properties based in the implementation of the intermediate-band concept. We have previously carried out ab-initio calculations of the electronic properties of these kinds of chalcopyrite metal alloys showing a narrow transition metal band isolated in the semiconductor band gap. The substitutes used in the present work are the 3d metal elements, Titanium and Chromium. For the theoretical calculations we use standard density functional theory at local density and generalized gradient approximation levels. We found that the optical phonon branches of the transition metal chalcopyrite, are very sensitive to the specific bonding geometry and small changes in the transition metal environment

  15. Low temperature characterization of the photocurrent produced by two-photon transitions in a quantum dot intermediate band solar cell

    International Nuclear Information System (INIS)

    Antolin, E.; Marti, A.; Stanley, C.R.; Farmer, C.D.; Canovas, E.; Lopez, N.; Linares, P.G.; Luque, A.

    2008-01-01

    Conceived to exceed the conversion efficiency of conventional photovoltaic devices, the intermediate band solar cell bases its operation on exploiting, besides the usual band-to-band optical transitions, the absorption of two sub-bandgap photons. For the present, the only technology used to implement an intermediate band in real devices has been the growth of an InAs/GaAs quantum dot superlattice. In practice, the obtained material shows two limitations: the narrow energy gap between conduction and intermediate band and the appearance of growth defects due to the lattice stress. The consequences are the presence of non-radiative recombination mechanisms and the thermal escape of electrons from the intermediate to the conduction band, hindering the splitting of the quasi-Fermi levels associated with the intermediate and conduction bands and the observation of photocurrent associated with the two-photon absorption. By reducing the temperature at which the devices are characterised we have suppressed the parasitic thermal mechanisms and have succeeded in measuring the photocurrent caused by the absorption of two below bandgap photons. In this work, the characterization of this photocurrent at low temperature is presented and discussed

  16. Insight into the transition between the open and closed conformations of Thermus thermophilus carboxypeptidase

    International Nuclear Information System (INIS)

    Okai, Masahiko; Yamamura, Akihiro; Hayakawa, Kou; Tsutsui, Shiho; Miyazono, Ken-ichi; Lee, Woo-Cheol; Nagata, Koji; Inoue, Yumiko; Tanokura, Masaru

    2017-01-01

    Carboxypeptidase cleaves the C-terminal amino acid residue from proteins and peptides. Here, we report the functional and structural characterizations of carboxypeptidase belonging to the M32 family from the thermophilic bacterium Thermus thermophilus HB8 (TthCP). TthCP exhibits a relatively broad specificity for both hydrophilic (neutral and basic) and hydrophobic (aliphatic and aromatic) residues at the C-terminus and shows optimal activity in the temperature range of 75–80 °C and in the pH range of 6.8–7.2. Enzyme activity was significantly enhanced by cobalt or cadmium and was moderately inhibited by Tris at 25 °C. We also determined the crystal structure of TthCP at 2.6 Å resolution. Two dimer types of TthCP are present in the crystal. One type consists of two subunits in different states, open and closed, with a C α RMSD value of 2.2 Å; the other type consists of two subunits in the same open state. This structure enables us to compare the open and closed states of an M32 carboxypeptidase. The TthCP subunit can be divided into two domains, L and S, which are separated by a substrate-binding groove. The L and S domains in the open state are almost identical to those in the closed state, with C α RMSD values of 0.84 and 0.53 Å, respectively, suggesting that the transition between the open and closed states proceeds with a large hinge-bending motion. The superimposition between the closed states of TthCP and BsuCP, another M32 family member, revealed that most putative substrate-binding residues in the grooves are oriented in the same direction. - Highlights: • The enzyme activity of TthCP was inhibited moderately by Tris molecule. • We solved the crystal structure of TthCP at 2.6 Å resolution. • The crystal structure of TthCP revealed both the open and closed conformations.

  17. Structural basis of lipid-driven conformational transitions in the KvAP voltage-sensing domain.

    Science.gov (United States)

    Li, Qufei; Wanderling, Sherry; Sompornpisut, Pornthep; Perozo, Eduardo

    2014-02-01

    Voltage-gated ion channels respond to transmembrane electric fields through reorientations of the positively charged S4 helix within the voltage-sensing domain (VSD). Despite a wealth of structural and functional data, the details of this conformational change remain controversial. Recent electrophysiological evidence showed that equilibrium between the resting ('down') and activated ('up') conformations of the KvAP VSD from Aeropyrum pernix can be biased through reconstitution in lipids with or without phosphate groups. We investigated the structural transition between these functional states, using site-directed spin-labeling and EPR spectroscopic methods. Solvent accessibility and interhelical distance determinations suggest that KvAP gates through S4 movements involving an ∼3-Å upward tilt and simultaneous ∼2-Å axial shift. This motion leads to large accessibly changes in the intracellular water-filled crevice and supports a new model of gating that combines structural rearrangements and electric-field remodeling.

  18. Reversible switching of fluorophore property based on intrinsic conformational transition of adenylate kinase during its catalytic cycle.

    Science.gov (United States)

    Fujii, Akira; Hirota, Shun; Matsuo, Takashi

    2013-07-17

    Adenylate kinase shows a conformational transition (OPEN and CLOSED forms) during substrate binding and product release to mediate the phosphoryl transfer between ADP and ATP/AMP. The protein motional characteristics will be useful to construct switching systems of fluorophore properties caused by the catalytic cycle of the enzyme. This paper demonstrates in situ reversible switching of a fluorophore property driven by the conformational transition of the enzyme. The pyrene-conjugated mutant adenylate kinase is able to switch the monomer/excimer emission property of pyrene on addition of ADP or P(1)P(5)-di(adenosine-5')pentaphosphate (Ap5A, a transition state analog). The observation under the dilute condition (~0.1 μM) indicates that the emission spectral change was caused by the motion of a protein molecule and not led by protein-protein interactions through π-π stacking of pyrene rings. The switching can be reversibly conducted by using hexokinase-coupling reaction. The fashion of the changes in emission intensities at various ligand concentrations is different between ADP, Mg(2+)-bound ADP, and Mg(2+)-bound Ap5A. The emission property switching is repeatable by a sequential addition of a substrate in a one-pot process. It is proposed that the property of a synthetic molecule on the enzyme surface is switchable in response to the catalytic cycle of adenylate kinase.

  19. Computer-Based Junior High/Intermediate School Program of Transitional Bilingual Education, Community School District 3, Manhattan. Final Evaluation Report, 1992-93. OREA Report.

    Science.gov (United States)

    Duque, Diana L.

    The Computer-Based Junior High/Intermediate School Program of Transitional Bilingual Education was a federally funded program in its third year of operation in one intermediate school and two junior high schools in Manhattan (New York) in 1992-93. During this period, it served 244 native Spanish-speaking, limited-English-proficient (LEP) students…

  20. Perturbation formalism for the complex poles and widths of the transition matrix with an application to intermediate structure phenomena

    International Nuclear Information System (INIS)

    Perez, R.B.; de Saussure, G.; Olsen, D.K.; Difilippo, F.C.

    1978-01-01

    The complex poles and widths of the transition T matrix are determined by the trajectory equations which consist of a set of first order nonlinear differential equations. A hierarchy of approximate solutions to the trajectory equations is developed by iterative methods. The results of this formalism are compared with exact solutions for the case of some strongly interacting pairs of resonances in two iron isotopes. In the presence of intermediate structure the average neutron reaction cross section is interpreted in terms of a resonant strength function which exhibits peaks at neutron energies corresponding to ''doorways'' levels

  1. Thermodynamics of single polyethylene and polybutylene glycols with hydrogen-bonding ends: A transition from looped to open conformations

    Science.gov (United States)

    Lee, Eunsang; Paul, Wolfgang

    2018-02-01

    A variety of linear polymer precursors with hydrogen bonding motifs at both ends enable us to design supramolecular polymer systems with tailored macroscopic properties including self-healing. In this study, we investigate thermodynamic properties of single polyethylene and polybutylene glycols with hydrogen bonding motifs. In this context, we first build a coarse-grained model of building blocks of the supramolecular polymer system based on all-atom molecular structures. The density of states of the single precursor is obtained using the stochastic approximation Monte Carlo method. Constructing canonical partition functions from the density of states, we find the transition from looped to open conformations at transition temperatures which are non-monotonously changing with an increasing degree of polymerization due to the competition between chain stiffness and loop-forming entropy penalty. In the complete range of chain length under investigation, a coexistence of the looped and open morphologies at the transition temperature is shown regardless of whether the transition is first-order-like or continuous. Polyethylene and polybutylene glycols show similar behavior in all the thermodynamic properties but the transition temperature of the more flexible polybutylene glycol is shown to change more gradually.

  2. Radio Detections During Two State Transitions of the Intermediate-Mass Black Hole HLX-1

    Science.gov (United States)

    Webb, Natalie; Cseh, David; Lenc, Emil; Godet, Olivier; Barret, Didier; Corbel, Stephane; Farrell, Sean; Fender, Robert; Gehrels, Neil; Heywood, Ian

    2012-01-01

    Relativistic jets are streams of plasma moving at appreciable fractions of the speed of light. They have been observed from stellar-mass black holes (approx. 3 to 20 solar masses) as well as supermassive black holes (approx.. 10(exp 6) to 10(exp 9) Solar Mass) found in the centers of most galaxies. Jets should also be produced by intermediate-mass black holes (approx. 10(exp 2) to 10(exp 5) Solar Mass), although evidence for this third class of black hole has, until recently, been weak. We report the detection of transient radio emission at the location of the intermediate-mass black hole candidate ESO 243-49 HLX-1, which is consistent with a discrete jet ejection event. These observations also allow us to refine the mass estimate of the black hole to be between approx. 9 × 10(exp 3) Solar Mass and approx. 9 × 10(exp 4) Solar Mass.

  3. Structure and phase transitions of monolayers of intermediate-length n-alkanes on graphite studied by neutron diffraction and molecular dynamics simulation

    Science.gov (United States)

    Diama, A.; Matthies, B.; Herwig, K. W.; Hansen, F. Y.; Criswell, L.; Mo, H.; Bai, M.; Taub, H.

    2009-08-01

    We present evidence from neutron diffraction measurements and molecular dynamics (MD) simulations of three different monolayer phases of the intermediate-length alkanes tetracosane (n-C24H50 denoted as C24) and dotriacontane (n-C32H66 denoted as C32) adsorbed on a graphite basal-plane surface. Our measurements indicate that the two monolayer films differ principally in the transition temperatures between phases. At the lowest temperatures, both C24 and C32 form a crystalline monolayer phase with a rectangular-centered (RC) structure. The two sublattices of the RC structure each consists of parallel rows of molecules in their all-trans conformation aligned with their long axis parallel to the surface and forming so-called lamellas of width approximately equal to the all-trans length of the molecule. The RC structure is uniaxially commensurate with the graphite surface in its [110] direction such that the distance between molecular rows in a lamella is 4.26 Å=√3 ag, where ag=2.46 Å is the lattice constant of the graphite basal plane. Molecules in adjacent rows of a lamella alternate in orientation between the carbon skeletal plane being parallel and perpendicular to the graphite surface. Upon heating, the crystalline monolayers transform to a "smectic" phase in which the inter-row spacing within a lamella expands by ˜10% and the molecules are predominantly oriented with the carbon skeletal plane parallel to the graphite surface. In the smectic phase, the MD simulations show evidence of broadening of the lamella boundaries as a result of molecules diffusing parallel to their long axis. At still higher temperatures, they indicate that the introduction of gauche defects into the alkane chains drives a melting transition to a monolayer fluid phase as reported previously.

  4. Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions.

    Directory of Open Access Journals (Sweden)

    Massimo Lai

    2015-01-01

    Full Text Available Calmodulin is a calcium-binding protein ubiquitous in eukaryotic cells, involved in numerous calcium-regulated biological phenomena, such as synaptic plasticity, muscle contraction, cell cycle, and circadian rhythms. It exibits a characteristic dumbell shape, with two globular domains (N- and C-terminal lobe joined by a linker region. Each lobe can take alternative conformations, affected by the binding of calcium and target proteins. Calmodulin displays considerable functional flexibility due to its capability to bind different targets, often in a tissue-specific fashion. In various specific physiological environments (e.g. skeletal muscle, neuron dendritic spines several targets compete for the same calmodulin pool, regulating its availability and affinity for calcium. In this work, we sought to understand the general principles underlying calmodulin modulation by different target proteins, and to account for simultaneous effects of multiple competing targets, thus enabling a more realistic simulation of calmodulin-dependent pathways. We built a mechanistic allosteric model of calmodulin, based on an hemiconcerted framework: each calmodulin lobe can exist in two conformations in thermodynamic equilibrium, with different affinities for calcium and different affinities for each target. Each lobe was allowed to switch conformation on its own. The model was parameterised and validated against experimental data from the literature. In spite of its simplicity, a two-state allosteric model was able to satisfactorily represent several sets of experiments, in particular the binding of calcium on intact and truncated calmodulin and the effect of different skMLCK peptides on calmodulin's saturation curve. The model can also be readily extended to include multiple targets. We show that some targets stabilise the low calcium affinity T state while others stabilise the high affinity R state. Most of the effects produced by calmodulin targets can be

  5. Liquid-gas phase transition and isospin fractionation in intermediate energy heavy ion collisions

    International Nuclear Information System (INIS)

    Xing Yongzhong; Liu Jianye; Guo Wenjun

    2004-01-01

    The liquid-gas phase transition in the heavy ion collisions and nuclear matter has been an important topic and got achievements, such as, based on the studies by H.Q. Song et al the critical temperature of liquid-gas phase transition enhances with increasing the mass of system and reduces as the increase of the neutron proton ratio of system. As authors know that both the liquid-gas phase transition and the isospin fractionation occur in the spinodal instability region at the nuclear density below the normal nuclear density. In particular, these two dynamical processes lead to the separation of nuclear matter into the liquid phase and gas phase. In this case to compare their dynamical behaviors is interested. The authors investigate the dependence of isospin fractionation degree on the mass and neutron proton ratio of system by using the isospin dependent quantum molecular dynamics model. The authors found that the degree of isospin fractionation (N/Z) n /(N/Z) imf decreases with increasing the mass of the system. This is just similar to the enhance of the critical temperature of liquid-gas phase transition T c as the increase of system mass. Because the enhance of T c is not favorable for the liquid-gas transition taking place, which reduces the isospin fractionation process and leads to decrease of (N/Z) n /(N/Z) imf . However the degree of isospin fractionation enhances with increasing the neutron proton ratio of the system. It is just corresponding to the reduce of T c of the liquid-gas phase transition as the increase of the isospin fractionation of the system. Because the reduce of T c enhances the liquid-gas phase transition process and also prompts the isospin fractionation process leading the increase of the isospin fractionation degree. To sum up, there are very similar dynamical behaviors for the degree of isospin fractionation and the critical temperature of the liquid-gas phase transition. So dynamical properties of the liquid-gas phase transition can

  6. Steered molecular dynamics simulations of a type IV pilus probe initial stages of a force-induced conformational transition.

    Directory of Open Access Journals (Sweden)

    Joseph L Baker

    2013-04-01

    Full Text Available Type IV pili are long, protein filaments built from a repeating subunit that protrudes from the surface of a wide variety of infectious bacteria. They are implicated in a vast array of functions, ranging from bacterial motility to microcolony formation to infection. One of the most well-studied type IV filaments is the gonococcal type IV pilus (GC-T4P from Neisseria gonorrhoeae, the causative agent of gonorrhea. Cryo-electron microscopy has been used to construct a model of this filament, offering insights into the structure of type IV pili. In addition, experiments have demonstrated that GC-T4P can withstand very large tension forces, and transition to a force-induced conformation. However, the details of force-generation, and the atomic-level characteristics of the force-induced conformation, are unknown. Here, steered molecular dynamics (SMD simulation was used to exert a force in silico on an 18 subunit segment of GC-T4P to address questions regarding the nature of the interactions that lead to the extraordinary strength of bacterial pili. SMD simulations revealed that the buried pilin α1 domains maintain hydrophobic contacts with one another within the core of the filament, leading to GC-T4P's structural stability. At the filament surface, gaps between pilin globular head domains in both the native and pulled states provide water accessible routes between the external environment and the interior of the filament, allowing water to access the pilin α1 domains as reported for VC-T4P in deuterium exchange experiments. Results were also compared to the experimentally observed force-induced conformation. In particular, an exposed amino acid sequence in the experimentally stretched filament was also found to become exposed during the SMD simulations, suggesting that initial stages of the force induced transition are well captured. Furthermore, a second sequence was shown to be initially hidden in the native filament and became exposed upon

  7. Steered molecular dynamics simulations of a type IV pilus probe initial stages of a force-induced conformational transition.

    Science.gov (United States)

    Baker, Joseph L; Biais, Nicolas; Tama, Florence

    2013-04-01

    Type IV pili are long, protein filaments built from a repeating subunit that protrudes from the surface of a wide variety of infectious bacteria. They are implicated in a vast array of functions, ranging from bacterial motility to microcolony formation to infection. One of the most well-studied type IV filaments is the gonococcal type IV pilus (GC-T4P) from Neisseria gonorrhoeae, the causative agent of gonorrhea. Cryo-electron microscopy has been used to construct a model of this filament, offering insights into the structure of type IV pili. In addition, experiments have demonstrated that GC-T4P can withstand very large tension forces, and transition to a force-induced conformation. However, the details of force-generation, and the atomic-level characteristics of the force-induced conformation, are unknown. Here, steered molecular dynamics (SMD) simulation was used to exert a force in silico on an 18 subunit segment of GC-T4P to address questions regarding the nature of the interactions that lead to the extraordinary strength of bacterial pili. SMD simulations revealed that the buried pilin α1 domains maintain hydrophobic contacts with one another within the core of the filament, leading to GC-T4P's structural stability. At the filament surface, gaps between pilin globular head domains in both the native and pulled states provide water accessible routes between the external environment and the interior of the filament, allowing water to access the pilin α1 domains as reported for VC-T4P in deuterium exchange experiments. Results were also compared to the experimentally observed force-induced conformation. In particular, an exposed amino acid sequence in the experimentally stretched filament was also found to become exposed during the SMD simulations, suggesting that initial stages of the force induced transition are well captured. Furthermore, a second sequence was shown to be initially hidden in the native filament and became exposed upon stretching.

  8. [Artificial Cysteine Bridges on the Surface of Green Fluorescent Protein Affect Hydration of Its Transition and Intermediate States].

    Science.gov (United States)

    Melnik, T N; Nagibina, G S; Surin, A K; Glukhova, K A; Melnik, B S

    2018-01-01

    Studying the effect of cysteine bridges on different energy levels of multistage folding proteins will enable a better understanding of the process of folding and functioning of globular proteins. In particular, it will create prospects for directed change in the stability and rate of protein folding. In this work, using the method of differential scanning microcalorimetry, we have studied the effect of three cysteine bridges introduced in different structural elements of the green fluorescent protein on the denaturation enthalpies, activation energies, and heat-capacity increments when this protein passes from native to intermediate and transition states. The studies have allowed us to confirm that, with this protein denaturation, the process hardly damages the structure initially, but then changes occur in the protein structure in the region of 4-6 beta sheets. The cysteine bridge introduced in this region decreases the hydration of the second transition state and increases the hydration of the second intermediate state during the thermal denaturation of the green fluorescent protein.

  9. Kinetics of disorder-to-fcc phase transition via an intermediate bcc state

    International Nuclear Information System (INIS)

    Liu Yongsheng; Nie Huifen; Bansil, Rama; Steinhart, Milos; Bang, Joona; Lodge, Timothy P.

    2006-01-01

    Time-resolved small-angle x-ray scattering measurements reveal that a long-lived intermediate bcc state forms when a poly(styrene-b-isoprene) diblock copolymer solution in an isoprene selective solvent is rapidly cooled from the disordered micellar fluid at high temperature to an equilibrium fcc state. The kinetics of the epitaxial growth of the [111] fcc peak from the [110] bcc peak was obtained by fitting the scattering data to a simple model of the transformation. The growth of the [111] fcc peak agrees with the Avrami model of nucleation and growth kinetics with an exponent n=1.4, as does the initial decay of the [110] bcc peak, with an exponent n=1.3. The data were also found to be in good agreement with the Cahn model of grain boundary nucleation and growth

  10. Thermodynamic Analysis of the Conformational Transition in Aqueous Solutions of Isotactic and Atactic Poly(Methacrylic Acid and the Hydrophobic Effect

    Directory of Open Access Journals (Sweden)

    Ksenija Kogej

    2016-04-01

    Full Text Available The affinity of amphiphilic compounds for water is important in various processes, e.g., in conformational transitions of biopolymers, protein folding/unfolding, partitioning of drugs in the living systems, and many others. Herein, we study the conformational transition of two isomer forms of poly(methacrylic acid (PMA, isotactic (iPMA and atactic (aPMA, in water. These isomers are chemically equivalent and differ only in the arrangement of functional groups along the chain. A complete thermodynamic analysis of the transition of the PMA chains from the compact to the extended form (comprising the conformational transition in water in the presence of three alkali chlorides is conducted by determining the free energy, enthalpy, and entropy changes of the process as a function of temperature, and therefrom also the heat capacity change. The heat capacity change of the transition is positive (+20 J/K mol for aPMA and negative (−50 J/K mol for iPMA. This result suggests a different affinity of PMA isomers for water. The conformational transition of iPMA is parallel to the transfer of polar solutes into water, whereas that of aPMA agrees with the transfer of nonpolar solutes into water.

  11. Isotope enrichment by electron spin resonance transitions of the intermediate radical pair

    International Nuclear Information System (INIS)

    Okazaki, M.; Shiga, T.; Sakata, S.; Konaka, R.; Toriyama, K.

    1988-01-01

    Microwave effects on the spin adduct yield were observed in the photoreduction of menadione in micellar solutions with ordinary sodium dodecyl sulfate (SDS), deuterium-labeled SDS, and a mixture of them. A large isotope effect was found in the microwave modulation of the spin adduct yield, which is due to the ESR transitions of the transient radical pair in the reaction. It is demonstrated for the first time that the microwave field can be used to enrich one of the isotopes which coexist in the system

  12. A signature for isoscalar-spin transitions in (d vector, d' vector) scattering at intermediate energy

    International Nuclear Information System (INIS)

    Morlet, M.; Bimbot, L.; Guillot, J.; Johnson, B.N.; Jourdan, F.; Langevin-Joliot, H.; Marty, N.; Rosier, L.; Wiele, J. van de; Willis, A.; Beatty, D.; Edwards, G.; Fergerson, R.W.; Glashausser, C.; Green, A.; Djalali, C.; Johnson, B.N.; Tomasi-Gustafsson, E.; Youn, M.Y.

    1991-05-01

    Three different signatures for isoscalar spin transitions in nuclei have been tested in the 12 C(d,d') 12 C reaction at 400 MeV. These signatures have values close to zero for the natural parity states, and range from 0.22 to 0.50 for the ΔS=1 ΔT=0, 12.7 MeV state. Preliminary results on 40 Ca(d,d') at 400 MeV are also presented. (author) 26 refs., 4 figs., 1 tab

  13. Emergence and stability of intermediate open vesicles in disk-to-vesicle transitions.

    Science.gov (United States)

    Li, Jianfeng; Zhang, Hongdong; Qiu, Feng; Shi, An-Chang

    2013-07-01

    The transition between two basic structures, a disk and an enclosed vesicle, of a finite membrane is studied by examining the minimum energy path (MEP) connecting these two states. The MEP is constructed using the string method applied to continuum elastic membrane models. The results reveal that, besides the commonly observed disk and vesicle, open vesicles (bowl-shaped vesicles or vesicles with a pore) can become stable or metastable shapes. The emergence, stability, and probability distribution of these open vesicles are analyzed. It is demonstrated that open vesicles can be stabilized by higher-order elastic energies. The estimated probability distribution of the different structures is in good agreement with available experiments.

  14. Conformation transitions of blood proteins under influence of physical factors on microwave dielectric method

    International Nuclear Information System (INIS)

    Gorobchenko, O.A.; Nikolov, O.T.; Gatash, S.V.

    2006-01-01

    In this article, the influence of γ-irradiation and temperature on albumin and fibrinogen conformation and dielectric properties of protein solutions have been studied by the microwave dielectric method. Both the values of the real part ε' (dielectric permittivity) and the imaginary part ε'' (dielectric losses) of the complex dielectric permittivity of the aqueous solution of bovine serum albumin and human fibrinogen as functions of temperature and γ-irradiation dose have been obtained. The time of dielectric relaxation of water molecules in the protein solutions was calculated. The hydration of the albumin and fibrinogen molecules was determined. The temperature dependencies of hydration are non-monotonous and have a number of characteristic features at the temperatures 30-34 and 44-47 deg. C for serum albumin, and 24 and 32 deg. C for fibrinogen

  15. Reversible and irreversible conformational transitions in myoglobin: role of hydrated amino acid ionic liquid.

    Science.gov (United States)

    Sankaranarayanan, Kamatchi; Sathyaraj, Gopal; Nair, B U; Dhathathreyan, A

    2012-04-12

    Hydrated phenylalanine ionic liquid (Phe-IL) has been used to solubilize myoglobin (Mb). Structural stability of Mb in Phe-IL analyzed using fluorescence and circular dichroism spectroscopy shows that for low levels of hydration of Phe-IL there is a large red shift in the fluorescence emission wavelength and the protein transforms to complete β sheet from its native helical conformation. Rehydration or dilution reverses the β sheet to an α helix which on aging organizes to micrometer-sized fibrils. At concentrations higher than 200 μM, the protein changes from β to a more random coiled structure. Organization of the protein in Phe-IL in a Langmuir film at the air/water interface has been investigated using the surface pressure-molecular area isotherm and shows nearly the same surface tension for both pure Mb and Mb in Phe-IL. Scanning electron microscopy of the films of Mb in Phe-IL transferred using the Langmuir-Blodgett film technique show layered morphology. This study shows that the conformation of Mb is completely reversible going from β → helix → β sheet up to 200 μM of Phe-IL. Similar surface tension values for Mb in water and in Phe-IL suggests that direct ion binding interactions with the protein coupled with the change in local viscosity from the IL seems to not only alter the secondary structure of individual proteins but also drives the self-assembly of the protein molecules leading finally to fibril formation.

  16. Spatial and kinematic distributions of transition populations in intermediate redshift galaxy clusters

    International Nuclear Information System (INIS)

    Crawford, Steven M.; Wirth, Gregory D.; Bershady, Matthew A.

    2014-01-01

    We analyze the spatial and velocity distributions of confirmed members in five massive clusters of galaxies at intermediate redshift (0.5 < z < 0.9) to investigate the physical processes driving galaxy evolution. Based on spectral classifications derived from broad- and narrow-band photometry, we define four distinct galaxy populations representing different evolutionary stages: red sequence (RS) galaxies, blue cloud (BC) galaxies, green valley (GV) galaxies, and luminous compact blue galaxies (LCBGs). For each galaxy class, we derive the projected spatial and velocity distribution and characterize the degree of subclustering. We find that RS, BC, and GV galaxies in these clusters have similar velocity distributions, but that BC and GV galaxies tend to avoid the core of the two z ≈ 0.55 clusters. GV galaxies exhibit subclustering properties similar to RS galaxies, but their radial velocity distribution is significantly platykurtic compared to the RS galaxies. The absence of GV galaxies in the cluster cores may explain their somewhat prolonged star-formation history. The LCBGs appear to have recently fallen into the cluster based on their larger velocity dispersion, absence from the cores of the clusters, and different radial velocity distribution than the RS galaxies. Both LCBG and BC galaxies show a high degree of subclustering on the smallest scales, leading us to conclude that star formation is likely triggered by galaxy-galaxy interactions during infall into the cluster.

  17. Transition Metal Donor-Peptide-Acceptor Complexes: From Intramolecular Electron Transfer Reactions to the Study of Reactive Intermediates

    Energy Technology Data Exchange (ETDEWEB)

    Isied, Stephan S.

    2003-03-11

    The trans-polyproline (PII) oligomers (Figure 1) are unusually rigid peptide structures which have been extensively studied by our group for peptide mediated intramolecular electron transfer (ET) at long distances. We have previously studied ET across a series of metal ion donor (D) acceptor (A) oligoproline peptides with different distances, driving forces and reorganizational energies. The majority of these experiments involve generating the ET intermediate using pulse radiolysis methods, although more recently photochemical methods are also used. Results of these studies showed that ET across peptides can vary by more than twelve orders of magnitude. Using ruthenium bipyridine donors, ET reaction rate constants across several proline residues (n = 4 - 9) occurred in the millisecond (ms) to {micro}s timescale, thus limiting the proline peptide conformational motions to only minor changes (far smaller than the large changes that occur on the ms to sec timescale, such as trans to cis proline isomerization). The present report describes our large data base of experimental results for D-peptide-A complexes in terms of a model where the involvement of both superexchange and hopping (hole and electron) mechanisms account for the long range ET rate constants observed. Our data shows that the change from superexchange to hopping mechanisms occurs at different distances depending on the type of D and A and their interactions with the peptides. Our model is also consistent with generalized models for superexchange and hopping which have been put forward by a number of theoretical groups to account for long range ET phenomena.

  18. Explosive to Effusive Transition in Intermediate Volcanism: An Analysis of Changing Magma System Conditions in Dominica

    Science.gov (United States)

    Bersson, J.; Waters, L. E.; Frey, H. M.; Nicolaysen, K. P.; Manon, M. R. F.

    2017-12-01

    The oscillation between explosive and effusive intermediate (59-62 wt% SiO2) volcanism in the Roseau Valley on Dominica, an island in the Lesser Antilles Arc, provides an opportunity to investigate temporal changes in the magmatic system. Here, we test the relationship between the Roseau ignimbrites (1-65 ka) and the Micotrin dome ( 1.1 ka) which are proposed to originate from the same magmatic system, with a detailed petrologic analysis of phenocrysts to determine commonalities or changes in pre-eruptive conditions (i.e., intensive variables). The ignimbrites are saturated in five phenocrysts (plagioclase + orthopyroxene + clinopyroxene + ilmenite + magnetite ± amphibole ± quartz), and the lava dome contains the same assemblage, but with notable differences: amphiboles are entirely reacted, and quartz occurs in greater abundance. Plagioclase in the ignimbrites ranges in composition from An46-93, and those in the dome range from An46-85. Two Fe-Ti oxide geo-thermometry reveal pre-eruptive temperatures from 730-820°C for three different ignimbrite units, whereas the pre-eruptive temperature for the dome is slightly hotter (850±23°C). Values of fO2 (relative to NNO) derived from Fe-Ti oxide oxygen-barometry range from +0.3 to +1.32 ΔNNO for the ignimbrites, which overlap with those from the dome (+0.5 to +0.9 ΔNNO). Pre-eruptive temperatures, plagioclase compositions, whole rock and glass compositions are incorporated into a plagioclase-liquid hygrometer to determine pre-eruptive melt H2O contents for each sample. H2O contents for ignimbrites range from 7.1-9.3 wt%, and those from the lava dome range from 6.7-7.1 wt%. Application of a H2O solubility model shows that water contents for the Roseau magmas correspond to pressures of 3-5 kbar. The most notable difference between the explosive and effusive magmas is that the lava dome has a higher pre-eruptive temperature than the ignimbrites. However, the results collectively suggest that more recent volcanism in

  19. Experimental study of the polyamorphism of water. II. The isobaric transitions between HDA and VHDA at intermediate and high pressures

    Science.gov (United States)

    Handle, Philip H.; Loerting, Thomas

    2018-03-01

    Since the first report of very-high density amorphous ice (VHDA) in 2001 [T. Loerting et al., Phys. Chem. Chem. Phys. 3, 5355-5357 (2001)], the status of VHDA as a distinct amorphous ice has been debated. We here study VHDA and its relation to expanded high density amorphous ice (eHDA) on the basis of isobaric heating experiments. VHDA was heated at 0.1 ≤ p ≤ 0.7 GPa, and eHDA was heated at 1.1 ≤ p ≤ 1.6 GPa to achieve interconversion. The behavior upon heating is monitored using in situ volumetry as well as ex situ X-ray diffraction and differential scanning calorimetry. We do not observe a sharp transition for any of the isobaric experiments. Instead, a continuous expansion (VHDA) or densification (eHDA) marks the interconversion. This suggests that a continuum of states exists between VHDA and HDA, at least in the temperature range studied here. This further suggests that VHDA is the most relaxed amorphous ice at high pressures and eHDA is the most relaxed amorphous ice at intermediate pressures. It remains unclear whether or not HDA and VHDA experience a sharp transition upon isothermal compression/decompression at low temperature.

  20. Prediction of the transition energies of atomic No and Lr by the intermediate Hamiltonian coupled cluster method

    International Nuclear Information System (INIS)

    Borschevsky, A.; Eliav, E.; Kaldor, U.; Vilkas, M.J.; Ishikawa, Y.

    2007-01-01

    Complete text of publication follows: Measurements of the spectroscopic properties of the superheavy elements present a serious challenge to the experimentalist. Their short lifetimes and the low quantities of their production necessitate reliable prediction of transition energies to avoid the need for broad wavelength scans and to assist in identifying the lines. Thus, reliable high-accuracy calculations are necessary prior and parallel to experimental research. Nobelium and Lawrencium are at present the two most likely candidates for spectroscopic measurements, with the first experiments planned at GSI, Darmstadt. The intermediate Hamiltonian (IH) coupled cluster method is applied to the ionization potentials, electron affinities, and excitation energies of atomic nobelium and lawrencium. Large basis sets are used (37s31p26d21f16g11h6i). All levels of a particular atom are obtained simultaneously by diagonalizing the IH matrix. The matrix elements correspond to all excitations from correlated occupied orbitals to virtual orbitals in a large P space, and are 'dressed' by folding in excitations to higher virtual orbitals (Q space) at the coupled cluster singles-and-doubles level. Lamb-shift corrections are included. The same approach was applied to the lighter homologues of Lr and No, lutetium and ytterbium, for which many transition energies are experimentally known, in order to assess the accuracy of the calculation. The average absolute error of 20 excitation energies of Lu is 423 cm -1 , and the error limits for Lr are therefore put at 700 cm -1 . Predicted Lr excitations with large transition moments in the prime range for the planned experiment, 20,000-30,000 cm -1 , are 7p → 8s at 20,100 cm -1 and 7p →p 7d at 28,100 cm -1 . In case of Yb, the calculated ionization potential was within 20 cm -1 of the experiment, and the average error of the 20 lowest calculated excitations was about 300 cm -1 . Hence, the error limits of nobelium are set to 800 cm -1

  1. Rates and equilibrium constants of the ligand-induced conformational transition of an HCN ion channel protein domain determined by DEER spectroscopy.

    Science.gov (United States)

    Collauto, Alberto; DeBerg, Hannah A; Kaufmann, Royi; Zagotta, William N; Stoll, Stefan; Goldfarb, Daniella

    2017-06-14

    Ligand binding can induce significant conformational changes in proteins. The mechanism of this process couples equilibria associated with the ligand binding event and the conformational change. Here we show that by combining the application of W-band double electron-electron resonance (DEER) spectroscopy with microfluidic rapid freeze quench (μRFQ) it is possible to resolve these processes and obtain both equilibrium constants and reaction rates. We studied the conformational transition of the nitroxide labeled, isolated carboxy-terminal cyclic-nucleotide binding domain (CNBD) of the HCN2 ion channel upon binding of the ligand 3',5'-cyclic adenosine monophosphate (cAMP). Using model-based global analysis, the time-resolved data of the μRFQ DEER experiments directly provide fractional populations of the open and closed conformations as a function of time. We modeled the ligand-induced conformational change in the protein using a four-state model: apo/open (AO), apo/closed (AC), bound/open (BO), bound/closed (BC). These species interconvert according to AC + L ⇌ AO + L ⇌ BO ⇌ BC. By analyzing the concentration dependence of the relative contributions of the closed and open conformations at equilibrium, we estimated the equilibrium constants for the two conformational equilibria and the open-state ligand dissociation constant. Analysis of the time-resolved μRFQ DEER data gave estimates for the intrinsic rates of ligand binding and unbinding as well as the rates of the conformational change. This demonstrates that DEER can quantitatively resolve both the thermodynamics and the kinetics of ligand binding and the associated conformational change.

  2. Protein conformational transitions at the liquid-gas interface as studied by dilational surface rheology.

    Science.gov (United States)

    Noskov, Boris A

    2014-04-01

    Experimental results on the dynamic dilational surface elasticity of protein solutions are analyzed and compared. Short reviews of the protein behavior at the liquid-gas interface and the dilational surface rheology precede the main sections of this work. The kinetic dependencies of the surface elasticity differ strongly for the solutions of globular and non-globular proteins. In the latter case these dependencies are similar to those for solutions of non-ionic amphiphilic polymers and have local maxima corresponding to the formation of the distal region of the surface layer (type I). In the former case the dynamic surface elasticity is much higher (>60 mN/m) and the kinetic dependencies are monotonical and similar to the data for aqueous dispersions of solid nanoparticles (type II). The addition of strong denaturants to solutions of bovine serum albumin and β-lactoglobulin results in an abrupt transition from the type II to type I dependencies if the denaturant concentration exceeds a certain critical value. These results give a strong argument in favor of the preservation of the protein globular structure in the course of adsorption without any denaturants. The addition of cationic surfactants also can lead to the non-monotonical kinetic dependencies of the dynamic surface elasticity indicating destruction of the protein tertiary and secondary structures. The addition of anionic surfactants gives similar results only for the protein solutions of high ionic strength. The influence of cationic surfactants on the local maxima of the kinetic dependencies of the dynamic surface elasticity for solutions of a non-globular protein (β-casein) differs from the influence of anionic surfactants due to the heterogeneity of the charge distribution along the protein chain. In this case one can use small admixtures of ionic surfactants as probes of the adsorption mechanism. The effect of polyelectrolytes on the kinetic dependencies of the dynamic surface elasticity of protein

  3. A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Trong-Nghia [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan (China); Department of Physical Chemistry, Hanoi University of Science and Technology, Hanoi (Viet Nam); Putikam, Raghunath; Lin, M. C., E-mail: chemmcl@emory.edu [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan (China)

    2015-03-28

    We have discovered a new and highly competitive product channel in the unimolecular decay process for small Criegee intermediates, CH{sub 2}OO and anti/syn-CH{sub 3}C(H)OO, occurring by intramolecular insertion reactions via a roaming-like transition state (TS) based on quantum-chemical calculations. Our results show that in the decomposition of CH{sub 2}OO and anti-CH{sub 3}C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH{sub 3}C(O)OH acids with >110 kcal/mol exothermicities via loose roaming-like insertion TSs involving the terminal O atom and the neighboring C–H bonds. For syn-CH{sub 3}C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH{sub 3} group by the terminal O atom producing CH{sub 2}C(H)O–OH. At 298 K, the intramolecular insertion process in CH{sub 2}OO was found to be 600 times faster than the commonly assumed ring-closing reaction.

  4. A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states

    International Nuclear Information System (INIS)

    Nguyen, Trong-Nghia; Putikam, Raghunath; Lin, M. C.

    2015-01-01

    We have discovered a new and highly competitive product channel in the unimolecular decay process for small Criegee intermediates, CH 2 OO and anti/syn-CH 3 C(H)OO, occurring by intramolecular insertion reactions via a roaming-like transition state (TS) based on quantum-chemical calculations. Our results show that in the decomposition of CH 2 OO and anti-CH 3 C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH 3 C(O)OH acids with >110 kcal/mol exothermicities via loose roaming-like insertion TSs involving the terminal O atom and the neighboring C–H bonds. For syn-CH 3 C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH 3 group by the terminal O atom producing CH 2 C(H)O–OH. At 298 K, the intramolecular insertion process in CH 2 OO was found to be 600 times faster than the commonly assumed ring-closing reaction

  5. A study on the development of regulatory guide to stability conformation and classification criteria of low and intermediate level radioactive waste

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Geon Jae; Paek, Min Hoon; Park, Jong Gil; Han, Byeong Seop; Cheong, Jae Hak; Lee, Hae Chan; Yang, Jin Yeong; Hong, Hei Kwan; Park, Jin Baek [Korea Advanced Institute of Science and Technology, Taejon (Korea, Republic of)

    1994-01-15

    The objectives of this study are to examine basic principles and terms and to suggest and recommend definite methods and criteria necessary for the classification and stability conformation of radioactive wastes. In this study, following studies were performed : investigate the domestic regulations related with the stability conformation and classification of radioactive wastes in order to keep mutual relationship and consistency between the regulations, investigate the sources, types and characteristics of domestic radioactive wastes as a basis for this study, investigate the classification criteria and methods of others countries in a general point of view and in the view point of disposal method, select the classification criteria factors for the domestic case and general case in the both general and domestic points of view, investigate the general test items for the stability conformation of radioactive waste forms and analysis on the test items and criteria of others countries for the mined cavity disposal and shallow land disposal in the view point of disposal method, experimental leaching and immersion tests for the borate and spent resin wastes as a study on the stability conformation of waste forms, selection of acceptance criteria for the both of disposal methods in the domestic and general cases.

  6. Conformality lost

    International Nuclear Information System (INIS)

    Kaplan, David B.; Lee, Jong-Wan; Son, Dam T.; Stephanov, Mikhail A.

    2009-01-01

    We consider zero-temperature transitions from conformal to nonconformal phases in quantum theories. We argue that there are three generic mechanisms for the loss of conformality in any number of dimensions: (i) fixed point goes to zero coupling, (ii) fixed point runs off to infinite coupling, or (iii) an IR fixed point annihilates with a UV fixed point and they both disappear into the complex plane. We give both relativistic and nonrelativistic examples of the last case in various dimensions and show that the critical behavior of the mass gap behaves similarly to the correlation length in the finite temperature Berezinskii-Kosterlitz-Thouless (BKT) phase transition in two dimensions, ξ∼exp(c/|T-T c | 1/2 ). We speculate that the chiral phase transition in QCD at large number of fermion flavors belongs to this universality class, and attempt to identify the UV fixed point that annihilates with the Banks-Zaks fixed point at the lower end of the conformal window.

  7. Matrix elements of intraband transitions in quantum dot intermediate band solar cells: the influence of quantum dot presence on the extended-state electron wave-functions

    International Nuclear Information System (INIS)

    Nozawa, Tomohiro; Arakawa, Yasuhiko

    2014-01-01

    The intraband transitions which are essential for quantum dot intermediate band solar cells (QD IBSCs) are theoretically investigated by estimating the matrix elements from a ground bound state, which is often regarded as an intermediate band (IB), to conduction band (CB) states for a structure with a quantum dot (QD) embedded in a matrix (a QD/matrix structure). We have found that the QD pushes away the electron envelope functions (probability densities) from the QD region in almost all quantum states above the matrix CB minimum. As a result, the matrix elements of the intraband transitions in the QD/matrix structure are largely reduced, compared to those calculated assuming the envelope functions of free electrons (i.e., plane-wave envelope functions) in a matrix structure as the final states of the intraband transitions. The result indicates the strong influence of the QD itself on the intraband transitions from the IB to the CB states in QD IBSC devices. This work will help in better understanding the problem of the intraband transitions and give new insight, that is, engineering of quantum states is indispensable for the realization of QD IBSCs with high solar energy conversion efficiencies. (paper)

  8. Kinetic and mechanistic studies of reactive intermediates in photochemical and transition metal-assisted oxidation, decarboxylation and alkyl transfer reactions

    Energy Technology Data Exchange (ETDEWEB)

    Carraher, Jack McCaslin [Iowa State Univ., Ames, IA (United States)

    2014-01-01

    Reactive species like high-valent metal-oxo complexes and carbon and oxygen centered radicals are important intermediates in enzymatic systems, atmospheric chemistry, and industrial processes. Understanding the pathways by which these intermediates form, their relative reactivity, and their fate after reactions is of the utmost importance. Herein are described the mechanistic detail for the generation of several reactive intermediates, synthesis of precursors, characterization of precursors, and methods to direct the chemistry to more desirable outcomes yielding ‘greener’ sources of commodity chemicals and fuels.

  9. Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft

    Directory of Open Access Journals (Sweden)

    MacKerell Alexander D

    2007-03-01

    Full Text Available Abstract Background The N-terminal SH2 domain (N-SH2 of the non-receptor tyrosine phosphatase SHP-2 is involved both in localization of SHP-2 by recognition of phosphotyrosine (pY peptides and self-inhibition of SHP-2 phosphatase activity through the formation of a protein – protein interface with the phosphatase domain. Mutations that disrupt this interface break the coupling between pY-peptide binding cleft conformation and self-inhibition, thereby increasing both SHP-2 phosphatase activity and pY-peptide binding affinity, and are associated with the congenital condition Noonan syndrome and various pediatric leukemias. To better characterize the molecular process involved in N-SH2 pY-dependent binding, we have applied explicit-solvent molecular dynamics simulations to study the closed-to-open transition of the N-SH2 pY-peptide binding cleft. Results The existence of stable conformations in the left-handed helical and the extended regions of Tyr66 φ/ψ space prevent rapid interconversion of the backbone and create a conformational switch such that Tyr66 in a left-handed helical backbone conformation results in an open cleft and in an extended backbone conformation results in a closed cleft. The stable conformations arise from deep, well-localized free-energy minima in the left-handed helical and extended regions of the Tyr66 φ/ψ map. Changing the Tyr66 backbone conformation from extended to left-handed helical induces a closed-to-open transition in the cleft, and the reverse change in backbone conformation induces the reverse, open-to-closed transition. In the open-cleft state, weak solvent-exposed interactions involving the sidechains of Tyr66, Asp40, Lys55, and Gln57 serve to anchor the Tyr66 sidechain to the surface of the protein and away from the binding cleft entrance, thereby facilitating pY-peptide access to the binding cleft. Conclusion The simulations point to a regulatory role for Tyr66 and surrounding residues in SHP-2 function

  10. Synthesis and conformational properties of oligonucleotides incorporating 2'-O-phosphorylated ribonucleotides as structural motifs of pre-tRNA splicing intermediates.

    Science.gov (United States)

    Tsuruoka, H; Shohda, K; Wada, T; Sekine, M

    2000-11-03

    To synthesize oligonucleotides containing 2'-O-phosphate groups, four kinds of ribonucleoside 3'-phosphoramidite building blocks 6a-d having the bis(2-cyano-1,1-dimethylethoxy)thiophosphoryl (BCMETP) group were prepared according to our previous phosphorylation procedure. These phosphoramidite units 6a-d were not contaminated with 3'-regioisomers and were successfully applied to solid-phase synthesis to give oligodeoxyuridylates 15, 16 and oligouridylates 21, 22. Self-complementary Drew-Dickerson DNA 12mers 24-28 replaced by a 2'-O-phosphorylated ribonucleotide at various positions were similarly synthesized. In these syntheses, it turned out that KI(3) was the most effective reagent for oxidative desulfurization of the initially generated thiophosphate group to the phosphate group on polymer supports. Without using this conversion step, a tridecadeoxyuridylate 17 incorporating a 2'-O-thiophosphorylated uridine derivative was also synthesized. To investigate the effect of the 2'-phosphate group on the thermal stability and 3D-structure of DNA(RNA) duplexes, T(m) measurement of the self-complementary oligonucleotides obtained and MD simulation of heptamer duplexes 33-36 were carried out. According to these analyses, it was suggested that the nucleoside ribose moiety phosphorylated at the 2'-hydroxyl function predominantly preferred C2'-endo to C3'-endo conformation in DNA duplexes so that it did not significantly affect the stability of the DNA duplex. On the other hand, the 2'-modified ribose moiety was expelled to give a C3'-endo conformation in RNA duplexes so that the RNA duplexes were extremely destabilized.

  11. Partially folded intermediates during trypsinogen denaturation

    Directory of Open Access Journals (Sweden)

    Martins N.F.

    1999-01-01

    Full Text Available The equilibrium unfolding of bovine trypsinogen was studied by circular dichroism, differential spectra and size exclusion HPLC. The change in free energy of denaturation was = 6.99 ± 1.40 kcal/mol for guanidine hydrochloride and = 6.37 ± 0.57 kcal/mol for urea. Satisfactory fits of equilibrium unfolding transitions required a three-state model involving an intermediate in addition to the native and unfolded forms. Size exclusion HPLC allowed the detection of an intermediate population of trypsinogen whose Stokes radii varied from 24.1 ± 0.4 Å to 26.0 ± 0.3 Å for 1.5 M and 2.5 M guanidine hydrochloride, respectively. During urea denaturation, the range of Stokes radii varied from 23.9 ± 0.3 Å to 25.7 ± 0.6 Å for 4.0 M and 6.0 M urea, respectively. Maximal intrinsic fluorescence was observed at about 3.8 M urea with 8-aniline-1-naphthalene sulfonate (ANS binding. These experimental data indicate that the unfolding of bovine trypsinogen is not a simple transition and suggest that the equilibrium intermediate population comprises one intermediate that may be characterized as a molten globule. To obtain further insight by studying intermediates representing different stages of unfolding, we hope to gain a better understanding of the complex interrelations between protein conformation and energetics.

  12. Liquid-vapor phase transition, collective flow and entropy determination from future measurements of intermediate mass fragments

    International Nuclear Information System (INIS)

    Coffin, J.P.

    1991-01-01

    Some global variables reflecting the highly collective character of nuclear matter produced in relativistic heavy-ion collisions are briefly reviewed on the basis of presently available experimental results and of Quantum Statistical Model and Quantum Molecular Dynamic Model predictions relative to intermediate mass fragments. Possible future measurements are suggested. (author) 27 refs., 8 figs

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

    Czech Academy of Sciences Publication Activity Database

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2016-07-01

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

  15. Holographic research on phase transitions for a five dimensional AdS black hole with conformally coupled scalar hair

    Energy Technology Data Exchange (ETDEWEB)

    Li, Hui-Ling, E-mail: LHL51759@126.com [School of Physical Electronics, University of Electronic Science and Technology of China, Chengdu, 610054 (China); College of Physics Science and Technology, Shenyang Normal University, Shenyang 110034 (China); Yang, Shu-Zheng, E-mail: szyangcwnu@126.com [Institute of Theoretical Physics, China West Normal University, Nanchong 637002 (China); Zu, Xiao-Tao, E-mail: xtzu@uestc.edu.cn [School of Physical Electronics, University of Electronic Science and Technology of China, Chengdu, 610054 (China)

    2017-01-10

    In the framework of holography, we survey the phase structure for a higher dimensional hairy black hole including the effects of the scalar field hair. It is worth emphasizing that, not only black hole entropy, but also entanglement entropy and two point correlation function exhibit the Van der Waals-like phase transition in a fixed scalar charge ensemble. Furthermore, by making use of numerical computation, we show that the Maxwell's equal area law is valid for the first order phase transition. In addition, we also discuss how the hair parameter affects the black hole's phase transition.

  16. Quantum Chemical Investigation of the Transition States and Intermediates for the Reaction of the Nitrosonium Ion with the Pentaammineazidocobalt(III) Ion.

    Science.gov (United States)

    Rotzinger, François P

    2016-12-19

    The water exchange reaction on Co(NH 3 ) 5 OH 2 3+ was investigated with various density functionals and basis sets. A Gibbs activation energy (ΔG ⧧ ) agreeing with experiment was obtained with the long-range-corrected functionals ωB97X-D3 and LC-BOP-LRD, SMD hydration, and modified Karlsruhe def2-TZVP basis sets. This computational technique was then applied to the reaction of NO + with Co(NH 3 ) 5 N 3 2+ . All of the possible pathways were investigated, NO + attack at the terminal N of Co(NH 3 ) 5 N 3 2+ via the E and the Z isomers of the transition states, and NO + attack at the bound N of azide, also via both isomers. The most favorable pathway proceeds via the attack at the bound N via the Z isomer. This leads to the intermediate with an oxatetrazole ligand bound to Co(III) at the N in the 3-position, Co(NH 3 ) 5 (cycl-N 4 O) 3+ , which undergoes N 2 elimination to yield the Co(NH 3 ) 5 N 2 O 3+ intermediate. The subsequent substitution of N 2 O by water follows the I d mechanism with retention of the configuration. No evidence for the existence of the square-pyramidal pentacoordinated intermediate Co(NH 3 ) 5 3+ was found. All of the investigated intermediates, Co(NH 3 ) 5 N 2 3+ , Co(NH 3 ) 5 [E-N(N 2 )(NO)] 3+ , Co(NH 3 ) 5 (E-ON 4 ) 3+ , Co(NH 3 ) 5 ON 2 3+ , Co(NH 3 ) 5 (cycl-N 4 O) 3+ , and Co(NH 3 ) 5 N 2 O 3+ , exhibit short lifetimes of less than ∼60 μs and react via the I d mechanism.

  17. Intermediate state trapping of a voltage sensor

    DEFF Research Database (Denmark)

    Lacroix, Jérôme J; Pless, Stephan Alexander; Maragliano, Luca

    2012-01-01

    Voltage sensor domains (VSDs) regulate ion channels and enzymes by undergoing conformational changes depending on membrane electrical signals. The molecular mechanisms underlying the VSD transitions are not fully understood. Here, we show that some mutations of I241 in the S1 segment of the Shaker...... Kv channel positively shift the voltage dependence of the VSD movement and alter the functional coupling between VSD and pore domains. Among the I241 mutants, I241W immobilized the VSD movement during activation and deactivation, approximately halfway between the resting and active states......, and drastically shifted the voltage activation of the ionic conductance. This phenotype, which is consistent with a stabilization of an intermediate VSD conformation by the I241W mutation, was diminished by the charge-conserving R2K mutation but not by the charge-neutralizing R2Q mutation. Interestingly, most...

  18. Effect of sugar addition on glass transition temperatures of cassava starch with low to intermediate moisture contents.

    Science.gov (United States)

    Figueroa, Yetzury; Guevara, Marvilan; Pérez, Adriana; Cova, Aura; Sandoval, Aleida J; Müller, Alejandro J

    2016-08-01

    This work studies how sucrose (S) addition modifies the thermal properties of cassava starch (CS). Neat CS and CS-S blends with 4, 6 and 8% sugar contents (CS-S-4%, CS-S-6% and CS-S-8%) were prepared and analyzed by differential scanning calorimetry (DSC) and dynamic mechanical thermal analysis (DMTA), in a wide range of moisture levels (2-20%). In equilibrated samples with moisture contents lower than 10%, twoendothermic steps were observed during first DSC heating scans and two corresponding relaxation maxima in tan δ were detected by DMTA. The first transition, detected at around 45-55°C by both DSC and DMTA, is frequently found in starchy foods, while the second observed at higher temperatures is associated to the glass transition temperature of the blends. At higher moisture contents, only one thermal transition was observed. Samples analyzed immediately after cooling from the melt (i.e., after erasing their thermal history), exhibited a single glass transition temperature, regardless of their moisture content. Addition of sugar promotes water plasticization of CS only at high moisture contents. In the low moisture content range, anti-plasticization was observed for both neat and sugar-added CS samples. Addition of sugar decreases the moisture content needed to achieve the maximum value of the glass transition temperature before plasticization starts. The results of this work may be valuable for the study of texture establishment in low moisture content extruded food products. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software.

    Science.gov (United States)

    Riniker, Sereina; Christ, Clara D; Hansen, Halvor S; Hünenberger, Philippe H; Oostenbrink, Chris; Steiner, Denise; van Gunsteren, Wilfred F

    2011-11-24

    The calculation of the relative free energies of ligand-protein binding, of solvation for different compounds, and of different conformational states of a polypeptide is of considerable interest in the design or selection of potential enzyme inhibitors. Since such processes in aqueous solution generally comprise energetic and entropic contributions from many molecular configurations, adequate sampling of the relevant parts of configurational space is required and can be achieved through molecular dynamics simulations. Various techniques to obtain converged ensemble averages and their implementation in the GROMOS software for biomolecular simulation are discussed, and examples of their application to biomolecules in aqueous solution are given. © 2011 American Chemical Society

  20. Quinine-Promoted, Enantioselective Boron-Tethered Diels-Alder Reaction by Anomeric Control of Transition State Conformation.

    Science.gov (United States)

    Scholl, Katie; Dillashaw, John; Timpy, Evan; Lam, Yu-Hong; DeRatt, Lindsey; Benton, Tyler R; Powell, Jacqueline P; Houk, Kendall N; Morgan, Jeremy B

    2018-05-01

    Diels-Alder reactions of tethered vinyl-metal species offer the opportunity to fashion highly functionalized diol intermediates for synthesis. We have developed the first enantioselective boron-tethered Diels-Alder reaction using quinine as a chiral promoter. Quinine recovery, enantioselectivity enhancement, and manipulation of the cyclohexene core are also investigated. DFT modeling calculations confirm the role of quinine as a bidentate ligand enhancing reaction rates. The enantioselectivity of the cycloaddition is proposed to originate from a boron-centered anomeric effect.

  1. MicroRNA Cluster miR-17-92 Regulates Neural Stem Cell Expansion and Transition to Intermediate Progenitors in the Developing Mouse Neocortex

    Directory of Open Access Journals (Sweden)

    Shan Bian

    2013-05-01

    Full Text Available During development of the embryonic neocortex, tightly regulated expansion of neural stem cells (NSCs and their transition to intermediate progenitors (IPs are critical for normal cortical formation and function. Molecular mechanisms that regulate NSC expansion and transition remain unclear. Here, we demonstrate that the microRNA (miRNA miR-17-92 cluster is required for maintaining proper populations of cortical radial glial cells (RGCs and IPs through repression of Pten and Tbr2 protein. Knockout of miR-17-92 and its paralogs specifically in the developing neocortex restricts NSC proliferation, suppresses RGC expansion, and promotes transition of RGCs to IPs. Moreover, Pten and Tbr2 protectors specifically block silencing activities of endogenous miR-17-92 and control proper numbers of RGCs and IPs in vivo. Our results demonstrate a critical role for miRNAs in promoting NSC proliferation and modulating the cell-fate decision of generating distinct neural progenitors in the developing neocortex.

  2. Structural Exploration and Conformational Transitions in MDM2 upon DHFR Interaction from Homo sapiens: A Computational Outlook for Malignancy via Epigenetic Disruption

    Directory of Open Access Journals (Sweden)

    Arundhati Banerjee

    2016-01-01

    Full Text Available Structural basis for exploration into MDM2 and MDM2-DHFR interaction plays a vital role in analyzing the obstruction in folate metabolism, nonsynthesis of purines, and further epigenetic regulation in Homo sapiens. Therefore, it leads to suppression of normal cellular behavior and malignancy. This has been earlier documented via yeast two-hybrid assays. So, with a novel outlook, this study explores the molecular level demonstration of the best satisfactory MDM2 model selection after performing manifold modeling techniques. Z-scores and other stereochemical features were estimated for comparison. Further, protein-protein docking was executed with MDM2 and the experimentally validated X-ray crystallographic DHFR. Residual disclosure from the best suited simulated protein complex disclosed 18 side chain and 3 ionic interactions to strongly accommodate MDM2 protein into the pocket-like zone in DHFR due to the positive environment by charged residues. Lysine residues from MDM2 played a predominant role. Moreover, evaluation from varied energy calculations, folding rate, and net area for solvent accessibility implied the active participation of MDM2 with DHFR. Fascinatingly, conformational transitions from coils to helices and β-sheets after interaction with DHFR affirm the conformational strength and firmer interaction of human MDM2-DHFR. Therefore, this probe instigates near-future clinical research and interactive computational investigations with mutations.

  3. Structural Exploration and Conformational Transitions in MDM2 upon DHFR Interaction from Homo sapiens: A Computational Outlook for Malignancy via Epigenetic Disruption.

    Science.gov (United States)

    Banerjee, Arundhati; Ray, Sujay

    2016-01-01

    Structural basis for exploration into MDM2 and MDM2-DHFR interaction plays a vital role in analyzing the obstruction in folate metabolism, nonsynthesis of purines, and further epigenetic regulation in Homo sapiens. Therefore, it leads to suppression of normal cellular behavior and malignancy. This has been earlier documented via yeast two-hybrid assays. So, with a novel outlook, this study explores the molecular level demonstration of the best satisfactory MDM2 model selection after performing manifold modeling techniques. Z-scores and other stereochemical features were estimated for comparison. Further, protein-protein docking was executed with MDM2 and the experimentally validated X-ray crystallographic DHFR. Residual disclosure from the best suited simulated protein complex disclosed 18 side chain and 3 ionic interactions to strongly accommodate MDM2 protein into the pocket-like zone in DHFR due to the positive environment by charged residues. Lysine residues from MDM2 played a predominant role. Moreover, evaluation from varied energy calculations, folding rate, and net area for solvent accessibility implied the active participation of MDM2 with DHFR. Fascinatingly, conformational transitions from coils to helices and β-sheets after interaction with DHFR affirm the conformational strength and firmer interaction of human MDM2-DHFR. Therefore, this probe instigates near-future clinical research and interactive computational investigations with mutations.

  4. Steered molecular dynamics simulations of a bacterial type IV pilus reveal characteristics of an experimentally-observed, force-induced conformational transition

    Science.gov (United States)

    Baker, Joseph; Biais, Nicolas; Tama, Florence

    2011-10-01

    Type IV pili (T4P) are long, filamentous structures that emanate from the cellular surface of many infectious bacteria. They are built from a 158 amino acid long subunit called pilin. T4P can grow to many micrometers in length, and can withstand large tension forces. During the infection process, pili attach themselves to host cells, and therefore naturally find themselves under tension. We investigated the response of a T4 pilus to a pulling force using the method of steered molecular dynamics (SMD) simulation. Our simulations expose to the external environment an amino acid sequence initially hidden in the native filament, in agreement with experimental data. Therefore, our simulations might be probing the initial stage of the transition to a force-induced conformation of the T4 pilus. Additional exposed amino acid sequences that might be useful targets for drugs designed to mitigate bacterial infection were also predicted.

  5. Resilience of a cerradão subjected to intermediate disturbance in the Cerrado-Amazonia transition, Mato Grosso, Brazil

    Directory of Open Access Journals (Sweden)

    Ben Hur Marimon-Junior

    2013-09-01

    Full Text Available The present study examined the hypothesis that remnant forests in small protected areas may be resilient to intermediate disturbances. We analyzed the diameter and height distributions of the tree community in a typical cerradão (14°42’02.3”S and 52°21’02.6”W and determined which species were most abundant, sampling at two- to three-year intervals over eight years. In 2002, 2005, 2008 and 2010, we measured all live trees with a diameter ≥ 5 cm at 0.3 m above ground in 50 plots of 10 x 10 m. Although significant variation was observed in the density of the trees and the distributions of their diameters and heights, the community maintained the “reverse-J” and unimodal patterns for these distributions, respectively. These results indicate continuous recruitment and little change in the structure of the community over the study period, supporting our hypothesis. Three different patterns of diametric distribution were observed among the analyzed species, likely reflecting different forest occupation strategies. Hirtella glandulosa was the speciesmost able to exploit its environment, as it possessed the greatest overall abundance and was represented by individuals in all diameter classes.

  6. Dynein Light Intermediate Chain 2 Facilitates the Metaphase to Anaphase Transition by Inactivating the Spindle Assembly Checkpoint.

    Directory of Open Access Journals (Sweden)

    Sagar P Mahale

    Full Text Available The multi-functional molecular motor cytoplasmic dynein performs diverse essential roles during mitosis. The mechanistic importance of the dynein Light Intermediate Chain homologs, LIC1 and LIC2 is unappreciated, especially in the context of mitosis. LIC1 and LIC2 are believed to exist in distinct cytoplasmic dynein complexes as obligate subunits. LIC1 had earlier been reported to be required for metaphase to anaphase progression by inactivating the kinetochore-microtubule attachment-sensing arm of the spindle assembly checkpoint (SAC. However, the functional importance of LIC2 during mitosis remains elusive. Here we report prominent novel roles for the LIC2 subunit of cytoplasmic dynein in regulating the spindle assembly checkpoint. LIC2 depletion in mammalian cells led to prolonged metaphase arrest in the presence of an active SAC and also to stretched kinetochores, thus implicating it in SAC inactivation. Quantitative fluorescence microscopy of SAC components revealed accumulation of both attachment- and tension-sensing checkpoint proteins at metaphase kinetochores upon LIC2 depletion. These observations support a stronger and more diverse role in checkpoint inactivation for LIC2 in comparison to its close homolog LIC1. Our study uncovers a novel functional hierarchy during mitotic checkpoint inactivation between the closely related but homologous LIC subunits of cytoplasmic dynein. These subtle functional distinctions between dynein subpopulations could be exploited to study specific aspects of the spindle assembly checkpoint, which is a key mediator of fidelity in eukaryotic cell division.

  7. Kinetic and mechanistic studies of reactive intermediates in photochemical and transition metal-assisted oxidation, decarboxylation and alkyl transfer reactions

    Science.gov (United States)

    Carraher, Jack McCaslin

    Reactive species like high-valent metal-oxo complexes and carbon and oxygen centered radicals are important intermediates in enzymatic systems, atmospheric chemistry, and industrial processes. Understanding the pathways by which these intermediates form, their relative reactivity, and their fate after reactions is of the utmost importance. Herein are described the mechanistic detail for the generation of several reactive intermediates, synthesis of precursors, characterization of precursors, and methods to direct the chemistry to more desirable outcomes yielding 'greener' sources of commodity chemicals and fuels. High-valent Chromium from Hydroperoxido-Chromium(III). The decomposition of pentaaquahydroperoxido chromium(III) ion (hereafter Cr aqOOH2+) in acidic aqueous solutions is kinetically complex and generates mixtures of products (Craq3+, HCrO 4-, H2O2, and O2). The yield of high-valent chromium products (known carcinogens) increased from a few percent at pH 1 to 70 % at pH 5.5 (near biological pH). Yields of H 2O2 increased with acid concentration. The reproducibility of the kinetic data was poor, but became simplified in the presence of H2O2 or 2,2‧-azinobis(3-ethylbenzothiazoline-6-sulfonate) dianion (ABTS2-). Both are capable of scavenging strongly oxidizing intermediates). The observed rate constants (pH 1, [O2] ≤ 0.03 mM) in the presence of these scavengers are independent of [scavenger] and within the error are the same (k,ABTS2- = (4.9 +/- 0.2) x 10-4 s-1 and kH2O2 = (5.3 +/- 0.7) x 10-4 s-1); indicating involvement of the scavengers in post-rate determining steps. In the presence of either scavenger, decomposition of CrOOH2+ obeyed a two-term rate law, k obs / s-1 = (6.7 +/- 0.7) x 10-4 + (7.6 +/- 1.1) x 10-4 [H+]. Effect of [H+] on the kinetics and the product distribution, cleaner kinetics in the presence of scavengers, and independence of kobs on [scavenger] suggest a dual-pathway mechanism for the decay of Craq OOH2+. The H+-catalyzed path

  8. 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.

  9. Magnetic ordering of CoCl2-GIC, a spin ceramic: hierarchical successive transitions and the intermediate glassy phase

    International Nuclear Information System (INIS)

    Suzuki, Masatsugu; Suzuki, Itsuko S; Matsuura, Motohiro

    2007-01-01

    Stage-2 CoCl 2 -graphite intercalation compound (GIC) is a spin ceramic which shows hierarchical successive transitions at T cu (= 8.9 K) and T cl (= 7.0 K) from the paramagnetic phase into an intra-cluster (two-dimensional ferromagnetic) order with inter-cluster disorder and then to an inter-cluster (three-dimensional antiferromagnetic like) order over the whole system. The nature of the inter-cluster disorder was suggested to be of spin glass by nonlinear magnetic response analyses around T cu and by studies on dynamical aspects of ordering between T cu and T cl . Here, we present a further extensive examination of a series of time dependence of zero-field cooled magnetization M ZFC after the ageing protocol below T cu . The time dependence of the relaxation rates S ZFC (t) = (1/H) dM ZFC (t)/dlnt dramatically changes from the curves of simple spin glass ageing effect below T cl to those of two peaks above T cl . The characteristic relaxation behaviour apparently indicates that there coexist two different kinds of glassy correlated region below T cu

  10. Effects of Catalytic Action and Ligand Binding on Conformational Ensembles of Adenylate Kinase.

    Science.gov (United States)

    Onuk, Emre; Badger, John; Wang, Yu Jing; Bardhan, Jaydeep; Chishti, Yasmin; Akcakaya, Murat; Brooks, Dana H; Erdogmus, Deniz; Minh, David D L; Makowski, Lee

    2017-08-29

    Crystal structures of adenylate kinase (AdK) from Escherichia coli capture two states: an "open" conformation (apo) obtained in the absence of ligands and a "closed" conformation in which ligands are bound. Other AdK crystal structures suggest intermediate conformations that may lie on the transition pathway between these two states. To characterize the transition from open to closed states in solution, X-ray solution scattering data were collected from AdK in the apo form and with progressively increasing concentrations of five different ligands. Scattering data from apo AdK are consistent with scattering predicted from the crystal structure of AdK in the open conformation. In contrast, data from AdK samples saturated with Ap5A do not agree with that calculated from AdK in the closed conformation. Using cluster analysis of available structures, we selected representative structures in five conformational states: open, partially open, intermediate, partially closed, and closed. We used these structures to estimate the relative abundances of these states for each experimental condition. X-ray solution scattering data obtained from AdK with AMP are dominated by scattering from AdK in the open conformation. For AdK in the presence of high concentrations of ATP and ADP, the conformational ensemble shifts to a mixture of partially open and closed states. Even when AdK is saturated with Ap5A, a significant proportion of AdK remains in a partially open conformation. These results are consistent with an induced-fit model in which the transition of AdK from an open state to a closed state is initiated by ATP binding.

  11. Intermediate treatments

    Science.gov (United States)

    John R. Jones; Wayne D. Shepperd

    1985-01-01

    Intermediate treatments are those applied after a new stand is successfully established and before the final harvest. These include not only intermediate cuttings - primarily thinning - but also fertilization, irrigation, and protection of the stand from damaging agents.

  12. 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...

  13. Binding mechanism and dynamic conformational change of C subunit of PKA with different pathways.

    Science.gov (United States)

    Chu, Wen-Ting; Chu, Xiakun; Wang, Jin

    2017-09-19

    The catalytic subunit of PKA (PKAc) exhibits three major conformational states (open, intermediate, and closed) during the biocatalysis process. Both ATP and substrate/inhibitor can effectively induce the conformational changes of PKAc from open to closed states. Aiming to explore the mechanism of this allosteric regulation, we developed a coarse-grained model and analyzed the dynamics of conformational changes of PKAc during binding by performing molecular dynamics simulations for apo PKAc, binary PKAc (PKAc with ATP, PKAc with PKI), and ternary PKAc (PKAc with ATP and PKI). Our results suggest a mixed binding mechanism of induced fit and conformational selection, with the induced fit dominant. The ligands can drive the movements of Gly-rich loop as well as some regions distal to the active site in PKAc and stabilize them at complex state. In addition, there are two parallel pathways (pathway with PKAc-ATP as an intermediate and pathway PKAc-PKI as an intermediate) during the transition from open to closed states. By molecular dynamics simulations and rate constant analyses, we find that the pathway through PKAc-ATP intermediate is the main binding route from open to closed state because of the fact that the bound PKI will hamper ATP from successful binding and significantly increase the barrier for the second binding subprocess. These findings will provide fundamental insights of the mechanisms of PKAc conformational change upon binding.

  14. Modulation of the Conformational Dynamics of Apo-Adenylate Kinase through a π-Cation Interaction.

    Science.gov (United States)

    Halder, Ritaban; Manna, Rabindra Nath; Chakraborty, Sandipan; Jana, Biman

    2017-06-15

    Large-scale conformational transition from open to closed state of adenylate kinase (ADK) is essential for its catalytic cycle. Apo-ADK undergoes conformational transition in a way that closely resembles an open-to-closed conformational transition. Here, equilibrium simulations, free-energy simulations, and quantum mechanics/molecular mechanics (QM/MM) calculations in combination with several bioinformatics approaches have been used to explore the molecular origin of this conformational transition in apo-ADK. In addition to its conventional open state, Escherichia coli apo-ADK adopts conformations that resemble a closed-like intermediate, the "half-open-half-closed" (HOHC) state, and a π-cation interaction can account for the stability of this HOHC state. Energetics and the electronic properties of this π-cation interaction have been explored using QM/MM calculations. Upon rescinding the π-cation interaction, the conformational landscape of the apo-ADK changes completely. The apo-ADK population is shifted completely toward the open state. This π-cation interaction is highly conserved in bacterial ADK; the cationic guanidinium moiety of a conserved ARG interacts with the delocalized π-electron cloud of either PHE or TYR. Interestingly, this study demonstrates the modulation of a principal protein dynamics by a conserved specific π-cation interaction across different organisms.

  15. The Building Game: From Enumerative Combinatorics to Conformational Diffusion

    Science.gov (United States)

    Johnson-Chyzhykov, Daniel; Menon, Govind

    2016-08-01

    We study a discrete attachment model for the self-assembly of polyhedra called the building game. We investigate two distinct aspects of the model: (i) enumerative combinatorics of the intermediate states and (ii) a notion of Brownian motion for the polyhedral linkage defined by each intermediate that we term conformational diffusion. The combinatorial configuration space of the model is computed for the Platonic, Archimedean, and Catalan solids of up to 30 faces, and several novel enumerative results are generated. These represent the most exhaustive computations of this nature to date. We further extend the building game to include geometric information. The combinatorial structure of each intermediate yields a systems of constraints specifying a polyhedral linkage and its moduli space. We use a random walk to simulate a reflected Brownian motion in each moduli space. Empirical statistics of the random walk may be used to define the rates of transition for a Markov process modeling the process of self-assembly.

  16. 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

  17. 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.

  18. 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.

  19. Conformal Infinity.

    Science.gov (United States)

    Frauendiener, Jörg

    2004-01-01

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

  20. 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.

  1. 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.

  2. Conformal Infinity

    OpenAIRE

    Frauendiener, J?rg

    2000-01-01

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

  3. Conformation radiotherapy and conformal radiotherapy

    International Nuclear Information System (INIS)

    Morita, Kozo

    1999-01-01

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

  4. TRANSIT

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. TRANSIT. SYSTEM: DETERMINE 2D-POSITION GLOBALLY BUT INTERMITTENT (POST-FACTO). IMPROVED ACCURACY. PRINCIPLE: POLAR SATELLITES WITH INNOVATIONS OF: GRAVITY-GRADIENT ATTITUDE CONTROL; DRAG COMPENSATION. WORKS ...

  5. Intermediate Fragment

    DEFF Research Database (Denmark)

    Kruse Aagaard, Anders

    2015-01-01

    This text and its connected exhibition are aiming to reflect both on the thoughts, the processes and the outcome of the design and production of the artefact ‘Intermediate Fragment’ and making as a contemporary architectural tool in general. Intermediate Fragment was made for the exhibition ‘Enga...... of realising an exhibition object was conceived, but expanded, refined and concretised through this process. The context of the work shown here is an interest in a tighter, deeper connection between experimentally obtained material knowledge and architectural design....

  6. Conformal Gravity

    International Nuclear Information System (INIS)

    Hooft, G.

    2012-01-01

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

  7. 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....

  8. Visualizing multistep elevator-like transitions of a nucleoside transporter.

    Science.gov (United States)

    Hirschi, Marscha; Johnson, Zachary Lee; Lee, Seok-Yong

    2017-05-04

    Membrane transporters move substrates across the membrane by alternating access of their binding sites between the opposite sides of the membrane. An emerging model of this process is the elevator mechanism, in which a substrate-binding transport domain moves a large distance across the membrane. This mechanism has been characterized by a transition between two states, but the conformational path that leads to the transition is not yet known, largely because the available structural information has been limited to the two end states. Here we present crystal structures of the inward-facing, intermediate, and outward-facing states of a concentrative nucleoside transporter from Neisseria wadsworthii. Notably, we determined the structures of multiple intermediate conformations, in which the transport domain is captured halfway through its elevator motion. Our structures present a trajectory of the conformational transition in the elevator model, revealing multiple intermediate steps and state-dependent conformational changes within the transport domain that are associated with the elevator-like motion.

  9. Structural basis and kinetics of force-induced conformational changes of an αA domain-containing integrin.

    Directory of Open Access Journals (Sweden)

    Xue Xiang

    Full Text Available Integrin α(Lβ₂ (lymphocyte function-associated antigen, LFA-1 bears force upon binding to its ligand intercellular adhesion molecule 1 (ICAM-1 when a leukocyte adheres to vascular endothelium or an antigen presenting cell (APC during immune responses. The ligand binding propensity of LFA-1 is related to its conformations, which can be regulated by force. Three conformations of the LFA-1 αA domain, determined by the position of its α₇-helix, have been suggested to correspond to three different affinity states for ligand binding.The kinetics of the force-driven transitions between these conformations has not been defined and dynamically coupled to the force-dependent dissociation from ligand. Here we show, by steered molecular dynamics (SMD simulations, that the αA domain was successively transitioned through three distinct conformations upon pulling the C-terminus of its α₇-helix. Based on these sequential transitions, we have constructed a mathematical model to describe the coupling between the αA domain conformational changes of LFA-1 and its dissociation from ICAM-1 under force. Using this model to analyze the published data on the force-induced dissociation of single LFA-1/ICAM-1 bonds, we estimated the force-dependent kinetic rates of interstate transition from the short-lived to intermediate-lived and from intermediate-lived to long-lived states. Interestingly, force increased these transition rates; hence activation of LFA-1 was accelerated by pulling it via an engaged ICAM-1.Our study defines the structural basis for mechanical regulation of the kinetics of LFA-1 αA domain conformational changes and relates these simulation results to experimental data of force-induced dissociation of single LFA-1/ICAM-1 bonds by a new mathematical model, thus provided detailed structural and kinetic characterizations for force-stabilization of LFA-1/ICAM-1 interaction.

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    activator inhibitor 1 (PAI-1). We report the first multi-microsecond atomistic molecular dynamics simulations of PAI-1 and compare the data with experimental hydrogen/deuterium-exchange data (HDXMS). The simulations reveal notable conformational flexibility of helices D, E and F and major fluctuations...... are observed in the W86-loop which occasionally leads to progressive detachment of β-strand 2 A from β-strand 3 A. An interesting correlation between Cα-RMSD values from simulations and experimental HDXMS data is observed. Helices D, E and F are known to be important for the overall stability of active PAI-1......Both function and dysfunction of serine protease inhibitors (serpins) involve massive conformational change in their tertiary structure but the dynamics facilitating these events remain poorly understood. We have studied the dynamic preludes to conformational change in the serpin plasminogen...

  11. Transitions of tethered chain molecules under tension.

    Science.gov (United States)

    Luettmer-Strathmann, Jutta; Binder, Kurt

    2014-09-21

    An applied tension force changes the equilibrium conformations of a polymer chain tethered to a planar substrate and thus affects the adsorption transition as well as the coil-globule and crystallization transitions. Conversely, solvent quality and surface attraction are reflected in equilibrium force-extension curves that can be measured in experiments. To investigate these effects theoretically, we study tethered chains under tension with Wang-Landau simulations of a bond-fluctuation lattice model. Applying our model to pulling experiments on biological molecules we obtain a good description of experimental data in the intermediate force range, where universal features dominate and finite size effects are small. For tethered chains in poor solvent, we observe the predicted two-phase coexistence at transitions from the globule to stretched conformations and also discover direct transitions from crystalline to stretched conformations. A phase portrait for finite chains constructed by evaluating the density of states for a broad range of solvent conditions and tensions shows how increasing tension leads to a disappearance of the globular phase. For chains in good solvents tethered to hard and attractive surfaces we find the predicted scaling with the chain length in the low-force regime and show that our results are well described by an analytical, independent-bond approximation for the bond-fluctuation model for the highest tensions. Finally, for a hard or slightly attractive surface the stretching of a tethered chain is a conformational change that does not correspond to a phase transition. However, when the surface attraction is sufficient to adsorb a chain it will undergo a desorption transition at a critical value of the applied force. Our results for force-induced desorption show the transition to be discontinuous with partially desorbed conformations in the coexistence region.

  12. Quantitative assessment of force fields on both low-energy conformational basins and transition-state regions of the (phi-psi) space

    NARCIS (Netherlands)

    Liu, Z.; Ensing, B.; Moore, P.B.

    2011-01-01

    The free energy surfaces (FESs) of alanine dipeptide are studied to illustrate a new strategy to assess the performance of classical molecular mechanics force field on the full range of the (phi-psi) conformational space. The FES is obtained from metadynamics simulations with five commonly used

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

    International Nuclear Information System (INIS)

    Zamolodchikov, A.B.

    1988-01-01

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

  14. Intermediate uveitis

    Directory of Open Access Journals (Sweden)

    Babu B

    2010-01-01

    Full Text Available Intermediate uveitis (IU is described as inflammation in the anterior vitreous, ciliary body and the peripheral retina. In the Standardization of Uveitis Nomenclature (SUN working group′s international workshop for reporting clinical data the consensus reached was that the term IU should be used for that subset of uveitis where the vitreous is the major site of the inflammation and if there is an associated infection (for example, Lyme disease or systemic disease (for example, sarcoidosis. The diagnostic term pars planitis should be used only for that subset of IU where there is snow bank or snowball formation occurring in the absence of an associated infection or systemic disease (that is, "idiopathic". This article discusses the clinical features, etiology, pathogenesis, investigations and treatment of IU.

  15. Structure and phase transitions of monolayers of intermediate-length n-alkanes on graphite studied by neutron diffraction and molecular dynamics simulation

    DEFF Research Database (Denmark)

    Diama, A.; Matthies, B.; Herwig, K. W.

    2009-01-01

    measurements indicate that the two monolayer films differ principally in the transition temperatures between phases. At the lowest temperatures, both C24 and C32 form a crystalline monolayer phase with a rectangular-centered (RC) structure. The two sublattices of the RC structure each consists of parallel rows...... show evidence of broadening of the lamella boundaries as a result of molecules diffusing parallel to their long axis. At still higher temperatures, they indicate that the introduction of gauche defects into the alkane chains drives a melting transition to a monolayer fluid phase as reported previously...

  16. Phase transition of a cobalt-free perovskite as a high-performance cathode for intermediate-temperature solid oxide fuel cells.

    Science.gov (United States)

    Jiang, Shanshan; Zhou, Wei; Niu, Yingjie; Zhu, Zhonghua; Shao, Zongping

    2012-10-01

    It is generally recognized that the phase transition of a perovskite may be detrimental to the connection between cathode and electrolyte. Moreover, certain phase transitions may induce the formation of poor electronic and ionic conducting phase(s), thereby lowering the electrochemical performance of the cathode. Here, we present a study on the phase transition of a cobalt-free perovskite (SrNb(0.1)Fe(0.9)O(3-δ), SNF) and evaluate its effect on the electrochemical performance of the fuel cell. SNF exists as a primitive perovskite structure with space group P4mm (99) at room temperature. As evidenced by in situ high-temperature X-ray diffraction measurements over the temperature range of 600 to 1000 °C, SNF undergoes a transformation to a tetragonal structure with a space group I4/m (87). This phase transition is accompanied by a moderate change in the volume, allowing a good cathode/electrolyte interface on thermal cycling. According to the electrochemical impedance spectroscopy evaluation, the I4/m phase exhibits positive effects on the cathode's performance, showing the highest oxygen reduction reaction activity of cobalt-free cathodes reported so far. This activity improvement is attributed to enhanced oxygen surface processes. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Energy Landscape and Pathways for Transitions between Watson-Crick and Hoogsteen Base Pairing in DNA.

    Science.gov (United States)

    Chakraborty, Debayan; Wales, David J

    2018-01-04

    The recent discovery that Hoogsteen (HG) base pairs are widespread in DNA across diverse sequences and positional contexts could have important implications for understanding DNA replication and DNA-protein recognition. While evidence is emerging that the Hoogsteen conformation could be a thermodynamically accessible conformation of the DNA duplex and provide a means to expand its functionality, relatively little is known about the molecular mechanism underlying the Watson-Crick (WC) to HG transition. In this Perspective, we describe pathways and kinetics for this transition at an atomic level of detail, using the energy landscape perspective. We show that competition between the duplex conformations results in a double funnel landscape, which explains some recent experimental observations. The interconversion pathways feature a number of intermediates, with a variable number of WC and HG base pairs. The relatively slow kinetics, with possible deviations from two-state behavior, suggest that this conformational switch is likely to be a challenging target for both simulation and experiment.

  18. Conformal invariance and two-dimensional physics

    International Nuclear Information System (INIS)

    Zuber, J.B.

    1993-01-01

    Actually, physicists and mathematicians are very interested in conformal invariance: geometric transformations which keep angles. This symmetry is very important for two-dimensional systems as phase transitions, string theory or node mathematics. In this article, the author presents the conformal invariance and explains its usefulness

  19. Targeted Molecular Dynamics to determine Focal Adhesion Targeting Domain Folding Intermediates

    Directory of Open Access Journals (Sweden)

    Pallavi Mohanty

    2017-10-01

    Full Text Available The Focal adhesion kinase (FAT domain of Focal Adhesion Kinase is a four helical bundle known for conformational plasticity. FAT adopts two distinctly different conformations i.e., close (cFAT and arm-exchanged (aeFAT states under native conditions [1]. The slow transition from cFAT to aeFAT is likely to proceed through an open intermediate state that allows YENV motif to attain β-turn conformation and phosphorylation of Y925 by Src kinases [2]. The two end states of FAT are known to interact with Paxillin and are responsible for maintaining steady state in Heart while intermediate conformation interacts with Grb2-SH2 leading to Pathological Cardiac Hypertrophy (PAH [2]. 10ns Targeted Molecular Dynamics (TMD was done between c- and aeFAT in order to explore the conformational transition and to capture pathologically relevant oFAT. Cluster and dynamic cross correlation analysis (DCCA of TMD generated trajectory was done and the selected FAT intermediate was docked with Grb2-SH2 using HADDOCK v2.2 docking followed by molecular dynamics. Conservation analysis of FAT-Grb2 binding site was done using CONSURF [3]. A Pharmacophore FAT-Grb2 complex was generated using SPARKv1.2 and submitted for Virtual screening using BLAZE v4. Drug likeliness and ADMET properties were calculated using MOLINSPIRATION tool. TMD reveals six clusters and DCCA showed positively and negatively correlated region along the transition pathway. Intermediates with competence for Grb2 interaction were docked with Grb2 and best binding complex was further refined. MMPBSA binding energy calculations revealed the best binding pose where the phosphorylated YENV motif of Human FAT interacted with a charged and hydrophobic pocket of Grb2. The conservation analysis showed that the charged pocket was more conserved in comparison with the hydrophobic pocket, hence providing useful insights on binding and specificity determining residues in Grb2. Virtual screening using the pharmacophore

  20. General Information for Transportation and Conformity

    Science.gov (United States)

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

  1. Global conformational dynamics of a Y-family DNA polymerase during catalysis.

    Directory of Open Access Journals (Sweden)

    Cuiling Xu

    2009-10-01

    Full Text Available Replicative DNA polymerases are stalled by damaged DNA while the newly discovered Y-family DNA polymerases are recruited to rescue these stalled replication forks, thereby enhancing cell survival. The Y-family DNA polymerases, characterized by low fidelity and processivity, are able to bypass different classes of DNA lesions. A variety of kinetic and structural studies have established a minimal reaction pathway common to all DNA polymerases, although the conformational intermediates are not well defined. Furthermore, the identification of the rate-limiting step of nucleotide incorporation catalyzed by any DNA polymerase has been a matter of long debate. By monitoring time-dependent fluorescence resonance energy transfer (FRET signal changes at multiple sites in each domain and DNA during catalysis, we present here a real-time picture of the global conformational transitions of a model Y-family enzyme: DNA polymerase IV (Dpo4 from Sulfolobus solfataricus. Our results provide evidence for a hypothetical DNA translocation event followed by a rapid protein conformational change prior to catalysis and a subsequent slow, post-chemistry protein conformational change. Surprisingly, the DNA translocation step was induced by the binding of a correct nucleotide. Moreover, we have determined the directions, rates, and activation energy barriers of the protein conformational transitions, which indicated that the four domains of Dpo4 moved in a synchronized manner. These results showed conclusively that a pre-chemistry conformational change associated with domain movements was too fast to be the rate-limiting step. Rather, the rearrangement of active site residues limited the rate of correct nucleotide incorporation. Collectively, the conformational dynamics of Dpo4 offer insights into how the inter-domain movements are related to enzymatic function and their concerted interactions with other proteins at the replication fork.

  2. Conformationally constrained dipeptide surrogates with aromatic side-chains: synthesis of 4-aryl indolizidin-9-one amino acids by conjugate addition to a common alpha,omega-diaminoazelate enone intermediate.

    Science.gov (United States)

    Cluzeau, Jérôme; Lubell, William D

    2004-03-05

    Four methyl 9-oxo-8-(N-(Boc)-amino)-4-phenyl-1-azabicyclo[4.3.0]nonane carboxylates (11, 4-Ph-I(9)aa-OMe) were synthesized from (2S,8S,5E)-di-tert-butyl-4-oxo-5-ene-2,8-bis[N-(PhF)amino]azelate [(5E)-7, PhF = 9-(9-phenylfluorenyl)] via a seven-step process featuring a conjugate addition/reductive amination/lactam cyclization sequence. Various nucleophiles were used in the conjugate addition reactions on enone (5E)-7 as a general route for making alpha,omega-diaminoazelates possessing different substituents in good yield albeit low diastereoselectivity except in the case of aryl Grignard reagents (9/1 to 15/1 drs). 6-Phenylazelates (6S)-8d and (6R)-8d were separated by chromatography and diastereoselective precipitation and independently transformed into 4-Ph-I(9)aa-OMe. From (6S)-8d, (2S,4R,6R,8S)-4-Ph-I(9)aa-OMe 11 was prepared selectively in 51% yield. Reductive amination of (6R)-8d provided the desired pipecolates 9 along with desamino compound 10, which was minimized by performing the hydrogenation in the presence of ammonium acetate. Subsequent ester exchange, lactam cyclization, and amine protection provided three products (2R,4S,6S,8R)-, (2R,4S,6S,8S)-, and (2S,4S,6R,8S)-4-Ph-I(9)aa-OMe 11 in 10, 6, and 6% yields, respectively, from (6R)-8d. Ester hydrolysis of (2S,4R,6R,8S)-11 furnished 4-phenyl indolizidin-9-one N-(Boc)amino acid 3 as a novel constrained Ala-Phe dipeptide surrogate for studying conformation-activity relationships of biologically active peptides.

  3. Conformal Tachyons

    CERN Document Server

    Tomaschitz, R

    2000-01-01

    We study tachyons conformally coupled to the background geometry of a Milne universe. The causality of superluminal signal transfer is scrutinized in this context. The cosmic time of the comoving frame determines a distinguished time order for events connected by superluminal signals. An observer can relate his rest frame to the galaxy frame, and compare so the time order of events in his proper time to the cosmic time order. All observers can in this way arrive at identical conclusions on the causality of events connected by superluminal signals. An unambiguous energy concept for tachyonic rays is defined by means of the cosmic time of the comoving reference frame, without resorting to an antiparticle interpretation. On that basis we give an explicit proof that no signals can be sent into the past of observers. Causality violating signals are energetically forbidden, as they would have negative energy in the rest frame of the emitting observer. If an observer emits a superluminal signal, the tachyonic respon...

  4. Regularities of intermediate adsorption complex relaxation

    International Nuclear Information System (INIS)

    Manukova, L.A.

    1982-01-01

    The experimental data, characterizing the regularities of intermediate adsorption complex relaxation in the polycrystalline Mo-N 2 system at 77 K are given. The method of molecular beam has been used in the investigation. The analytical expressions of change regularity in the relaxation process of full and specific rates - of transition from intermediate state into ''non-reversible'', of desorption into the gas phase and accumUlation of the particles in the intermediate state are obtained

  5. Conformal field theory in conformal space

    International Nuclear Information System (INIS)

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

    1999-01-01

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

  6. Transition to intermediate valence state and x-ray photoemission in Sm/sub 1-x/Gd/sub x/S

    International Nuclear Information System (INIS)

    Campagna, M.; Chui, S.T.; Wertheim, G.K.; Tosatti, E.

    1976-01-01

    We report a systematic x-ray photoemission study of the alloys Sm 1 /sub -//subx/Gd/subx/S for 0 2+ → Sm 3+ photoemission line shape using a model which has some similarities with the Jaccarino-Walker model for magnetic alloys. It assumes the existence of only two different kinds of Sm 2+ ions in Sm 1 /sub -//subx/Gd/subx/S for x approximately-less-than 16%. We discuss possible reasons for the fact that Gd does not show the usual clustering effects known to occur in many substitutional rare-earth alloys. Lattice-constant measurements for various substituents further illustrate the importance of electronic effects in the phase transition

  7. Synthesis and structures of six closely related N-[3-(2-chlorobenzoyl)-5-ethylthiophen-2-yl]arylamides, together with an isolated reaction intermediate: order versus disorder, molecular conformations and hydrogen bonding in zero, one and two dimensions.

    Science.gov (United States)

    Sagar, Belakavadi K; Yathirajan, Hemmige S; Rathore, Ravindranath S; Glidewell, Christopher

    2018-02-01

    Six closely related N-[3-(2-chlorobenzoyl)-5-ethylthiophen-2-yl]arylamides have been synthesized and structurally characterized, together with a representative reaction intermediate. In each of N-[3-(2-chlorobenzoyl)-5-ethylthiophen-2-yl]benzamide, C 20 H 16 ClNO 2 S, (I), N-[3-(2-chlorobenzoyl)-5-ethylthiophen-2-yl]-4-phenylbenzamide, C 26 H 20 ClNO 2 S, (II), and 2-bromo-N-[3-(2-chlorobenzoyl)-5-ethylthiophen-2-yl]benzamide, C 20 H 15 BrClNO 2 S, (III), the molecules are disordered over two sets of atomic sites, with occupancies of 0.894 (8) and 0.106 (8) in (I), 0.832 (5) and 0.168 (5) in (II), and 0.7006 (12) and 0.2994 (12) in (III). In each of N-[3-(2-chlorobenzoyl)-5-ethylthiophen-2-yl]-2-iodobenzamide, C 20 H 15 ClINO 2 S, (IV), and N-[3-(2-chlorobenzoyl)-5-ethylthiophen-2-yl]-2-methoxybenzamide, C 21 H 18 ClNO 3 S, (V), the molecules are fully ordered, but in N-[3-(2-chlorobenzoyl)-5-ethylthiophen-2-yl]-2,6-difluorobenzamide, C 20 H 14 ClF 2 NO 2 S, (VI), which crystallizes with Z' = 2 in the space group C2/c, one of the two independent molecules is fully ordered, while the other is disordered over two sets of atomic sites having occupancies of 0.916 (3) and 0.084 (3). All of the molecules in compounds (I)-(VI) exhibit an intramolecular N-H...O hydrogen bond. The molecules of (I) and (VI) are linked by C-H...O hydrogen bonds to form finite zero-dimensional dimers, which are cyclic in (I) and acyclic in (VI), those of (III) are linked by C-H...π(arene) hydrogen bonds to form simple chains, and those of (IV) and (V) are linked into different types of chains of rings, built in each case from a combination of C-H...O and C-H...π(arene) hydrogen bonds. Two C-H...O hydrogen bonds link the molecules of (II) into sheets containing three types of ring. In benzotriazol-1-yl 3,4-dimethoxybenzoate, C 15 H 13 N 3 O 4 , (VII), the benzoate component is planar and makes a dihedral angle of 84.51 (6)° with the benzotriazole unit. Comparisons are made

  8. Louisiana SIP: LAC 33:III Ch. 14 Subchap B, 1431 to 1434--Conformity to State or Federal Implementation Plans of Transportation Plans, Programs, and Projects Developed, Funded, or Approved Under Title 23 U.S.C. or the Federal Transit Laws

    Science.gov (United States)

    Louisiana SIP: LAC 33:III Ch. 14 Subchap B, 1431 to 1434--Conformity to State or Federal Implementation Plans of Transportation Plans, Programs, and Projects Developed, Funded, or Approved Under Title 23 U.S.C. or the Federal Transit Laws

  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. Holographic multiverse and conformal invariance

    International Nuclear Information System (INIS)

    Garriga, Jaume; Vilenkin, Alexander

    2009-01-01

    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

  11. Conformational kinetics of aliphatic tails

    Science.gov (United States)

    Ferrarini, Alberta; Moro, Giorgio; Nordio, Pier Luigi

    The master equation describing the random walk between sites identified with the stable conformers of a chain molecule, represents the extension to the time domain of the Rotational Isomeric State model. The asymptotic analysis of the multidimensional diffusion equation in the continuous torsional variables subjected to the configurational potential, provides a rigorous justification for the discrete models, and it supplies, without resorting to phenomenological parameters, molecular definitions of the kinetic rates for the conformational transitions occurring at each segment of the chain. The coupling between the torsional variables is fully taken into account, giving rise to cooperative effects. A complete calculation of the specific correlation functions which describe the time evolution of the angular functions probed by N.M.R. and dielectric relaxation measurements, has been performed for alkyl chains attached to a massive core. The resulting behaviour has been compared with the decay of trans and gauche populations of specific bonds, expressed in terms of suitable correlation functions whose time integrals lead quite naturally to the definition of effective kinetic constants for the conformational transitions.

  12. 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....

  13. Conformal Einstein spaces

    International Nuclear Information System (INIS)

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

    1985-01-01

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

  14. Carbonyl Activation by Borane Lewis Acid Complexation: Transition States of H2 Splitting at the Activated Carbonyl Carbon Atom in a Lewis Basic Solvent and the Proton-Transfer Dynamics of the Boroalkoxide Intermediate.

    Science.gov (United States)

    Heshmat, Mojgan; Privalov, Timofei

    2017-07-06

    By using transition-state (TS) calculations, we examined how Lewis acid (LA) complexation activates carbonyl compounds in the context of hydrogenation of carbonyl compounds by H 2 in Lewis basic (ethereal) solvents containing borane LAs of the type (C 6 F 5 ) 3 B. According to our calculations, LA complexation does not activate a ketone sufficiently enough for the direct addition of H 2 to the O=C unsaturated bond; but, calculations indicate a possibly facile heterolytic cleavage of H 2 at the activated and thus sufficiently Lewis acidic carbonyl carbon atom with the assistance of the Lewis basic solvent (i.e., 1,4-dioxane or THF). For the solvent-assisted H 2 splitting at the carbonyl carbon atom of (C 6 F 5 ) 3 B adducts with different ketones, a number of TSs are computed and the obtained results are related to insights from experiment. By using the Born-Oppenheimer molecular dynamics with the DFT for electronic structure calculations, the evolution of the (C 6 F 5 ) 3 B-alkoxide ionic intermediate and the proton transfer to the alkoxide oxygen atom were investigated. The results indicate a plausible hydrogenation mechanism with a LA, that is, (C 6 F 5 ) 3 B, as a catalyst, namely, 1) the step of H 2 cleavage that involves a Lewis basic solvent molecule plus the carbonyl carbon atom of thermodynamically stable and experimentally identifiable (C 6 F 5 ) 3 B-ketone adducts in which (C 6 F 5 ) 3 B is the "Lewis acid promoter", 2) the transfer of the solvent-bound proton to the oxygen atom of the (C 6 F 5 ) 3 B-alkoxide intermediate giving the (C 6 F 5 ) 3 B-alcohol adduct, and 3) the S N 2-style displacement of the alcohol by a ketone or a Lewis basic solvent molecule. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. 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.

  16. Superspace conformal field theory

    International Nuclear Information System (INIS)

    Quella, Thomas

    2013-07-01

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

  17. Non-conformable, partial and conformable transposition

    DEFF Research Database (Denmark)

    König, Thomas; Mäder, Lars Kai

    2013-01-01

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

  18. Electronic Transitions in Conformationally Controlled Peralkylated Hexasilanes

    Czech Academy of Sciences Publication Activity Database

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

    2016-01-01

    Roč. 17, č. 19 (2016), s. 3010-3022 ISSN 1439-4235 Institutional support: RVO:61388963 Keywords : configuration interaction * density functional calculations * magnetic circular dichroism * oligosilanes * UV/Vis spectroscopy Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.075, year: 2016

  19. Dry molten globule intermediates and the mechanism of protein unfolding.

    Science.gov (United States)

    Baldwin, Robert L; Frieden, Carl; Rose, George D

    2010-10-01

    New experimental results show that either gain or loss of close packing can be observed as a discrete step in protein folding or unfolding reactions. This finding poses a significant challenge to the conventional two-state model of protein folding. Results of interest involve dry molten globule (DMG) intermediates, an expanded form of the protein that lacks appreciable solvent. When an unfolding protein expands to the DMG state, side chains unlock and gain conformational entropy, while liquid-like van der Waals interactions persist. Four unrelated proteins are now known to form DMGs as the first step of unfolding, suggesting that such an intermediate may well be commonplace in both folding and unfolding. Data from the literature show that peptide amide protons are protected in the DMG, indicating that backbone structure is intact despite loss of side-chain close packing. Other complementary evidence shows that secondary structure formation provides a major source of compaction during folding. In our model, the major free-energy barrier separating unfolded from native states usually occurs during the transition between the unfolded state and the DMG. The absence of close packing at this barrier provides an explanation for why phi-values, derived from a Brønsted-Leffler plot, depend primarily on structure at the mutational site and not on specific side-chain interactions. The conventional two-state folding model breaks down when there are DMG intermediates, a realization that has major implications for future experimental work on the mechanism of protein folding. 2010 Wiley-Liss, Inc.

  20. The Fusion Loops of the Initial Prefusion Conformation of Herpes Simplex Virus 1 Fusion Protein Point Toward the Membrane

    Directory of Open Access Journals (Sweden)

    Juan Fontana

    2017-08-01

    Full Text Available All enveloped viruses, including herpesviruses, must fuse their envelope with the host membrane to deliver their genomes into target cells, making this essential step subject to interference by antibodies and drugs. Viral fusion is mediated by a viral surface protein that transits from an initial prefusion conformation to a final postfusion conformation. Strikingly, the prefusion conformation of the herpesvirus fusion protein, gB, is poorly understood. Herpes simplex virus (HSV, a model system for herpesviruses, causes diseases ranging from mild skin lesions to serious encephalitis and neonatal infections. Using cryo-electron tomography and subtomogram averaging, we have characterized the structure of the prefusion conformation and fusion intermediates of HSV-1 gB. To this end, we have set up a system that generates microvesicles displaying full-length gB on their envelope. We confirmed proper folding of gB by nondenaturing electrophoresis-Western blotting with a panel of monoclonal antibodies (MAbs covering all gB domains. To elucidate the arrangement of gB domains, we labeled them by using (i mutagenesis to insert fluorescent proteins at specific positions, (ii coexpression of gB with Fabs for a neutralizing MAb with known binding sites, and (iii incubation of gB with an antibody directed against the fusion loops. Our results show that gB starts in a compact prefusion conformation with the fusion loops pointing toward the viral membrane and suggest, for the first time, a model for gB’s conformational rearrangements during fusion. These experiments further illustrate how neutralizing antibodies can interfere with the essential gB structural transitions that mediate viral entry and therefore infectivity.

  1. Conformal solids and holography

    Science.gov (United States)

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

    2017-12-01

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

  2. Toward TeV Conformality

    International Nuclear Information System (INIS)

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

    2010-01-01

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

  3. Conformational effects in photoelectron circular dichroism

    Science.gov (United States)

    Turchini, S.

    2017-12-01

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

  4. Conformational Diffusion and Helix Formation Kinetics

    International Nuclear Information System (INIS)

    Hummer, Gerhard; Garcia, Angel E.; Garde, Shekhar

    2000-01-01

    The time, temperature, and sequence dependences of helix formation kinetics of fully atomistic peptide models in explicit solvent are described quantitatively by a diffusive search within the coil state with barrierless transitions into the helical state. Conformational diffusion leads to nonexponential kinetics and jump-width dependences in temperature jump experiments. (c) 2000 The American Physical Society

  5. Conformational Diffusion and Helix Formation Kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Hummer, Gerhard [Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520 (United States); Garcia, Angel E. [Theoretical Biology and Biophysics Group T-10, MS K710, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Garde, Shekhar [Department of Chemical Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180 (United States)

    2000-09-18

    The time, temperature, and sequence dependences of helix formation kinetics of fully atomistic peptide models in explicit solvent are described quantitatively by a diffusive search within the coil state with barrierless transitions into the helical state. Conformational diffusion leads to nonexponential kinetics and jump-width dependences in temperature jump experiments. (c) 2000 The American Physical Society.

  6. Intermediality and media change

    OpenAIRE

    2012-01-01

    This book is about intermediality as an approach to analysing and understanding media change. Intermediality and Media Change is critical of technological determinism that characterises 'new media discourse' about the ongoing digitalization, framed as a revolution and creating sharp contrasts between old and new media. Intermediality instead emphasises paying attention to continuities between media of all types and privileges a comparative perspective on technological changes in media over ti...

  7. An alternative conformation of the gp41 heptad repeat 1 region coiled coil exists in the human immunodeficiency virus (HIV-1) envelope glycoprotein precursor

    International Nuclear Information System (INIS)

    Mische, Claudia C.; Yuan Wen; Strack, Bettina; Craig, Stewart; Farzan, Michael; Sodroski, Joseph

    2005-01-01

    The human immunodeficiency virus (HIV-1) transmembrane envelope glycoprotein, gp41, which mediates virus-cell fusion, exists in at least three different conformations within the trimeric envelope glycoprotein complex. The structures of the prefusogenic and intermediate states are unknown; structures representing the postfusion state have been solved. In the postfusion conformation, three helical heptad repeat 2 (HR2) regions pack in an antiparallel fashion into the hydrophobic grooves on the surface of a triple-helical coiled coil formed by the heptad repeat 1 (HR1) regions. We studied the prefusogenic conformation of gp41 by mutagenic alteration of membrane-anchored and soluble forms of the HIV-1 envelope glycoproteins. Our results indicate that, in the HIV-1 envelope glycoprotein precursor, the gp41 HR1 region is in a conformation distinct from that of a trimeric coiled coil. Thus, the central gp41 coiled coil is formed during the transition of the HIV-1 envelope glycoproteins from the precursor state to the receptor-bound intermediate

  8. Induced quantum conformal gravity

    International Nuclear Information System (INIS)

    Novozhilov, Y.V.; Vassilevich, D.V.

    1988-11-01

    Quantum gravity is considered as induced by matter degrees of freedom and related to the symmetry breakdown in the low energy region of a non-Abelian gauge theory of fundamental fields. An effective action for quantum conformal gravity is derived where both the gravitational constant and conformal kinetic term are positive. Relation with induced classical gravity is established. (author). 15 refs

  9. Thickenings and conformal gravity

    Science.gov (United States)

    Lebrun, Claude

    1991-07-01

    A twistor correspondence is given for complex conformal space-times with vanishing Bach and Eastwood-Dighton tensors; when the Weyl curvature is algebraically general, these equations are precisely the conformal version of Einstein's vacuum equations with cosmological constant. This gives a fully curved version of the linearized correspondence of Baston and Mason [B-M].

  10. Thickenings and conformal gravity

    Energy Technology Data Exchange (ETDEWEB)

    LeBrun, C. (State Univ. of New York, Stony Brook, NY (USA). Dept. of Mathematics)

    1991-07-01

    A twistor correspondence is given for complex conformal space-times with vanishing Bach and Eastwood-Dighton tensors; when the Weyl curvature is algebraically general, these equations are precisely the conformal version of Einstein's vacuum equations with cosmological constant. This gives a fully curved version of the linearized correspondence of Baston and Mason (B-M). (orig.).

  11. Thickenings and conformal gravity

    International Nuclear Information System (INIS)

    LeBrun, C.

    1991-01-01

    A twistor correspondence is given for complex conformal space-times with vanishing Bach and Eastwood-Dighton tensors; when the Weyl curvature is algebraically general, these equations are precisely the conformal version of Einstein's vacuum equations with cosmological constant. This gives a fully curved version of the linearized correspondence of Baston and Mason [B-M]. (orig.)

  12. Conformal transformations in superspace

    International Nuclear Information System (INIS)

    Dao Vong Duc

    1977-01-01

    The spinor extension of the conformal algebra is investigated. The transformation law of superfields under the conformal coordinate inversion R defined in the superspace is derived. Using R-technique, the superconformally covariant two-point and three-point correlation functions are found

  13. 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....

  14. Conformity index: A review

    International Nuclear Information System (INIS)

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

    2006-01-01

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

  15. Conformal invariance in supergravity

    International Nuclear Information System (INIS)

    Bergshoeff, E.A.

    1983-01-01

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

  16. Stepwise expansion of the bacteriophage ϕ6 procapsid: possible packaging intermediates.

    Science.gov (United States)

    Nemecek, Daniel; Cheng, Naiqian; Qiao, Jian; Mindich, Leonard; Steven, Alasdair C; Heymann, J Bernard

    2011-11-25

    The initial assembly product of bacteriophage ϕ6, the procapsid, undergoes major structural transformation during the sequential packaging of its three segments of single-stranded RNA. The procapsid, a compact icosahedrally symmetric particle with deeply recessed vertices, expands to the spherical mature capsid, increasing the volume available to accommodate the genome by 2.5-fold. It has been proposed that expansion and packaging are linked, with each stage in expansion presenting a binding site for a particular RNA segment. To investigate procapsid transformability, we induced expansion by acidification, heating, and elevated salt concentration. Cryo-electron microscopy reconstructions after all three treatments yielded the same partially expanded particle. Analysis by cryo-electron tomography showed that all vertices of a given capsid were either in a compact or an expanded state, indicating a highly cooperative transition. To benchmark the mature capsid, we analyzed filled (in vivo packaged) capsids. When these particles were induced to release their RNA, they reverted to the same intermediate state as expanded procapsids (intermediate 1) or to a second, further expanded state (intermediate 2). This partial reversibility of expansion suggests that the mature spherical capsid conformation is obtained only when sufficient outward pressure is exerted by packaged RNA. The observation of two intermediates is consistent with the proposed three-step packaging process. The model is further supported by the observation that a mutant capable of packaging the second RNA segment without previously packaging the first segment has enhanced susceptibility for switching spontaneously from the procapsid to the first intermediate state. Published by Elsevier Ltd.

  17. Conformal expansions and renormalons

    Energy Technology Data Exchange (ETDEWEB)

    Rathsman, J.

    2000-02-07

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

  18. Hydrogen-deuterium exchange and mass spectrometry reveal the pH-dependent conformational changes of diphtheria toxin T domain.

    Science.gov (United States)

    Li, Jing; Rodnin, Mykola V; Ladokhin, Alexey S; Gross, Michael L

    2014-11-04

    The translocation (T) domain of diphtheria toxin plays a critical role in moving the catalytic domain across the endosomal membrane. Translocation/insertion is triggered by a decrease in pH in the endosome where conformational changes of T domain occur through several kinetic intermediates to yield a final trans-membrane form. High-resolution structural studies are only applicable to the static T-domain structure at physiological pH, and studies of the T-domain translocation pathway are hindered by the simultaneous presence of multiple conformations. Here, we report the application of hydrogen-deuterium exchange mass spectrometry (HDX-MS) for the study of the pH-dependent conformational changes of the T domain in solution. Effects of pH on intrinsic HDX rates were deconvolved by converting the on-exchange times at low pH into times under our "standard condition" (pH 7.5). pH-Dependent HDX kinetic analysis of T domain clearly reveals the conformational transition from the native state (W-state) to a membrane-competent state (W(+)-state). The initial transition occurs at pH 6 and includes the destabilization of N-terminal helices accompanied by the separation between N- and C-terminal segments. The structural rearrangements accompanying the formation of the membrane-competent state expose a hydrophobic hairpin (TH8-9) to solvent, prepare it to insert into the membrane. At pH 5.5, the transition is complete, and the protein further unfolds, resulting in the exposure of its C-terminal hydrophobic TH8-9, leading to subsequent aggregation in the absence of membranes. This solution-based study complements high resolution crystal structures and provides a detailed understanding of the pH-dependent structural rearrangement and acid-induced oligomerization of T domain.

  19. Hydrogen–Deuterium Exchange and Mass Spectrometry Reveal the pH-Dependent Conformational Changes of Diphtheria Toxin T Domain

    Science.gov (United States)

    2015-01-01

    The translocation (T) domain of diphtheria toxin plays a critical role in moving the catalytic domain across the endosomal membrane. Translocation/insertion is triggered by a decrease in pH in the endosome where conformational changes of T domain occur through several kinetic intermediates to yield a final trans-membrane form. High-resolution structural studies are only applicable to the static T-domain structure at physiological pH, and studies of the T-domain translocation pathway are hindered by the simultaneous presence of multiple conformations. Here, we report the application of hydrogen–deuterium exchange mass spectrometry (HDX-MS) for the study of the pH-dependent conformational changes of the T domain in solution. Effects of pH on intrinsic HDX rates were deconvolved by converting the on-exchange times at low pH into times under our “standard condition” (pH 7.5). pH-Dependent HDX kinetic analysis of T domain clearly reveals the conformational transition from the native state (W-state) to a membrane-competent state (W+-state). The initial transition occurs at pH 6 and includes the destabilization of N-terminal helices accompanied by the separation between N- and C-terminal segments. The structural rearrangements accompanying the formation of the membrane-competent state expose a hydrophobic hairpin (TH8–9) to solvent, prepare it to insert into the membrane. At pH 5.5, the transition is complete, and the protein further unfolds, resulting in the exposure of its C-terminal hydrophobic TH8–9, leading to subsequent aggregation in the absence of membranes. This solution-based study complements high resolution crystal structures and provides a detailed understanding of the pH-dependent structural rearrangement and acid-induced oligomerization of T domain. PMID:25290210

  20. Conformal sequestering simplified

    International Nuclear Information System (INIS)

    Schmaltz, Martin; Sundrum, Raman

    2006-01-01

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

  1. Conformally connected universes

    International Nuclear Information System (INIS)

    Cantor, M.; Piran, T.

    1983-01-01

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

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

    International Nuclear Information System (INIS)

    Alkalaev, Konstantin; Belavin, Vladimir

    2016-01-01

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

  3. an intermediate moisture meat

    African Journals Online (AJOL)

    STORAGESEVER

    2008-07-04

    Jul 4, 2008 ... traditional SM muscle without compromising quality. ... technique is intermediate moisture food processing. ... Traditionally, most tsire suya producers use ..... quality of Chinese purebred and European X Chinese crossbred ...

  4. Bacterial intermediate filaments

    DEFF Research Database (Denmark)

    Charbon, Godefroid; Cabeen, M.; Jacobs-Wagner, C.

    2009-01-01

    Crescentin, which is the founding member of a rapidly growing family of bacterial cytoskeletal proteins, was previously proposed to resemble eukaryotic intermediate filament (IF) proteins based on structural prediction and in vitro polymerization properties. Here, we demonstrate that crescentin...

  5. Mapping Intermediality in Performance

    NARCIS (Netherlands)

    2010-01-01

    Mapping Intermediality in Performance benadert het vraagstuk van intermedialiteit met betrekking tot performance (vooral theater) vanuit vijf verschillende invalshoeken: performativiteit en lichaam; tijd en ruimte; digitale cultuur en posthumanisme; netwerken; pedagogiek en praxis. In deze boeiende

  6. Intermediate algebra & analytic geometry

    CERN Document Server

    Gondin, William R

    1967-01-01

    Intermediate Algebra & Analytic Geometry Made Simple focuses on the principles, processes, calculations, and methodologies involved in intermediate algebra and analytic geometry. The publication first offers information on linear equations in two unknowns and variables, functions, and graphs. Discussions focus on graphic interpretations, explicit and implicit functions, first quadrant graphs, variables and functions, determinate and indeterminate systems, independent and dependent equations, and defective and redundant systems. The text then examines quadratic equations in one variable, system

  7. Control of the conformations of ion Coulomb crystals in a Penning trap

    Science.gov (United States)

    Mavadia, Sandeep; Goodwin, Joseph F.; Stutter, Graham; Bharadia, Shailen; Crick, Daniel R.; Segal, Daniel M.; Thompson, Richard C.

    2013-01-01

    Laser-cooled atomic ions form ordered structures in radiofrequency ion traps and in Penning traps. Here we demonstrate in a Penning trap the creation and manipulation of a wide variety of ion Coulomb crystals formed from small numbers of ions. The configuration can be changed from a linear string, through intermediate geometries, to a planar structure. The transition from a linear string to a zigzag geometry is observed for the first time in a Penning trap. The conformations of the crystals are set by the applied trap potential and the laser parameters, and agree with simulations. These simulations indicate that the rotation frequency of a small crystal is mainly determined by the laser parameters, independent of the number of ions and the axial confinement strength. This system has potential applications for quantum simulation, quantum information processing and tests of fundamental physics models from quantum field theory to cosmology. PMID:24096901

  8. Conformable variational iteration method

    Directory of Open Access Journals (Sweden)

    Omer Acan

    2017-02-01

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

  9. 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....

  10. Essential role of conformational selection in ligand binding.

    Science.gov (United States)

    Vogt, Austin D; Pozzi, Nicola; Chen, Zhiwei; Di Cera, Enrico

    2014-02-01

    Two competing and mutually exclusive mechanisms of ligand recognition - conformational selection and induced fit - have dominated our interpretation of ligand binding in biological macromolecules for almost six decades. Conformational selection posits the pre-existence of multiple conformations of the macromolecule from which the ligand selects the optimal one. Induced fit, on the other hand, postulates the existence of conformational rearrangements of the original conformation into an optimal one that are induced by binding of the ligand. In the former case, conformational transitions precede the binding event; in the latter, conformational changes follow the binding step. Kineticists have used a facile criterion to distinguish between the two mechanisms based on the dependence of the rate of relaxation to equilibrium, kobs, on the ligand concentration, [L]. A value of kobs decreasing hyperbolically with [L] has been seen as diagnostic of conformational selection, while a value of kobs increasing hyperbolically with [L] has been considered diagnostic of induced fit. However, this simple conclusion is only valid under the rather unrealistic assumption of conformational transitions being much slower than binding and dissociation events. In general, induced fit only produces values of kobs that increase with [L] but conformational selection is more versatile and is associated with values of kobs that increase with, decrease with or are independent of [L]. The richer repertoire of kinetic properties of conformational selection applies to kinetic mechanisms with single or multiple saturable relaxations and explains the behavior of nearly all experimental systems reported in the literature thus far. Conformational selection is always sufficient and often necessary to account for the relaxation kinetics of ligand binding to a biological macromolecule and is therefore an essential component of any binding mechanism. On the other hand, induced fit is never necessary and

  11. Glutamate Induced Thermal Equilibrium Intermediate and Counteracting Effect on Chemical Denaturation of Proteins.

    Science.gov (United States)

    Anumalla, Bramhini; Prabhu, N Prakash

    2018-01-25

    When organisms are subjected to stress conditions, one of their adaptive responses is accumulation of small organic molecules called osmolytes. These osmolytes affect the structure and stability of the biological macromolecules including proteins. The present study examines the effect of a negatively charged amino acid osmolyte, glutamate (Glu), on two model proteins, ribonuclease A (RNase A) and α-lactalbumin (α-LA), which have positive and negative surface charges at pH 7, respectively. These proteins follow two-state unfolding transitions during both heat and chemical induced denaturation processes. The addition of Glu stabilizes the proteins against temperature and induces an early equilibrium intermediate during unfolding. The stability is found to be enthalpy-driven, and the free energy of stabilization is more for α-LA compared to RNase A. The decrease in the partial molar volume and compressibility of both of the proteins in the presence of Glu suggests that the proteins attain a more compact state through surface hydration which could provide a more stable conformation. This is also supported by molecule dynamic simulation studies which demonstrate that the water density around the proteins is increased upon the addition of Glu. Further, the intermediates could be completely destabilized by lower concentrations (∼0.5 M) of guanidinium chloride and salt. However, urea subverts the Glu-induced intermediate formed by α-LA, whereas it only slightly destabilizes in the case of RNase A which has a positive surface charge and could possess charge-charge interactions with Glu. This suggests that, apart from hydration, columbic interactions might also contribute to the stability of the intermediate. Gdm-induced denaturation of RNase A and α-LA in the absence and the presence of Glu at different temperatures was carried out. These results also show the Glu-induced stabilization of both of the proteins; however, all of the unfolding transitions followed two

  12. Focused conformational sampling in proteins

    Science.gov (United States)

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

    2017-11-01

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

  13. Enhanced conformational sampling using enveloping distribution sampling.

    Science.gov (United States)

    Lin, Zhixiong; van Gunsteren, Wilfred F

    2013-10-14

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

  14. A new fundamental type of conformational isomerism

    Science.gov (United States)

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

    2018-06-01

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

  15. In vivo dose estimations through transit signal measured with thimble chamber positioned along the central axis at electronic portal imaging device level in medical linear accelerator in carcinoma of the middle-third esophagus patients undergoing three-dimensional conformal radiotherapy.

    Science.gov (United States)

    Kumar, Putha Suman; Banerjee, S; Arun Kumar, E S; Srinivas, Challapalli; Vadhiraja, B M; Saxena, P U; Ravichandran, Ramamoorthy; Kasturi, Dinesh Pai

    2018-01-01

    This study presents a method to estimate midplane dose (D iso, transit ) in vivo from transit signal (S t ) measured with thimble ionization chamber in cancer of the middle-third esophagus patients treated with three-dimensional radiotherapy (RT). This detector is positioned at the level of electronic portal imaging device in the gantry of a medical linear accelerator. Efficacy of inhomogeneity corrections of three dose calculation algorithms available in XiO treatment planning system (TPS) for planned dose (for open fields) (D iso, TPS ) was studied with three heterogeneous phantoms. D iso, transit represents measured signal at transit point (S t ) far away correlating to dose at isocenter. A locally fabricated thorax phantom was used to measure the in vivo midplane dose (D iso, mid ) which was also estimated through S t . Thirteen patients with carcinoma of the middle-third esophagus treated with three-dimensional conformal RT were studied. S t was recorded (three times, with a gap of 5-6 fractions during the treatment) to estimate D iso, transit , which was compared with the doses calculated by TPS. The dose predictions by superposition algorithm were superior compared to the other algorithms. Percentage deviation of D iso, transit , D iso, mid with D iso, TPS combined all fields was 2.7 and -2.6%, respectively, with the thorax phantom. The mean percentage deviation with standard deviation of estimated D iso, transit with D iso, TPS observed in patients was within standard deviation -0.73% ±2.09% (n = 39). Midplane dose estimates in vivo using this method provide accurate determination of delivered dose in the middle-third esophagus RT treatments. This method could be useful in similar clinical circumstances for dose confirmation and documentation.

  16. Conformity and statistical tolerancing

    Science.gov (United States)

    Leblond, Laurent; Pillet, Maurice

    2018-02-01

    Statistical tolerancing was first proposed by Shewhart (Economic Control of Quality of Manufactured Product, (1931) reprinted 1980 by ASQC), in spite of this long history, its use remains moderate. One of the probable reasons for this low utilization is undoubtedly the difficulty for designers to anticipate the risks of this approach. The arithmetic tolerance (worst case) allows a simple interpretation: conformity is defined by the presence of the characteristic in an interval. Statistical tolerancing is more complex in its definition. An interval is not sufficient to define the conformance. To justify the statistical tolerancing formula used by designers, a tolerance interval should be interpreted as the interval where most of the parts produced should probably be located. This tolerance is justified by considering a conformity criterion of the parts guaranteeing low offsets on the latter characteristics. Unlike traditional arithmetic tolerancing, statistical tolerancing requires a sustained exchange of information between design and manufacture to be used safely. This paper proposes a formal definition of the conformity, which we apply successively to the quadratic and arithmetic tolerancing. We introduce a concept of concavity, which helps us to demonstrate the link between tolerancing approach and conformity. We use this concept to demonstrate the various acceptable propositions of statistical tolerancing (in the space decentring, dispersion).

  17. Axiomatic conformal field theory

    International Nuclear Information System (INIS)

    Gaberdiel, M.R.; Goddard, P.

    2000-01-01

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

  18. Mechanistic Insights from the Crystal Structure of Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase Complexed with the Adenylate Intermediate.

    Science.gov (United States)

    Chen, Yaozong; Jiang, Yiping; Guo, Zhihong

    2016-12-06

    o-Succinylbenzoyl-CoA (OSB-CoA) synthetase, or MenE, catalyzes an essential step in vitamin K biosynthesis and is a valuable drug target. Like many other adenylating enzymes, it changes its structure to accommodate substrate binding, catalysis, and product release along the path of a domain alternation catalytic mechanism. We have determined the crystal structure of its complex with the adenylation product, o-succinylbenzoyl-adenosine monophosphate (OSB-AMP), and captured a new postadenylation state. This structure presents unique features such as a strained conformation for the bound adenylate intermediate to indicate that it represents the enzyme state after completion of the adenylation reaction but before release of the C domain in its transition to the thioesterification conformation. By comparison to the ATP-bound preadenylation conformation, structural changes are identified in both the reactants and the active site to allow inference about how these changes accommodate and facilitate the adenylation reaction and to directly support an in-line backside attack nucleophilic substitution mechanism for the first half-reaction. Mutational analysis suggests that the conserved His196 plays an important role in desolvation of the active site rather than stabilizing the transition state of the adenylation reaction. In addition, comparison of the new structure with a previously determined OSB-AMP-bound structure of the same enzyme allows us to propose a release mechanism of the C domain in its alteration to form the thioesterification conformation. These findings allow us to better understand the domain alternation catalytic mechanism of MenE as well as many other adenylating enzymes.

  19. [Therapy of intermediate uveitis].

    Science.gov (United States)

    Doycheva, D; Deuter, C; Zierhut, M

    2014-12-01

    Intermediate uveitis is a form of intraocular inflammation in which the vitreous body is the major site of inflammation. Intermediate uveitis is primarily treated medicinally and systemic corticosteroids are the mainstay of therapy. When recurrence of uveitis or side effects occur during corticosteroid therapy an immunosuppressive treatment is required. Cyclosporine A is the only immunosuppressive agent that is approved for therapy of uveitis in Germany; however, other immunosuppressive drugs have also been shown to be effective and well-tolerated in patients with intermediate uveitis. In severe therapy-refractory cases when conventional immunosuppressive therapy has failed, biologics can be used. In patients with unilateral uveitis or when the systemic therapy is contraindicated because of side effects, an intravitreal steroid treatment can be carried out. In certain cases a vitrectomy may be used.

  20. Mobile communication and intermediality

    DEFF Research Database (Denmark)

    Helles, Rasmus

    2013-01-01

    communicative affordances of mobile devices in order to understand how people choose between them for different purposes. It is argued that mobile communication makes intermediality especially central, as the choice of medium is detached from the location of stationary media and begins to follow the user across......The article argues the importance of intermediality as a concept for research in mobile communication and media. The constant availability of several, partially overlapping channels for communication (texting, calls, email, Facebook, etc.) requires that we adopt an integrated view of the various...

  1. Money distribution with intermediation

    OpenAIRE

    Teles, Caio Augusto Colnago

    2013-01-01

    This pap er analyzes the distribution of money holdings in a commo dity money search-based mo del with intermediation. Intro ducing heterogeneity of costs to the Kiyotaki e Wright ( 1989 ) mo del, Cavalcanti e Puzzello ( 2010) gives rise to a non-degenerated distribution of money. We extend further this mo del intro ducing intermediation in the trading pro cess. We show that the distribution of money matters for savings decisions. This gives rises to a xed p oint problem for the ...

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

    International Nuclear Information System (INIS)

    Croci, S.; Achterhold, K.; Ortalli, I.; Parak, F. G.

    2008-01-01

    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 (ΔG). 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.

  3. Conditions for the test emplacement of intermediate-level radioactive wastes in chamber 8a of the 511 m level of the Asse Salt Mine

    International Nuclear Information System (INIS)

    1984-01-01

    The Gesellschaft fuer Strahlen- und Umweltforschung mbH (GSF) emplaces intermediate-level radioactive wastes which accumulate in an activity involving the use of radioactive materials that is licensed or reported in the Federal Republic of Germany or which are stored on an interim basis by the appropriate licensing or inspection agencies in chamber 8a of the 511 m level of the Asse Salt Mine in Remlingen near Wolfenbuettel in conjunction with an engineering test program. The type and form of the intermediate-level wastes must conform to certain conditions so that there are no hazards to personnel and the repository during transfer and subsequent storage. It is therefore necessary for the radioactive wastes to be treated and packaged before delivery in such a way that they satisfy the conditions presented in this document. The GSF shall inform the companies and organizations delivering wastes about its experiences with emplacement operations. The Conditions for the Test Emplacement of Intermediate-Level Radioactive Wastes in Chamber 8a of the 511 m Level of the Asse Salt Mine must be adapted to conform to the latest state of science and the art. The GSF must therefore reserve the right to modify the conditions, allowing for an appropriate transition period

  4. Extended conformal algebras

    International Nuclear Information System (INIS)

    Goddard, Peter

    1990-01-01

    The algebra of the group of conformal transformations in two dimensions consists of two commuting copies of the Virasoro algebra. In many mathematical and physical contexts, the representations of ν which are relevant satisfy two conditions: they are unitary and they have the ''positive energy'' property that L o is bounded below. In an irreducible unitary representation the central element c takes a fixed real value. In physical contexts, the value of c is a characteristic of a theory. If c < 1, it turns out that the conformal algebra is sufficient to ''solve'' the theory, in the sense of relating the calculation of the infinite set of physically interesting quantities to a finite subset which can be handled in principle. For c ≥ 1, this is no longer the case for the algebra alone and one needs some sort of extended conformal algebra, such as the superconformal algebra. It is these algebras that this paper aims at addressing. (author)

  5. Algebraic conformal field theory

    International Nuclear Information System (INIS)

    Fuchs, J.; Nationaal Inst. voor Kernfysica en Hoge-Energiefysica

    1991-11-01

    Many conformal field theory features are special versions of structures which are present in arbitrary 2-dimensional quantum field theories. So it makes sense to describe 2-dimensional conformal field theories in context of algebraic theory of superselection sectors. While most of the results of the algebraic theory are rather abstract, conformal field theories offer the possibility to work out many formulae explicitly. In particular, one can construct the full algebra A-bar of global observables and the endomorphisms of A-bar which represent the superselection sectors. Some explicit results are presented for the level 1 so(N) WZW theories; the algebra A-bar is found to be the enveloping algebra of a Lie algebra L-bar which is an extension of the chiral symmetry algebra of the WZW theory. (author). 21 refs., 6 figs

  6. Killing tensors and conformal Killing tensors from conformal Killing vectors

    International Nuclear Information System (INIS)

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

    2003-01-01

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

  7. Can Morphing Methods Predict Intermediate Structures?

    Science.gov (United States)

    Weiss, Dahlia R.; Levitt, Michael

    2009-01-01

    Movement is crucial to the biological function of many proteins, yet crystallographic structures of proteins can give us only a static snapshot. The protein dynamics that are important to biological function often happen on a timescale that is unattainable through detailed simulation methods such as molecular dynamics as they often involve crossing high-energy barriers. To address this coarse-grained motion, several methods have been implemented as web servers in which a set of coordinates is usually linearly interpolated from an initial crystallographic structure to a final crystallographic structure. We present a new morphing method that does not extrapolate linearly and can therefore go around high-energy barriers and which can produce different trajectories between the same two starting points. In this work, we evaluate our method and other established coarse-grained methods according to an objective measure: how close a coarse-grained dynamics method comes to a crystallographically determined intermediate structure when calculating a trajectory between the initial and final crystal protein structure. We test this with a set of five proteins with at least three crystallographically determined on-pathway high-resolution intermediate structures from the Protein Data Bank. For simple hinging motions involving a small conformational change, segmentation of the protein into two rigid sections outperforms other more computationally involved methods. However, large-scale conformational change is best addressed using a nonlinear approach and we suggest that there is merit in further developing such methods. PMID:18996395

  8. Molecular dynamics studies of the conformation of sorbitol

    Science.gov (United States)

    Lerbret, A.; Mason, P.E.; Venable, R.M.; Cesàro, A.; Saboungi, M.-L.; Pastor, R.W.; Brady, J.W.

    2009-01-01

    Molecular dynamics simulations of a 3 m aqueous solution of D-sorbitol (also called D-glucitol) have been performed at 300 K, as well as at two elevated temperatures to promote conformational transitions. In principle, sorbitol is more flexible than glucose since it does not contain a constraining ring. However, a conformational analysis revealed that the sorbitol chain remains extended in solution, in contrast to the bent conformation found experimentally in the crystalline form. While there are 243 staggered conformations of the backbone possible for this open-chain polyol, only a very limited number were found to be stable in the simulations. Although many conformers were briefly sampled, only eight were significantly populated in the simulation. The carbon backbones of all but two of these eight conformers were completely extended, unlike the bent crystal conformation. These extended conformers were stabilized by a quite persistent intramolecular hydrogen bond between the hydroxyl groups of carbon C-2 and C-4. The conformational populations were found to be in good agreement with the limited available NMR data except for the C-2–C-3 torsion (spanned by the O-2–O-4 hydrogen bond), where the NMR data supports a more bent structure. PMID:19744646

  9. Massive Conformal Gravity

    International Nuclear Information System (INIS)

    Faria, F. F.

    2014-01-01

    We construct a massive theory of gravity that is invariant under conformal transformations. The massive action of the theory depends on the metric tensor and a scalar field, which are considered the only field variables. We find the vacuum field equations of the theory and analyze its weak-field approximation and Newtonian limit.

  10. Taming the conformal zoo

    International Nuclear Information System (INIS)

    Moore, G.; Seiberg, N.

    1989-01-01

    All known rational conformal field theories may be obtained from (2+1)-dimensional Chern-Simons gauge theories by appropriate choice of gauge group. We conjecture that all rational field theories are classified by groups via (2+1)-dimensional Chern-Simons gauge theories. (orig.)

  11. Conformal special relativity

    International Nuclear Information System (INIS)

    Maia, M.D.

    2006-01-01

    It is shown that the information loss/recovery theorem based on the ADS/CFT correspondence is not consistent with the stability of the Schwarzschild or Reissner-Nordstrom black holes. Nonetheless, the conformal invariance of Yang-Mills theory points to new relativity principle compatible with quantum unitarity near those black holes

  12. 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. Copyright © 2012 Elsevier Ltd. All rights reserved.

  13. Parafermionic conformal field theory

    International Nuclear Information System (INIS)

    Kurak, V.

    1989-09-01

    Conformal parafermionic field theories are reviewed with emphasis on the computation of their OPE estructure constants. It is presented a simple computational of these for the Z(N) parafermions, unveilling their Lie algebra content. (A.C.A.S.) [pt

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

    Science.gov (United States)

    Sullivan, David C; Lim, Carmay

    2006-08-24

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

  15. 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

  16. The Intermediate Neutrino Program

    CERN Document Server

    Adams, C.; Ankowski, A.M.; Asaadi, J.A.; Ashenfelter, J.; Axani, S.N.; Babu, K.; Backhouse, C.; Band, H.R.; Barbeau, P.S.; Barros, N.; Bernstein, A.; Betancourt, M.; Bishai, M.; Blucher, E.; Bouffard, J.; Bowden, N.; Brice, S.; Bryan, C.; Camilleri, L.; Cao, J.; Carlson, J.; Carr, R.E.; Chatterjee, A.; Chen, M.; Chen, S.; Chiu, M.; Church, E.D.; Collar, J.I.; Collin, G.; Conrad, J.M.; Convery, M.R.; Cooper, R.L.; Cowen, D.; Davoudiasl, H.; de Gouvea, A.; Dean, D.J.; Deichert, G.; Descamps, F.; DeYoung, T.; Diwan, M.V.; Djurcic, Z.; Dolinski, M.J.; Dolph, J.; Donnelly, B.; Dwyer, D.A.; Dytman, S.; Efremenko, Y.; Everett, L.L.; Fava, A.; Figueroa-Feliciano, E.; Fleming, B.; Friedland, A.; Fujikawa, B.K.; Gaisser, T.K.; Galeazzi, M.; Galehouse, D.C.; Galindo-Uribarri, A.; Garvey, G.T.; Gautam, S.; Gilje, K.E.; Gonzalez-Garcia, M.; Goodman, M.C.; Gordon, H.; Gramellini, E.; Green, M.P.; Guglielmi, A.; Hackenburg, R.W.; Hackenburg, A.; Halzen, F.; Han, K.; Hans, S.; Harris, D.; Heeger, K.M.; Herman, M.; Hill, R.; Holin, A.; Huber, P.; Jaffe, D.E.; Johnson, R.A.; Joshi, J.; Karagiorgi, G.; Kaufman, L.J.; Kayser, B.; Kettell, S.H.; Kirby, B.J.; Klein, J.R.; Kolomensky, Yu. G.; Kriske, R.M.; Lane, C.E.; Langford, T.J.; Lankford, A.; Lau, K.; Learned, J.G.; Ling, J.; Link, J.M.; Lissauer, D.; Littenberg, L.; Littlejohn, B.R.; Lockwitz, S.; Lokajicek, M.; Louis, W.C.; Luk, K.; Lykken, J.; Marciano, W.J.; Maricic, J.; Markoff, D.M.; Martinez Caicedo, D.A.; Mauger, C.; Mavrokoridis, K.; McCluskey, E.; McKeen, D.; McKeown, R.; Mills, G.; Mocioiu, I.; Monreal, B.; Mooney, M.R.; Morfin, J.G.; Mumm, P.; Napolitano, J.; Neilson, R.; Nelson, J.K.; Nessi, M.; Norcini, D.; Nova, F.; Nygren, D.R.; Orebi Gann, G.D.; Palamara, O.; Parsa, Z.; Patterson, R.; Paul, P.; Pocar, A.; Qian, X.; Raaf, J.L.; Rameika, R.; Ranucci, G.; Ray, H.; Reyna, D.; Rich, G.C.; Rodrigues, P.; Romero, E.Romero; Rosero, R.; Rountree, S.D.; Rybolt, B.; Sanchez, M.C.; Santucci, G.; Schmitz, D.; Scholberg, K.; Seckel, D.; Shaevitz, M.; Shrock, R.; Smy, M.B.; Soderberg, M.; Sonzogni, A.; Sousa, A.B.; Spitz, J.; St. John, J.M.; Stewart, J.; Strait, J.B.; Sullivan, G.; Svoboda, R.; Szelc, A.M.; Tayloe, R.; Thomson, M.A.; Toups, M.; Vacheret, A.; Vagins, M.; Van de Water, R.G.; Vogelaar, R.B.; Weber, M.; Weng, W.; Wetstein, M.; White, C.; White, B.R.; Whitehead, L.; Whittington, D.W.; Wilking, M.J.; Wilson, R.J.; Wilson, P.; Winklehner, D.; Winn, D.R.; Worcester, E.; Yang, L.; Yeh, M.; Yokley, Z.W.; Yoo, J.; Yu, B.; Yu, J.; Zhang, C.

    2015-01-01

    The US neutrino community gathered at the Workshop on the Intermediate Neutrino Program (WINP) at Brookhaven National Laboratory February 4-6, 2015 to explore opportunities in neutrino physics over the next five to ten years. Scientists from particle, astroparticle and nuclear physics participated in the workshop. The workshop examined promising opportunities for neutrino physics in the intermediate term, including possible new small to mid-scale experiments, US contributions to large experiments, upgrades to existing experiments, R&D plans and theory. The workshop was organized into two sets of parallel working group sessions, divided by physics topics and technology. Physics working groups covered topics on Sterile Neutrinos, Neutrino Mixing, Neutrino Interactions, Neutrino Properties and Astrophysical Neutrinos. Technology sessions were organized into Theory, Short-Baseline Accelerator Neutrinos, Reactor Neutrinos, Detector R&D and Source, Cyclotron and Meson Decay at Rest sessions.This report summ...

  17. The Intermediate Neutrino Program

    Energy Technology Data Exchange (ETDEWEB)

    Adams, C.; et al.

    2015-03-23

    The US neutrino community gathered at the Workshop on the Intermediate Neutrino Program (WINP) at Brookhaven National Laboratory February 4-6, 2015 to explore opportunities in neutrino physics over the next five to ten years. Scientists from particle, astroparticle and nuclear physics participated in the workshop. The workshop examined promising opportunities for neutrino physics in the intermediate term, including possible new small to mid-scale experiments, US contributions to large experiments, upgrades to existing experiments, R&D plans and theory. The workshop was organized into two sets of parallel working group sessions, divided by physics topics and technology. Physics working groups covered topics on Sterile Neutrinos, Neutrino Mixing, Neutrino Interactions, Neutrino Properties and Astrophysical Neutrinos. Technology sessions were organized into Theory, Short-Baseline Accelerator Neutrinos, Reactor Neutrinos, Detector R&D and Source, Cyclotron and Meson Decay at Rest sessions.This report summarizes discussion and conclusions from the workshop.

  18. The Intermediate Neutrino Program

    Energy Technology Data Exchange (ETDEWEB)

    Adams, C. [Yale Univ., New Haven, CT (United States); Alonso, J. R. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Ankowski, A. M. [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Asaadi, J. A. [Syracuse Univ., NY (United States); Ashenfelter, J. [Yale Univ., New Haven, CT (United States); Axani, S. N. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Babu, K [Oklahoma State Univ., Stillwater, OK (United States); Backhouse, C. [California Inst. of Technology (CalTech), Pasadena, CA (United States); Band, H. R. [Yale Univ., New Haven, CT (United States); Barbeau, P. S. [Duke Univ., Durham, NC (United States); Barros, N. [Univ. of Pennsylvania, Philadelphia, PA (United States); Bernstein, A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Betancourt, M. [Illinois Inst. of Technology, Chicago, IL (United States); Bishai, M. [Brookhaven National Lab. (BNL), Upton, NY (United States); Blucher, E. [Univ. of Chicago, IL (United States); Bouffard, J. [State Univ. of New York (SUNY), Albany, NY (United States); Bowden, N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Brice, S. [Illinois Inst. of Technology, Chicago, IL (United States); Bryan, C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Camilleri, L. [Columbia Univ., New York, NY (United States); Cao, J. [Inst. of High Energy Physics, Beijing (China); Carlson, J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Carr, R. E. [Columbia Univ., New York, NY (United States); Chatterjee, A. [Univ. of Texas, Arlington, TX (United States); Chen, M. [Univ. of California, Irvine, CA (United States); Chen, S. [Tsinghua Univ., Beijing (China); Chiu, M. [Brookhaven National Lab. (BNL), Upton, NY (United States); Church, E. D. [Illinois Inst. of Technology, Chicago, IL (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Collar, J. I. [Univ. of Chicago, IL (United States); Collin, G. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Conrad, J. M. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Convery, M. R. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Cooper, R. L. [Indiana Univ., Bloomington, IN (United States); Cowen, D. [Pennsylvania State Univ., University Park, PA (United States); Davoudiasl, H. [Brookhaven National Lab. (BNL), Upton, NY (United States); Gouvea, A. D. [Northwestern Univ., Evanston, IL (United States); Dean, D. J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Deichert, G. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Descamps, F. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); DeYoung, T. [Michigan State Univ., East Lansing, MI (United States); Diwan, M. V. [Brookhaven National Lab. (BNL), Upton, NY (United States); Djurcic, Z. [Argonne National Lab. (ANL), Argonne, IL (United States); Dolinski, M. J. [Drexel Univ., Philadelphia, PA (United States); Dolph, J. [Brookhaven National Lab. (BNL), Upton, NY (United States); Donnelly, B. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Dwyer, D. A. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Dytman, S. [Univ. of Pittsburgh, PA (United States); Efremenko, Y. [Univ. of Tennessee, Knoxville, TN (United States); Everett, L. L. [Univ. of Wisconsin, Madison, WI (United States); Fava, A. [University of Padua, Padova (Italy); Figueroa-Feliciano, E. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Fleming, B. [Yale Univ., New Haven, CT (United States); Friedland, A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Fujikawa, B. K. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Gaisser, T. K. [Univ. of Delaware, Newark, DE (United States); Galeazzi, M. [Univ. of Miami, FL (United States); Galehouse, DC [Univ. of Akron, OH (United States); Galindo-Uribarri, A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Garvey, G. T. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Gautam, S. [Tribhuvan Univ., Kirtipur (Nepal); Gilje, K. E. [Illinois Inst. of Technology, Chicago, IL (United States); Gonzalez-Garcia, M. [Stony Brook Univ., NY (United States); Goodman, M. C. [Argonne National Lab. (ANL), Argonne, IL (United States); Gordon, H. [Brookhaven National Lab. (BNL), Upton, NY (United States); Gramellini, E. [Yale Univ., New Haven, CT (United States); Green, M. P. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Guglielmi, A. [University of Padua, Padova (Italy); Hackenburg, R. W. [Brookhaven National Lab. (BNL), Upton, NY (United States); Hackenburg, A. [Yale Univ., New Haven, CT (United States); Halzen, F. [Univ. of Wisconsin, Madison, WI (United States); Han, K. [Yale Univ., New Haven, CT (United States); Hans, S. [Brookhaven National Lab. (BNL), Upton, NY (United States); Harris, D. [Illinois Inst. of Technology, Chicago, IL (United States); Heeger, K. M. [Yale Univ., New Haven, CT (United States); Herman, M. [Brookhaven National Lab. (BNL), Upton, NY (United States); Hill, R. [Univ. of Chicago, IL (United States); Holin, A. [Univ. College London, Bloomsbury (United Kingdom); Huber, P. [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Jaffe, D. E. [Brookhaven National Lab. (BNL), Upton, NY (United States); Johnson, R. A. [Univ. of Cincinnati, OH (United States); Joshi, J. [Brookhaven National Lab. (BNL), Upton, NY (United States); Karagiorgi, G. [Univ. of Manchester (United Kingdom); Kaufman, L. J. [Indiana Univ., Bloomington, IN (United States); Kayser, B. [Illinois Inst. of Technology, Chicago, IL (United States); Kettell, S. H. [Brookhaven National Lab. (BNL), Upton, NY (United States); Kirby, B. J. [Brookhaven National Lab. (BNL), Upton, NY (United States); Klein, J. R. [Univ. of Texas, Arlington, TX (United States); Kolomensky, Y. G. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States); Kriske, R. M. [Univ. of Minnesota, Minneapolis, MN (United States); Lane, C. E. [Drexel Univ., Philadelphia, PA (United States); Langford, T. J. [Yale Univ., New Haven, CT (United States); Lankford, A. [Univ. of California, Irvine, CA (United States); Lau, K. [Univ. of Houston, TX (United States); Learned, J. G. [Univ. of Hawaii, Honolulu, HI (United States); Ling, J. [Univ. of Illinois, Urbana-Champaign, IL (United States); Link, J. M. [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Lissauer, D. [Brookhaven National Lab. (BNL), Upton, NY (United States); Littenberg, L. [Brookhaven National Lab. (BNL), Upton, NY (United States); Littlejohn, B. R. [Illinois Inst. of Technology, Chicago, IL (United States); Lockwitz, S. [Illinois Inst. of Technology, Chicago, IL (United States); Lokajicek, M. [Inst. of Physics of the Academy of Sciences of Czech Republic, Prague (Czech Republic); Louis, W. C. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Luk, K. [Univ. of California, Berkeley, CA (United States); Lykken, J. [Illinois Inst. of Technology, Chicago, IL (United States); Marciano, W. J. [Brookhaven National Lab. (BNL), Upton, NY (United States); Maricic, J. [Univ. of Hawaii, Honolulu, HI (United States); Markoff, D. M. [North Carolina Central Univ., Durham, NC (United States); Caicedo, D. A. M. [Illinois Inst. of Technology, Chicago, IL (United States); Mauger, C. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Mavrokoridis, K. [Univ. of Liverpool (United Kingdom); McCluskey, E. [Illinois Inst. of Technology, Chicago, IL (United States); McKeen, D. [Univ. of Washington, Seattle, WA (United States); McKeown, R. [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States); Mills, G. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Mocioiu, I. [Pennsylvania State Univ., University Park, PA (United States); Monreal, B. [Univ. of California, Santa Barbara, CA (United States); Mooney, M. R. [Brookhaven National Lab. (BNL), Upton, NY (United States); Morfin, J. G. [Illinois Inst. of Technology, Chicago, IL (United States); Mumm, P. [National Inst. of Standards and Technology (NIST), Boulder, CO (United States); Napolitano, J. [Temple Univ., Philadelphia, PA (United States); Neilson, R. [Drexel Univ., Philadelphia, PA (United States); Nelson, J. K. [College of William and Mary, Williamsburg, VA (United States); Nessi, M. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Norcini, D. [Yale Univ., New Haven, CT (United States); Nova, F. [Univ. of Texas, Austin, TX (United States); Nygren, D. R. [Univ. of Texas, Arlington, TX (United States); Gann, GDO [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States); Palamara, O. [Illinois Inst. of Technology, Chicago, IL (United States); Parsa, Z. [Brookhaven National Lab. (BNL), Upton, NY (United States); Patterson, R. [California Inst. of Technology (CalTech), Pasadena, CA (United States); Paul, P. [Stony Brook Univ., NY (United States); Pocar, A. [Univ. of Massachusetts, Amherst, MA (United States); Qian, X. [Brookhaven National Lab. (BNL), Upton, NY (United States); Raaf, J. L. [Illinois Inst. of Technology, Chicago, IL (United States); Rameika, R. [Illinois Inst. of Technology, Chicago, IL (United States); Ranucci, G. [National Inst. of Nuclear Physics, Milano (Italy); Ray, H. [Univ. of Florida, Gainesville, FL (United States); Reyna, D. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Rich, G. C. [Triangle Universities Nuclear Lab., Durham, NC (United States); Rodrigues, P. [Univ. of Rochester, NY (United States); Romero, E. R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States); Rosero, R. [Brookhaven National Lab. (BNL), Upton, NY (United States); Rountree, S. D. [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Rybolt, B. [Univ. of Tennessee, Knoxville, TN (United States); Sanchez, M. C. [Iowa State Univ., Ames, IA (United States); Santucci, G. [Stony Brook Univ., NY (United States); Schmitz, D. [Univ. of Chicago, IL (United States); Scholberg, K. [Duke Univ., Durham, NC (United States); Seckel, D. [Univ. of Delaware, Newark, DE (United States); Shaevitz, M. [Columbia Univ., New York, NY (United States); Shrock, R. [Stony Brook Univ., NY (United States); Smy, M. B. [Univ. of California, Irvine, CA (United States); Soderberg, M. [Syracuse Univ., NY (United States); Sonzogni, A. [Brookhaven National Lab. (BNL), Upton, NY (United States); Sousa, A. B. [Univ. of Cincinnati, OH (United States); Spitz, J. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); John, J. M. S. [Univ. of Cincinnati, OH (United States); Stewart, J. [Brookhaven National Lab. (BNL), Upton, NY (United States); Strait, J. B. [Illinois Inst. of Technology, Chicago, IL (United States); Sullivan, G. [Univ. of Maryland, College Park, MD (United States); Svoboda, R. [Univ. of California, Davis, CA (United States); Szelc, A. M. [Yale Univ., New Haven, CT (United States); Tayloe, R. [Indiana Univ., Bloomington, IN (United States); Thomson, M. A. [Univ. of Cambridge (United Kingdom); Toups, M. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Vacheret, A. [Univ. of Oxford (United Kingdom); Vagins, M. [Univ. of California, Irvine, CA (United States); Water, R. G. V. D. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Vogelaar, R. B. [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Weber, M. [Bern (Switzerland); Weng, W. [Brookhaven National Lab. (BNL), Upton, NY (United States); Wetstein, M. [Univ. of Chicago, IL (United States); White, C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); White, B. R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Whitehead, L. [Univ. of Houston, TX (United States); Whittington, D. W. [Indiana Univ., Bloomington, IN (United States); Wilking, M. J. [Stony Brook Univ., NY (United States); Wilson, R. J. [Colorado State Univ., Fort Collins, CO (United States); Wilson, P. [Illinois Inst. of Technology, Chicago, IL (United States); Winklehner, D. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Winn, D. R. [Fairfield Univ., CT (United States); Worcester, E. [Brookhaven National Lab. (BNL), Upton, NY (United States); Yang, L. [Univ. of Illinois, Urbana-Champaign, IL (United States); Yeh, M [Brookhaven National Lab. (BNL), Upton, NY (United States); Yokley, Z. W. [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Yoo, J. [Illinois Inst. of Technology, Chicago, IL (United States); Yu, B. [Brookhaven National Lab. (BNL), Upton, NY (United States); Yu, J. [Univ. of Texas, Arlington, TX (United States); Zhang, C. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2017-04-03

    The US neutrino community gathered at the Workshop on the Intermediate Neutrino Program (WINP) at Brookhaven National Laboratory February 4-6, 2015 to explore opportunities in neutrino physics over the next five to ten years. Scientists from particle, astroparticle and nuclear physics participated in the workshop. The workshop examined promising opportunities for neutrino physics in the intermediate term, including possible new small to mid-scale experiments, US contributions to large experiments, upgrades to existing experiments, R&D plans and theory. The workshop was organized into two sets of parallel working group sessions, divided by physics topics and technology. Physics working groups covered topics on Sterile Neutrinos, Neutrino Mixing, Neutrino Interactions, Neutrino Properties and Astrophysical Neutrinos. Technology sessions were organized into Theory, Short-Baseline Accelerator Neutrinos, Reactor Neutrinos, Detector R&D and Source, Cyclotron and Meson Decay at Rest sessions.This report summarizes discussion and conclusions from the workshop.

  19. Intermediate energy data

    International Nuclear Information System (INIS)

    Koning, A.J.; Fukahori, T.; Hasegawa, A.

    1998-01-01

    Subgroup 13 (SG13) on Intermediate Energy Nuclear data was formed by NEA Nuclear Science Committee to solve common problems of these types of data for nuclear applications. An overview is presented in this final report of the present activities of SG13, including data needs, high-priority nuclear data request list (nuclides), compilation of experimental data, specialists meetings and benchmarks, data formats and data libraries. Some important accomplishments are summarized, and recommendations are presented. (R.P.)

  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. 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.

  2. Hot Conformal Gauge Theories

    DEFF Research Database (Denmark)

    Mojaza, Matin; Pica, Claudio; Sannino, Francesco

    2010-01-01

    of flavors. Surprisingly this number, if computed to the order g^2, agrees with previous predictions for the lower boundary of the conformal window for nonsupersymmetric gauge theories. The higher order results tend to predict a higher number of critical flavors. These are universal properties, i......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...

  3. 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. © 2016 Wiley Periodicals, Inc.

  4. 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.

  5. Conformal description of spinning particles

    International Nuclear Information System (INIS)

    Todorov, I.T.

    1986-01-01

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

  6. 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....

  7. Conformal radiotherapy: a glossary

    International Nuclear Information System (INIS)

    Dubray, B.; Giraud, P.; Beaudre, A.

    1999-01-01

    Most of the concepts and terms related to conformal radiotherapy were produced by English-speaking authors and eventually validated by international groups of experts, whose working language was also English. Therefore, a significant part of this literature is poorly accessible to the French-speaking radiation oncology community. The present paper gathers the 'official' definitions already published in French, along with propositions for the remaining terms which should be submitted to a more formal and representative validation process. (author)

  8. Normal mode-guided transition pathway generation in proteins.

    Directory of Open Access Journals (Sweden)

    Byung Ho Lee

    Full Text Available The biological function of proteins is closely related to its structural motion. For instance, structurally misfolded proteins do not function properly. Although we are able to experimentally obtain structural information on proteins, it is still challenging to capture their dynamics, such as transition processes. Therefore, we need a simulation method to predict the transition pathways of a protein in order to understand and study large functional deformations. Here, we present a new simulation method called normal mode-guided elastic network interpolation (NGENI that performs normal modes analysis iteratively to predict transition pathways of proteins. To be more specific, NGENI obtains displacement vectors that determine intermediate structures by interpolating the distance between two end-point conformations, similar to a morphing method called elastic network interpolation. However, the displacement vector is regarded as a linear combination of the normal mode vectors of each intermediate structure, in order to enhance the physical sense of the proposed pathways. As a result, we can generate more reasonable transition pathways geometrically and thermodynamically. By using not only all normal modes, but also in part using only the lowest normal modes, NGENI can still generate reasonable pathways for large deformations in proteins. This study shows that global protein transitions are dominated by collective motion, which means that a few lowest normal modes play an important role in this process. NGENI has considerable merit in terms of computational cost because it is possible to generate transition pathways by partial degrees of freedom, while conventional methods are not capable of this.

  9. 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.

  10. Perspective: Spectroscopy and kinetics of small gaseous Criegee intermediates

    International Nuclear Information System (INIS)

    Lee, Yuan-Pern

    2015-01-01

    The Criegee intermediates, carbonyl oxides proposed by Criegee in 1949 as key intermediates in the ozonolysis of alkenes, play important roles in many aspects of atmospheric chemistry. Because direct detection of these gaseous intermediates was unavailable until recently, previous understanding of their reactions, derived from indirect experimental evidence, had great uncertainties. Recent laboratory detection of the simplest Criegee intermediate CH 2 OO and some larger members, produced from ultraviolet irradiation of corresponding diiodoalkanes in O 2 , with various methods such as photoionization, ultraviolet absorption, infrared absorption, and microwave spectroscopy opens a new door to improved understanding of the roles of these Criegee intermediates. Their structures and spectral parameters have been characterized; their significant zwitterionic nature is hence confirmed. CH 2 OO, along with other products, has also been detected directly with microwave spectroscopy in gaseous ozonolysis reactions of ethene. The detailed kinetics of the source reaction, CH 2 I + O 2 , which is critical to laboratory studies of CH 2 OO, are now understood satisfactorily. The kinetic investigations using direct detection identified some important atmospheric reactions, including reactions with NO 2 , SO 2 , water dimer, carboxylic acids, and carbonyl compounds. Efforts toward the characterization of larger Criegee intermediates and the investigation of related reactions are in progress. Some reactions of CH 3 CHOO are found to depend on conformation. This perspective examines progress toward the direct spectral characterization of Criegee intermediates and investigations of the associated reaction kinetics, and indicates some unresolved problems and prospective challenges for this exciting field of research

  11. The intermediate state in Patd

    African Journals Online (AJOL)

    ) Jesus had assumed. (concerning the 'intermediate state') as existing, anything which does not exist. Three basic things about the intermediate state emerge from the parable: (a) Jesus recognizes that at the moment of death, in ipso articulo.

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

    Science.gov (United States)

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

    2018-01-01

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

  13. Cooperative structural transitions in amyloid-like aggregation

    Science.gov (United States)

    Steckmann, Timothy; Bhandari, Yuba R.; Chapagain, Prem P.; Gerstman, Bernard S.

    2017-04-01

    Amyloid fibril aggregation is associated with several horrific diseases such as Alzheimer's, Creutzfeld-Jacob, diabetes, Parkinson's, and others. Although proteins that undergo aggregation vary widely in their primary structure, they all produce a cross-β motif with the proteins in β-strand conformations perpendicular to the fibril axis. The process of amyloid aggregation involves forming myriad different metastable intermediate aggregates. To better understand the molecular basis of the protein structural transitions and aggregation, we report on molecular dynamics (MD) computational studies on the formation of amyloid protofibrillar structures in the small model protein ccβ, which undergoes many of the structural transitions of the larger, naturally occurring amyloid forming proteins. Two different structural transition processes involving hydrogen bonds are observed for aggregation into fibrils: the breaking of intrachain hydrogen bonds to allow β-hairpin proteins to straighten, and the subsequent formation of interchain H-bonds during aggregation into amyloid fibrils. For our MD simulations, we found that the temperature dependence of these two different structural transition processes results in the existence of a temperature window that the ccβ protein experiences during the process of forming protofibrillar structures. This temperature dependence allows us to investigate the dynamics on a molecular level. We report on the thermodynamics and cooperativity of the transformations. The structural transitions that occurred in a specific temperature window for ccβ in our investigations may also occur in other amyloid forming proteins but with biochemical parameters controlling the dynamics rather than temperature.

  14. [Intermediate energy nuclear physics

    International Nuclear Information System (INIS)

    1989-01-01

    This report summarizes work in experimental Intermediate Energy Nuclear Physics carried out between October 1, 1988 and October 1, 1989 at the Nuclear Physics Laboratory of the University of Colorado, Boulder, under grant DE-FG02-86ER-40269 with the United States Department of Energy. The experimental program is very broadly based, including pion-nucleon studies at TRIUMF, inelastic pion scattering and charge exchange reactions at LAMPF, and nucleon charge exchange at LAMPF/WNR. In addition, a number of other topics related to accelerator physics are described in this report

  15. Atomic cranks and levers control sugar ring conformations

    International Nuclear Information System (INIS)

    Zhang Qingmin; Lee, Gwangrog; Marszalek, Piotr E

    2005-01-01

    In this paper we review the conformational analysis of sugar rings placed under tension during mechanical manipulations of single polysaccharide molecules with the atomic force microscope and during steered molecular dynamics simulations. We examine the role of various chemical bonds and linkages between sugar rings in inhibiting or promoting their conformational transitions by means of external forces. Small differences in the orientation of one chemical bond on the sugar ring can produce significantly different mechanical properties at the polymer level as exemplified by two polysaccharides: cellulose, composed of β-1→4-linked D-glucose, and amylose, composed of α-1→4-linked D-glucose. In contrast to β-glucose rings, which are mechanically stable and produce simple entropic elasticity of the chain, α-glucose rings flip under tension from their chair to a boat-like structure and these transitions produce deviations of amylose elasticity from the freely jointed chain model. We also examine the deformation of two mechanically complementary 1→6-linked polysaccharides: pustulan, a β-1→6-linked glucan, and dextran, a α-1→6-linked glucan. Forced rotations about the C 5 -C 6 bonds govern the elasticity of pustulan, and complex conformational transitions that involve simultaneous C 5 -C 6 rotations and chair-boat transitions govern the elasticity of dextran. Finally, we discuss the likelihood of various conformational transitions in sugar rings in biological settings and speculate on their significance

  16. Experiments in intermediate energy physics

    International Nuclear Information System (INIS)

    Dehnhard, D.

    2003-01-01

    Research in experimental nuclear physics was done from 1979 to 2002 primarily at intermediate energy facilities that provide pion, proton, and kaon beams. Particularly successful has been the work at the Los Alamos Meson Physics Facility (LAMPF) on unraveling the neutron and proton contributions to nuclear ground state and transition densities. This work was done on a wide variety of nuclei and with great detail on the carbon, oxygen, and helium isotopes. Some of the investigations involved the use of polarized targets which allowed the extraction of information on the spin-dependent part of the triangle-nucleon interaction. At the Indiana University Cyclotron Facility (IUCF) we studied proton-induced charge exchange reactions with results of importance to astrophysics and the nuclear few-body problem. During the first few years, the analysis of heavy-ion nucleus scattering data that had been taken prior to 1979 was completed. During the last few years we created hypernuclei by use of a kaon beam at Brookhaven National Laboratory (BNL) and an electron beam at Jefferson Laboratory (JLab). The data taken at BNL for a study of the non-mesonic weak decay of the A particle in a nucleus are still under analysis by our collaborators. The work at JLab resulted in the best resolution hypernuclear spectra measured thus far with magnetic spectrometers

  17. Experiments in intermediate energy physics

    Energy Technology Data Exchange (ETDEWEB)

    Dehnhard, D.

    2003-02-28

    Research in experimental nuclear physics was done from 1979 to 2002 primarily at intermediate energy facilities that provide pion, proton, and kaon beams. Particularly successful has been the work at the Los Alamos Meson Physics Facility (LAMPF) on unraveling the neutron and proton contributions to nuclear ground state and transition densities. This work was done on a wide variety of nuclei and with great detail on the carbon, oxygen, and helium isotopes. Some of the investigations involved the use of polarized targets which allowed the extraction of information on the spin-dependent part of the triangle-nucleon interaction. At the Indiana University Cyclotron Facility (IUCF) we studied proton-induced charge exchange reactions with results of importance to astrophysics and the nuclear few-body problem. During the first few years, the analysis of heavy-ion nucleus scattering data that had been taken prior to 1979 was completed. During the last few years we created hypernuclei by use of a kaon beam at Brookhaven National Laboratory (BNL) and an electron beam at Jefferson Laboratory (JLab). The data taken at BNL for a study of the non-mesonic weak decay of the A particle in a nucleus are still under analysis by our collaborators. The work at JLab resulted in the best resolution hypernuclear spectra measured thus far with magnetic spectrometers.

  18. Conformational analysis by intersection: CONAN.

    Science.gov (United States)

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

    2003-01-15

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

  19. Conformal superalgebras via tractor calculus

    Science.gov (United States)

    Lischewski, Andree

    2015-01-01

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

  20. Catalytic transitions in the human MDR1 P-glycoprotein drug binding sites.

    Science.gov (United States)

    Wise, John G

    2012-06-26

    Multidrug resistance proteins that belong to the ATP-binding cassette family like the human P-glycoprotein (ABCB1 or Pgp) are responsible for many failed cancer and antiviral chemotherapies because these membrane transporters remove the chemotherapeutics from the targeted cells. Understanding the details of the catalytic mechanism of Pgp is therefore critical to the development of inhibitors that might overcome these resistances. In this work, targeted molecular dynamics techniques were used to elucidate catalytically relevant structures of Pgp. Crystal structures of homologues in four different conformations were used as intermediate targets in the dynamics simulations. Transitions from conformations that were wide open to the cytoplasm to transition state conformations that were wide open to the extracellular space were studied. Twenty-six nonredundant transitional protein structures were identified from these targeted molecular dynamics simulations using evolutionary structure analyses. Coupled movement of nucleotide binding domains (NBDs) and transmembrane domains (TMDs) that form the drug binding cavities were observed. Pronounced twisting of the NBDs as they approached each other as well as the quantification of a dramatic opening of the TMDs to the extracellular space as the ATP hydrolysis transition state was reached were observed. Docking interactions of 21 known transport ligands or inhibitors were analyzed with each of the 26 transitional structures. Many of the docking results obtained here were validated by previously published biochemical determinations. As the ATP hydrolysis transition state was approached, drug docking in the extracellular half of the transmembrane domains seemed to be destabilized as transport ligand exit gates opened to the extracellular space.

  1. Characterization of a structural intermediate of flavivirus membrane fusion.

    Directory of Open Access Journals (Sweden)

    Karin Stiasny

    2007-02-01

    Full Text Available Viral membrane fusion proceeds through a sequence of steps that are driven by triggered conformational changes of viral envelope glycoproteins, so-called fusion proteins. Although high-resolution structural snapshots of viral fusion proteins in their prefusion and postfusion conformations are available, it has been difficult to define intermediate structures of the fusion pathway because of their transient nature. Flaviviruses possess a class II viral fusion protein (E mediating fusion at acidic pH that is converted from a dimer to a trimer with a hairpin-like structure during the fusion process. Here we show for tick-borne encephalitis virus that exposure of virions to alkaline instead of acidic pH traps the particles in an intermediate conformation in which the E dimers dissociate and interact with target membranes via the fusion peptide without proceeding to the merger of the membranes. Further treatment to low pH, however, leads to fusion, suggesting that these monomers correspond to an as-yet-elusive intermediate required to convert the prefusion dimer into the postfusion trimer. Thus, the use of nonphysiological conditions allows a dissection of the flavivirus fusion process and the identification of two separate steps, in which membrane insertion of multiple copies of E monomers precedes the formation of hairpin-like trimers. This sequence of events provides important new insights for understanding the dynamic process of viral membrane fusion.

  2. Classical extended conformal symmetries

    International Nuclear Information System (INIS)

    Viswanathan, R.

    1990-02-01

    Extensions of the Virasoro algebra are constructed as Poisson brackets of higher spin fields which appear as coefficient fields in certain covariant derivative operators of order N. These differential operators are constructed so as to be covariant under reparametrizations on fields of definite conformal dimension. Factorization of such an N-th order operator in terms of first order operators, together with the inclusion of a spin one U(1) current, is shown to lead to a two-parameter W-algebra. One of these parameters plays the role of interpolating between W-algebras based on different Lie algebras of the same rank. (author). 11 refs

  3. Comments on intermediate-scale models

    Energy Technology Data Exchange (ETDEWEB)

    Ellis, J.; Enqvist, K.; Nanopoulos, D.V.; Olive, K.

    1987-04-23

    Some superstring-inspired models employ intermediate scales m/sub I/ of gauge symmetry breaking. Such scales should exceed 10/sup 16/ GeV in order to avoid prima facie problems with baryon decay through heavy particles and non-perturbative behaviour of the gauge couplings above m/sub I/. However, the intermediate-scale phase transition does not occur until the temperature of the Universe falls below O(m/sub W/), after which an enormous excess of entropy is generated. Moreover, gauge symmetry breaking by renormalization group-improved radiative corrections is inapplicable because the symmetry-breaking field has not renormalizable interactions at scales below m/sub I/. We also comment on the danger of baryon and lepton number violation in the effective low-energy theory.

  4. Comments on intermediate-scale models

    International Nuclear Information System (INIS)

    Ellis, J.; Enqvist, K.; Nanopoulos, D.V.; Olive, K.

    1987-01-01

    Some superstring-inspired models employ intermediate scales m I of gauge symmetry breaking. Such scales should exceed 10 16 GeV in order to avoid prima facie problems with baryon decay through heavy particles and non-perturbative behaviour of the gauge couplings above m I . However, the intermediate-scale phase transition does not occur until the temperature of the Universe falls below O(m W ), after which an enormous excess of entropy is generated. Moreover, gauge symmetry breaking by renormalization group-improved radiative corrections is inapplicable because the symmetry-breaking field has not renormalizable interactions at scales below m I . We also comment on the danger of baryon and lepton number violation in the effective low-energy theory. (orig.)

  5. Conformally symmetric traversable wormholes

    International Nuclear Information System (INIS)

    Boehmer, Christian G.; Harko, Tiberiu; Lobo, Francisco S. N.

    2007-01-01

    Exact solutions of traversable wormholes are found under the assumption of spherical symmetry and the existence of a nonstatic conformal symmetry, which presents a more systematic approach in searching for exact wormhole solutions. In this work, a wide variety of solutions are deduced by considering choices for the form function, a specific linear equation of state relating the energy density and the pressure anisotropy, and various phantom wormhole geometries are explored. A large class of solutions impose that the spatial distribution of the exotic matter is restricted to the throat neighborhood, with a cutoff of the stress-energy tensor at a finite junction interface, although asymptotically flat exact solutions are also found. Using the 'volume integral quantifier', it is found that the conformally symmetric phantom wormhole geometries may, in principle, be constructed by infinitesimally small amounts of averaged null energy condition violating matter. Considering the tidal acceleration traversability conditions for the phantom wormhole geometry, specific wormhole dimensions and the traversal velocity are also deduced

  6. 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

  7. Single molecule insights on conformational selection and induced fit mechanism

    DEFF Research Database (Denmark)

    Hatzakis, Nikos

    2014-01-01

    . To describe the molecular basis of this behavior, two main mechanisms have been advanced: 'induced fit' and 'conformational selection'. Our understanding of these models relies primarily on NMR, computational studies and kinetic measurements. These techniques report the average behavior of a large ensemble...... of unsynchronized molecules, often masking intrinsic dynamic behavior of proteins and biologically significant transient intermediates. Single molecule measurements are emerging as a powerful tool for characterizing protein function. They offer the direct observation and quantification of the activity, abundance...

  8. An Expression of Periodic Phenomena of Fashion on Sexual Selection Model with Conformity Genes and Memes

    Science.gov (United States)

    Mutoh, Atsuko; Tokuhara, Shinya; Kanoh, Masayoshi; Oboshi, Tamon; Kato, Shohei; Itoh, Hidenori

    It is generally thought that living things have trends in their preferences. The mechanism of occurrence of another trends in successive periods is concerned in their conformity. According to social impact theory, the minority is always exists in the group. There is a possibility that the minority make the transition to the majority by conforming agents. Because of agent's promotion of their conform actions, the majority can make the transition. We proposed an evolutionary model with both genes and memes, and elucidated the interaction between genes and memes on sexual selection. In this paper, we propose an agent model for sexual selection imported the concept of conformity. Using this model we try an environment where male agents and female agents are existed, we find that periodic phenomena of fashion are expressed. And we report the influence of conformity and differentiation on the transition of their preferences.

  9. Ligand induced change of β2 adrenergic receptor from active to inactive conformation and its implication for the closed/open state of the water channel: insight from molecular dynamics simulation, free energy calculation and Markov state model analysis.

    Science.gov (United States)

    Bai, Qifeng; Pérez-Sánchez, Horacio; Zhang, Yang; Shao, Yonghua; Shi, Danfeng; Liu, Huanxiang; Yao, Xiaojun

    2014-08-14

    The reported crystal structures of β2 adrenergic receptor (β2AR) reveal that the open and closed states of the water channel are correlated with the inactive and active conformations of β2AR. However, more details about the process by which the water channel states are affected by the active to inactive conformational change of β2AR remain illusive. In this work, molecular dynamics simulations are performed to study the dynamical inactive and active conformational change of β2AR induced by inverse agonist ICI 118,551. Markov state model analysis and free energy calculation are employed to explore the open and close states of the water channel. The simulation results show that inverse agonist ICI 118,551 can induce water channel opening during the conformational transition of β2AR. Markov state model (MSM) analysis proves that the energy contour can be divided into seven states. States S1, S2 and S5, which represent the active conformation of β2AR, show that the water channel is in the closed state, while states S4 and S6, which correspond to the intermediate state conformation of β2AR, indicate the water channel opens gradually. State S7, which represents the inactive structure of β2AR, corresponds to the full open state of the water channel. The opening mechanism of the water channel is involved in the ligand-induced conformational change of β2AR. These results can provide useful information for understanding the opening mechanism of the water channel and will be useful for the rational design of potent inverse agonists of β2AR.

  10. RHIZOME AND DISCOURSE OF INTERMEDIALITY

    Directory of Open Access Journals (Sweden)

    Л Н Синельникова

    2017-12-01

    Full Text Available Rhizomaticity is a strategy and a regularity of text creation in a lot of modern commu-nicative discourse practices. What remains urgent is the problem of the systematic interdisciplinary de-scription of texts whose structure and language qualities are determined by the signs of the rhizome - a concept of post-modern philosophy introduced into the scientific field by the French philosopher Gilles Deleuze and the psychotherapist Félix Guattari (Deleuze, Guattari 1996. The rhizome (Fr. rhizome - rootstock, tuber, bulb, mycelium possesses the following qualities: it is non-linear, open and directed towards the unpredictability of discourse transformations through the possibilities of structure development in any direction; there is no centre or periphery in the rhizome, and any discourse element can become ‘a vital structure’ for text-creation. The rhizome does not have non-intersecting boundaries; and in the space of the rhizomatic discourse environment, an increase of reality facets takes place, non-standard associative con-nections appear, multiplication effects are formed, which create new meanings. Rhizomaticity is the quality of texts being organised by the laws of rhizomatic logic (V.F. Sharkov 2007, by the terms of which ‘su-perposition’ of discourses can take place, a transition from one semiotic system to another. The article makes an attempt to correlate the qualities of the rhizome with the signs of the intermedia discourse, which is built on the semiotic interaction of different media. The moving lines of the rhizome, its ‘branch-ing’ qualities can be found in poetic texts, in the evaluating segments of political discourse, in advertising discourse, in internet communications, which represent rhizomorphic environments. An analysis of examples from these spheres has shown that the rhizomatic approach opens new facets of intermediality. The author uses the methods of discourse analysis to prove that the openness and non

  11. ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations.

    Science.gov (United States)

    Parvatikar, Akash; Vacaliuc, Gabriel S; Ramanathan, Arvind; Chennubhotla, S Chakra

    2018-05-08

    Anharmonicity in time-dependent conformational fluctuations is noted to be a key feature of functional dynamics of biomolecules. Although anharmonic events are rare, long-timescale (μs-ms and beyond) simulations facilitate probing of such events. We have previously developed quasi-anharmonic analysis to resolve higher-order spatial correlations and characterize anharmonicity in biomolecular simulations. In this article, we have extended this toolbox to resolve higher-order temporal correlations and built a scalable Python package called anharmonic conformational analysis (ANCA). ANCA has modules to: 1) measure anharmonicity in the form of higher-order statistics and its variation as a function of time, 2) output a storyboard representation of the simulations to identify key anharmonic conformational events, and 3) identify putative anharmonic conformational substates and visualization of transitions between these substates. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  12. Quality assurance of the reactor pressure vessel of nuclear power plants. Determination of the fracture toughness KIC above the ductile-brittle transition region on small test specimens by means of a conformal mapping

    International Nuclear Information System (INIS)

    Ullrich, G.; Krompholz, K.

    1994-01-01

    The ''surveillance-programs'' for the determination of the mechanical properties of reactor pressure vessel (RPV) materials, as a function of the neutron dose, include impact and tensile tests for the boiling water reactor; while for pressurized water reactors additional wedge opening load specimens (WOL), for the measurement of the fracture toughness K IC at low temperatures, are utilized. While the Charpy impact toughness gives the total magnitude of energy, which indicates the change of the material state, e.g. the state of embrittlement, the fracture toughness, I IC , gives a base for mechanical calculations. This is of importance for components in which cracks or flaws are assumed. The mechanical analysis, and its relevance to safety assessments, depends on the knowledge of different parameters such as geometry of the structure and flaws, and load history of the structure. Fracture mechanical methods play an important role, if the leak-before-fracture problem is considered. Within the frame work of fracture mechanical methods, only the influence of assumed macroscopic cracks on the structural behaviour can be handled. Flaw formation processes in flaw-free structures, as well as the treatment of short flaws, can not currently be included. In the regime of low and intermediate temperatures (for ferritic and austenitic materials, normally below 400 o C), the rules of linear elastic fracture mechanics (LEFM) and elasto-plastic fracture mechanics (EPFM) are applied, some of which are already part of the code cases. (author) 5 figs., 32 refs

  13. Ward identities for conformal models

    International Nuclear Information System (INIS)

    Lazzarini, S.; Stora, R.

    1988-01-01

    Ward identities which express the symmetry of conformal models are treated. Diffeomorphism invariance or locally holomorphic coordinate transformations are used. Diffeomorphism invariance is then understood in terms of Riemannian geometry. Two different sets of Ward identities expressing diffeomorphism invariance in a conformally invariant way are found for the free bosonic string. Using a geometrical argument, the correct invariance for a large class of conformal models is given

  14. Conformational analysis of lignin models

    International Nuclear Information System (INIS)

    Santos, Helio F. dos

    2001-01-01

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

  15. On the linear conformal gravitation

    International Nuclear Information System (INIS)

    Pal'chik, M.Ya.; Fradkin, E.S.

    1984-01-01

    Conformal gravitation is analyzed under the assumption that its solution possesses the property of conformal symmetry. This assumption has sense in the case of small distances and only for definite types of matter fields, namely: at special choice of matter fields and their interactions, providing a lack of conformal anomalies; or at definite magnitudes of binding constants, coinciding with the zeroes of the Gell-Mann-Low function. The field equations, of the group-theoretical natura are obtained

  16. Fermion-scalar conformal blocks

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-04-13

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

  17. Instantons in conformal gravity

    International Nuclear Information System (INIS)

    Strominger, A.; Horowitz, G.T.; Perry, M.J.

    1984-01-01

    Fe study extrema of the general conformally invariant action: Ssub(c)=∫1/sub(α) 2 Csup(abcd)Csub(abcd)+γRsup(abcd*)Rsup(*)sub(abcd)+iTHETARsup(abcd)*Rsub(abcd). We find the first examples in four dimensions of asymptotically euclidean gravitational instantons. These have arbitrary Euler number and Hirzebruch signature. Some of these instantons represent tunneling between zero-curvature vacua that are not related by small gauge transformations. Others represent tunneling between flat space and topologically non-trivial zero-energy initial data. A general formula for the one-loop determinant is derived in terms of the renormalization group invariant masses, the volume of space-time, the Euler number and the Hirzebruch signature. (orig.)

  18. 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 10...... interviews with first-time reporting companies and six interviews with companies that failed to comply with the new law. It is concluded that coercive pressures from government have an impact on CSR reporting practices. Further, the analysis finds traces of mimetic isomorphism which inspires a homogenisation...... 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....

  19. Reflections on Conformal Spectra

    CERN Multimedia

    CERN. Geneva

    2015-01-01

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

  20. Conformal boundary loop models

    International Nuclear Information System (INIS)

    Jacobsen, Jesper Lykke; Saleur, Hubert

    2008-01-01

    We study a model of densely packed self-avoiding loops on the annulus, related to the Temperley-Lieb algebra with an extra idempotent boundary generator. Four different weights are given to the loops, depending on their homotopy class and whether they touch the outer rim of the annulus. When the weight of a contractible bulk loop x≡q+q -1 element of (-2,2], this model is conformally invariant for any real weight of the remaining three parameters. We classify the conformal boundary conditions and give exact expressions for the corresponding boundary scaling dimensions. The amplitudes with which the sectors with any prescribed number and types of non-contractible loops appear in the full partition function Z are computed rigorously. Based on this, we write a number of identities involving Z which hold true for any finite size. When the weight of a contractible boundary loop y takes certain discrete values, y r ≡([r+1] q )/([r] q ) with r integer, other identities involving the standard characters K r,s of the Virasoro algebra are established. The connection with Dirichlet and Neumann boundary conditions in the O(n) model is discussed in detail, and new scaling dimensions are derived. When q is a root of unity and y=y r , exact connections with the A m type RSOS model are made. These involve precise relations between the spectra of the loop and RSOS model transfer matrices, valid in finite size. Finally, the results where y=y r are related to the theory of Temperley-Lieb cabling

  1. Conformal Aspects of QCD

    Energy Technology Data Exchange (ETDEWEB)

    Brodsky, S

    2003-11-19

    Theoretical and phenomenological evidence is now accumulating that the QCD coupling becomes constant at small virtuality; i.e., {alpha}{sub s}(Q{sup 2}) develops an infrared fixed point in contradiction to the usual assumption of singular growth in the infrared. For example, the hadronic decays of the {tau} lepton can be used to determine the effective charge {alpha}{sub {tau}}(m{sub {tau}{prime}}{sup 2}) for a hypothetical {tau}-lepton with mass in the range 0 < m{sub {tau}{prime}} < m{sub {tau}}. The {tau} decay data at low mass scales indicates that the effective charge freezes at a value of s = m{sub {tau}{prime}}{sup 2} of order 1 GeV{sup 2} with a magnitude {alpha}{sub {tau}} {approx} 0.9 {+-} 0.1. The near-constant behavior of effective couplings suggests that QCD can be approximated as a conformal theory even at relatively small momentum transfer and why there are no significant running coupling corrections to quark counting rules for exclusive processes. The AdS/CFT correspondence of large N{sub c} supergravity theory in higher-dimensional anti-de Sitter space with supersymmetric QCD in 4-dimensional space-time also has interesting implications for hadron phenomenology in the conformal limit, including an all-orders demonstration of counting rules for exclusive processes and light-front wavefunctions. The utility of light-front quantization and light-front Fock wavefunctions for analyzing nonperturbative QCD and representing the dynamics of QCD bound states is also discussed.

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

    International Nuclear Information System (INIS)

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

    1987-01-01

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

  3. Discourses and Models of Intermediality

    OpenAIRE

    Schröter, Jens

    2011-01-01

    In his article "Discourses and Models of Intermediality" Jens Schröter discusses the question as to what relations do different discourses pose between different "media." Schröter identifies four models of discourse: 1) synthetic intermediality: a "fusion" of different media to super-media, a model with roots in the Wagnerian concept of Gesamtkunstwerk with political connotations, 2) formal (or transmedial) intermediality: a concept based on formal structures not "specific" to one medium but ...

  4. Information acquisition and financial intermediation

    OpenAIRE

    Boyarchenko, Nina

    2012-01-01

    This paper considers the problem of information acquisition in an intermediated market, where the specialists have access to superior technology for acquiring information. These informational advantages of specialists relative to households lead to disagreement between the two groups, changing the shape of the intermediation-constrained region of the economy and increasing the frequency of periods when the intermediation constraint binds. Acquiring the additional information is, however, cost...

  5. Logarithmic conformal field theory through nilpotent conformal dimensions

    International Nuclear Information System (INIS)

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

    2001-01-01

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

  6. Conformational inversion-topomerization mechanism of ethylcyclohexyl isomers and its role in combustion kinetics

    KAUST Repository

    Bian, Huiting; Wang, Zhandong; Sun, Jinhua; Zhang, Feng

    2016-01-01

    the formation of subsequent decomposition products. In this work, the conformational inversion-topomerization mechanism and H-migration reactions for six ethylcyclohexyl radical isomers were systematically studied by ab initio calculations and the transition

  7. Glycine Perturbs Local and Global Conformational Flexibility of a Transmembrane Helix

    DEFF Research Database (Denmark)

    Högel, Philipp; Götz, Alexander; Kuhne, Felix

    2018-01-01

    Flexible transmembrane helices frequently support the conformational transitions between different functional states of membrane proteins. While proline is well known to distort and destabilize transmembrane helices, the role of glycine is still debated. Here, we systematically investigated the e...

  8. Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies.

    Science.gov (United States)

    Kim, Do-Nyun; Altschuler, Josiah; Strong, Campbell; McGill, Gaël; Bathe, Mark

    2011-01-01

    The conformational dynamics data bank (CDDB, http://www.cdyn.org) is a database that aims to provide comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis is performed using a recently introduced coarse-grained computational approach that is applied to the majority of structures present in the electron microscopy data bank (EMDB). Results include equilibrium thermal fluctuations and elastic strain energy distributions that identify rigid versus flexible protein domains generally, as well as those associated with specific functional transitions, and correlations in molecular motions that identify molecular regions that are highly coupled dynamically, with implications for allosteric mechanisms. A practical web-based search interface enables users to easily collect conformational dynamics data in various formats. The data bank is maintained and updated automatically to include conformational dynamics results for new structural entries as they become available in the EMDB. The CDDB complements static structural information to facilitate the investigation and interpretation of the biological function of proteins and protein assemblies essential to cell function.

  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. α-helix to β-hairpin transition of human amylin monomer

    Science.gov (United States)

    Singh, Sadanand; Chiu, Chi-cheng; Reddy, Allam S.; de Pablo, Juan J.

    2013-04-01

    The human islet amylin polypeptide is produced along with insulin by pancreatic islets. Under some circumstances, amylin can aggregate to form amyloid fibrils, whose presence in pancreatic cells is a common pathological feature of Type II diabetes. A growing body of evidence indicates that small, early stage aggregates of amylin are cytotoxic. A better understanding of the early stages of the amylin aggregation process and, in particular, of the nucleation events leading to fibril growth could help identify therapeutic strategies. Recent studies have shown that, in dilute solution, human amylin can adopt an α-helical conformation, a β-hairpin conformation, or an unstructured coil conformation. While such states have comparable free energies, the β-hairpin state exhibits a large propensity towards aggregation. In this work, we present a detailed computational analysis of the folding pathways that arise between the various conformational states of human amylin in water. A free energy surface for amylin in explicit water is first constructed by resorting to advanced sampling techniques. Extensive transition path sampling simulations are then employed to identify the preferred folding mechanisms between distinct minima on that surface. Our results reveal that the α-helical conformer of amylin undergoes a transformation into the β-hairpin monomer through one of two mechanisms. In the first, misfolding begins through formation of specific contacts near the turn region, and proceeds via a zipping mechanism. In the second, misfolding occurs through an unstructured coil intermediate. The transition states for these processes are identified. Taken together, the findings presented in this work suggest that the inter-conversion of amylin between an α-helix and a β-hairpin is an activated process and could constitute the nucleation event for fibril growth.

  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. On Associative Conformal Algebras of Linear Growth

    OpenAIRE

    Retakh, Alexander

    2000-01-01

    Lie conformal algebras appear in the theory of vertex algebras. Their relation is similar to that of Lie algebras and their universal enveloping algebras. Associative conformal algebras play a role in conformal representation theory. We introduce the notions of conformal identity and unital associative conformal algebras and classify finitely generated simple unital associative conformal algebras of linear growth. These are precisely the complete algebras of conformal endomorphisms of finite ...

  13. Twelve massless flavors and three colors below the conformal window

    International Nuclear Information System (INIS)

    Fodor, Zoltan; Holland, Kieran; Kuti, Julius; Nogradi, Daniel; Schroeder, Chris

    2011-01-01

    We report new results for a frequently discussed gauge theory with twelve fermion flavors in the fundamental representation of the SU(3) color gauge group. The model, controversial with respect to its conformality, is important in non-perturbative studies searching for a viable composite Higgs mechanism beyond the Standard Model (BSM). In comparison with earlier work, our new simulations apply larger volumes and probe deeper in fermion and pion masses toward the chiral limit. Investigating the controversy, we subject the model to opposite hypotheses with respect to the conformal window. In the first hypothesis, below the conformal window, we test chiral symmetry breaking (χSB) with its Goldstone spectrum, F π , the χSB condensate, and several composite hadron states as analytic functions of the fermion mass when varied in a limited range with our best effort to control finite volume effects. In the second test, for the alternate hypothesis inside the conformal window, we probe conformal behavior driven by a single anomalous mass dimension under the assumption of unbroken chiral symmetry at vanishing fermion mass. Our results at fixed gauge coupling, based on the assumptions of the two hypotheses we define, show low level of confidence in the conformal scenario with leading order scaling analysis. Relaxing the important assumption of leading mass-deformed conformality with its conformal finite size scaling would require added theoretical understanding of the scaling violation terms in the conformal analysis and a comprehensive test of its effects on the confidence level of the fits. Results for the running coupling, based on the force between static sources, and preliminary indications for the finite temperature transition are also presented. Staggered lattice fermions with stout-suppressed taste breaking are used throughout the simulations.

  14. The MHD intermediate shock interaction with an intermediate wave: Are intermediate shocks physical?

    International Nuclear Information System (INIS)

    Wu, C.C.

    1988-01-01

    Contrary to the usual belief that MHD intermediate shocks are extraneous, the authors have recently shown by numerical solutions of dissipative MHD equations that intermediate shocks are admissible and can be formed through nonlinear steepening from a continuous wave. In this paper, he clarifies the differences between the conventional view and the results by studying the interaction of an MHD intermediate shock with an intermediate wave. The study reaffirms his results. In addition, the study shows that there exists a larger class of shocklike solutions in the time-dependent dissiaptive MHD equations than are given by the MHD Rankine-Hugoniot relations. it also suggests a mechanism for forming rotational discontinuities through the interaction of an intermediate shock with an intermediate wave. The results are of importance not only to the MHD shock theory but also to studies such as magnetic field reconnection models

  15. Multifragmentation in intermediate energy heavy ion collisions

    International Nuclear Information System (INIS)

    Jacak, B.V.; Britt, H.C.; Claesson, G.

    1986-01-01

    There has been considerable recent interest in the production of intermediate mass fragments (A > 4) in intermediate and high energy nucleus-nucleus collisions. The mechanism for production of these fragments is not well understood and has been described by models employing a variety of assumptions. Some examples are: disassembly of a system in thermal equilibrium into nucleons and nuclear fragments, liquid-vapor phase transitions in nuclear matter, final state coalescence of nucleons and dynamical correlations between nucleons at breakup. Previous studies of fragment production, with one exception, have been single particle inclusive measurements; the observed fragment mass (or charge) distributions can be described by all of the models above. To gain insight into the fragment production mechanism, the authors used the GSI/LBL Plastic Ball detector system to get full azimuthal coverage for intermediate mass fragments in the forward hemisphere in the center of mass system while measuring all the light particles in each event. The authors studied the systems 200 MeV/nucleon Au + Au and Au + Fe

  16. Recent advancements in conformal gravity

    International Nuclear Information System (INIS)

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

    2017-01-01

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

  17. Conformal invariance in harmonic superspace

    International Nuclear Information System (INIS)

    Galperin, A.; Ivanov, E.; Ogievetsky, V.; Sokatchev, E.

    1985-01-01

    N=2 conformal supersymmetry is realized in harmonic superspace, its peculiarities are analyzed. The coordinate group and analytical prepotentials for N=2 conformal supergravity are found. A new version of the N=2 Einstein supergravity with infinite number of auxiliary fields is suggested. A hypermultiplet without central charges and constraints is used as a compensator

  18. 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.

  19. Intermediate valence spectroscopy

    International Nuclear Information System (INIS)

    Gunnarsson, O.; Schoenhammer, K.

    1987-01-01

    Spectroscopic properties of intermediate valence compounds are studied using the Anderson model. Due to the large orbital and spin degeneracy N/sub f/ of the 4f-level, 1/N/sub f/ can be treated as a small parameter. This approach provides exact T = 0 results for the Anderson impurity model in the limit N/sub f/ → ∞, and by adding 1/N/sub f/ corrections some properties can be calculated accurately even for N/sub f/ = 1 or 2. In particular valence photoemission and resonance photoemission spectroscopies are studied. A comparison of theoretical and experimental spectra provides an estimate of the parameters in the model. Core level photoemission spectra provide estimates of the coupling between the f-level and the conduction states and of the f-level occupancy. With these parameters the model gives a fair description of other electron spectroscopies. For typical parameters the model predicts two structures in the f-spectrum, namely one structure at the f-level and one at the Fermi energy. The resonance photoemission calculation gives a photon energy dependence for these two peaks in fair agreement with experiment. The peak at the Fermi energy is partly due to a narrow Kondo resonance, resulting from many-body effects and the presence of a continuous, partly filled conduction band. This resonance is related to a large density of low-lying excitations, which explains the large susceptibility and specific heat observed for these systems at low temperatures. 38 references, 11 figures, 2 tables

  20. 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.

  1. Conformal algebra of Riemann surfaces

    International Nuclear Information System (INIS)

    Vafa, C.

    1988-01-01

    It has become clear over the last few years that 2-dimensional conformal field theories are a crucial ingredient of string theory. Conformal field theories correspond to vacuum solutions of strings; or more precisely we know how to compute string spectrum and scattering amplitudes by starting from a formal theory (with a proper value of central charge of the Virasoro algebra). Certain non-linear sigma models do give rise to conformal theories. A lot of progress has been made in the understanding of conformal theories. The author discusses a different view of conformal theories which was motivated by the development of operator formalism on Riemann surfaces. The author discusses an interesting recent work from this point of view

  2. The logarithmic conformal field theories

    International Nuclear Information System (INIS)

    Rahimi Tabar, M.R.; Aghamohammadi, A.; Khorrami, M.

    1997-01-01

    We study the correlation functions of logarithmic conformal field theories. First, assuming conformal invariance, we explicitly calculate two- and three-point functions. This calculation is done for the general case of more than one logarithmic field in a block, and more than one set of logarithmic fields. Then we show that one can regard the logarithmic field as a formal derivative of the ordinary field with respect to its conformal weight. This enables one to calculate any n-point function containing the logarithmic field in terms of ordinary n-point functions. Finally, we calculate the operator product expansion (OPE) coefficients of a logarithmic conformal field theory, and show that these can be obtained from the corresponding coefficients of ordinary conformal theory by a simple derivation. (orig.)

  3. Welding. Performance Objectives. Intermediate Course.

    Science.gov (United States)

    Vincent, Kenneth

    Several intermediate performance objectives and corresponding criterion measures are listed for each of nine terminal objectives for an intermediate welding course. The materials were developed for a 36-week (3 hours daily) course designed to prepare the student for employment in the field of welding. Electric welding and specialized (TIG & MIG)…

  4. Intermediate structure and threshold phenomena

    International Nuclear Information System (INIS)

    Hategan, Cornel

    2004-01-01

    The Intermediate Structure, evidenced through microstructures of the neutron strength function, is reflected in open reaction channels as fluctuations in excitation function of nuclear threshold effects. The intermediate state supporting both neutron strength function and nuclear threshold effect is a micro-giant neutron threshold state. (author)

  5. Conformational Dynamics of Thermus aquaticus DNA Polymerase I during Catalysis

    Science.gov (United States)

    Suo, Zucai

    2014-01-01

    Despite the fact that DNA polymerases have been investigated for many years and are commonly used as tools in a number of molecular biology assays, many details of the kinetic mechanism they use to catalyze DNA synthesis remain unclear. Structural and kinetic studies have characterized a rapid, pre-catalytic open-to-close conformational change of the Finger domain during nucleotide binding for many DNA polymerases including Thermus aquaticus DNA polymerase I (Taq Pol), a thermostable enzyme commonly used for DNA amplification in PCR. However, little has been done to characterize the motions of other structural domains of Taq Pol or any other DNA polymerase during catalysis. Here, we used stopped-flow Förster resonance energy transfer (FRET) to investigate the conformational dynamics of all five structural domains of the full-length Taq Pol relative to the DNA substrate during nucleotide binding and incorporation. Our study provides evidence for a rapid conformational change step induced by dNTP binding and a subsequent global conformational transition involving all domains of Taq Pol during catalysis. Additionally, our study shows that the rate of the global transition was greatly increased with the truncated form of Taq Pol lacking the N-terminal domain. Finally, we utilized a mutant of Taq Pol containing a de novo disulfide bond to demonstrate that limiting protein conformational flexibility greatly reduced the polymerization activity of Taq Pol. PMID:24931550

  6. Intensity modulated conformal radiotherapy

    International Nuclear Information System (INIS)

    Noel, Georges; Moty-Monnereau, Celine; Meyer, Aurelia; David, Pauline; Pages, Frederique; Muller, Felix; Lee-Robin, Sun Hae; David, Denis Jean

    2006-12-01

    This publication reports the assessment of intensity-modulated conformal radiotherapy (IMCR). This assessment is based on a literature survey which focussed on indications, efficiency and safety on the short term, on the risk of radio-induced cancer on the long term, on the role in the therapeutic strategy, on the conditions of execution, on the impact on morbidity-mortality and life quality, on the impact on the health system and on public health policies and program. This assessment is also based on the opinion of a group of experts regarding the technical benefit of IMCR, its indications depending on the cancer type, safety in terms of radio-induced cancers, and conditions of execution. Before this assessment, the report thus indicates indications for which the use of IMCR can be considered as sufficient or not determined. It also proposes a technical description of IMCR and helical tomo-therapy, discusses the use of this technique for various pathologies or tumours, analyses the present situation of care in France, and comments the identification of this technique in foreign classifications

  7. 6d Conformal matter

    International Nuclear Information System (INIS)

    Zotto, Michele Del; Heckman, Jonathan J.; Tomasiello, Alessandro; Vafa, Cumrun

    2015-01-01

    A single M5-brane probing G, an ADE-type singularity, leads to a system which has G×G global symmetry and can be viewed as “bifundamental” (G,G) matter. For the A N series, this leads to the usual notion of bifundamental matter. For the other cases it corresponds to a strongly interacting (1,0) superconformal system in six dimensions. Similarly, an ADE singularity intersecting the Hořava-Witten wall leads to a superconformal matter system with E 8 ×G global symmetry. Using the F-theory realization of these theories, we elucidate the Coulomb/tensor branch of (G,G ′ ) conformal matter. This leads to the notion of fractionalization of an M5-brane on an ADE singularity as well as fractionalization of the intersection point of the ADE singularity with the Hořava-Witten wall. Partial Higgsing of these theories leads to new 6d SCFTs in the infrared, which we also characterize. This generalizes the class of (1,0) theories which can be perturbatively realized by suspended branes in IIA string theory. By reducing on a circle, we arrive at novel duals for 5d affine quiver theories. Introducing many M5-branes leads to large N gravity duals.

  8. On the stability of rotational discontinuities and intermediate shocks

    International Nuclear Information System (INIS)

    Lee, L.C.; Huang, L.; Chao, J.K.

    1989-01-01

    The stability of rotational discontinuities and intermediate shocks is studied based on a hybrid simulation code. The simulation results show that rotational discontinuities are stable and intermediate shocks are not stationary. Intermediate shocks tend to evolve to rotational discontinuities and waves. The authors employ several different initial profiles for the magnetic field in the transition region and find that the final structure of the discontinuities or shocks is not sensitive to the initial magnetic field profile. The present results are different from those obtained from the resistive MHD simulations. Furthermore, their study indicates that the kinetic effect of particles plays an important role in the structure and stability of rotational discontinuities and intermediate shocks

  9. Intermediate neutron spectrum problems and the intermediate neutron spectrum experiment

    International Nuclear Information System (INIS)

    Jaegers, P.J.; Sanchez, R.G.

    1996-01-01

    Criticality benchmark data for intermediate energy spectrum systems does not exist. These systems are dominated by scattering and fission events induced by neutrons with energies between 1 eV and 1 MeV. Nuclear data uncertainties have been reported for such systems which can not be resolved without benchmark critical experiments. Intermediate energy spectrum systems have been proposed for the geological disposition of surplus fissile materials. Without the proper benchmarking of the nuclear data in the intermediate energy spectrum, adequate criticality safety margins can not be guaranteed. The Zeus critical experiment now under construction will provide this necessary benchmark data

  10. Milestoning with transition memory

    Science.gov (United States)

    Hawk, Alexander T.; Makarov, Dmitrii E.

    2011-12-01

    Milestoning is a method used to calculate the kinetics and thermodynamics of molecular processes occurring on time scales that are not accessible to brute force molecular dynamics (MD). In milestoning, the conformation space of the system is sectioned by hypersurfaces (milestones), an ensemble of trajectories is initialized on each milestone, and MD simulations are performed to calculate transitions between milestones. The transition probabilities and transition time distributions are then used to model the dynamics of the system with a Markov renewal process, wherein a long trajectory of the system is approximated as a succession of independent transitions between milestones. This approximation is justified if the transition probabilities and transition times are statistically independent. In practice, this amounts to a requirement that milestones are spaced such that trajectories lose position and velocity memory between subsequent transitions. Unfortunately, limiting the number of milestones limits both the resolution at which a system's properties can be analyzed, and the computational speedup achieved by the method. We propose a generalized milestoning procedure, milestoning with transition memory (MTM), which accounts for memory of previous transitions made by the system. When a reaction coordinate is used to define the milestones, the MTM procedure can be carried out at no significant additional expense as compared to conventional milestoning. To test MTM, we have applied its version that allows for the memory of the previous step to the toy model of a polymer chain undergoing Langevin dynamics in solution. We have computed the mean first passage time for the chain to attain a cyclic conformation and found that the number of milestones that can be used, without incurring significant errors in the first passage time is at least 8 times that permitted by conventional milestoning. We further demonstrate that, unlike conventional milestoning, MTM permits

  11. Conformational analysis and circular dichroism of bilirubin, the yellow pigment of jaundice

    Science.gov (United States)

    Lightner, David A.; Person, Richard; Peterson, Blake; Puzicha, Gisbert; Pu, Yu-Ming; Bojadziev, Stefan

    1991-06-01

    Conformational analysis of (4Z, 15Z)-bilirubin-IX(alpha) by molecular mechanics computations reveals a global energy minimum folded conformation. Powerful added stabilization is achieved through intramolecular hydrogen bonding. Theoretical treatment of bilirubin as a molecular exciton predicts an intense bisignate circular dichroism spectrum for the folded conformation: (Delta) (epsilon) is congruent to 270 L (DOT) mole-1 (DOT) cm-1 for the $OM450 nm electronic transition(s). Synthesis of bilirubin analogs with propionic acid groups methylated at the (alpha) or (beta) position introduces an allosteric effect that allows for an optical resolution of the pigments, with enantiomers exhibiting the theoretically predicted circular dichroism.

  12. Towards conformal loop quantum gravity

    International Nuclear Information System (INIS)

    Wang, Charles H-T

    2006-01-01

    A discussion is given of recent developments in canonical gravity that assimilates the conformal analysis of gravitational degrees of freedom. The work is motivated by the problem of time in quantum gravity and is carried out at the metric and the triad levels. At the metric level, it is shown that by extending the Arnowitt-Deser-Misner (ADM) phase space of general relativity (GR), a conformal form of geometrodynamics can be constructed. In addition to the Hamiltonian and Diffeomorphism constraints, an extra first class constraint is introduced to generate conformal transformations. This phase space consists of York's mean extrinsic curvature time, conformal three-metric and their momenta. At the triad level, the phase space of GR is further enlarged by incorporating spin-gauge as well as conformal symmetries. This leads to a canonical formulation of GR using a new set of real spin connection variables. The resulting gravitational constraints are first class, consisting of the Hamiltonian constraint and the canonical generators for spin-gauge and conformorphism transformations. The formulation has a remarkable feature of being parameter-free. Indeed, it is shown that a conformal parameter of the Barbero-Immirzi type can be absorbed by the conformal symmetry of the extended phase space. This gives rise to an alternative approach to loop quantum gravity that addresses both the conceptual problem of time and the technical problem of functional calculus in quantum gravity

  13. Benchmarking Commercial Conformer Ensemble Generators.

    Science.gov (United States)

    Friedrich, Nils-Ole; de Bruyn Kops, Christina; Flachsenberg, Florian; Sommer, Kai; Rarey, Matthias; Kirchmair, Johannes

    2017-11-27

    We assess and compare the performance of eight commercial conformer ensemble generators (ConfGen, ConfGenX, cxcalc, iCon, MOE LowModeMD, MOE Stochastic, MOE Conformation Import, and OMEGA) and one leading free algorithm, the distance geometry algorithm implemented in RDKit. The comparative study is based on a new version of the Platinum Diverse Dataset, a high-quality benchmarking dataset of 2859 protein-bound ligand conformations extracted from the PDB. Differences in the performance of commercial algorithms are much smaller than those observed for free algorithms in our previous study (J. Chem. Inf. 2017, 57, 529-539). For commercial algorithms, the median minimum root-mean-square deviations measured between protein-bound ligand conformations and ensembles of a maximum of 250 conformers are between 0.46 and 0.61 Å. Commercial conformer ensemble generators are characterized by their high robustness, with at least 99% of all input molecules successfully processed and few or even no substantial geometrical errors detectable in their output conformations. The RDKit distance geometry algorithm (with minimization enabled) appears to be a good free alternative since its performance is comparable to that of the midranked commercial algorithms. Based on a statistical analysis, we elaborate on which algorithms to use and how to parametrize them for best performance in different application scenarios.

  14. Monitoring conformational dynamics with solid-state R1ρ experiments

    International Nuclear Information System (INIS)

    Quinn, Caitlin M.; McDermott, Ann E.

    2009-01-01

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

  15. Conformal invariance in harmonic superspace

    International Nuclear Information System (INIS)

    Galperin, A.; Ivanov, E.; Ogievetsky, V.; Sokatchev, E.

    1987-01-01

    In the present paper we show how the N = 2 superconformal group is realised in harmonic superspace and examine conformal invariance of N = 2 off-shell theories. We believe that the example of N = O self-dual Yang-Mills equations can serve as an instructive introduction to the subject of harmonic superspace and this is examined. The rigid N = 2 conformal supersymmetry and its local version, i.e. N = 2 conformal supergravity is also discussed. The paper is a contribution to the book commemorating the sixtieth birthday of E.S. Fradkin. (author)

  16. Two dimensional infinite conformal symmetry

    International Nuclear Information System (INIS)

    Mohanta, N.N.; Tripathy, K.C.

    1993-01-01

    The invariant discontinuous (discrete) conformal transformation groups, namely the Kleinian and Fuchsian groups Gamma (with an arbitrary signature) of H (the Poincare upper half-plane l) and the unit disc Delta are explicitly constructed from the fundamental domain D. The Riemann surface with signatures of Gamma and conformally invariant automorphic forms (functions) with Peterson scalar product are discussed. The functor, where the category of complex Hilbert spaces spanned by the space of cusp forms constitutes the two dimensional conformal field theory. (Author) 7 refs

  17. Harmony of spinning conformal blocks

    Energy Technology Data Exchange (ETDEWEB)

    Schomerus, Volker [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Theory Group; Sobko, Evgeny [Stockholm Univ. (Sweden); Nordita, Stockholm (Sweden); Isachenkov, Mikhail [Weizmann Institute of Science, Rehovoth (Israel). Dept. of Particle Physics and Astrophysics

    2016-12-07

    Conformal blocks for correlation functions of tensor operators play an increasingly important role for the conformal bootstrap programme. We develop a universal approach to such spinning blocks through the harmonic analysis of certain bundles over a coset of the conformal group. The resulting Casimir equations are given by a matrix version of the Calogero-Sutherland Hamiltonian that describes the scattering of interacting spinning particles in a 1-dimensional external potential. The approach is illustrated in several examples including fermionic seed blocks in 3D CFT where they take a very simple form.

  18. Harmony of spinning conformal blocks

    Energy Technology Data Exchange (ETDEWEB)

    Schomerus, Volker [DESY Hamburg, Theory Group,Notkestraße 85, 22607 Hamburg (Germany); Sobko, Evgeny [Nordita and Stockholm University,Roslagstullsbacken 23, SE-106 91 Stockholm (Sweden); Isachenkov, Mikhail [Department of Particle Physics and Astrophysics, Weizmann Institute of Science,Rehovot 7610001 (Israel)

    2017-03-15

    Conformal blocks for correlation functions of tensor operators play an increasingly important role for the conformal bootstrap programme. We develop a universal approach to such spinning blocks through the harmonic analysis of certain bundles over a coset of the conformal group. The resulting Casimir equations are given by a matrix version of the Calogero-Sutherland Hamiltonian that describes the scattering of interacting spinning particles in a 1-dimensional external potential. The approach is illustrated in several examples including fermionic seed blocks in 3D CFT where they take a very simple form.

  19. Mass generation within conformal invariant theories

    International Nuclear Information System (INIS)

    Flato, M.; Guenin, M.

    1981-01-01

    The massless Yang-Mills theory is strongly conformally invariant and renormalizable; however, when masses are introduced the theory becomes nonrenormalizable and weakly conformally invariant. Conditions which recover strong conformal invariance are discussed in the letter. (author)

  20. Molecular insight into conformational transmission of human P-glycoprotein

    International Nuclear Information System (INIS)

    Chang, Shan-Yan; Liu, Fu-Feng; Dong, Xiao-Yan; Sun, Yan

    2013-01-01

    P-glycoprotein (P-gp), a kind of ATP-binding cassette transporter, can export candidates through a channel at the two transmembrane domains (TMDs) across the cell membranes using the energy released from ATP hydrolysis at the two nucleotide-binding domains (NBDs). Considerable evidence has indicated that human P-gp undergoes large-scale conformational changes to export a wide variety of anti-cancer drugs out of the cancer cells. However, molecular mechanism of the conformational transmission of human P-gp from the NBDs to the TMDs is still unclear. Herein, targeted molecular dynamics simulations were performed to explore the atomic detail of the conformational transmission of human P-gp. It is confirmed that the conformational transition from the inward- to outward-facing is initiated by the movement of the NBDs. It is found that the two NBDs move both on the two directions (x and y). The movement on the x direction leads to the closure of the NBDs, while the movement on the y direction adjusts the conformations of the NBDs to form the correct ATP binding pockets. Six key segments (KSs) protruding from the TMDs to interact with the NBDs are identified. The relative movement of the KSs along the y axis driven by the NBDs can be transmitted through α-helices to the rest of the TMDs, rendering the TMDs to open towards periplasm in the outward-facing conformation. Twenty eight key residue pairs are identified to participate in the interaction network that contributes to the conformational transmission from the NBDs to the TMDs of human P-gp. In addition, 9 key residues in each NBD are also identified. The studies have thus provided clear insight into the conformational transmission from the NBDs to the TMDs in human P-gp

  1. Higher-derivative generalization of conformal mechanics

    Science.gov (United States)

    Baranovsky, Oleg

    2017-08-01

    Higher-derivative analogs of multidimensional conformal particle and many-body conformal mechanics are constructed. Their Newton-Hooke counterparts are derived by applying appropriate coordinate transformations.

  2. Naturality in conformal field theory

    International Nuclear Information System (INIS)

    Moore, G.; Seiberg, N.

    1989-01-01

    We discuss constraints on the operator product coefficients in diagonal and nondiagonal rational conformal field theories. Nondiagonal modular invariants always arise from automorphisms of the fusion rule algebra or from extensions of the chiral algebra. Moreover, when the chiral algebra has been maximally extended a strong form of the naturality principle of field theory can be proven for rational conformal field theory: operator product coefficients vanish if and only if the corresponding fusion rules vanish; that is, if and only if the vanishing can be understood in terms of a symmetry. We illustrate these ideas with several examples. We also generalize our ideas about rational conformal field theories to a larger class of theories: 'quasi-rational conformal field theories' and we explore some of their properties. (orig.)

  3. Steady states in conformal theories

    CERN Multimedia

    CERN. Geneva

    2015-01-01

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

  4. 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...

  5. Aspect of the conformal invariance

    International Nuclear Information System (INIS)

    Bauer, M.

    1990-11-01

    This thesis is about the study of several physical and mathematical aspects of critical phenomena at two dimensions. These phenomena have remarkable symmetry properties in the coordonnates changes keeping the angles. They are named conformal theories

  6. 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.

  7. 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.

  8. Inverse bootstrapping conformal field theories

    Science.gov (United States)

    Li, Wenliang

    2018-01-01

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

  9. Intermediate Levels of Visual Processing

    National Research Council Canada - National Science Library

    Nakayama, Ken

    1998-01-01

    ...) surface representation, here we have shown that there is an intermediate level of visual processing, between the analysis of the image and higher order representations related to specific objects; (2...

  10. Towards an Approximate Conformance Relation for Hybrid I/O Automata

    Directory of Open Access Journals (Sweden)

    Morteza Mohaqeqi

    2016-12-01

    Full Text Available Several notions of conformance have been proposed for checking the behavior of cyber-physical systems against their hybrid systems models. In this paper, we explore the initial idea of a notion of approximate conformance that allows for comparison of both observable discrete actions and (sampled continuous trajectories. As such, this notion will consolidate two earlier notions, namely the notion of Hybrid Input-Output Conformance (HIOCO by M. van Osch and the notion of Hybrid Conformance by H. Abbas and G.E. Fainekos. We prove that our proposed notion of conformance satisfies a semi-transitivity property, which makes it suitable for a step-wise proof of conformance or refinement.

  11. Conformational stability analyses of alpha subunit I domain of LFA-1 and Mac-1.

    Directory of Open Access Journals (Sweden)

    Debin Mao

    Full Text Available β₂ integrin of lymphocyte function-associated antigen-1 (LFA-1 or macrophage-1 antigen (Mac-1 binds to their common ligand of intercellular adhesion molecule-1 (ICAM-1 and mediates leukocyte-endothelial cell (EC adhesions in inflammation cascade. Although the two integrins are known to have distinct functions, the corresponding micro-structural bases remain unclear. Here (steered-molecular dynamics simulations were employed to elucidate the conformational stability of α subunit I domains of LFA-1 and Mac-1 in different affinity states and relevant I domain-ICAM-1 interaction features. Compared with low affinity (LA Mac-1, the LA LFA-1 I domain was unstable in the presence or absence of ICAM-1 ligand, stemming from diverse orientations of its α₇-helix with different motifs of zipper-like hydrophobic junction between α₁- and α₇-helices. Meanwhile, spontaneous transition of LFA-1 I domain from LA state to intermediate affinity (IA state was first visualized. All the LA, IA, and high affinity (HA states of LFA-1 I domain and HA Mac-1 I domain were able to bind to ICAM-1 ligand effectively, while LA Mac-1 I domain was unfavorable for binding ligand presumably due to the specific orientation of S144 side-chain that capped the MIDAS ion. These results furthered our understanding in correlating the structural bases with their functions of LFA-1 and Mac-1 integrins from the viewpoint of I domain conformational stability and of the characteristics of I domain-ICAM-1 interactions.

  12. Conformal radiotherapy: principles and classification

    International Nuclear Information System (INIS)

    Rosenwald, J.C.; Gaboriaud, G.; Pontvert, D.

    1999-01-01

    'Conformal radiotherapy' is the name fixed by usage and given to a new form of radiotherapy resulting from the technological improvements observed during the last ten years. While this terminology is now widely used, no precise definition can be found in the literature. Conformal radiotherapy refers to an approach in which the dose distribution is more closely 'conformed' or adapted to the actual shape of the target volume. However, the achievement of a consensus on a more specific definition is hampered by various difficulties, namely in characterizing the degree of 'conformality'. We have therefore suggested a classification scheme be established on the basis of the tools and the procedures actually used for all steps of the process, i.e., from prescription to treatment completion. Our classification consists of four levels: schematically, at level 0, there is no conformation (rectangular fields); at level 1, a simple conformation takes place, on the basis of conventional 2D imaging; at level 2, a 3D reconstruction of the structures is used for a more accurate conformation; and level 3 includes research and advanced dynamic techniques. We have used our personal experience, contacts with colleagues and data from the literature to analyze all the steps of the planning process, and to define the tools and procedures relevant to a given level. The corresponding tables have been discussed and approved at the European level within the Dynarad concerted action. It is proposed that the term 'conformal radiotherapy' be restricted to procedures where all steps are at least at level 2. (author)

  13. Conformal Cosmology and Supernova Data

    OpenAIRE

    Behnke, Danilo; Blaschke, David; Pervushin, Victor; Proskurin, Denis

    2000-01-01

    We define the cosmological parameters $H_{c,0}$, $\\Omega_{m,c}$ and $\\Omega_{\\Lambda, c}$ within the Conformal Cosmology as obtained by the homogeneous approximation to the conformal-invariant generalization of Einstein's General Relativity theory. We present the definitions of the age of the universe and of the luminosity distance in the context of this approach. A possible explanation of the recent data from distant supernovae Ia without a cosmological constant is presented.

  14. Scalar perturbations and conformal transformation

    International Nuclear Information System (INIS)

    Fabris, J.C.; Tossa, J.

    1995-11-01

    The non-minimal coupling of gravity to a scalar field can be transformed into a minimal coupling through a conformal transformation. We show how to connect the results of a perturbation calculation, performed around a Friedman-Robertson-Walker background solution, before and after the conformal transformation. We work in the synchronous gauge, but we discuss the implications of employing other frames. (author). 16 refs

  15. Low temperature intermediate band metallic behavior in Ti implanted Si

    Energy Technology Data Exchange (ETDEWEB)

    Olea, Javier, E-mail: oleaariza@fis.ucm.es; Pastor, David; Garcia-Hemme, Eric; Garcia-Hernansanz, Rodrigo; Prado, Alvaro del; Martil, Ignacio; Gonzalez-Diaz, German

    2012-08-31

    Si samples implanted with very high Ti doses and subjected to Pulsed-Laser Melting (PLM) have been electrically analyzed in the scope of a two-layer model previously reported based on the Intermediate Band (IB) theory. Conductivity and Hall effect measurements using the van der Pauw technique suggest that the insulator-metal transition takes place for implantation doses in the 10{sup 14}-10{sup 16} cm{sup -2} range. Results of the sample implanted with the 10{sup 16} cm{sup -2} dose show a metallic behavior at low temperature that is explained by the formation of a p-type IB out of the Ti deep levels. This suggests that the IB would be semi-filled, which is essential for IB photovoltaic devices. - Highlights: Black-Right-Pointing-Pointer We fabricated high dose Ti implanted Si samples for intermediate band research. Black-Right-Pointing-Pointer We measured the electronic transport properties in the 7-300 K range. Black-Right-Pointing-Pointer We show an insulator to metallic transition when the intermediate band is formed. Black-Right-Pointing-Pointer The intermediate band is semi-filled and populated by holes. Black-Right-Pointing-Pointer We satisfactorily explain the electrical behavior by an intermediate band model.

  16. Conformational Stability of the NH2-Terminal Propeptide of the Precursor of Pulmonary Surfactant Protein SP-B.

    Directory of Open Access Journals (Sweden)

    Ángeles Bañares-Hidalgo

    Full Text Available Assembly of pulmonary surfactant lipid-protein complexes depends on conformational changes coupled with proteolytic maturation of proSP-B, the precursor of pulmonary surfactant protein B (SP-B, along the surfactant biogenesis pathway in pneumocytes. Conformational destabilization of the N-terminal propeptide of proSP-B (SP-BN triggers exposure of the mature SP-B domain for insertion into surfactant lipids. We have studied the conformational stability during GdmCl- or urea-promoted unfolding of SP-BN with trp fluorescence and circular dichroism spectroscopies. Binding of the intermediate states to bis-ANS suggests their molten globule-like character. ΔG0H2O was ~ 12.7 kJ·mol-1 either with urea or GdmCl. None of the thermal transitions of SP-BN detected by CD correspond to protein unfolding. Differential scanning calorimetry of SP-BN evidenced two endothermic peaks involved in oligomer dissociation as confirmed with 2 M urea. Ionic strength was relevant since at 150 mM NaCl, the process originating the endotherm at the highest temperature was irreversible (Tm2 = 108.5°C with an activation energy of 703.8 kJ·mol-1. At 500 mM NaCl the process became reversible (Tm2 = 114.4°C and data were fitted to the Non-two States model with two subpeaks. No free thiols in the propeptide could be titrated by DTNB with or without 5.7 M GdmCl, indicating disulfide bonds establishment.

  17. Quantum Conformal Algebras and Closed Conformal Field Theory

    CERN Document Server

    Anselmi, D

    1999-01-01

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

  18. Probing Conformational Stability and Dynamics of Erythroid and Nonerythroid Spectrin: Effects of Urea and Guanidine Hydrochloride

    Science.gov (United States)

    Patra, Malay; Mukhopadhyay, Chaitali; Chakrabarti, Abhijit

    2015-01-01

    We have studied the conformational stability of the two homologous membrane skeletal proteins, the erythroid and non-erythroid spectrins, in their dimeric and tetrameric forms respectively during unfolding in the presence of urea and guanidine hydrochloride (GuHCl). Fluorescence and circular dichroism (CD) spectroscopy have been used to study the changes of intrinsic tryptophan fluorescence, anisotropy, far UV-CD and extrinsic fluorescence of bound 1-anilinonapthalene-8-sulfonic acid (ANS). Chemical unfolding of both proteins were reversible and could be described as a two state transition. The folded erythroid spectrin and non-erythroid spectrin were directly converted to unfolded monomer without formation of any intermediate. Fluorescence quenching, anisotropy, ANS binding and dynamic light scattering data suggest that in presence of low concentrations of the denaturants (up-to 1M) hydrogen bonding network and van der Waals interaction play a role inducing changes in quaternary as well as tertiary structures without complete dissociation of the subunits. This is the first report of two large worm like, multi-domain proteins obeying twofold rule which is commonly found in small globular proteins. The free energy of stabilization (ΔGu H 2 0) for the dimeric spectrin has been 20 kcal/mol lesser than the tetrameric from. PMID:25617632

  19. Synthesis of Α-azido-oximes from chiral cyclo-hexanones. Conformation monitoring by NMR

    International Nuclear Information System (INIS)

    Alves, R.J.; Fontes Prado, M.A.; Oliveira, A.B. de; Souza Filho, J.D. de; GArcia, J.I.; Olesker, A.; Lukacs, G.

    1993-01-01

    Carbon hydrates are the greatest source of chirality due to a large number of functional groups. Such compounds present preferential conformations, which result in reactions which high level of stereo-selectivity. This work is concerned to the preparation of intermediates to several other synthesis of biological interest and how the above mentioned properties influence these synthesis

  20. A surprising role for conformational entropy in protein function

    Science.gov (United States)

    Wand, A. Joshua; Moorman, Veronica R.; Harpole, Kyle W.

    2014-01-01

    Formation of high-affinity complexes is critical for the majority of enzymatic reactions involving proteins. The creation of the family of Michaelis and other intermediate complexes during catalysis clearly involves a complicated manifold of interactions that are diverse and complex. Indeed, computing the energetics of interactions between proteins and small molecule ligands using molecular structure alone remains a grand challenge. One of the most difficult contributions to the free energy of protein-ligand complexes to experimentally access is that due to changes in protein conformational entropy. Fortunately, recent advances in solution nuclear magnetic resonance (NMR) relaxation methods have enabled the use of measures-of-motion between conformational states of a protein as a proxy for conformational entropy. This review briefly summarizes the experimental approaches currently employed to characterize fast internal motion in proteins, how this information is used to gain insight into conformational entropy, what has been learned and what the future may hold for this emerging view of protein function. PMID:23478875

  1. Slab tears and intermediate-depth seismicity

    Science.gov (United States)

    Meighan, Hallie E.; ten Brink, Uri S.; Pulliam, Jay

    2013-01-01

    Active tectonic regions where plate boundaries transition from subduction to strike slip can take several forms, such as triple junctions, acute, and obtuse corners. Well-documented slab tears that are associated with high rates of intermediate-depth seismicity are considered here: Gibraltar arc, the southern and northern ends of the Lesser Antilles arc, and the northern end of Tonga trench. Seismicity at each of these locations occurs, at times, in the form of swarms or clusters, and various authors have proposed that each marks an active locus of tear propagation. The swarms and clusters start at the top of the slab below the asthenospheric wedge and extend 30–60 km vertically downward within the slab. We propose that these swarms and clusters are generated by fluid-related embrittlement of mantle rocks. Focal mechanisms of these swarms generally fit the shear motion that is thought to be associated with the tearing process.

  2. Conformational changes in DNA gyrase revealed by limited proteolysis

    DEFF Research Database (Denmark)

    Kampranis, S C; Maxwell, A

    1998-01-01

    We have used limited proteolysis to identify conformational changes in DNA gyrase. Gyrase exhibits a proteolytic fingerprint dominated by two fragments, one of approximately 62 kDa, deriving from the A protein, and another of approximately 25 kDa from the B protein. Quinolone binding to the enzyme......-DNA intermediate by calcium ions does not reveal any protection, suggesting that the quinolone-induced conformational change is different from an "open-gate" state of the enzyme. A quinolone-resistant mutant of gyrase fails to give the characteristic quinolone-associated proteolytic signature. The ATP...... does not prevent dimerization since incubation of the enzyme-DNA complex with both ADPNP and quinolones gives rise to a complex whose proteolytic pattern retains the characteristic signature of dimerization but has lost the quinolone-induced protection. As a result, the quinolone-gyrase complex can...

  3. Physics of intermediate shocks: A review

    Science.gov (United States)

    Karimabadi, H.

    1995-01-01

    Intermediate shocks (ISs) lead to a transition from super-Alfvenic to sub-Alfvenic flow and are different from slow and fast shocks in that an IS rotates the component of the magnetic field tangent to the shock plane by 180 deg. Another peculiarity of ISs is that for the same upstream conditions an IS can have two different downstream states. There also exist a second class of ISs which rotate the magnetic field by an angle other than 180 deg. Due to their noncoplanar nature they cannot be time-stationary and are referred to as time-dependent intermediate shocks (TDIS). The existence of ISs has been the subject of much controversy over the years. Early studies questioned the physical reality of ISs. However, the studies of ISs found a new impetus when C.C. Wu showed that ISs do exist and are stable within the resistive MHD framework. In this paper, after a brief historical overview of the subject, we will review the latest developments in the study of ISs. In particular, we will address the questions of stability and structure of ISs and the relationship between ISs and other discontinuities. One of the recent developments has been the finding that ISs can be unsteady, reforming in time. Details of this process will be discussed. Finally, we examine the effect of anisotropy on the resolutions and discuss the relevance of ISs to the observed field rotations at the Earth's magnetopause.

  4. BANKING INTERMEDIATION AND CONSEQUENCES OF FINANCIAL CRISIS

    Directory of Open Access Journals (Sweden)

    Medar Lucian-Ion

    2012-12-01

    Full Text Available The financial intermediation of bank institutions, has an essential role in mobilising of the available funds and their distribution in various products and services, for economic growth. The extent that banking system is in distress or passing through a period of crisis, then, everything turns into a general crisis, especially that, in some states, natural and legal persons have been learned ,,to live’’ on the credits.The effectiveness of banking intermediation activity in Romania depends on how fast the market is enabled under the influence of the new European regulations. The Romanian market in all its forms is the second largest in the EU, and the banking system is almost entirely made up of banks with foreign capital. The romanian banking market has not suffered so much because of the financial crisis. To the extent that banking institutions provide the necessary funds, Romania has important resources for the transition to a new economic cycle based on sustainable development.

  5. Gauge fixing problem in the conformal QED

    International Nuclear Information System (INIS)

    Ichinose, Shoichi

    1986-01-01

    The gauge fixing problem in the conformal (spinor and scalar) QED is examined. For the analysis, we generalize Dirac's manifestly conformal-covariant formalism. It is shown that the (vector and matter) fields must obey a certain mixed (conformal and gauge) type of transformation law in order to fix the local gauge symmetry preserving the conformal invariance in the Lagrangian. (orig.)

  6. 40 CFR 93.154 - Conformity analysis.

    Science.gov (United States)

    2010-07-01

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

  7. Reactions of stabilized Criegee Intermediates

    Science.gov (United States)

    Vereecken, Luc; Harder, Hartwig; Novelli, Anna

    2014-05-01

    Carbonyl oxides (Criegee intermediates) were proposed as key intermediates in the gas phase ozonolysis of alkenes in 1975 by Rudolf Criegee. Despite the importance of ozonolysis in atmospheric chemistry, direct observation of these intermediates remained elusive, with only indirect experimental evidence for their role in the oxidation of hydrocarbons, e.g. through scavenging experiments. Direct experimental observation of stabilized CI has only been achieved since 2008. Since then, a concerted effort using experimental and theoretical means is in motion to characterize the chemistry and kinetics of these reactive intermediates. We present the results of theoretical investigations of the chemistry of Criegee intermediates with a series of coreactants which may be of importance in the atmosphere, in experimental setups, or both. This includes the CI+CI cross-reaction, which proceeds with a rate coefficient near the collision limit and can be important in experimental conditions. The CI + alkene reactions show strong dependence of the rate coefficient depending on the coreactants, but is generally found to be rather slow. The CI + ozone reaction is sufficiently fast to occur both in experiment and the free troposphere, and acts as a sink for CI. The reaction of CI with hydroperoxides, ROOH, is complex, and leads both to the formation of oligomers, as to the formation of reactive etheroxides, with a moderately fast rate coefficient. The importance of these reactions is placed in the context of the reaction conditions in different atmospheric environments ranging from unpolluted to highly polluted.

  8. Conformational elasticity can facilitate TALE-DNA recognition.

    Science.gov (United States)

    Lei, Hongxing; Sun, Jiya; Baldwin, Enoch P; Segal, David J; Duan, Yong

    2014-01-01

    Sequence-programmable transcription activator-like effector (TALE) proteins have emerged as a highly efficient tool for genome engineering. Recent crystal structures depict a transition between an open unbound solenoid and more compact DNA-bound solenoid formed by the 34 amino acid repeats. How TALEs switch conformation between these two forms without substantial energetic compensation, and how the repeat-variable di-residues (RVDs) discriminate between the cognate base and other bases still remain unclear. Computational analysis on these two aspects of TALE-DNA interaction mechanism has been conducted in order to achieve a better understanding of the energetics. High elasticity was observed in the molecular dynamics simulations of DNA-free TALE structure that started from the bound conformation where it sampled a wide range of conformations including the experimentally determined apo and bound conformations. This elastic feature was also observed in the simulations starting from the apo form which suggests low free energy barrier between the two conformations and small compensation required upon binding. To analyze binding specificity, we performed free energy calculations of various combinations of RVDs and bases using Poisson-Boltzmann surface area (PBSA) and other approaches. The PBSA calculations indicated that the native RVD-base structures had lower binding free energy than mismatched structures for most of the RVDs examined. Our theoretical analyses provided new insight on the dynamics and energetics of TALE-DNA binding mechanism. © 2014 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2017-07-15

    Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. Despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groups of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation. The source code, binaries and data are available at https://simtk.org/home/kgs . amelie.heliou@polytechnique.edu or vdbedem@stanford.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  10. Escherichia coli Phosphoenolpyruvate Dependent Phosphotransferase System. NMR Studies of the Conformation of HPr and P-HPr and the Mechanism of Energy Coupling

    NARCIS (Netherlands)

    Dooijewaard, G.; Roossien, F.F.; Robillard, G.T.

    1979-01-01

    1H and 31P nuclear magnetic resonance investigations of the phosphoprotein intermediate P-HPr and the parent molecule HPr of the E. coli phosphoenolpyruvate dependent phosphotransferase system (PTS) show that HPr can exist in two conformations. These conformations influence the protonation state of

  11. Conformational Clusters of Phosphorylated Tyrosine.

    Science.gov (United States)

    Abdelrasoul, Maha; Ponniah, Komala; Mao, Alice; Warden, Meghan S; Elhefnawy, Wessam; Li, Yaohang; Pascal, Steven M

    2017-12-06

    Tyrosine phosphorylation plays an important role in many cellular and intercellular processes including signal transduction, subcellular localization, and regulation of enzymatic activity. In 1999, Blom et al., using the limited number of protein data bank (PDB) structures available at that time, reported that the side chain structures of phosphorylated tyrosine (pY) are partitioned into two conserved conformational clusters ( Blom, N.; Gammeltoft, S.; Brunak, S. J. Mol. Biol. 1999 , 294 , 1351 - 1362 ). We have used the spectral clustering algorithm to cluster the increasingly growing number of protein structures with pY sites, and have found that the pY residues cluster into three distinct side chain conformations. Two of these pY conformational clusters associate strongly with a narrow range of tyrosine backbone conformation. The novel cluster also highly correlates with the identity of the n + 1 residue, and is strongly associated with a sequential pYpY conformation which places two adjacent pY side chains in a specific relative orientation. Further analysis shows that the three pY clusters are associated with distinct distributions of cognate protein kinases.

  12. Intermediate coupling collision strengths from LS coupled R-matrix elements

    International Nuclear Information System (INIS)

    Clark, R.E.H.

    1978-01-01

    Fine structure collision strength for transitions between two groups of states in intermediate coupling and with inclusion of configuration mixing are obtained from LS coupled reactance matrix elements (R-matrix elements) and a set of mixing coefficients. The LS coupled R-matrix elements are transformed to pair coupling using Wigner 6-j coefficients. From these pair coupled R-matrix elements together with a set of mixing coefficients, R-matrix elements are obtained which include the intermediate coupling and configuration mixing effects. Finally, from the latter R-matrix elements, collision strengths for fine structure transitions are computed (with inclusion of both intermediate coupling and configuration mixing). (Auth.)

  13. Evidence for close side-chain packing in an early protein folding intermediate previously assumed to be a molten globule.

    Science.gov (United States)

    Rosen, Laura E; Connell, Katelyn B; Marqusee, Susan

    2014-10-14

    The molten globule, a conformational ensemble with significant secondary structure but only loosely packed tertiary structure, has been suggested to be a ubiquitous intermediate in protein folding. However, it is difficult to assess the tertiary packing of transiently populated species to evaluate this hypothesis. Escherichia coli RNase H is known to populate an intermediate before the rate-limiting barrier to folding that has long been thought to be a molten globule. We investigated this hypothesis by making mimics of the intermediate that are the ground-state conformation at equilibrium, using two approaches: a truncation to generate a fragment mimic of the intermediate, and selective destabilization of the native state using point mutations. Spectroscopic characterization and the response of the mimics to further mutation are consistent with studies on the transient kinetic intermediate, indicating that they model the early intermediate. Both mimics fold cooperatively and exhibit NMR spectra indicative of a closely packed conformation, in contrast to the hypothesis of molten tertiary packing. This result is important for understanding the nature of the subsequent rate-limiting barrier to folding and has implications for the assumption that many other proteins populate molten globule folding intermediates.

  14. Hierarchical Conformational Analysis of Native Lysozyme Based on Sub-Millisecond Molecular Dynamics Simulations.

    Directory of Open Access Journals (Sweden)

    Kai Wang

    Full Text Available Hierarchical organization of free energy landscape (FEL for native globular proteins has been widely accepted by the biophysics community. However, FEL of native proteins is usually projected onto one or a few dimensions. Here we generated collectively 0.2 milli-second molecular dynamics simulation trajectories in explicit solvent for hen egg white lysozyme (HEWL, and carried out detailed conformational analysis based on backbone torsional degrees of freedom (DOF. Our results demonstrated that at micro-second and coarser temporal resolutions, FEL of HEWL exhibits hub-like topology with crystal structures occupying the dominant structural ensemble that serves as the hub of conformational transitions. However, at 100 ns and finer temporal resolutions, conformational substates of HEWL exhibit network-like topology, crystal structures are associated with kinetic traps that are important but not dominant ensembles. Backbone torsional state transitions on time scales ranging from nanoseconds to beyond microseconds were found to be associated with various types of molecular interactions. Even at nanoseconds temporal resolution, the number of conformational substates that are of statistical significance is quite limited. These observations suggest that detailed analysis of conformational substates at multiple temporal resolutions is both important and feasible. Transition state ensembles among various conformational substates at microsecond temporal resolution were observed to be considerably disordered. Life times of these transition state ensembles are found to be nearly independent of the time scales of the participating torsional DOFs.

  15. Search for intermediate vector bosons

    International Nuclear Information System (INIS)

    Cline, D.B.; Rubbia, C.; van der Meer, S.

    1982-01-01

    Over the past 15 years a new class of unified theories has been developed to describe the forces acting between elementary particles. The most successful of the new theories establishes a link between electromagnetism and the weak force. A crucial prediction of this unified electroweak theory is the existence of three massive particles called intermediate vector bosons. If these intermediate vector bosons exist and if they have properties attributed to them by electroweak theory, they should soon be detected, as the world's first particle accelerator with enough energy to create such particles has recently been completed at the European Organization for Nuclear Research (CERN) in Geneva. The accelerator has been converted to a colliding beam machine in which protons and antiprotons collide head on. According to electroweak theory, intermediate vector bosons can be created in proton-antiproton collisions. (SC)

  16. Search for intermediate vector bosons

    International Nuclear Information System (INIS)

    Klajn, D.B.; Rubbia, K.; Meer, S.

    1983-01-01

    Problem of registration and search for intermediate vector bosons is discussed. According to weak-current theory there are three intermediate vector bosons with +1(W + )-1(W - ) and zero (Z 0 ) electric charges. It was suggested to conduct the investigation into particles in 1976 by cline, Rubbia and Makintair using proton-antiproton beams. Major difficulties of the experiment are related to the necessity of formation of sufficient amount of antiparticles and the method of antiproton beam ''cooling'' for the purpose of reduction of its random movements. The stochastic method was suggested by van der Meer in 1968 as one of possible cooling methods. Several large detectors were designed for searching intermediate vector bosons

  17. Gravity with Intermediate Goods Trade

    Directory of Open Access Journals (Sweden)

    Sujin Jang

    2017-12-01

    Full Text Available This paper derives the gravity equation with intermediate goods trade. We extend a standard monopolistic competition model to incorporate intermediate goods trade, and show that the gravity equation with intermediates trade is identical to the one without it except in that gross output should be used as the output measure instead of value added. We also show that the output elasticity of trade is significantly underestimated when value added is used as the output measure. This implies that with the conventional gravity equation, the contribution of output growth can be substantially underestimated and the role of trade costs reduction can be exaggerated in explaining trade expansion, as we demonstrate for the case of Korea's trade growth between 1995 and 2007.

  18. Applications of Molecular Modeling to Transition State Energies and Conformations

    Science.gov (United States)

    1992-05-08

    reactivity trends for similar systems are known. Illuminati and Mandolini have done research on the lactone formation from w-bromoalkane-carboxylate...strikingly similar to that determined for Illuminati and Mandolini’s similar lactonization system (see Figure 20). The AE, for the 4- 69 membered ring...Brown, F.K.; Spellmeyer, D.C.; Metz, J.T.; Li, Y.; Loncharich, R.L. Science. 1986, 231, 1108-17. Illuminati , G.; Mandolini, L. Accts. of Chem. Res. 1981

  19. Water Evaporation and Conformational Changes from Partially Solvated Ubiquitin

    Directory of Open Access Journals (Sweden)

    Saravana Prakash Thirumuruganandham

    2010-01-01

    Full Text Available Using molecular dynamics simulation, we study the evaporation of water molecules off partially solvated ubiquitin. The evaporation and cooling rates are determined for a molecule at the initial temperature of 300 K. The cooling rate is found to be around 3 K/ns, and decreases with water temperature in the course of the evaporation. The conformation changes are monitored by studying a variety of intermediate partially solvated ubiquitin structures. We find that ubiquitin shrinks with decreasing hydration shell and exposes more of its hydrophilic surface area to the surrounding.

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

    Science.gov (United States)

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

    2015-08-20

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

  1. 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.

  2. Conformal dimension theory and application

    CERN Document Server

    Mackay, John M

    2010-01-01

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

  3. Elementary introduction to conformal invariance

    International Nuclear Information System (INIS)

    Grandati, Y.

    1992-01-01

    These notes constitute an elementary introduction to the concept of conformal invariance and its applications to the study of bidimensional critical phenomena. The aim is to give an access as pedestrian as possible to this vast subject. After a brief account of the general properties of conformal transformation in D dimensions, we study more specifically the case D = 2. The center of the discussion is then the consequences of the action of this symmetry group on bidimensional field theories, and in particular the links between the representations of the Virasoro algebra and the structure of the correlation functions of conformal field theories. Finally after showing how the Ising model reduces to a Majorana fermionic field theory, we see how the general formalism previously discussed can be applied to the Ising case at the critical point. (orig.)

  4. Conformal geometry and quasiregular mappings

    CERN Document Server

    Vuorinen, Matti

    1988-01-01

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

  5. Renyi entropy and conformal defects

    International Nuclear Information System (INIS)

    Bianchi, Lorenzo; Myers, Robert C.; Smolkin, Michael

    2016-01-01

    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.

  6. Future possibilities with intermediate-energy neutron beams

    International Nuclear Information System (INIS)

    Brady, F.P.

    1987-01-01

    Future possibilities for using neutrons of intermediate energies (50 - 200 MeV) as a probe of the nucleus are discussed. Some of the recent thinking concerning a systematic approach for studying elastic and inelastic scattering of electrons and hadrons and the important role of medium- and intermediate-energy neutrons in such a programme is reviewed. The advantages of neutrons in this energy range over neutrons with lower energies and over intermediate-energy pions for determining nuclear-transition and ground state densities, and for distinguishing proton from neutron density (isovector sensitivity), are noted. The important role of (n,p) charge exchange reactions in nuclear excitation studies is also reviewed. Experimental methods for utilizing neutrons as probes in elastic, inelastic, and charge exchange studies at these energies are discussed

  7. About the structure of quantum intermediate state of superconductors

    International Nuclear Information System (INIS)

    Ledenev, O.P.

    2008-01-01

    The calculation of spatial structure of a quantum intermediate state in Type I superconductors is completed. Theoretical model of thermodynamics of considered state was proposed by Andreev. It is shown, that in a quantum case, the period of structure appears significantly smaller and has different dependence on both the magnetic field and temperature than in the classical intermediate Landau state. The decrease of thickness of normal layers results in increase of characteristic distance between the quantum Andreev levels of electronic excitations, and the transition to the quantum intermediate from classical state is realized at higher temperatures ∼1 K, than it was supposed in previous works. The comparison of calculation data with experimental results, for example using the sample of mono-crystal gallium, is conducted

  8. SUSY Unparticle and Conformal Sequestering

    Energy Technology Data Exchange (ETDEWEB)

    Nakayama, Yu; Nakayama, Yu

    2007-07-17

    We investigate unparticle physics with supersymmetry (SUSY). The SUSY breaking effects due to the gravity mediation induce soft masses for the SUSY unparticles and hence break the conformal invariance. The unparticle physics observable in near future experiments is only consistent if the SUSY breakingeffects from the hidden sector to the standard model sector are dominated by the gauge mediation, or if the SUSY breaking effects to the unparticle sector are sufficiently sequestered. We argue that the natural realization of the latter possibility is the conformal sequestering scenario.

  9. 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

  10. Topics in conformal field theory

    International Nuclear Information System (INIS)

    Kiritsis, E.B.

    1988-01-01

    In this work two major topics in Conformal Field Theory are discussed. First a detailed investigation of N = 2 Superconformal theories is presented. The structure of the representations of the N = 2 superconformal algebras is investigated and the character formulae are calculated. The general structure of N = 2 superconformal theories is elucidated and the operator algebra of the minimal models is derived. The first minimal system is discussed in more detail. Second, applications of the conformal techniques are studied in the Ashkin-Teller model. The c = 1 as well as the c = 1/2 critical lines are discussed in detail

  11. Larval helminths in intermediate hosts

    DEFF Research Database (Denmark)

    Fredensborg, Brian Lund; Poulin, R

    2005-01-01

    Density-dependent effects on parasite fitness have been documented from adult helminths in their definitive hosts. There have, however, been no studies on the cost of sharing an intermediate host with other parasites in terms of reduced adult parasite fecundity. Even if larval parasites suffer a ...

  12. Intermediate statistics in quantum maps

    Energy Technology Data Exchange (ETDEWEB)

    Giraud, Olivier [H H Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL (United Kingdom); Marklof, Jens [School of Mathematics, University of Bristol, University Walk, Bristol BS8 1TW (United Kingdom); O' Keefe, Stephen [School of Mathematics, University of Bristol, University Walk, Bristol BS8 1TW (United Kingdom)

    2004-07-16

    We present a one-parameter family of quantum maps whose spectral statistics are of the same intermediate type as observed in polygonal quantum billiards. Our central result is the evaluation of the spectral two-point correlation form factor at small argument, which in turn yields the asymptotic level compressibility for macroscopic correlation lengths. (letter to the editor)

  13. Intermediality and the Child Performer

    Science.gov (United States)

    Budd, Natasha

    2016-01-01

    This report details examples of praxis in the creation and presentation of "Joy Fear and Poetry": an intermedial theatre performance in which children aged 7-12 years generated aesthetic gestures using a range of new media forms. The impetus for the work's development was a desire to make an intervention into habituated patterns of…

  14. Material Voices: Intermediality and Autism

    Science.gov (United States)

    Trimingham, Melissa; Shaughnessy, Nicola

    2016-01-01

    Autism continues to be regarded enigmatically; a community that is difficult to access due to perceived disruptions of interpersonal connectedness. Through detailed observations of two children participating in the Arts and Humanities Research Council funded project "Imagining Autism: Drama, Performance and Intermediality as Interventions for…

  15. Magnetic re-entrance in intermediate valence compounds

    International Nuclear Information System (INIS)

    Allub, R.; Machiavelli, O.; Balseiro, C.; Alascio, B.

    1980-01-01

    The possibility is explored of magnetic re-entrance in intermediate valence compounds. Using a simplified Anderson-Lattice model the pressure-temperature magnetic phase diagram is obtained. This diagram shows that for some value of the microscopic parameters the temperature induced two transitions (non-magnetic to magnetically ordered to paramagnetic). The magnetization and the average occupation number of the localized state are calculated. Estimations of the observability of the effect in systems like CeAl 2 are made. (author)

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

    CERN Document Server

    Karevski, Dragi

    2012-01-01

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

  17. Classical model of intermediate statistics

    International Nuclear Information System (INIS)

    Kaniadakis, G.

    1994-01-01

    In this work we present a classical kinetic model of intermediate statistics. In the case of Brownian particles we show that the Fermi-Dirac (FD) and Bose-Einstein (BE) distributions can be obtained, just as the Maxwell-Boltzmann (MD) distribution, as steady states of a classical kinetic equation that intrinsically takes into account an exclusion-inclusion principle. In our model the intermediate statistics are obtained as steady states of a system of coupled nonlinear kinetic equations, where the coupling constants are the transmutational potentials η κκ' . We show that, besides the FD-BE intermediate statistics extensively studied from the quantum point of view, we can also study the MB-FD and MB-BE ones. Moreover, our model allows us to treat the three-state mixing FD-MB-BE intermediate statistics. For boson and fermion mixing in a D-dimensional space, we obtain a family of FD-BE intermediate statistics by varying the transmutational potential η BF . This family contains, as a particular case when η BF =0, the quantum statistics recently proposed by L. Wu, Z. Wu, and J. Sun [Phys. Lett. A 170, 280 (1992)]. When we consider the two-dimensional FD-BE statistics, we derive an analytic expression of the fraction of fermions. When the temperature T→∞, the system is composed by an equal number of bosons and fermions, regardless of the value of η BF . On the contrary, when T=0, η BF becomes important and, according to its value, the system can be completely bosonic or fermionic, or composed both by bosons and fermions

  18. Spin-4 extended conformal algebras

    International Nuclear Information System (INIS)

    Kakas, A.C.

    1988-01-01

    We construct spin-4 extended conformal algebras using the second hamiltonian structure of the KdV hierarchy. In the presence of a U(1) current a family of spin-4 algebras exists but the additional requirement that the spin-1 and spin-4 currents commute fixes the algebra uniquely. (orig.)

  19. Defects in conformal field theory

    International Nuclear Information System (INIS)

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

    2016-01-01

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

  20. Conformal symmetry and holographic cosmology

    NARCIS (Netherlands)

    Bzowski, A.W.

    2013-01-01

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

  1. Checking behavioral conformance of artifacts

    NARCIS (Netherlands)

    Fahland, D.; Leoni, de M.; Dongen, van B.F.; Aalst, van der W.M.P.

    2011-01-01

    The usefulness of process models (e.g., for analysis, improvement, or execution) strongly depends on their ability to describe reality. Conformance checking is a technique to validate how good a given process model describes recorded executions of the actual process. Recently, artifacts have been

  2. Conformation analysis of oligomeric flavanoids

    Science.gov (United States)

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

    1995-01-01

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

  3. Conformational analysis of oligomeric flavanoids

    Science.gov (United States)

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

    1995-01-01

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

  4. Inversion theory and conformal mapping

    CERN Document Server

    Blair, David E

    2000-01-01

    It is rarely taught in an undergraduate or even graduate curriculum that the only conformal maps in Euclidean space of dimension greater than two are those generated by similarities and inversions in spheres. This is in stark contrast to the wealth of conformal maps in the plane. The principal aim of this text is to give a treatment of this paucity of conformal maps in higher dimensions. The exposition includes both an analytic proof in general dimension and a differential-geometric proof in dimension three. For completeness, enough complex analysis is developed to prove the abundance of conformal maps in the plane. In addition, the book develops inversion theory as a subject, along with the auxiliary theme of circle-preserving maps. A particular feature is the inclusion of a paper by Carath�odory with the remarkable result that any circle-preserving transformation is necessarily a M�bius transformation, not even the continuity of the transformation is assumed. The text is at the level of advanced undergr...

  5. Defects in conformal field theory

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-04-15

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

  6. Supertwistor connection and conformal supergravity

    International Nuclear Information System (INIS)

    Merkulov, S.A.

    1985-01-01

    Supersymmetry expansion of the geometry of local twistors is suggested. Definition of the space of local supertwistors is given and its differential geometry is formulated. Variational principles are discussed, and it is shown that corresponding Euler-Lagrange equations also coincide and result in superzero equations of N=1 conformal supergravitation, which generalize Bach equations

  7. Conformal symmetry and string theories

    International Nuclear Information System (INIS)

    Kumar, A.

    1987-01-01

    This thesis is devoted to the study of various aspects of the 2-dimensional conformal field theory and its applications to strings. We make a short review of the conformal field theory and its supersymmetric extension, called superconformal field theory. We present an elegant superspace formulation of these theories and solve the condition for the closure of the superconformal algebra. The we go on to classify the superconformal field theories according to these solutions. We prove that N ≥ 5 superconformal algebra, with N being the number of supersymmetries, does not have central charge. We find the primary representations of all the interesting superconformal algebra. We study the quantization of the superconformal theories and derive the constraints on the central charge of the algebra that has to be satisfied for a consistent quantum theory. This quantization process also determines the ground state energy of the system and the spectrum of the model. We study the global aspects of the conformal symmetry and its role in the construction of consistent heterotic string theories. We prove the uniqueness of heterotic superstring theories in 10 dimensions in the fermionic constructions. We show how the vertex operators are closely associated with the primary field representation of the conformal algebra. We utilize these vertex operator constructions to obtain tree amplitudes in the 10-dimensional heterotic string theory. We show by explicit calculation at the 3-point level that the scattering amplitudes derived from the heterotic superstring are same as the ones obtained from 10-dimensional supergravity theories

  8. 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...

  9. 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...

  10. Trickle-Down Preferences: Preferential Conformity to High Status Peers in Fashion Choices

    Science.gov (United States)

    Galak, Jeff; Gray, Kurt; Elbert, Igor; Strohminger, Nina

    2016-01-01

    How much do our choices represent stable inner preferences versus social conformity? We examine conformity and consistency in sartorial choices surrounding a common life event of new norm exposure: relocation. A large-scale dataset of individual purchases of women’s shoes (16,236 transactions) across five years and 2,007 women reveals a balance of conformity and consistency, moderated by changes in location socioeconomic status. Women conform to new local norms (i.e., average heel size) when moving to relatively higher status locations, but mostly ignore new local norms when moving to relatively lower status locations. In short, at periods of transition, it is the fashion norms of the rich that trickle down to consumers. These analyses provide the first naturalistic large-scale demonstration of the tension between psychological conformity and consistency, with real decisions in a highly visible context. PMID:27144595

  11. Trickle-Down Preferences: Preferential Conformity to High Status Peers in Fashion Choices.

    Directory of Open Access Journals (Sweden)

    Jeff Galak

    Full Text Available How much do our choices represent stable inner preferences versus social conformity? We examine conformity and consistency in sartorial choices surrounding a common life event of new norm exposure: relocation. A large-scale dataset of individual purchases of women's shoes (16,236 transactions across five years and 2,007 women reveals a balance of conformity and consistency, moderated by changes in location socioeconomic status. Women conform to new local norms (i.e., average heel size when moving to relatively higher status locations, but mostly ignore new local norms when moving to relatively lower status locations. In short, at periods of transition, it is the fashion norms of the rich that trickle down to consumers. These analyses provide the first naturalistic large-scale demonstration of the tension between psychological conformity and consistency, with real decisions in a highly visible context.

  12. Trickle-Down Preferences: Preferential Conformity to High Status Peers in Fashion Choices.

    Science.gov (United States)

    Galak, Jeff; Gray, Kurt; Elbert, Igor; Strohminger, Nina

    2016-01-01

    How much do our choices represent stable inner preferences versus social conformity? We examine conformity and consistency in sartorial choices surrounding a common life event of new norm exposure: relocation. A large-scale dataset of individual purchases of women's shoes (16,236 transactions) across five years and 2,007 women reveals a balance of conformity and consistency, moderated by changes in location socioeconomic status. Women conform to new local norms (i.e., average heel size) when moving to relatively higher status locations, but mostly ignore new local norms when moving to relatively lower status locations. In short, at periods of transition, it is the fashion norms of the rich that trickle down to consumers. These analyses provide the first naturalistic large-scale demonstration of the tension between psychological conformity and consistency, with real decisions in a highly visible context.

  13. Restricted conformal invariance in QCD and its predictive power for virtual two-photon processes

    CERN Document Server

    Müller, D

    1998-01-01

    The conformal algebra provides powerful constraints, which guarantee that renormalized conformally covariant operators exist in the hypothetical conformal limit of the theory, where the $\\beta$-function vanishes. Thus, in this limit also the conformally covariant operator product expansion on the light cone holds true. This operator product expansion has predictive power for two-photon processes in the generalized Bjorken region. Only the Wilson coefficients and the anomalous dimensions that are known from deep inelastic scattering are required for the prediction of all other two-photon processes in terms of the process-dependent off-diagonal expectation values of conformal operators. It is checked that the next-to-leading order calculations for the flavour non-singlet meson transition form factors are consistent with the corrections to the corresponding Wilson coefficients in deep inelasitic scattering.

  14. Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Zeynab Mohammad Hosseini Naveh

    Full Text Available Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of the acetylcholine binding protein (AChBP, a widely accepted model for the full receptor extracellular domain. Using unbiased Molecular Dynamics (MD and Temperature Accelerated Molecular Dynamics (TAMD simulations we investigate the AChBP transition between the apo and the agonist-bound state. In long standard MD simulations, both conformations of the native protein are stable, while the agonist-bound structure evolves toward the apo one if the orientation of few key sidechains in the orthosteric cavity is modified. Conversely, TAMD simulations initiated from the native conformations are able to produce the spontaneous transition. With respect to the modified conformations, TAMD accelerates the transition by at least a factor 10. The analysis of some specific residue-residue interactions points out that the transition mechanism is based on the disruption/formation of few key hydrogen bonds. Finally, while early events of ligand dissociation are observed already in standard MD, TAMD accelerates the ligand detachment and, at the highest TAMD effective temperature, it is able to produce a complete dissociation path in one AChBP subunit.

  15. Structure of a low-population intermediate state in the release of an enzyme product.

    Science.gov (United States)

    De Simone, Alfonso; Aprile, Francesco A; Dhulesia, Anne; Dobson, Christopher M; Vendruscolo, Michele

    2015-01-09

    Enzymes can increase the rate of biomolecular reactions by several orders of magnitude. Although the steps of substrate capture and product release are essential in the enzymatic process, complete atomic-level descriptions of these steps are difficult to obtain because of the transient nature of the intermediate conformations, which makes them largely inaccessible to standard structure determination methods. We describe here the determination of the structure of a low-population intermediate in the product release process by human lysozyme through a combination of NMR spectroscopy and molecular dynamics simulations. We validate this structure by rationally designing two mutations, the first engineered to destabilise the intermediate and the second to stabilise it, thus slowing down or speeding up, respectively, product release. These results illustrate how product release by an enzyme can be facilitated by the presence of a metastable intermediate with transient weak interactions between the enzyme and product.

  16. Probing Protein Multidimensional Conformational Fluctuations by Single-Molecule Multiparameter Photon Stamping Spectroscopy

    Science.gov (United States)

    2015-01-01

    Conformational motions of proteins are highly dynamic and intrinsically complex. To capture the temporal and spatial complexity of conformational motions and further to understand their roles in protein functions, an attempt is made to probe multidimensional conformational dynamics of proteins besides the typical one-dimensional FRET coordinate or the projected conformational motions on the one-dimensional FRET coordinate. T4 lysozyme hinge-bending motions between two domains along α-helix have been probed by single-molecule FRET. Nevertheless, the domain motions of T4 lysozyme are rather complex involving multiple coupled nuclear coordinates and most likely contain motions besides hinge-bending. It is highly likely that the multiple dimensional protein conformational motions beyond the typical enzymatic hinged-bending motions have profound impact on overall enzymatic functions. In this report, we have developed a single-molecule multiparameter photon stamping spectroscopy integrating fluorescence anisotropy, FRET, and fluorescence lifetime. This spectroscopic approach enables simultaneous observations of both FRET-related site-to-site conformational dynamics and molecular rotational (or orientational) motions of individual Cy3-Cy5 labeled T4 lysozyme molecules. We have further observed wide-distributed rotational flexibility along orientation coordinates by recording fluorescence anisotropy and simultaneously identified multiple intermediate conformational states along FRET coordinate by monitoring time-dependent donor lifetime, presenting a whole picture of multidimensional conformational dynamics in the process of T4 lysozyme open-close hinge-bending enzymatic turnover motions under enzymatic reaction conditions. By analyzing the autocorrelation functions of both lifetime and anisotropy trajectories, we have also observed the dynamic and static inhomogeneity of T4 lysozyme multidimensional conformational fluctuation dynamics, providing a fundamental

  17. 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.

    2013-01-01

    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. PMID:23649628

  18. Effects of macromolecular crowding on protein conformational changes.

    Directory of Open Access Journals (Sweden)

    Hao Dong

    2010-07-01

    Full Text Available Many protein functions can be directly linked to conformational changes. Inside cells, the equilibria and transition rates between different conformations may be affected by macromolecular crowding. We have recently developed a new approach for modeling crowding effects, which enables an atomistic representation of "test" proteins. Here this approach is applied to study how crowding affects the equilibria and transition rates between open and closed conformations of seven proteins: yeast protein disulfide isomerase (yPDI, adenylate kinase (AdK, orotidine phosphate decarboxylase (ODCase, Trp repressor (TrpR, hemoglobin, DNA beta-glucosyltransferase, and Ap(4A hydrolase. For each protein, molecular dynamics simulations of the open and closed states are separately run. Representative open and closed conformations are then used to calculate the crowding-induced changes in chemical potential for the two states. The difference in chemical-potential change between the two states finally predicts the effects of crowding on the population ratio of the two states. Crowding is found to reduce the open population to various extents. In the presence of crowders with a 15 A radius and occupying 35% of volume, the open-to-closed population ratios of yPDI, AdK, ODCase and TrpR are reduced by 79%, 78%, 62% and 55%, respectively. The reductions for the remaining three proteins are 20-44%. As expected, the four proteins experiencing the stronger crowding effects are those with larger conformational changes between open and closed states (e.g., as measured by the change in radius of gyration. Larger proteins also tend to experience stronger crowding effects than smaller ones [e.g., comparing yPDI (480 residues and TrpR (98 residues]. The potentials of mean force along the open-closed reaction coordinate of apo and ligand-bound ODCase are altered by crowding, suggesting that transition rates are also affected. These quantitative results and qualitative trends will

  19. Lid opening and conformational stability of T1 Lipase is mediated by increasing chain length polar solvents

    Directory of Open Access Journals (Sweden)

    Jonathan Maiangwa

    2017-05-01

    Full Text Available The dynamics and conformational landscape of proteins in organic solvents are events of potential interest in nonaqueous process catalysis. Conformational changes, folding transitions, and stability often correspond to structural rearrangements that alter contacts between solvent molecules and amino acid residues. However, in nonaqueous enzymology, organic solvents limit stability and further application of proteins. In the present study, molecular dynamics (MD of a thermostable Geobacillus zalihae T1 lipase was performed in different chain length polar organic solvents (methanol, ethanol, propanol, butanol, and pentanol and water mixture systems to a concentration of 50%. On the basis of the MD results, the structural deviations of the backbone atoms elucidated the dynamic effects of water/organic solvent mixtures on the equilibrium state of the protein simulations in decreasing solvent polarity. The results show that the solvent mixture gives rise to deviations in enzyme structure from the native one simulated in water. The drop in the flexibility in H2O, MtOH, EtOH and PrOH simulation mixtures shows that greater motions of residues were influenced in BtOH and PtOH simulation mixtures. Comparing the root mean square fluctuations value with the accessible solvent area (SASA for every residue showed an almost correspondingly high SASA value of residues to high flexibility and low SASA value to low flexibility. The study further revealed that the organic solvents influenced the formation of more hydrogen bonds in MtOH, EtOH and PrOH and thus, it is assumed that increased intraprotein hydrogen bonding is ultimately correlated to the stability of the protein. However, the solvent accessibility analysis showed that in all solvent systems, hydrophobic residues were exposed and polar residues tended to be buried away from the solvent. Distance variation of the tetrahedral intermediate packing of the active pocket was not conserved in organic solvent

  20. Correlated Default and Financial Intermediation

    OpenAIRE

    Gregory Phelan

    2015-01-01

    Financial intermediation naturally arises when knowledge about the aggregate state is valuable for managing investments and lenders cannot easily observe the aggregate state. I show this using a costly enforcement model in which lenders need ex-post incentives to enforce payments from defaulted loans and borrowers' payoffs are correlated. When projects have correlated outcomes, learning the state of one project (via enforcement) provides information about the states of other projects. A large...

  1. Conformal and Nearly Conformal Theories at Large N

    Science.gov (United States)

    Tarnoplskiy, Grigory M.

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

  2. Conformal invariance in the quantum field theory

    International Nuclear Information System (INIS)

    Kurak, V.

    1975-09-01

    Basic features concerning the present knowledge of conformal symmetry are illustrated in a simple model. Composite field dimensions of this model are computed and related to the conformal group. (author) [pt

  3. Gauge theory of glass transition

    International Nuclear Information System (INIS)

    Vasin, Mikhail

    2011-01-01

    A new analytical approach for the description of the glass transition in a frustrated system is suggested. The theory is based on the non-equilibrium dynamics technique, and takes into account the interaction of the local order field with the massive gauge field, which describes frustration-induced plastic deformation. The glass transition is regarded as a phase transition interrupted because of the premature critical slowing-down of one of the degrees of freedom caused by the frustrations. It is shown that freezing of the system appears when the correlation length and relaxation time of the gauge field diverge. The Vogel–Fulcher–Tammann relation for the transition kinetics and the critical exponent for the nonlinear susceptibility, 2.5∼ t correlation function dependence on time, and explains the boson peak appearance on this curve. In addition, the function of the glass transition temperature value with cooling rate is derived; this dependence fully conforms with known experimental data

  4. 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.

  5. Conformal invariance from nonconformal gravity

    International Nuclear Information System (INIS)

    Meissner, Krzysztof A.; Nicolai, Hermann

    2009-01-01

    We discuss the conditions under which classically conformally invariant models in four dimensions can arise out of nonconformal (Einstein) gravity. As an 'existence proof' that this is indeed possible we show how to derive N=4 super Yang-Mills theory with any compact gauge group G from nonconformal gauged N=4 supergravity as a special flat space limit. We stress the role that the anticipated UV finiteness of the (so far unknown) underlying theory of quantum gravity would have to play in such a scheme, as well as the fact that the masses of elementary particles would have to arise via quantum gravitational effects which mimic the conformal anomalies of standard (flat space) UV divergent quantum field theory.

  6. 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.

  7. Gel dosimetry for conformal radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-07-01

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

  8. Conformal FDTD modeling wake fields

    Energy Technology Data Exchange (ETDEWEB)

    Jurgens, T.; Harfoush, F.

    1991-05-01

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

  9. Conformal manifolds: ODEs from OPEs

    Science.gov (United States)

    Behan, Connor

    2018-03-01

    The existence of an exactly marginal deformation in a conformal field theory is very special, but it is not well understood how this is reflected in the allowed dimensions and OPE coefficients of local operators. To shed light on this question, we compute perturbative corrections to several observables in an abstract CFT, starting with the beta function. This yields a sum rule that the theory must obey in order to be part of a conformal manifold. The set of constraints relating CFT data at different values of the coupling can in principle be written as a dynamical system that allows one to flow arbitrarily far. We begin the analysis of it by finding a simple form for the differential equations when the spacetime and theory space are both one-dimensional. A useful feature we can immediately observe is that our system makes it very difficult for level crossing to occur.

  10. Conformal field theories and critical phenomena

    International Nuclear Information System (INIS)

    Xu, Bowei

    1993-01-01

    In this article we present a brief review of the conformal symmetry and the two dimensional conformal quantum field theories. As concrete applications of the conformal theories to the critical phenomena in statistical systems, we calculate the value of central charge and the anomalous scale dimensions of the Z 2 symmetric quantum chain with boundary condition. The results are compatible with the prediction of the conformal field theories

  11. Conformal group actions and Segal's cosmology

    International Nuclear Information System (INIS)

    Werth, J.-E.

    1984-01-01

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

  12. Boundary and interface CFTs from the conformal bootstrap

    Energy Technology Data Exchange (ETDEWEB)

    Gliozzi, Ferdinando [Dipartimento di Fisica, Università di Torino,Via P. Giuria 1 I-10125 Torino (Italy); Istituto Nazionale di Fisica Nucleare - sezione di Torino,Via P. Giuria 1 I-10125 Torino (Italy); Liendo, Pedro [IMIP, Humboldt-Universität zu Berlin, IRIS Adelershof,Zum Großen Windkanal 6, 12489 Berlin (Germany); Meineri, Marco [Scuola Normale Superiore,Piazza dei Cavalieri 7 I-56126 Pisa (Italy); Istituto Nazionale di Fisica Nucleare - sezione di Pisa,Largo B. Pontecorvo, 3, 56127 Pisa (Italy); Rago, Antonio [Centre for Mathematical Sciences, Plymouth University,Drake Circus, Plymouth, PL4 8AA (United Kingdom)

    2015-05-07

    We explore some consequences of the crossing symmetry for defect conformal field theories, focusing on codimension one defects like flat boundaries or interfaces. We study surface transitions of the 3d Ising and other O(N) models through numerical solutions to the crossing equations with the method of determinants. In the extraordinary transition, where the low-lying spectrum of the surface operators is known, we use the bootstrap equations to obtain information on the bulk spectrum of the theory. In the ordinary transition the knowledge of the low-lying bulk spectrum allows to calculate the scale dimension of the relevant surface operator, which compares well with known results of two-loop calculations in 3d. Estimates of various OPE coefficients are also obtained. We also analyze in 4-ϵ dimensions the renormalization group interface between the O(N) model and the free theory and check numerically the results in 3d.

  13. MHD intermediate shock discontinuities: Pt. 1

    International Nuclear Information System (INIS)

    Kennel, C.F.; Blandford, R.D.; Coppi, P.

    1989-01-01

    Recent numerical investigations have focused attention once more on the role of intermediate shocks in MHD. Four types of intermediate shock are identified using a graphical representation of the MHD Rankine-Hugoniot conditions. This same representation can be used to exhibit the close relationship of intermediate shocks to switch-on shocks and rotational discontinuities. The conditions under which intermediate discontinuities can be found are elucidated. The variations in velocity, pressure, entropy and magnetic-field jumps with upstream parameters in intermediate shocks are exhibited graphically. The evolutionary arguments traditionally advanced against intermediate shocks may fail because the equations of classical MHD are not strictly hyperbolic. (author)

  14. Generative Models of Conformational Dynamics

    OpenAIRE

    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...

  15. Integrability of conformal fishnet theory

    Science.gov (United States)

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

    2018-01-01

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

  16. Cryo-EM structures of two bovine adenovirus type 3 intermediates

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Lingpeng; Huang, Xiaoxing; Li, Xiaomin [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Xiong, Wei [State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Luo-jia-shan, Wuhan, Hubei 430072 (China); Sun, Wei; Yang, Chongwen; Zhang, Kai; Wang, Ying [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Liu, Hongrong [College of Physics and Information Science, Hunan Normal University, Changsha, Hunan 410081 (China); Huang, Xiaojun; Ji, Gang; Sun, Fei [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Zheng, Congyi, E-mail: cctcc202@whu.edu.cn [State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Luo-jia-shan, Wuhan, Hubei 430072 (China); Zhu, Ping, E-mail: zhup@ibp.ac.cn [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)

    2014-02-15

    Adenoviruses (Ads) infect hosts from all vertebrate species and have been investigated as vaccine vectors. We report here near-atomic structures of two bovine Ad type 3 (BAd3) intermediates obtained by cryo-electron microscopy. A comparison between the two intermediate structures reveals that the differences are localized in the fivefold vertex region, while their facet structures are identical. The overall facet structure of BAd3 exhibits a similar structure to human Ads; however, BAd3 protein IX has a unique conformation. Mass spectrometry and cryo-electron tomography analyses indicate that one intermediate structure represents the stage during DNA encapsidation, whilst the other intermediate structure represents a later stage. These results also suggest that cleavage of precursor protein VI occurs during, rather than after, the DNA encapsidation process. Overall, our results provide insights into the mechanism of Ad assembly, and allow the first structural comparison between human and nonhuman Ads at backbone level. - Highlights: • First structure of bovine adenovirus type 3. • Some channels are located at the vertex of intermediate during DNA encapsidation. • Protein IX exhibits a unique conformation of trimeric coiled–coiled structure. • Cleavage of precursor protein VI occurs during the DNA encapsidation process.

  17. Cryo-EM structures of two bovine adenovirus type 3 intermediates

    International Nuclear Information System (INIS)

    Cheng, Lingpeng; Huang, Xiaoxing; Li, Xiaomin; Xiong, Wei; Sun, Wei; Yang, Chongwen; Zhang, Kai; Wang, Ying; Liu, Hongrong; Huang, Xiaojun; Ji, Gang; Sun, Fei; Zheng, Congyi; Zhu, Ping

    2014-01-01

    Adenoviruses (Ads) infect hosts from all vertebrate species and have been investigated as vaccine vectors. We report here near-atomic structures of two bovine Ad type 3 (BAd3) intermediates obtained by cryo-electron microscopy. A comparison between the two intermediate structures reveals that the differences are localized in the fivefold vertex region, while their facet structures are identical. The overall facet structure of BAd3 exhibits a similar structure to human Ads; however, BAd3 protein IX has a unique conformation. Mass spectrometry and cryo-electron tomography analyses indicate that one intermediate structure represents the stage during DNA encapsidation, whilst the other intermediate structure represents a later stage. These results also suggest that cleavage of precursor protein VI occurs during, rather than after, the DNA encapsidation process. Overall, our results provide insights into the mechanism of Ad assembly, and allow the first structural comparison between human and nonhuman Ads at backbone level. - Highlights: • First structure of bovine adenovirus type 3. • Some channels are located at the vertex of intermediate during DNA encapsidation. • Protein IX exhibits a unique conformation of trimeric coiled–coiled structure. • Cleavage of precursor protein VI occurs during the DNA encapsidation process

  18. 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.

  19. Anomalies, conformal manifolds, and spheres

    Energy Technology Data Exchange (ETDEWEB)

    Gomis, Jaume [Perimeter Institute for Theoretical Physics,Waterloo, Ontario, N2L 2Y5 (Canada); Hsin, Po-Shen [Department of Physics, Princeton University,Princeton, NJ 08544 (United States); Komargodski, Zohar; Schwimmer, Adam [Weizmann Institute of Science,Rehovot 76100 (Israel); Seiberg, Nathan [School of Natural Sciences, Institute for Advanced Study,Princeton, NJ 08540 (United States); Theisen, Stefan [Max-Planck-Institut für Gravitationsphysik, Albert-Einstein-Institut,14476 Golm (Germany)

    2016-03-04

    The two-point function of exactly marginal operators leads to a universal contribution to the trace anomaly in even dimensions. We study aspects of this trace anomaly, emphasizing its interpretation as a sigma model, whose target space M is the space of conformal field theories (a.k.a. the conformal manifold). When the underlying quantum field theory is supersymmetric, this sigma model has to be appropriately supersymmetrized. As examples, we consider in some detail N=(2,2) and N=(0,2) supersymmetric theories in d=2 and N=2 supersymmetric theories in d=4. This reasoning leads to new information about the conformal manifolds of these theories, for example, we show that the manifold is Kähler-Hodge and we further argue that it has vanishing Kähler class. For N=(2,2) theories in d=2 and N=2 theories in d=4 we also show that the relation between the sphere partition function and the Kähler potential of M follows immediately from the appropriate sigma models that we construct. Along the way we find several examples of potential trace anomalies that obey the Wess-Zumino consistency conditions, but can be ruled out by a more detailed analysis.

  20. Electrophysiological precursors of social conformity

    Science.gov (United States)

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

    2013-01-01

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

  1. CONFORMITY IN CHRIST 1. THE TRANSFORMATION PROCESS

    African Journals Online (AJOL)

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

  2. 40 CFR 52.938 - General conformity.

    Science.gov (United States)

    2010-07-01

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

  3. 40 CFR 51.854 - Conformity analysis.

    Science.gov (United States)

    2010-07-01

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

  4. 40 CFR 52.2133 - General conformity.

    Science.gov (United States)

    2010-07-01

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

  5. Conformity in Christ | Waaijman | Acta Theologica

    African Journals Online (AJOL)

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

  6. Comparative Incidence of Conformational, Neurodegenerative Disorders.

    Directory of Open Access Journals (Sweden)

    Jesús de Pedro-Cuesta

    Full Text Available The purpose of this study was to identify incidence and survival patterns in conformational neurodegenerative disorders (CNDDs.We identified 2563 reports on the incidence of eight conditions representing sporadic, acquired and genetic, protein-associated, i.e., conformational, NDD groups and age-related macular degeneration (AMD. We selected 245 papers for full-text examination and application of quality criteria. Additionally, data-collection was completed with detailed information from British, Swedish, and Spanish registries on Creutzfeldt-Jakob disease (CJD forms, amyotrophic lateral sclerosis (ALS, and sporadic rapidly progressing neurodegenerative dementia (sRPNDd. For each condition, age-specific incidence curves, age-adjusted figures, and reported or calculated median survival were plotted and examined.Based on 51 valid reported and seven new incidence data sets, nine out of eleven conditions shared specific features. Age-adjusted incidence per million person-years increased from ≤1.5 for sRPNDd, different CJD forms and Huntington's disease (HD, to 1589 and 2589 for AMD and Alzheimer's disease (AD respectively. Age-specific profiles varied from (a symmetrical, inverted V-shaped curves for low incidences to (b those increasing with age for late-life sporadic CNDDs and for sRPNDd, with (c a suggested, intermediate, non-symmetrical inverted V-shape for fronto-temporal dementia and Parkinson's disease. Frequently, peak age-specific incidences from 20-24 to ≥90 years increased with age at onset and survival. Distinct patterns were seen: for HD, with a low incidence, levelling off at middle age, and long median survival, 20 years; and for sRPNDd which displayed the lowest incidence, increasing with age, and a short median disease duration.These results call for a unified population view of NDDs, with an age-at-onset-related pattern for acquired and sporadic CNDDs. The pattern linking age at onset to incidence magnitude and survival might

  7. Comparative Incidence of Conformational, Neurodegenerative Disorders

    Science.gov (United States)

    de Pedro-Cuesta, Jesús; Rábano, Alberto; Martínez-Martín, Pablo; Ruiz-Tovar, María; Alcalde-Cabero, Enrique; Almazán-Isla, Javier; Avellanal, Fuencisla; Calero, Miguel

    2015-01-01

    Background The purpose of this study was to identify incidence and survival patterns in conformational neurodegenerative disorders (CNDDs). Methods We identified 2563 reports on the incidence of eight conditions representing sporadic, acquired and genetic, protein-associated, i.e., conformational, NDD groups and age-related macular degeneration (AMD). We selected 245 papers for full-text examination and application of quality criteria. Additionally, data-collection was completed with detailed information from British, Swedish, and Spanish registries on Creutzfeldt-Jakob disease (CJD) forms, amyotrophic lateral sclerosis (ALS), and sporadic rapidly progressing neurodegenerative dementia (sRPNDd). For each condition, age-specific incidence curves, age-adjusted figures, and reported or calculated median survival were plotted and examined. Findings Based on 51 valid reported and seven new incidence data sets, nine out of eleven conditions shared specific features. Age-adjusted incidence per million person-years increased from ≤1.5 for sRPNDd, different CJD forms and Huntington's disease (HD), to 1589 and 2589 for AMD and Alzheimer's disease (AD) respectively. Age-specific profiles varied from (a) symmetrical, inverted V-shaped curves for low incidences to (b) those increasing with age for late-life sporadic CNDDs and for sRPNDd, with (c) a suggested, intermediate, non-symmetrical inverted V-shape for fronto-temporal dementia and Parkinson's disease. Frequently, peak age-specific incidences from 20–24 to ≥90 years increased with age at onset and survival. Distinct patterns were seen: for HD, with a low incidence, levelling off at middle age, and long median survival, 20 years; and for sRPNDd which displayed the lowest incidence, increasing with age, and a short median disease duration. Interpretation These results call for a unified population view of NDDs, with an age-at-onset-related pattern for acquired and sporadic CNDDs. The pattern linking age at onset to

  8. Transitional Justice

    DEFF Research Database (Denmark)

    Gissel, Line Engbo

    This presentation builds on an earlier published article, 'Contemporary Transitional Justice: Normalising a Politics of Exception'. It argues that the field of transitional justice has undergone a shift in conceptualisation and hence practice. Transitional justice is presently understood to be th...... to be the provision of ordinary criminal justice in contexts of exceptional political transition.......This presentation builds on an earlier published article, 'Contemporary Transitional Justice: Normalising a Politics of Exception'. It argues that the field of transitional justice has undergone a shift in conceptualisation and hence practice. Transitional justice is presently understood...

  9. Role of Intermediate Filaments in Vesicular Traffic

    Directory of Open Access Journals (Sweden)

    Azzurra Margiotta

    2016-04-01

    Full Text Available Intermediate filaments are an important component of the cellular cytoskeleton. The first established role attributed to intermediate filaments was the mechanical support to cells. However, it is now clear that intermediate filaments have many different roles affecting a variety of other biological functions, such as the organization of microtubules and microfilaments, the regulation of nuclear structure and activity, the control of cell cycle and the regulation of signal transduction pathways. Furthermore, a number of intermediate filament proteins have been involved in the acquisition of tumorigenic properties. Over the last years, a strong involvement of intermediate filament proteins in the regulation of several aspects of intracellular trafficking has strongly emerged. Here, we review the functions of intermediate filaments proteins focusing mainly on the recent knowledge gained from the discovery that intermediate filaments associate with key proteins of the vesicular membrane transport machinery. In particular, we analyze the current understanding of the contribution of intermediate filaments to the endocytic pathway.

  10. Conformal symmetry inheritance in null fluid spacetimes

    International Nuclear Information System (INIS)

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

    2003-01-01

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

  11. Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

    International Nuclear Information System (INIS)

    Shi, Jade; Schwantes, Christian; Bilsel, Osman

    2017-01-01

    The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. We report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble. The resulting prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. We then predict incisive single molecule FRET experiments, using these results, as a means of model validation. Our study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.

  12. ESL intermediate/advanced writing

    CERN Document Server

    Munoz Page, Mary Ellen; Jaskiewicz, Mary

    2011-01-01

    Master ESL (English as a Second Language) Writing with the study guide designed for non-native speakers of English. Skill-building lessons relevant to today's topics help ESL students write complete sentences, paragraphs, and even multi-paragraph essays. It's perfect for classroom use or self-guided writing preparation.DETAILS- Intermediate drills for improving skills with parallel structure, mood, correct shifting errors & dangling participles- Advanced essay drills focusing on narrative, descriptive, process, reaction, comparison and contrast- Superb preparation for students taking the TOEFL

  13. Photonuclear reactions at intermediate energy

    International Nuclear Information System (INIS)

    Koch, J.H.

    1982-01-01

    The dominant feature of photonuclear reactions at intermediate energies is the excitation of the δ resonance and one can therefore use such reactions to study the dynamics of δ propagation in a nucleus. Following an introductory section the author comments on photoabsorption on a single nucleon in Section II. A review of the δ-n Greens function and of the photonuclear amplitude is given in Section III. Results for photoabsorption on 4 He are shown in Section IV and compared with the data. Coherent π 0 photoproduction is discussed in Section V and calculations for 12 C are compared to recent measurements. (Auth.)

  14. Pelamis WEC - intermediate scale demonstration

    Energy Technology Data Exchange (ETDEWEB)

    Yemm, R.

    2003-07-01

    This report describes the successful building and commissioning of an intermediate 1/7th scale model of the Pelamis Wave Energy Converter (WEC) and its testing in the wave climate of the Firth of Forth. Details are given of the design of the semi-submerged articulated structure of cylindrical elements linked by hinged joints. The specific programme objectives and conclusions, development issues addressed, and key remaining risks are discussed along with development milestones to be passed before the Pelamis WEC is ready for full-scale prototype testing.

  15. Conformation and hydrogen bonding in 4-Aminobutanol

    Science.gov (United States)

    Khalil, Andrew S.; Duguay, Taylor M.; Lavrich, Richard J.

    2017-06-01

    Rotational spectra of the most abundant and four 13C isotopomers of 4-aminobutanol have been recorded in natural abundance using a Fourier-transform microwave spectrometer. For the most abundant isotopomer, 56 hyperfine components from the fifteen a- and b-type transitions measured were fit to the quadupole coupling constants, χaa = -3.843(3) MHz, χbb = 1.971(3) MHz. Rotational and centrifugal distortion constants determined from fits of the resulting unsplit line centers to the Watson A-reduction Hamiltonian are A = 4484.893(3) MHz, B = 2830.721(1) MHz, C = 1942.9710(3) MHz, ΔJ = 0.98(3) kHz, ΔJK = 1.4(1) kHz, ΔK = - 2.6(5) kHz, δJ = 0.27(1) kHz, and δK = 1.7(1) kHz. Between nine and eleven rotational transitions were measured for the 13C isotopes and rotational constants were determined by fixing the distortion constants to the values found for the normal isotope. The five sets of moments of inertia were used to determine the 4-aminobutanol substitution structure as well to perform a least-squares fit of the lowest energy ab initio structure. The heavy atom coordinates determined from these two methods are in excellent agreement. The conformation of 4-aminobutanol is stabilized by an intramolecular hydrogen bond from the alcohol proton to amino nitrogen with a resulting hydrogen bond distance of 1.891 Å. The experimental structure is consistent with the lowest energy ab initio [MP2/6-311++G(d,p)] structure.

  16. Intermediality: Bridge to Critical Media Literacy.

    Science.gov (United States)

    Pailliotet, Ann Watts; Semali, Ladislaus; Rodenberg, Rita K.; Giles, Jackie K.; Macaul, Sherry L.

    2000-01-01

    Defines "intermediality" as the ability to critically read and write with and across varied symbol systems. Relates it to critical media literacy. Offers rationales for teaching critical media literacy in general, and intermedial instruction in particular. Identifies seven guiding intermedial elements: theory, texts, processes, contexts,…

  17. 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.)

  18. Kinetic intermediates en route to the final serpin-protease complex: studies of complexes of α1-protease inhibitor with trypsin.

    Science.gov (United States)

    Maddur, Ashoka A; Swanson, Richard; Izaguirre, Gonzalo; Gettins, Peter G W; Olson, Steven T

    2013-11-01

    Serpin protein protease inhibitors inactivate their target proteases through a unique mechanism in which a major serpin conformational change, resulting in a 70-Å translocation of the protease from its initial reactive center loop docking site to the opposite pole of the serpin, kinetically traps the acyl-intermediate complex. Although the initial Michaelis and final trapped acyl-intermediate complexes have been well characterized structurally, the intermediate stages involved in this remarkable transformation are not well understood. To better characterize such intermediate steps, we undertook rapid kinetic studies of the FRET and fluorescence perturbation changes of site-specific fluorophore-labeled derivatives of the serpin, α1-protease inhibitor (α1PI), which report the serpin and protease conformational changes involved in transforming the Michaelis complex to the trapped acyl-intermediate complex in reactions with trypsin. Two kinetically resolvable conformational changes were observed in the reactions, ascribable to (i) serpin reactive center loop insertion into sheet A with full protease translocation but incomplete protease distortion followed by, (ii) full conformational distortion and movement of the protease and coupled serpin conformational changes involving the F helix-sheet A interface. Kinetic studies of calcium effects on the labeled α1PI-trypsin reactions demonstrated both inactive and low activity states of the distorted protease in the final complex that were distinct from the intermediate distorted state. These studies provide new insights into the nature of the serpin and protease conformational changes involved in trapping the acyl-intermediate complex in serpin-protease reactions and support a previously proposed role for helix F in the trapping mechanism.

  19. Lifetime enhancement for multiphoton absorption in intermediate band solar cells

    International Nuclear Information System (INIS)

    Bezerra, Anibal T; Studart, Nelson

    2017-01-01

    A semiconductor structure consisting of two coupled quantum wells embedded into the intrinsic region of a p – i–n junction is proposed as an intermediate band solar cell with a photon ratchet state, which would lead to increasing the cell efficiency. The conduction subband of the right-hand side quantum well works as the intermediated band, whereas the excited conduction subband of the left-hand side quantum well operates as the ratchet state. The photoelectrons in the intermediate band are scattered through the thin wells barrier and accumulated into the ratchet subband. A rate equation model for describing the charge transport properties is presented. The efficiency of the current generation is analyzed by studying the occupation of the wells subbands, taking into account the charge dynamic behavior provided by the electrical contacts connected to the cell. The current generation efficiency depends essentially from the relations between the generation, recombination rates and the scattering rate to the ratchet state. The inclusion of the ratchet states led to both an increase and a decrease in the cell current depending on the transition rates. This suggests that the coupling between the intermediate band and the ratchet state is a key point in developing an efficient solar cell. (paper)

  20. Lifetime enhancement for multiphoton absorption in intermediate band solar cells

    Science.gov (United States)

    Bezerra, Anibal T.; Studart, Nelson

    2017-08-01

    A semiconductor structure consisting of two coupled quantum wells embedded into the intrinsic region of a p-i-n junction is proposed as an intermediate band solar cell with a photon ratchet state, which would lead to increasing the cell efficiency. The conduction subband of the right-hand side quantum well works as the intermediated band, whereas the excited conduction subband of the left-hand side quantum well operates as the ratchet state. The photoelectrons in the intermediate band are scattered through the thin wells barrier and accumulated into the ratchet subband. A rate equation model for describing the charge transport properties is presented. The efficiency of the current generation is analyzed by studying the occupation of the wells subbands, taking into account the charge dynamic behavior provided by the electrical contacts connected to the cell. The current generation efficiency depends essentially from the relations between the generation, recombination rates and the scattering rate to the ratchet state. The inclusion of the ratchet states led to both an increase and a decrease in the cell current depending on the transition rates. This suggests that the coupling between the intermediate band and the ratchet state is a key point in developing an efficient solar cell.

  1. Post-crisis financial intermediation

    Directory of Open Access Journals (Sweden)

    Ilie MIHAI

    2015-09-01

    Full Text Available The recent financial crisis that begun in 2007 in the US, which then swept around the world, has left deep scars on the already wrinkled face of the global economy. Some national and regional economies, which had money for expensive makeup, or created money[1], managed to blur or hide the scars left by the crisis, others are still facing difficulties in overcoming the effects of this. The rapacity of banks, their greed and risk ignorance, were the origin of the outbreak of the last major economic and financial crisis but unfortunately those who were responsible or, rather, irresponsible, paid little or nothing at all for the burden of their bad loan portfolio. This cost has been supported by the population, either directly by paying high interest and fees [Mihai I., 2007], or indirectly, through the use of public budgets to cover the losses of banks, most of which had private capital. In this context, we intend to examine the state of financial intermediation in Romania in the post-crisis period, and to primarily follow: (i The structure and evolution of the banking system; (ii Non-government credit situation; (iii The level of savings; (iiii Loan-deposit ratio; (v The degree of financial intermediation and disintegration phenomenon etc., and to articulate some conclusions and suggestions on the matters that have been explored.

  2. Intermediate-Mass Black Holes

    Science.gov (United States)

    Miller, M. Coleman; Colbert, E. J. M.

    2004-01-01

    The mathematical simplicity of black holes, combined with their links to some of the most energetic events in the universe, means that black holes are key objects for fundamental physics and astrophysics. Until recently, it was generally believed that black holes in nature appear in two broad mass ranges: stellar-mass (M~3 20 M⊙), which are produced by the core collapse of massive stars, and supermassive (M~106 1010 M⊙), which are found in the centers of galaxies and are produced by a still uncertain combination of processes. In the last few years, however, evidence has accumulated for an intermediate-mass class of black holes, with M~102 104 M⊙. If such objects exist they have important implications for the dynamics of stellar clusters, the formation of supermassive black holes, and the production and detection of gravitational waves. We review the evidence for intermediate-mass black holes and discuss future observational and theoretical work that will help clarify numerous outstanding questions about these objects.

  3. The Biological Bases of Conformity

    Science.gov (United States)

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

    2012-01-01

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

  4. 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

  5. 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

  6. Optimal design of the cable metro with unified intermediate supports

    Directory of Open Access Journals (Sweden)

    Lagerev A.V.

    2017-12-01

    slope of the surface relief also has discrete-step type. The transition to a larger height unified intermediate supports determines the need for installation of supports with a large pitch. Its value then begins to decrease monotonically with further increase of the angle of the longitudinal slope of the surface relief until it needs to transition to the new size of supports. Synchronous change in the optimal values of the height and step of the installation of intermediate supports, depending on the angle of the longitudinal slope of the sur-face relief leads to the fact that the optimal cost characteristics of the cable metro lines are smooth functions. It has an extreme character with a minimum at angles of inclination of the surface elevation ~5 degrees, which is associated with the form of sagging of the load-bearing ropes. Unification of intermediate supports has little effect on the optimal cost characteristics of the cable metro lines. Even for a sufficiently large step of the unification the largest difference in op-timal value is almost insignificant: it lies in the range of 2...3%, increasing with increasing the angle of the longitudinal slope of the surface relief and unit cost of the intermediate support. Unification of intermediate supports according to the height and their step practically does not affect the optimal value for horizontal tension on the load-bearing ropes. It determined mainly by the angle of the longitudinal slope of the surface relief. Deviation of horizontal tension on the load-bearing ropes for the nonstandard supports and the unified supports within the range of angles of inclination of the terrain surface 0...60 degrees is not more than 0.5 to 0.8 %.

  7. Conformal covariance of general relativity

    International Nuclear Information System (INIS)

    Ionescu-Pallas, N.; Gottlieb, I.

    1980-01-01

    The Einstein's equations of General Relativity are written in a conformal metric, resulting as a consequence of geometrizing the pressure forces. Accordingly, the trajectory of a test body pursues a geodetic line even inside the source of gravitational field. Moreover, the pressure, entering the perfect fluid scheme, may be replaced by a certain scalar interaction. This new manner of interpreting General Relativity is then applied to Cosmology, in order to build up a model of Universe whose static limit should coincide with that of Einstein. At the same time, the cosmological constant is connected to the scalar interaction acquiring a plausible explanation. (author)

  8. Introduction to twisted conformal fields

    International Nuclear Information System (INIS)

    Kazama, Y.

    1988-01-01

    A pedagogical account is given of the recent developments in the theory of twisted conformal fields. Among other things, the main part of the lecture concerns the construction of the twist-emission vertex operator, which is a generalization of the fermion emission vertex in the superstring theory. Several different forms of the vertex are derived and their mutural relationships are clarified. In this paper, the authors include a brief survey of the history of the fermion emission vertex, as it offers a good perspective in which to appreciate the logical development

  9. Direct observation of unimolecular decay of CH{sub 3}CH{sub 2}CHOO Criegee intermediates to OH radical products

    Energy Technology Data Exchange (ETDEWEB)

    Fang, Yi; Liu, Fang; Lester, Marsha I., E-mail: milester@sas.upenn.edu [Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323 (United States); Klippenstein, Stephen J. [Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States)

    2016-07-28

    The unimolecular decay of carbonyl oxide intermediates, known as Criegee intermediates, produced in alkene ozonolysis is a significant source of OH radicals in the troposphere. Here, the rate of appearance of OH radical products is examined directly in the time-domain for a prototypical alkyl-substituted Criegee intermediate, CH{sub 3}CH{sub 2}CHOO, following vibrational activation under collision-free conditions. Complementary statistical Rice–Ramsperger–Kassel–Marcus calculations of the microcanonical unimolecular decay rate for CH{sub 3}CH{sub 2}CHOO are also carried out at energies in the vicinity of the barrier for 1,4 hydrogen atom transfer that leads to OH products. Tunneling through the barrier, derived from high level electronic structure calculations, contributes significantly to the decay rate. Infrared transitions of CH{sub 3}CH{sub 2}CHOO are identified in the CH stretch overtone region, which are detected by ultraviolet laser-induced fluorescence of the resultant OH products. The features observed are attributed to CH vibrational excitations and conformational forms utilizing insights from theory. Both experiment and theory yield unimolecular decay rates for CH{sub 3}CH{sub 2}CHOO of ca. 10{sup 7} s{sup −1}, which are slower than those obtained for syn-CH{sub 3}CHOO or (CH{sub 3}){sub 2}COO reported previously [Fang et al., J. Chem. Phys. 144, 061102 (2016)] at similar energies. Master equation modeling is also utilized to predict the thermal decay rate of CH{sub 3}CH{sub 2}CHOO under atmospheric conditions, giving a rate of 279 s{sup −1} at 298 K.

  10. Poly (3, 4-ethylendioxithiophene) (PEDOT) oxidation: activation energy and conformational energy

    International Nuclear Information System (INIS)

    Otero, T F; Romero, M C

    2008-01-01

    The oxidation kinetics of films of the conducting polymer PEDOT-C1O4 after electrochemical reduction by polarization at increasing cathodic potential was studied by potential steps. The response i/t presents a maximum at intermediate oxidation times. At the maximum the reaction occurs under chemical kinetic control following the expected current variations from the Chemical and Electrochemical Kinetics, when reactant concentrations or temperatures are changed. The obtained activation energy of the oxidation present two ranges as a function of the cathodic potential of prepolarization: constant values after prepolarization at low cathodic potentials and a lineal variation after prepolarization at increasing high cathodic potentials. According with the conformational relaxation model during electrochemical reduction the polymer shrinks, closes and packs the conformational structure. The activation energy for the subsequent oxidation includes two terms: the constant chemical activation energy and the conformational energy required to relax the packed polymeric structure. The conformational energy only appears after prepolarization at more cathodic potentials than the closing potential where more packed conformations were obtained. The conformational activation energy accounts the energetic requirements to relax and unfold the polymeric chains generating the required free volume to lodge balancing counterions; meanwhile the chemical activation energy accounts the energetic requirements for the electrochemical reaction to occur.

  11. Parity Doubling and the S Parameter below the Conformal Window

    International Nuclear Information System (INIS)

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

    2011-01-01

    We describe a lattice simulation of the masses and decay constants of the lowest-lying vector and axial resonances, and the electroweak S parameter, in an SU(3) gauge theory with N f =2 and 6 fermions in the fundamental representation. The spectrum becomes more parity doubled and the S parameter per electroweak doublet decreases when N f is increased from 2 to 6, motivating study of these trends as N f is increased further, toward the critical value for transition from confinement to infrared conformality.

  12. Generative Models of Conformational Dynamics

    Science.gov (United States)

    Langmead, Christopher James

    2014-01-01

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

  13. On bidimensional Lagrangian conformal models

    International Nuclear Information System (INIS)

    Lazzarini, S.

    1990-04-01

    The main topic of this thesis is the study of Conformal Field Theories defined on an arbitrary compact Riemann surface without boundary. The Beltrami parametrization of complexe structures endowing such a surface provides a local bidimensional diffeomorphism invariance of the theory and the holomorphic factorization. The perturbative quantization a la Feynman is then constrained by local factorized Ward identities. The renormalization is analysed in the Esptein-Glaser scheme. A first part deals with the simplest free field models where one checks the interesting conjecture that renormalized perturbative expansions could be resumed by a Polyakov's formula which is a Wess-Zumino action for the diffeomorphism anomaly. For a higher genus surface, only a differential version is proposed. The second part of this thesis is devoted to the characterization of some observables of the free bosonic string in the corresponding gauge theory with the aid of the nilpotent Slavnov s-operator. It is conjectured that part of the observables of this theory is labelled by the local cohomology of s modulo d and corresponds to the vertex operators, as it is verified for the tachyon vertex in the conformal gauge [fr

  14. Supporting Transition

    Science.gov (United States)

    Qureshi, Asima; Petrucco, James

    2018-01-01

    Meadowbrook Primary School has explored the use of The Teacher Assessment in Primary Science (TAPS) to support transition, initially for transfer to secondary school and now for transition from Early Years Foundation Stage (EYFS) into Key Stage 1 (ages 5-7). This article will consider an example of a secondary transition project and discuss the…

  15. Conformal symmetries of FRW accelerating cosmologies

    International Nuclear Information System (INIS)

    Kehagias, A.; Riotto, A.

    2014-01-01

    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

  16. Maxwell equations in conformal invariant electrodynamics

    International Nuclear Information System (INIS)

    Fradkin, E.S.; AN SSSR, Novosibirsk. Inst. Avtomatiki i Ehlektrometrii); Kozhevnikov, A.A.; Palchik, M.Ya.; Pomeransky, A.A.

    1983-01-01

    We consider a conformal invariant formulation of quantum electrodynamics. Conformal invariance is achieved with a specific mathematical construction based on the indecomposable representations of the conformal group associated with the electromagnetic potential and current. As a corolary of this construction modified expressions for the 3-point Green functions are obtained which both contain transverse parts. They make it possible to formulate a conformal invariant skeleton perturbation theory. It is also shown that the Euclidean Maxwell equations in conformal electrodynamics are manifestations of its kinematical structure: in the case of the 3-point Green functions these equations follow (up to constants) from the conformal invariance while in the case of higher Green functions they are equivalent to the equality of the kernels of the partial wave expansions. This is the manifestation of the mathematical fast of a (partial) equivalence of the representations associated with the potential, current and the field tensor. (orig.)

  17. Operator algebras and conformal field theory

    International Nuclear Information System (INIS)

    Gabbiani, F.; Froehlich, J.

    1993-01-01

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

  18. 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.

  19. Conformational transformations induced by the charge-curvature interaction at finite temperature

    DEFF Research Database (Denmark)

    Gaididei, Yuri Borisovich; Gorria, Carlos; Christiansen, Peter Leth

    2008-01-01

    The role of thermal fluctuations on the conformational dynamics of a single closed filament is studied. It is shown that, due to the interaction between charges and bending degrees of freedom, initially circular aggregates may undergo transformation to polygonal shape. The transition occurs both...

  20. Lattice models and conformal field theories

    International Nuclear Information System (INIS)

    Saleur, H.

    1988-01-01

    Theoretical studies concerning the connection between critical physical systems and the conformal theories are reviewed. The conformal theory associated to a critical (integrable) lattice model is derived. The obtention of the central charge, critical exponents and torus partition function, using renormalization group arguments, is shown. The quantum group structure, in the integrable lattice models, and the theory of Visaro algebra representations are discussed. The relations between off-critical integrable models and conformal theories, in finite geometries, are studied

  1. Multichannel conformal blocks for scattering amplitudes

    Science.gov (United States)

    Belitsky, A. V.

    2018-05-01

    By performing resummation of small fermion-antifermion pairs within the pentagon form factor program to scattering amplitudes in planar N = 4 superYang-Mills theory, we construct multichannel conformal blocks within the flux-tube picture for N-sided NMHV polygons. This procedure is equivalent to summation of descendants of conformal primaries in the OPE framework. The resulting conformal partial waves are determined by multivariable hypergeometric series of Lauricella-Saran type.

  2. Conformal hyperbolicity of Lorentzian warped products

    International Nuclear Information System (INIS)

    Markowitz, M.J.

    1982-01-01

    A space-time M is said to be conformally hyperbolic if the intrinsic conformal Lorentz pseudodistance dsub(M) is a true distance. In this paper criteria are derived which insure the conformal hyperbolicity of certain space-times which are generalizations of the Robertson-Walker spaces. Then dsub(M) is determined explicitly for Einstein-de Sitter space, and important cosmological model. (author)

  3. Conformal hyperbolicity of Lorentzian warped products

    Energy Technology Data Exchange (ETDEWEB)

    Markowitz, M.J. (Chicago Univ., IL (USA). Dept. of Mathematics)

    1982-12-01

    A space-time M is said to be conformally hyperbolic if the intrinsic conformal Lorentz pseudodistance dsub(M) is a true distance. In this paper criteria are derived which insure the conformal hyperbolicity of certain space-times which are generalizations of the Robertson-Walker spaces. Then dsub(M) is determined explicitly for Einstein-de Sitter space, and important cosmological model.

  4. Fluorescence lifetime components reveal kinetic intermediate states upon equilibrium denaturation of carbonic anhydrase II.

    Science.gov (United States)

    Nemtseva, Elena V; Lashchuk, Olesya O; Gerasimova, Marina A; Melnik, Tatiana N; Nagibina, Galina S; Melnik, Bogdan S

    2017-12-21

    In most cases, intermediate states of multistage folding proteins are not 'visible' under equilibrium conditions but are revealed in kinetic experiments. Time-resolved fluorescence spectroscopy was used in equilibrium denaturation studies. The technique allows for detecting changes in the conformation and environment of tryptophan residues in different structural elements of carbonic anhydrase II which in its turn has made it possible to study the intermediate states of carbonic anhydrase II under equilibrium conditions. The results of equilibrium and kinetic experiments using wild-type bovine carbonic anhydrase II and its mutant form with the substitution of leucine for alanine at position 139 (L139A) were compared. The obtained lifetime components of intrinsic tryptophan fluorescence allowed for revealing that, the same as in kinetic experiments, under equilibrium conditions the unfolding of carbonic anhydrase II ensues through formation of intermediate states.

  5. Angular correlations and fragmentation in intermediate energy heavy ion collisions

    International Nuclear Information System (INIS)

    Kristiansson, Anders.

    1990-05-01

    Intermediate energy heavy-ion collisions have been studied from 35 A MeV up to 94 A MeV at various accelerators. Angular correlations between light particles and detection of projectile- and target-fragments have been used to investigate the reaction mechanisms in this transition region between low- and high energy. An excess of correlations is observed in the particle-particle elastic scattering plane. This excess increases with particle mass and can be understood in terms of momentum conservation. The fragmentation measurements gives an indication that both energy and momentum transfer to the spectator volumes does occur. (author)

  6. Geometrical formulation of the conformal Ward identity

    International Nuclear Information System (INIS)

    Kachkachi, M.

    2002-08-01

    In this paper we use deep ideas in complex geometry that proved to be very powerful in unveiling the Polyakov measure on the moduli space of Riemann surfaces and lead to obtain the partition function of perturbative string theory for 2, 3, 4 loops. Indeed, a geometrical interpretation of the conformal Ward identity in two dimensional conformal field theory is proposed: the conformal anomaly is interpreted as a deformation of the complex structure of the basic Riemann surface. This point of view is in line with the modern trend of geometric quantizations that are based on deformations of classical structures. Then, we solve the conformal Ward identity by using this geometrical formalism. (author)

  7. Fabrication challenges associated with conformal optics

    Science.gov (United States)

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

    2001-09-01

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

  8. Gluon amplitudes as 2 d conformal correlators

    Science.gov (United States)

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

    2017-10-01

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

  9. Noncommutative geometry and twisted conformal symmetry

    International Nuclear Information System (INIS)

    Matlock, Peter

    2005-01-01

    The twist-deformed conformal algebra is constructed as a Hopf algebra with twisted coproduct. This allows for the definition of conformal symmetry in a noncommutative background geometry. The twisted coproduct is reviewed for the Poincare algebra and the construction is then extended to the full conformal algebra. The case of Moyal-type noncommutativity of the coordinates is considered. It is demonstrated that conformal invariance need not be viewed as incompatible with noncommutative geometry; the noncommutativity of the coordinates appears as a consequence of the twisting, as has been shown in the literature in the case of the twisted Poincare algebra

  10. Unconstrained multiplet in N=2 conformal supergravity

    International Nuclear Information System (INIS)

    Hayashi, Masahito; Uehara, Shozo.

    1985-02-01

    An unconstrained (general) multiplet was studied in N = 2 conformal supergravity. Transformation law, embedding formula and multiplication rule are explicitly presented at the linearized level. (author)

  11. Superintegrability of d-dimensional conformal blocks

    International Nuclear Information System (INIS)

    Isachenkov, Mikhail

    2016-02-01

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

  12. Superintegrability of d-dimensional conformal blocks

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-02-15

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

  13. Riemann monodromy problem and conformal field theories

    International Nuclear Information System (INIS)

    Blok, B.

    1989-01-01

    A systematic analysis of the use of the Riemann monodromy problem for determining correlators (conformal blocks) on the sphere is presented. The monodromy data is constructed in terms of the braid matrices and gives a constraint on the noninteger part of the conformal dimensions of the primary fields. To determine the conformal blocks we need to know the order of singularities. We establish a criterion which tells us when the knowledge of the conformal dimensions of primary fields suffice to determine the blocks. When zero modes of the extended algebra are present the analysis is more difficult. In this case we give a conjecture that works for the SU(2) WZW case. (orig.)

  14. 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.

  15. Conformal Dimensions via Large Charge Expansion.

    Science.gov (United States)

    Banerjee, Debasish; Chandrasekharan, Shailesh; Orlando, Domenico

    2018-02-09

    We construct an efficient Monte Carlo algorithm that overcomes the severe signal-to-noise ratio problems and helps us to accurately compute the conformal dimensions of large-Q fields at the Wilson-Fisher fixed point in the O(2) universality class. Using it, we verify a recent proposal that conformal dimensions of strongly coupled conformal field theories with a global U(1) charge can be obtained via a series expansion in the inverse charge 1/Q. We find that the conformal dimensions of the lowest operator with a fixed charge Q are almost entirely determined by the first few terms in the series.

  16. Conformal maps between pseudo-Finsler spaces

    Science.gov (United States)

    Voicu, Nicoleta

    The paper aims to initiate a systematic study of conformal mappings between Finsler spacetimes and, more generally, between pseudo-Finsler spaces. This is done by extending several results in pseudo-Riemannian geometry which are necessary for field-theoretical applications and by proposing a technique that reduces some problems involving pseudo-Finslerian conformal vector fields to their pseudo-Riemannian counterparts. Also, we point out, by constructing classes of examples, that conformal groups of flat (locally Minkowskian) pseudo-Finsler spaces can be much richer than both flat Finslerian and pseudo-Euclidean conformal groups.

  17. Conformal frame dependence of inflation

    International Nuclear Information System (INIS)

    Domènech, Guillem; Sasaki, Misao

    2015-01-01

    Physical equivalence between different conformal frames in scalar-tensor theory of gravity is a known fact. However, assuming that matter minimally couples to the metric of a particular frame, which we call the matter Jordan frame, the matter point of view of the universe may vary from frame to frame. Thus, there is a clear distinction between gravitational sector (curvature and scalar field) and matter sector. In this paper, focusing on a simple power-law inflation model in the Einstein frame, two examples are considered; a super-inflationary and a bouncing universe Jordan frames. Then we consider a spectator curvaton minimally coupled to a Jordan frame, and compute its contribution to the curvature perturbation power spectrum. In these specific examples, we find a blue tilt at short scales for the super-inflationary case, and a blue tilt at large scales for the bouncing case

  18. Conformable eddy current array delivery

    Science.gov (United States)

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

    2016-02-01

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

  19. Conformal frame dependence of inflation

    Energy Technology Data Exchange (ETDEWEB)

    Domènech, Guillem; Sasaki, Misao, E-mail: guillem.domenech@yukawa.kyoto-u.ac.jp, E-mail: misao@yukawa.kyoto-u.ac.jp [Yukawa Institute for Theoretical Physics, Kyoto University, Kyoto 606-8502 (Japan)

    2015-04-01

    Physical equivalence between different conformal frames in scalar-tensor theory of gravity is a known fact. However, assuming that matter minimally couples to the metric of a particular frame, which we call the matter Jordan frame, the matter point of view of the universe may vary from frame to frame. Thus, there is a clear distinction between gravitational sector (curvature and scalar field) and matter sector. In this paper, focusing on a simple power-law inflation model in the Einstein frame, two examples are considered; a super-inflationary and a bouncing universe Jordan frames. Then we consider a spectator curvaton minimally coupled to a Jordan frame, and compute its contribution to the curvature perturbation power spectrum. In these specific examples, we find a blue tilt at short scales for the super-inflationary case, and a blue tilt at large scales for the bouncing case.

  20. Strings, conformal fields and topology

    International Nuclear Information System (INIS)

    Kaku, Michio

    1991-01-01

    String Theory has advanced at an astonishing pace in the last few years, and this book aims to acquaint the reader with the most active topics of research in the field. Building on the foundations laid in his Introduction to Superstrings, Professor Kaku discusses such topics as the classification of conformal string theories, knot theory, the Yang-Baxter relation, quantum groups, the non-polynominal closed string field theory, matrix models, and topological field theory. Several chapters review the fundamentals of string theory, making the presentation of the material self-contained while keeping overlap with the earlier book to a minimum. The book conveys the vitality of current research in string theory and places readers at its forefront. (orig.) With 40 figs. in 50 parts

  1. Light gauginos and conformal sequestering

    International Nuclear Information System (INIS)

    Hanaki, Kentaro; Ookouchi, Yutaka

    2011-01-01

    In a wide class of direct and semidirect gauge mediation models, it has been observed that the gaugino masses vanish at leading order. It implies that there is a hierarchy between the gaugino and sfermion masses, invoking a fine-tuning problem in the Higgs sector via radiative corrections. In this paper, we explore the possibility of solving this anomalously light gaugino problem exploiting strong conformal dynamics in the hidden sector. With a mild assumption on the anomalous dimensions of the hidden sector operators, we show that the next-to-leading order contributions to the gaugino masses can naturally be in the same order as the sfermion masses. The μ/B μ problem is also discussed.

  2. Dissecting Protein Configurational Entropy into Conformational and Vibrational Contributions.

    Science.gov (United States)

    Chong, Song-Ho; Ham, Sihyun

    2015-10-01

    Quantifying how the rugged nature of the underlying free-energy landscape determines the entropic cost a protein must incur upon folding and ligand binding is a challenging problem. Here, we present a novel computational approach that dissects the protein configurational entropy on the basis of the classification of protein dynamics on the landscape into two separate components: short-term vibrational dynamics related to individual free-energy wells and long-term conformational dynamics associated with transitions between wells. We apply this method to separate the configurational entropy of the protein villin headpiece subdomain into its conformational and vibrational components. We find that the change in configurational entropy upon folding is dominated by the conformational entropy despite the fact that the magnitude of the vibrational entropy is the significantly larger component in each of the folded and unfolded states, which is in accord with the previous empirical estimations. The straightforward applicability of our method to unfolded proteins promises a wide range of applications, including those related to intrinsically disordered proteins.

  3. Conformational dependence of a protein kinase phosphate transfer reaction

    Science.gov (United States)

    Labute, Montiago; Henkelman, Graeme; Tung, Chang-Shung; Fenimore, Paul; McMahon, Ben

    2007-03-01

    Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase have been calculated using plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In TC, we calculate that the reactants and products are nearly isoenergetic with a 20-kJ/mol barrier, whereas phosphate transfer is unfavorable by 120 kJ/mol in the RC, with an even higher barrier. Our results demonstrate that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an angstrom in the catalytic site [1]. [1] G.H. Henkelman, M.X. LaBute, C.-S. Tung, P.W. Fenimore, B.H. McMahon, Proc. Natl. Acad. Sci. USA vol. 102, no. 43:15347-15351 (2005).

  4. 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.

  5. Calibration of laboratory equipment and its intermediate verification

    International Nuclear Information System (INIS)

    Remedi, Jorge O.

    2011-01-01

    When a laboratory wants to prove that he has technical competence to carry out tests or calibrations must demonstrate that it has complied with certain requirements that establish , among others, the mandatory : calibrate or verify equipment before putting it into service in order to ensure that it meets to the specifications of laboratory equipment to keep records evidencing the checks that equipment complies with the specification ; perform intermediate checks for maintain confidence in the calibration status of the equipment , ensure that the operation is checked and calibration status of equipment when the equipment goes outside the direct control of the laboratory , before be returned to service, establish a program and procedure for the calibration of equipment; show how determined the calibration periods of their equipment as well as evidence that intermediate checks are suitable for the calibration periods. However, some confusion is observed as to the meaning of the terms 'calibration' and 'verification' of a computer. This paper analyzes applicable documentation and suggests that the differences are generated in part by translations and by characterization concepts upon its usage, that is, if it is legal metrology or assessment conformity. Therefore, this study aims to characterize both concepts , fundamentals to zoom distinguish , outline appropriate strategies for calibration and verification activities to ensure the compliance with regulatory requirements [es

  6. FINANCIAL INTERMEDIATION, ENTREPRENEURSHIP AND ECONOMIC GROWTH

    OpenAIRE

    Wenli Cheng

    2007-01-01

    This paper presents a simple general equilibrium model of financial intermediation, entrepreneurship and economic growth. In this model, the role of financial intermediation is to pool savings and to lend the pooled funds to an entrepreneur, who in turn invests the funds in a new production technology. The adoption of the new production technology improves individual real income. Thus financial intermediation promotes economic growth through affecting individuals’ saving behaviour and enabl...

  7. Biocatalytic Synthesis of Chiral Pharmaceutical Intermediates

    Directory of Open Access Journals (Sweden)

    Ramesh N. Patel

    2004-01-01

    Full Text Available The production of single enantiomers of drug intermediates has become increasingly important in the pharmaceutical industry. Chiral intermediates and fine chemicals are in high demand from both the pharmaceutical and agrochemical industries for the preparation of bulk drug substances and agricultural products. The enormous potential of microorganisms and enzymes for the transformation of synthetic chemicals with high chemo-, regio- and enantioselectivities has been demonstrated. In this article, biocatalytic processes are described for the synthesis of chiral pharmaceutical intermediates.

  8. Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method

    International Nuclear Information System (INIS)

    Ovchinnikov, Victor; Karplus, Martin

    2014-01-01

    A parallel implementation of the finite-temperature string method is described, which takes into account the invariance of coordinates with respect to rigid-body motions. The method is applied to the complex α-helix↔β-sheet transition in a β-hairpin miniprotein in implicit solvent, which exhibits much of the complexity of conformational changes in proteins. Two transition paths are considered, one derived from a linear interpolant between the endpoint structures and the other derived from a targeted dynamics simulation. Two methods for computing the conformational free energy (FE) along the string are compared, a restrained method, and a tessellation method introduced by E. Vanden-Eijnden and M. Venturoli [J. Chem. Phys. 130, 194103 (2009)]. It is found that obtaining meaningful free energy profiles using the present atom-based coordinates requires restricting sampling to a vicinity of the converged path, where the hyperplanar approximation to the isocommittor surface is sufficiently accurate. This sampling restriction can be easily achieved using restraints or constraints. The endpoint FE differences computed from the FE profiles are validated by comparison with previous calculations using a path-independent confinement method. The FE profiles are decomposed into the enthalpic and entropic contributions, and it is shown that the entropy difference contribution can be as large as 10 kcal/mol for intermediate regions along the path, compared to 15–20 kcal/mol for the enthalpy contribution. This result demonstrates that enthalpic barriers for transitions are offset by entropic contributions arising from the existence of different paths across a barrier. The possibility of using systematically coarse-grained representations of amino acids, in the spirit of multiple interaction site residue models, is proposed as a means to avoid ad hoc sampling restrictions to narrow transition tubes

  9. Mechanistic Insights on Human Phosphoglucomutase Revealed by Transition Path Sampling and Molecular Dynamics Calculations.

    Science.gov (United States)

    Brás, Natércia F; Fernandes, Pedro A; Ramos, Maria J; Schwartz, Steven D

    2018-02-06

    Human α-phosphoglucomutase 1 (α-PGM) catalyzes the isomerization of glucose-1-phosphate into glucose-6-phosphate (G6P) through two sequential phosphoryl transfer steps with a glucose-1,6-bisphosphate (G16P) intermediate. Given that the release of G6P in the gluconeogenesis raises the glucose output levels, α-PGM represents a tempting pharmacological target for type 2 diabetes. Here, we provide the first theoretical study of the catalytic mechanism of human α-PGM. We performed transition-path sampling simulations to unveil the atomic details of the two catalytic chemical steps, which could be key for developing transition state (TS) analogue molecules with inhibitory properties. Our calculations revealed that both steps proceed through a concerted S N 2-like mechanism, with a loose metaphosphate-like TS. Even though experimental data suggests that the two steps are identical, we observed noticeable differences: 1) the transition state ensemble has a well-defined TS region and a late TS for the second step, and 2) larger coordinated protein motions are required to reach the TS of the second step. We have identified key residues (Arg23, Ser117, His118, Lys389), and the Mg 2+ ion that contribute in different ways to the reaction coordinate. Accelerated molecular dynamics simulations suggest that the G16P intermediate may reorient without leaving the enzymatic binding pocket, through significant conformational rearrangements of the G16P and of specific loop regions of the human α-PGM. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Transition radiation and transition scattering

    International Nuclear Information System (INIS)

    Ginzburg, V.L.

    1982-01-01

    Transition radiation is a process of a rather general character. It occurs when some source, which does not have a proper frequency (for example, a charge) moves at a constant velocity in an inhomogeneous and (or) nonstationary medium or near such a medium. The simplest type of transition radiation takes place when a charge crosses a boundary between two media (the role of one of the media may be played by vacuum). In the case of periodic variation of the medium, transition radiation possesses some specific features (resonance transition radiation or transition scattering). Transition scattering occurs, in particular, when a permittivity wave falls onto an nonmoving (fixed) charge. Transition scattering is closely connected with transition bremsstrahlung radiation. All these transition processes are essential for plasma physics. Transition radiation and transition scattering have analogues outside the framework of electrodynamics (like in the case of Vavilov-Cherenkov radiation). In the present report the corresponding range of phenomena is elucidated, as far as possible, in a generally physical aspect. (Auth.)

  11. Tribological Behavior of Oil-Lubricated Laser Textured Steel Surfaces in Conformal Flat and Non-Conformal Contacts

    Energy Technology Data Exchange (ETDEWEB)

    Kovalchenko, A. M. [Inst. for Problems of Materials Science, Dept. 7, 3 Krzhizhanovsky Street, Kyiv 03142, UA (Corresponding author), e-mail: andrii.kovalchenko@gatech.edu; Erdemir, A. [Argonne National Lab., Energy Systems Division, 9700 South Cass Avenue, Argonne, IL 60439 US; Ajayi, O. O. [Argonne National Lab., Energy Systems Division, 9700 South Cass Avenue, Argonne, IL 60439 US; Etsion, I. [Technion-Israel Inst. of Technology, Dept. of Mechanical Engineering, Haifa 32000, IL

    2017-01-30

    Changing the surface texture of sliding surfaces is an effective way to manipulate friction and wear of lubricated surfaces. Having realized its potential, we have done very extensive studies on the effects of laser surface texturing (LST, which involves the creation of an array of microdimples on a surface) on friction and wear behavior of oil-lubricated steel surfaces in the early 2000s. In this paper, we reviewed some of our research accomplishments and assessed future directions of the laser texturing field in many diverse industrial applications. Our studies specifically addressed the impact of laser texturing on friction and wear of both the flat conformal and initial non-conformal point contact configurations using a pin-on-disk test rig under fully-flooded synthetic oil lubricants with different viscosities. Electrical resistance measurement between pin and LST disks was also used to determine the operating lubrication regimes in relation to friction. In conformal contact, we confirmed that LST could significantly expand the operating conditions for hydrodynamic lubrication to significantly much higher loads and slower speeds. In particular, with LST and higher viscosity oils, the low-friction full hydrodynamic regime was shifted to the far left in the Stribeck diagram. Overall, the beneficial effects of laser surface texturing were more pronounced at higher speeds and loads and with higher viscosity oil. LST was also observed to reduce the magnitude of friction coefficients in the boundary regime. For the non-conformal contact configuration, we determined that LST would produce more abrasive wear on the rubbing counterface compared to the untreated surfaces due to a reduction in lubricant fluid film thickness, as well as the highly uneven and rough nature of the textured surfaces. However, this higher initial wear rate has led to faster generation of a conformal contact, and thus transition from the high-friction boundary to lower friction mixed

  12. Conformal standard model with an extended scalar sector

    Energy Technology Data Exchange (ETDEWEB)

    Latosiński, Adam [Max-Planck-Institut für Gravitationsphysik (Albert-Einstein-Institut),Mühlenberg 1, D-14476 Potsdam (Germany); Lewandowski, Adrian; Meissner, Krzysztof A. [Faculty of Physics, University of Warsaw,Pasteura 5, 02-093 Warsaw (Poland); Nicolai, Hermann [Max-Planck-Institut für Gravitationsphysik (Albert-Einstein-Institut),Mühlenberg 1, D-14476 Potsdam (Germany)

    2015-10-26

    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. The scalar potential and the Yukawa couplings involving only right-chiral neutrinos are invariant under a new global symmetry SU(3){sub N} that complements the standard U(1){sub B−L} symmetry, and is broken explicitly only by the Yukawa interaction, of order O(10{sup −6}), coupling right-chiral neutrinos and the electroweak lepton doublets. We point out four main advantages of this 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){sub N} symmetry are natural Dark Matter candidates with calculable small masses and couplings; and (4) the Majorana Yukawa coupling matrix acquires a form naturally adapted to leptogenesis. The model is made perturbatively consistent up to the Planck scale by imposing the vanishing of quadratic divergences at the Planck scale (‘softly broken conformal symmetry’). Observable consequences of the model occur mainly via the mixing of the new scalars and the standard model Higgs boson.

  13. Quantum cosmology of a conformal multiverse

    Science.gov (United States)

    Robles-Pérez, Salvador J.

    2017-09-01

    This paper studies the cosmology of a homogeneous and isotropic spacetime endorsed with a conformally coupled massless scalar field. We find six different solutions of the Friedmann equation that represent six different types of universes, and all of them are periodically distributed along the complex time axis. From a classical point of view, they are then isolated, separated by Euclidean regions that represent quantum mechanical barriers. Quantum mechanically, however, there is a nonzero probability for the state of the universes to tunnel out through a Euclidean instanton and suffer a sudden transition to another state of the spacetime. We compute the probability of transition for this and other nonlocal processes like the creation of universes in entangled pairs and, generally speaking, in multipartite entangled states. We obtain the quantum state of a single universe within the formalism of the Wheeler-DeWitt equation and give the semiclassical state of the universes that describes the quantum mechanics of a scalar field propagating in a de Sitter background spacetime. We show that the superposition principle of the quantum mechanics of matter fields alone is an emergent feature of the semiclassical description of the universe that is not valid, for instance, in the spacetime foam. We use the third quantization formalism to describe the creation of an entangled pair of universes with opposite signs of the momentum conjugated to the scale factor. Each universe of the entangled pair represents an expanding spacetime in terms of the Wentzel-Kramers-Brillouin (WKB) time experienced by internal observers in their particle physics experiments. We compute the effective value of the Friedmann equation of the background spacetime of the two entangled universes, and thus, the effect that the entanglement would have in their expansion rates. We analyze as well the effects of the interuniversal entanglement in the properties of the scalar fields that propagate in each

  14. The butane condensed matter conformational problem

    NARCIS (Netherlands)

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

    2010-01-01

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

  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. Dissecting the large-scale galactic conformity

    Science.gov (United States)

    Seo, Seongu

    2018-01-01

    Galactic conformity is an observed phenomenon that galaxies located in the same region have similar properties such as star formation rate, color, gas fraction, and so on. The conformity was first observed among galaxies within in the same halos (“one-halo conformity”). The one-halo conformity can be readily explained by mutual interactions among galaxies within a halo. Recent observations however further witnessed a puzzling connection among galaxies with no direct interaction. In particular, galaxies located within a sphere of ~5 Mpc radius tend to show similarities, even though the galaxies do not share common halos with each other ("two-halo conformity" or “large-scale conformity”). Using a cosmological hydrodynamic simulation, Illustris, we investigate the physical origin of the two-halo conformity and put forward two scenarios. First, back-splash galaxies are likely responsible for the large-scale conformity. They have evolved into red galaxies due to ram-pressure stripping in a given galaxy cluster and happen to reside now within a ~5 Mpc sphere. Second, galaxies in strong tidal field induced by large-scale structure also seem to give rise to the large-scale conformity. The strong tides suppress star formation in the galaxies. We discuss the importance of the large-scale conformity in the context of galaxy evolution.

  17. Conformal deformation of Riemann space and torsion

    International Nuclear Information System (INIS)

    Pyzh, V.M.

    1981-01-01

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

  18. Fusion rules in conformal field theory

    International Nuclear Information System (INIS)

    Fuchs, J.

    1993-06-01

    Several aspects of fusion rings and fusion rule algebras, and of their manifestations in two-dimensional (conformal) field theory, are described: diagonalization and the connection with modular invariance; the presentation in terms of quotients of polynomial rings; fusion graphs; various strategies that allow for a partial classification; and the role of the fusion rules in the conformal bootstrap programme. (orig.)

  19. A viewpoint on nearly conformally symmetric manifold

    International Nuclear Information System (INIS)

    Rahman, M.S.

    1990-06-01

    Some observations, with definition, on Nearly Conformally Symmetric (NCS) manifold are made. A number of theorems concerning conformal change of metric and parallel tensors on NCS manifolds are presented. It is illustrated that a manifold M = R n-1 x R + 1 , endowed with a special metric, is NCS but not of harmonic curvature. (author). 8 refs

  20. Closed forms for conformally flat Green's functions

    International Nuclear Information System (INIS)

    Brown, M.R.; Grove, P.G.; Ottewill, A.C.

    1981-01-01

    A closed form is obtained for the massless scalar Green's function on Rindler space. This is related by conformal transformation to the Green's function for a massless, conformally coupled scalar field on the open Einstein universe. A closed form is also obtained for the corresponding Green's function on the Einstein static universe. (author)

  1. Full conformational landscape of 3-Methoxyphenol revealed by room temperature mm-wave rotational spectroscopy supported by quantum chemical calculations.

    Science.gov (United States)

    Roucou, Anthony; Fontanari, Daniele; Dhont, Guillaume; Jabri, Atef; Bray, Cédric; Hindle, Francis; Mouret, Gaël; Bocquet, Robin; Cuisset, Arnaud

    2018-03-30

    Room temperature millimeter-wave rotational spectroscopy supported by high level of theory calculations have been employed to fully characterise the conformational landscape of 3-Methoxyphenol, a semi-volatile polar oxygenated aromatic compound precursor of secondary organic aerosols in the atmosphere arising from biomass combustion. While previous rotationally-resolved spectroscopic studies in the microwave and in the UV domains failed to observe the complete conformational landscape, the 70 - 330 GHz rotational spectrum measured in this study reveals the ground state rotational signatures of the four stable conformations theoretically predicted. Moreover, rotational transitions in the lowest energy vibrationally excited states were assigned for two conformers. While the inertial defect of methoxyphenol does not signicantly change between conformers and isomers, the excitation of the methoxy out-of-plane bending is the main contribution to the non-planarity of the molecule. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Effect of hyperons on nuclear phase transition

    International Nuclear Information System (INIS)

    Das, P.; Mallik, S.; Chaudhuri, G.

    2016-01-01

    Phase transition of nuclear system in heavy ion-collisions at intermediate energy has been studied well for many years and it has also been extended to strange nuclear matter. Recently, using the Canonical Thermodynamical Model (CTM), detailed work on multiplicity distribution of fragments produced from fragmentation of hypernuclear system shows the existence of phase transition or phase coexistence in strange system with Λ-hyperons. In present work we want to continue the investigation on phase transition with respect to some other thermodynamic observables like free energy, specific heat etc. in order to be confirmed about the nature of the transition

  3. Vertex operator algebras and conformal field theory

    International Nuclear Information System (INIS)

    Huang, Y.Z.

    1992-01-01

    This paper discusses conformal field theory, an important physical theory, describing both two-dimensional critical phenomena in condensed matter physics and classical motions of strings in string theory. The study of conformal field theory will deepen the understanding of these theories and will help to understand string theory conceptually. Besides its importance in physics, the beautiful and rich mathematical structure of conformal field theory has interested many mathematicians. New relations between different branches of mathematics, such as representations of infinite-dimensional Lie algebras and Lie groups, Riemann surfaces and algebraic curves, the Monster sporadic group, modular functions and modular forms, elliptic genera and elliptic cohomology, Calabi-Yau manifolds, tensor categories, and knot theory, are revealed in the study of conformal field theory. It is therefore believed that the study of the mathematics involved in conformal field theory will ultimately lead to new mathematical structures which would be important to both mathematics and physics

  4. Conformation Generation: The State of the Art.

    Science.gov (United States)

    Hawkins, Paul C D

    2017-08-28

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

  5. Conformal Symmetry Patterns in Baryon Spectra

    International Nuclear Information System (INIS)

    Kirchbach, Mariana; Compean, Cliffor B

    2011-01-01

    Attention is drawn to the fact that the spectra of the baryons of the lightest flavors, the nucleon and the Δ, carry quantum numbers characteristic for an unitary representation of the conformal group. We show that the above phenomenon is well explained for baryons whose internal structure is dominated by a quark-diquark configuration that resides in a conformally compactified Minkowski space time, R 1 x S 3 , and is described by means of the conformal scale equation there. The R 1 x S 3 space-time represents the boundary of the conformally compactified AdS 5 , on which one expects to encounter a conformal theory in accord with the gauge-gravity duality. Within this context, our model is congruent with AdS 5 /CFT 4 .

  6. An Intermediate in the evolution of superfast sonic muscles

    Directory of Open Access Journals (Sweden)

    Mok Hin-Kiu

    2011-11-01

    Full Text Available Abstract Background Intermediate forms in the evolution of new adaptations such as transitions from water to land and the evolution of flight are often poorly understood. Similarly, the evolution of superfast sonic muscles in fishes, often considered the fastest muscles in vertebrates, has been a mystery because slow bladder movement does not generate sound. Slow muscles that stretch the swimbladder and then produce sound during recoil have recently been discovered in ophidiiform fishes. Here we describe the disturbance call (produced when fish are held and sonic mechanism in an unrelated perciform pearl perch (Glaucosomatidae that represents an intermediate condition in the evolution of super-fast sonic muscles. Results The pearl perch disturbance call is a two-part sound produced by a fast sonic muscle that rapidly stretches the bladder and an antagonistic tendon-smooth muscle combination (part 1 causing the tendon and bladder to snap back (part 2 generating a higher-frequency and greater-amplitude pulse. The smooth muscle is confirmed by electron microscopy and protein analysis. To our knowledge smooth muscle attachment to a tendon is unknown in animals. Conclusion The pearl perch, an advanced perciform teleost unrelated to ophidiiform fishes, uses a slow type mechanism to produce the major portion of the sound pulse during recoil, but the swimbladder is stretched by a fast muscle. Similarities between the two unrelated lineages, suggest independent and convergent evolution of sonic muscles and indicate intermediate forms in the evolution of superfast muscles.

  7. Intermediates and the folding of proteins L and G

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Scott; Head-Gordon, Teresa

    2003-07-01

    We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G that are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted {beta}-1 and {beta}-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third {beta}-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment.

  8. Nuclear structure at intermediate energies

    International Nuclear Information System (INIS)

    Bonner, B.E.; Mutchler, G.S.

    1991-01-01

    The theme that unites the sometimes seemingly disparate experiments undertaken by the Bonner Lab Medium Energy Group is a determination to understand in detail the many facets and manifestations of the strong interaction, that which is now referred to as nonperturbative QCD. Whether we are investigating the question of just what does carry the spin of baryons, or the extent of the validity of the SU(6) wavefunctions for the excited hyperons (as will be measured in their radiative decays in our CEBAF experiment), or questions associated with the formation of a new state of matter predicted by QCD (the subject of our BNL experiments E810, E854, as well as our approved experiment at RHIC), -- all these projects share this common goal. Our other experiments represent different approaches to the same broad undertaking. LAMPF E1097 will provide definitive answers to the question of the spin dependence of the inelastic channel of pion production in the n-p interaction. FNAL E683 may well open a new field of investigation in nuclear physics: that of just how quarks and gluons interact with nuclear matter as they transverse nuclei of different sizes. In most all of the experiments mentioned above, the Bonner Lab Group is playing major leadership roles as well as doing a big fraction of the hard work that such experiments require. We use many of the facilities that are unavailable to the intermediate energy physics community and we use our expertise to design and fabricate the detectors and instrumentation that are required to perform the measurements which we decide to do

  9. Solution conformation of 2-aminopurine dinucleotide determined by ultraviolet two-dimensional fluorescence spectroscopy

    International Nuclear Information System (INIS)

    Widom, Julia R; Marcus, Andrew H; Johnson, Neil P; Von Hippel, Peter H

    2013-01-01

    We have observed the conformation-dependent electronic coupling between the monomeric subunits of a dinucleotide of 2-aminopurine (2-AP), a fluorescent analogue of the nucleic acid base adenine. This was accomplished by extending two-dimensional fluorescence spectroscopy (2D FS)—a fluorescence-detected variation of 2D electronic spectroscopy—to excite molecular transitions in the ultraviolet (UV) regime. A collinear sequence of four ultrafast laser pulses centered at 323 nm was used to resonantly excite the coupled transitions of 2-AP dinucleotide. The phases of the optical pulses were continuously swept at kilohertz frequencies, and the ensuing nonlinear fluorescence was phase-synchronously detected at 370 nm. Upon optimization of a point–dipole coupling model to our data, we found that in aqueous buffer the 2-AP dinucleotide adopts an average conformation in which the purine bases are non-helically stacked (center-to-center distance R 12 = 3.5 ± 0.5 Å , twist angle θ 12 = 5° ± 5° ), which differs from the conformation of such adjacent bases in duplex DNA. These experiments establish UV–2D FS as a method for examining the local conformations of an adjacent pair of fluorescent nucleotides substituted into specific DNA or RNA constructs, which will serve as a powerful probe to interpret, in structural terms, biologically significant local conformational changes within the nucleic acid framework of protein–nucleic acid complexes. (paper)

  10. Phase Transitions for Flat Anti - de Sitter Black Holes

    International Nuclear Information System (INIS)

    Surya, Sumati; Schleich, Kristin; Witt, Donald M.

    2001-01-01

    We reexamine the thermodynamics of anti - de Sitter (adS) black holes with Ricci flat horizons using the adS soliton as the thermal background. We find that there is a phase transition which is dependent not only on the temperature but also on the black hole area, which is an independent parameter. As in the spherical adS black hole, this phase transition is related via the adS/conformal-field-theory correspondence to a confinement-deconfinement transition in the large-N gauge theory on the conformal boundary at infinity

  11. Using Peephole Optimization on Intermediate Code

    NARCIS (Netherlands)

    Tanenbaum, A.S.; van Staveren, H.; Stevenson, J.W.

    1982-01-01

    Many portable compilers generate an intermediate code that is subsequently translated into the target machine's assembly language. In this paper a stack-machine-based intermediate code suitable for algebraic languages (e.g., PASCAL, C, FORTRAN) and most byte-addressed mini- and microcomputers is

  12. Gasoline Engine Mechanics. Performance Objectives. Intermediate Course.

    Science.gov (United States)

    Jones, Marion

    Several intermediate performance objectives and corresponding criterion measures are listed for each of six terminal objectives presented in this curriculum guide for an intermediate gasoline engine mechanics course at the secondary level. (For the beginning course guide see CE 010 947.) The materials were developed for a two-semester (2 hour…

  13. Some Intermediate-Level Violin Concertos.

    Science.gov (United States)

    Abramson, Michael

    1997-01-01

    Contends that many violin students attempt difficult concertos before they are technically or musically prepared. Identifies a variety of concertos at the intermediate and advanced intermediate-level for students to study and master before attempting the advanced works by Bach and Mozart. Includes concertos by Vivaldi, Leclair, Viotti, Haydn,…

  14. 39 CFR 3001.39 - Intermediate decisions.

    Science.gov (United States)

    2010-07-01

    ... 39 Postal Service 1 2010-07-01 2010-07-01 false Intermediate decisions. 3001.39 Section 3001.39 Postal Service POSTAL REGULATORY COMMISSION PERSONNEL RULES OF PRACTICE AND PROCEDURE Rules of General Applicability § 3001.39 Intermediate decisions. (a) Initial decision by presiding officer. In any proceedings in...

  15. Pair production of intermediate vector bosons

    International Nuclear Information System (INIS)

    Mikaelian, K.O.

    1979-01-01

    The production of intermediate vector boson pairs W + W - , Z 0 Z 0 , W +- Z 0 and W +- γ in pp and p anti p collisions is discussed. The motivation is to detect the self-interactions among the four intermediate vector bosons

  16. Conformal invariance in hydrodynamic turbulence

    International Nuclear Information System (INIS)

    Falkovich, Gregory

    2007-01-01

    This short survey is written by a physicist. It contains neither theorems nor precise definitions. Its main content is a description of the results of numerical solution of the equations of fluid mechanics in the regime of developed turbulence. Due to limitations of computers, the results are not very precise. Despite being neither exact nor rigorous, the findings may nevertheless be of interest for mathematicians. The main result is that the isolines of some scalar fields (vorticity, temperature) in two-dimensional turbulence belong to the class of conformally invariant curves called SLE (Scramm-Loewner evolution) curves. First, this enables one to predict and find a plethora of quantitative relations going far beyond what was known previously about turbulence. Second, it suggests relations between phenomena that seemed unrelated, like the Euler equation and critical percolation. Third, it shows that one is able to get exact analytic results in statistical hydrodynamics. In short, physicists have found something unexpected and hope that mathematicians can help to explain it.

  17. 47 CFR 2.1072 - Limitation on Declaration of Conformity.

    Science.gov (United States)

    2010-10-01

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

  18. Electron-atom scattering at intermediate energies

    International Nuclear Information System (INIS)

    Kingston, A.E.; Walters, H.R.J.

    1982-01-01

    The problems of intermediate energy scattering are approached from the low and high energy ends. At low intermediate energies difficulties associated with the use of pseudostates and correlation terms are discussed, special consideration being given to nonphysical pseudoresonances. Perturbation methods appropriate to high intermediate energies are described and attempts to extend these high energy approximations down to low intermediate energies are studied. It is shown how the importance of electron exchange effects develops with decreasing energy. The problem of assessing the 'effective completeness' of pseudostate sets at intermediate energies is mentioned and an instructive analysis of a 2p pseudostate approximation to elastic e - -H scattering is given. It is suggested that at low energies the Pauli Exclusion Principle can act to hide short range defects in pseudostate approximations. (author)

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-02-15

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

  20. Conformational targeting of fibrillar polyglutamine proteins in live cells escalates aggregation and cytotoxicity.

    Directory of Open Access Journals (Sweden)

    Erik Kvam

    2009-05-01

    Full Text Available Misfolding- and aggregation-prone proteins underlying Parkinson's, Huntington's and Machado-Joseph diseases, namely alpha-synuclein, huntingtin, and ataxin-3 respectively, adopt numerous intracellular conformations during pathogenesis, including globular intermediates and insoluble amyloid-like fibrils. Such conformational diversity has complicated research into amyloid-associated intracellular dysfunction and neurodegeneration. To this end, recombinant single-chain Fv antibodies (scFvs are compelling molecular tools that can be selected against specific protein conformations, and expressed inside cells as intrabodies, for investigative and therapeutic purposes.Using atomic force microscopy (AFM and live-cell fluorescence microscopy, we report that a human scFv selected against the fibrillar form of alpha-synuclein targets isomorphic conformations of misfolded polyglutamine proteins. When expressed in the cytoplasm of striatal cells, this conformation-specific intrabody co-localizes with intracellular aggregates of misfolded ataxin-3 and a pathological fragment of huntingtin, and enhances the aggregation propensity of both disease-linked polyglutamine proteins. Using this intrabody as a tool for modulating the kinetics of amyloidogenesis, we show that escalating aggregate formation of a pathologic huntingtin fragment is not cytoprotective in striatal cells, but rather heightens oxidative stress and cell death as detected by flow cytometry. Instead, cellular protection is achieved by suppressing aggregation using a previously described intrabody that binds to the amyloidogenic N-terminus of huntingtin. Analogous cytotoxic results are observed following conformational targeting of normal or polyglutamine-expanded human ataxin-3, which partially aggregate through non-polyglutamine domains.These findings validate that the rate of aggregation modulates polyglutamine-mediated intracellular dysfunction, and caution that molecules designed to