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Sample records for solvent-dependent conformational transitions

  1. An experimental study of the solvent-dependent self-assembly/disassembly and conformer preferences of gramicidin A.

    PubMed

    Chen, Liuxi; Chen, Shu-Hua; Russell, David H

    2013-08-20

    The solvent dependence of self-assembly/disassembly kinetics and conformer preferences of the gramicidin A (GA) dimer is investigated using a combination of techniques, viz., electrospray ionization-ion mobility-mass spectrometry (IM-MS), collision-induced dissociation (CID), and hydrogen/deuterium exchange (HDX)-MS. IM-MS measurements reveal that there are possibly three distinct GA dimeric species, detected as sodium ion adduct ions [2GA + 2Na](2+), and these are assigned as the parallel ?-helix, antiparallel ?-helix, and head-to-head dimer. The monomerization kinetics and equilibrium abundances of the dimer ions depend upon solvent polarity. The antiparallel ?-helix was the thermodynamically preferred species in less polar solvents. HDX measurements and collision-induced dissociation (CID) of the intermediate complex confirm the well-protected dimer geometry with strong intermolecular hydrogen bonds. This combined IM-HDX-CID methodology provides a comprehensive view of GA self-assembly/disassembly in low dielectric solutions, showing its potential utility in solving solution-phase protein self-assembly/disassembly kinetics and providing structural information of the multimers at the same time. PMID:23855712

  2. Conformational Transitions of Heteropolymers

    E-print Network

    Michael Bachmann; Wolfhard Janke

    2007-10-22

    We study conformational transitions of simple coarse-grained models for protein-like heteropolymers on the simple cubic lattice and off-lattice, respectively, by means of multicanonical sampling algorithms. The effective hydrophobic/polar models do not require the knowledge of the native topology for a given sequence of residues as input. Therefore these models are eligible to investigate general properties of the tertiary folding behaviour of such protein-like heteropolymers.

  3. A mononuclear iron(ii) complex: cooperativity, kinetics and activation energy of the solvent-dependent spin transition.

    PubMed

    Bushuev, Mark B; Pishchur, Denis P; Logvinenko, Vladimir A; Gatilov, Yuri V; Korolkov, Ilya V; Shundrina, Inna K; Nikolaenkova, Elena B; Krivopalov, Viktor P

    2015-12-14

    The system [FeL2](BF4)2 ()-EtOH-H2O (L is 4-(3,5-dimethyl-1H-pyrazol-1-yl)-2-(pyridin-2-yl)-6-methylpyrimidine) shows a complicated balance between the relative stabilities of solvatomorphs and polymorphs of the complex [FeL2](BF4)2. New solvatomorphs, (LS)·EtOH·H2O and ?-(LS)·xH2O, were isolated in this system. They were converted into four daughter phases, (A/LS), (D/LS), (E/LS)·yEtOH·zH2O and (F/LS). On thermal cycling in sealed ampoules, the phases (LS)·EtOH·H2O and ?-(LS)·xH2O transform into the anhydrous phase (A/LS). The hysteresis loop width for the (A/LS) ? (A/HS) spin transition depends on the water and ethanol contents in the ampoule and varies from ca. 30 K up to 145 K. The reproducible hysteresis loop of 145 K is the widest ever reported one for a spin crossover complex. The phase (A/LS) combines the outstanding spin crossover properties with thermal robustness allowing for multiple cycling in sealed ampoules without degradation. The kinetics of the (A/LS) ? (A/HS) transition is sigmoidal which is indicative of strong cooperative interactions. The cooperativity of the (A/LS) ? (A/HS) transition is related to the formation of a 2D supramolecular structure of the phase (A/LS). The activation energy for the spin transition is very high (hundreds of kJ mol(-1)). The kinetics of the (A/HS) ? (A/LS) transition can either be sigmoidal or exponential depending on the water and ethanol contents in the ampoule. The phases (D/LS) and (F/LS) show gradual crossover, whereas the phase (E/LS)·yEtOH·yH2O shows a reversible hysteretic transition associated with the solvent molecule release and uptake. PMID:26599731

  4. Quantifying macromolecular conformational transition pathways

    NASA Astrophysics Data System (ADS)

    Seyler, Sean; Kumar, Avishek; Thorpe, Michael; Beckstein, Oliver

    2015-03-01

    Diverse classes of proteins function through large-scale conformational changes that are challenging for computer simulations. A range of fast path-sampling techniques have been used to generate transitions, but it has been difficult to compare paths from (and assess the relative strengths of) different methods. We introduce a comprehensive method (pathway similarity analysis, PSA) for quantitatively characterizing and comparing macromolecular pathways. The Hausdorff and Fréchet metrics (known from computational geometry) are used to quantify the degree of similarity between polygonal curves in configuration space. A strength of PSA is its use of the full information available from the 3 N-dimensional configuration space trajectory without requiring additional specific knowledge about the system. We compare a sample of eleven different methods for the closed-to-open transitions of the apo enzyme adenylate kinase (AdK) and also apply PSA to an ensemble of 400 AdK trajectories produced by dynamic importance sampling MD and the Geometrical Pathways algorithm. We discuss the method's potential to enhance our understanding of transition path sampling methods, validate them, and help guide future research toward deeper physical insights into conformational transitions.

  5. Conformational Transitions in Molecular Systems

    E-print Network

    Michael Bachmann; Wolfhard Janke

    2009-02-17

    Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as molecular motors in the complex machinery of molecular synthetization processes. Due to their significance, misfolds and malfunctions of proteins typically entail disastrous diseases, such as Alzheimer's disease and bovine spongiform encephalopathy (BSE). Therefore, the understanding of the trinity of amino acid composition, geometric structure, and biological function is one of the most essential challenges for the natural sciences. Here, we glance at conformational transitions accompanying the structure formation in protein folding processes.

  6. Conformational Transitions in Molecular Systems

    NASA Astrophysics Data System (ADS)

    Bachmann, M.; Janke, W.

    2008-11-01

    Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as molecular motors in the complex machinery of molecular synthetization processes. Due to their significance, misfolds and malfunctions of proteins typically entail disastrous diseases, such as Alzheimer's disease and bovine spongiform encephalopathy (BSE). Therefore, the understanding of the trinity of amino acid composition, geometric structure, and biological function is one of the most essential challenges for the natural sciences. Here, we glance at conformational transitions accompanying the structure formation in protein folding processes.

  7. Electroweak phase transition in nearly conformal technicolor

    SciTech Connect

    Cline, James M.; Jaervinen, Matti; Sannino, Francesco

    2008-10-01

    We examine the temperature-dependent electroweak phase transition in extensions of the standard model in which the electroweak symmetry is spontaneously broken via strongly coupled, nearly conformal dynamics. In particular, we focus on the low energy effective theory used to describe minimal walking technicolor at the phase transition. Using the one-loop effective potential with ring improvement, we identify significant regions of parameter space which yield a sufficiently strong first-order transition for electroweak baryogenesis. The composite particle spectrum corresponding to these regions can be produced and studied at the Large Hadron Collider experiment. We note the possible emergence of a second phase transition at lower temperatures. This occurs when the underlying technicolor theory possesses a nontrivial center symmetry.

  8. Conformational transitions of a weak polyampholyte

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

    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.

  9. Peptide-Induced Amyloid-Like Conformational Transitions in Proteins

    PubMed Central

    Egorov, Vladimir; Grudinina, Natalia; Vasin, Andrey; Lebedev, Dmitry

    2015-01-01

    Changes in protein conformation can occur both as part of normal protein functioning and during disease pathogenesis. The most common conformational diseases are amyloidoses. Sometimes the development of a number of diseases which are not traditionally related to amyloidoses is associated with amyloid-like conformational transitions of proteins. Also, amyloid-like aggregates take part in normal physiological processes such as memorization and cell signaling. Several primary structural features of a protein are involved in conformational transitions. Also the protein proteolytic fragments can cause the conformational transitions in the protein. Short peptides which could be produced during the protein life cycle or which are encoded by short open reading frames can affect the protein conformation and function. PMID:26435719

  10. Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations

    E-print Network

    de Groot, Bert

    Conformational Transitions upon Ligand Binding: Holo- Structure Prediction from Apo Conformations in the ligand- bound state (holo structures), however, are a prerequisite for successful structure-based drug of the holo structure. The method is applied to ten cases in which proteins undergo structural rearrangements

  11. Water-Peptide Dynamics during Conformational Transitions Dmitry Nerukh*,

    E-print Network

    Nerukh, Dmitry

    Water-Peptide Dynamics during Conformational Transitions Dmitry Nerukh*, and Sergey Karabasov are investigated using classical molecular dynamics simulation with explicit water molecules. The distribution of the surrounding water at different moments before the transitions and the dynamical correlations of water

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

    NASA Astrophysics Data System (ADS)

    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-?s canonical MD simulation failed to sample such a rare event.

  13. Conformational transitions in random heteropolymer models

    NASA Astrophysics Data System (ADS)

    Blavatska, Viktoria; Janke, Wolfhard

    2014-01-01

    We study the conformational properties of heteropolymers containing two types of monomers A and B, modeled as self-attracting self-avoiding random walks on a regular lattice. Such a model can describe in particular the sequences of hydrophobic and hydrophilic residues in proteins [K. F. Lau and K. A. Dill, Macromolecules 22, 3986 (1989)] and polyampholytes with oppositely charged groups [Y. Kantor and M. Kardar, Europhys. Lett. 28, 169 (1994)]. Treating the sequences of the two types of monomers as quenched random variables, we provide a systematic analysis of possible generalizations of this model. To this end we apply the pruned-enriched Rosenbluth chain-growth algorithm, which allows us to obtain the phase diagrams of extended and compact states coexistence as function of both the temperature and fraction of A and B monomers along the heteropolymer chain.

  14. Native proteins trap high-energy transit conformations

    PubMed Central

    Brereton, Andrew E.; Karplus, P. Andrew

    2015-01-01

    During protein folding and as part of some conformational changes that regulate protein function, the polypeptide chain must traverse high-energy barriers that separate the commonly adopted low-energy conformations. How distortions in peptide geometry allow these barrier-crossing transitions is a fundamental open question. One such important transition involves the movement of a non-glycine residue between the left side of the Ramachandran plot (that is, ? < 0°) and the right side (that is, ? > 0°). We report that high-energy conformations with ? ~ 0°, normally expected to occur only as fleeting transition states, are stably trapped in certain highly resolved native protein structures and that an analysis of these residues provides a detailed, experimentally derived map of the bond angle distortions taking place along the transition path. This unanticipated information lays to rest any uncertainty about whether such transitions are possible and how they occur, and in doing so lays a firm foundation for theoretical studies to better understand the transitions between basins that have been little studied but are integrally involved in protein folding and function. Also, the context of one such residue shows that even a designed highly stable protein can harbor substantial unfavorable interactions. PMID:26601321

  15. Folding funnels and conformational transitions via hinge-bending motions.

    PubMed

    Kumar, S; Ma, B; Tsai, C J; Wolfson, H; Nussinov, R

    1999-01-01

    In this article we focus on presenting a broad range of examples illustrating low-energy transitions via hinge-bending motions. The examples are divided according to the type of hinge-bending involved; namely, motions involving fragments of the protein chains, hinge-bending motions involving protein domains, and hinge-bending motions between the covalently unconnected subunits. We further make a distinction between allosterically and nonallosterically regulated proteins. These transitions are discussed within the general framework of folding and binding funnels. We propose that the conformers manifesting such swiveling motions are not the outcome of "induced fit" binding mechanism; instead, molecules exist in an ensemble of conformations that are in equilibrium in solution. These ensembles, which populate the bottoms of the funnels, a priori contain both the "open" and the "closed" conformational isomers. Furthermore, we argue that there are no fundamental differences among the physical principles behind the folding and binding funnels. Hence, there is no basic difference between funnels depicting ensembles of conformers of single molecules with fragment, or domain motions, as compared to subunits in multimeric quaternary structures, also showing such conformational transitions. The difference relates only to the size and complexity of the system. The larger the system, the more complex its corresponding fused funnel(s). In particular, funnels associated with allosterically regulated proteins are expected to be more complicated, because allostery is frequently involved with movements between subunits, and consequently is often observed in multichain and multimolecular complexes. This review centers on the critical role played by flexibility and conformational fluctuations in enzyme activity. Internal motions that extend over different time scales and with different amplitudes are known to be essential for the catalytic cycle. The conformational change observed in enzyme-substrate complexes as compared to the unbound enzyme state, and in particular the hinge-bending motions observed in enzymes with two domains, have a substantial effect on the enzymatic catalytic activity. The examples we review span the lipolytic enzymes that are particularly interesting, owing to their activation at the water-oil interface; an allosterically controlled dehydrogenase (lactate dehydrogenase); a DNA methyltransferase, with a covalently-bound intermediate; large-scale flexible loop motions in a glycolytic enzyme (TIM); domain motion in PGK, an enzyme which is essential in most cells, both for ATP generation in aerobes and for fermentation in anaerobes; adenylate kinase, showing large conformational changes, owing to their need to shield their catalytic centers from water; a calcium-binding protein (calmodulin), involved in a wide range of cellular calcium-dependent signaling; diphtheria toxin, whose large domain motion has been shown to yield "domain swapping;" the hexameric glutamate dehydrogenase, which has been studied both in a thermophile and in a mesophile; an allosteric enzyme, showing subunit motion between the R and the T states (aspartate transcarbamoylase), and the historically well-studied lac repressor. Nonallosteric subunit transitions are also addressed, with some examples (aspartate receptor and BamHI endonuclease). Hence, using this enzyme-catalysis-centered discussion, we address energy funnel landscapes of large-scale conformational transitions, rather than the faster, quasi-harmonic, thermal fluctuations. PMID:10593256

  16. Conformational Transition of H-shaped Branched Polymers

    E-print Network

    Ashok Kumar Dasmahapatra; Venkata Mahanth Sanka

    2013-10-15

    We report dynamic Monte Carlo simulation on conformational transition of H-shaped branched polymers by varying main chain (backbone) and side chain (branch) length. H-shaped polymers in comparison with equivalent linear polymers exhibit a depression of theta temperature accompanying with smaller chain dimensions. We observed that the effect of branches on backbone dimension is more pronounced than the reverse, and is attributed to the conformational heterogeneity prevails within the molecule. With increase in branch length, backbone is slightly stretched out in coil and globule state. However, in the pre-collapsed (cf. crumpled globule) state, backbone size decreases with the increase of branch length. We attribute this non-monotonic behavior as the interplay between excluded volume interaction and intra-chain bead-bead attractive interaction during collapse transition. Structural analysis reveals that the inherent conformational heterogeneity promotes the formation of a collapsed structure with segregated backbone and branch units (resembles to 'sandwich' or 'Janus' morphology) rather an evenly distributed structure comprising of all the units. The shape of the collapsed globule becomes more spherical with increasing either backbone or branch length.

  17. Protein behavior at surfaces: orientation, conformational transitions and transport.

    PubMed

    Yu, Linling; Zhang, Lin; Sun, Yan

    2015-02-20

    Chromatography is the key technology in protein purification as well as in protein refolding. Taking the scientific development and technological innovation of protein chromatography as the objective, this article is devoted to an overview of protein behavior at chromatographic surfaces, including protein orientation, conformational transitions (unfolding and refolding), and protein transport. Recent advances achieved by using molecular simulations as well as theoretical and experimental investigations are elaborated and discussed with emphasis on their implications to the rational design of novel chromatographic surfaces or materials and mobile phase conditions for the development of high-performance protein chromatography. PMID:25601319

  18. Sequence Recognition of DNA by Protein-Induced Conformational Transitions

    SciTech Connect

    Watkins, Derrick; Mohan, Srividya; Koudelka, Gerald B.; Williams, Loren Dean

    2010-11-09

    The binding of proteins to specific sequences of DNA is an important feature of virtually all DNA transactions. Proteins recognize specific DNA sequences using both direct readout (sensing types and positions of DNA functional groups) and indirect readout (sensing DNA conformation and deformability). Previously we showed that the P22 c2 repressor N-terminal domain (P22R NTD) forces the central non-contacted 5{prime}-ATAT-3{prime} sequence of the DNA operator into the B{prime} state, a state known to affect DNA hydration, rigidity and bending. Usually the B{prime} state, with a narrow minor groove and a spine of hydration, is reserved for A-tract DNA (TpA steps disrupt A-tracts). Here, we have co-crystallized P22R NTD with an operator containing a central 5{prime}-ACGT-3{prime} sequence in the non-contacted region. C {center_dot} G base pairs have not previously been observed in the B{prime} state and are thought to prevent it. However, P22R NTD induces a narrow minor groove and a spine of hydration to 5{prime}-ACGT-3{prime}. We observe that C {center_dot} G base pairs have distinctive destabilizing and disordering effects on the spine of hydration. It appears that the reduced stability of the spine results in a higher energy cost for the B to B{prime} transition. The differential effect of DNA sequence on the barrier to this transition allows the protein to sense the non-contacted DNA sequence.

  19. Conformational transitions of subunit epsilon in ATP synthase from thermophilic Bacillus PS3.

    PubMed

    Feniouk, Boris A; Kato-Yamada, Yasuyuki; Yoshida, Masasuke; Suzuki, Toshiharu

    2010-02-01

    Subunit epsilon of bacterial and chloroplast F(O)F(1)-ATP synthase is responsible for inhibition of ATPase activity. In Bacillus PS3 enzyme, subunit epsilon can adopt two conformations. In the "extended", inhibitory conformation, its two C-terminal alpha-helices are stretched along subunit gamma. In the "contracted", noninhibitory conformation, these helices form a hairpin. The transition of subunit epsilon from an extended to a contracted state was studied in ATP synthase incorporated in Bacillus PS3 membranes at 59 degrees C. Fluorescence energy resonance transfer between fluorophores introduced in the C-terminus of subunit epsilon and in the N-terminus of subunit gamma was used to follow the conformational transition in real time. It was found that ATP induced the conformational transition from the extended to the contracted state (half-maximum transition extent at 140 microM ATP). ADP could neither prevent nor reverse the ATP-induced conformational change, but it did slow it down. Acid residues in the DELSEED region of subunit beta were found to stabilize the extended conformation of epsilon. Binding of ATP directly to epsilon was not essential for the ATP-induced conformational change. The ATP concentration necessary for the half-maximal transition (140 microM) suggests that subunit epsilon probably adopts the extended state and strongly inhibits ATP hydrolysis only when the intracellular ATP level drops significantly below the normal value. PMID:20141757

  20. Picosecond conformational transition and equilibration of a cyclic peptide

    PubMed Central

    Bredenbeck, Jens; Helbing, Jan; Sieg, Arne; Schrader, Tobias; Zinth, Wolfgang; Renner, Christian; Behrendt, Raymond; Moroder, Luis; Wachtveitl, Josef; Hamm, Peter

    2003-01-01

    Ultrafast IR spectroscopy is used to monitor the nonequilibrium backbone dynamics of a cyclic peptide in the amide I vibrational range with picosecond time resolution. A conformational change is induced by means of a photoswitch integrated into the peptide backbone. Although the main conformational change of the backbone is completed after only 20 ps, the subsequent equilibration in the new region of conformational space continues for times >16 ns. Relaxation and equilibration processes of the peptide backbone occur on a discrete hierarchy of time scales. Albeit possessing only a few conformational degrees of freedom compared with a protein, the peptide behaves highly nontrivially and provides insights into the complexity of fast protein folding. PMID:12736378

  1. Entropic mechanism of allosteric communication in conformational transitions of dihydrofolate reductase.

    PubMed

    Terada, Tomoki P; Kimura, Toru; Sasai, Masaki

    2013-10-24

    The mechanism of allosteric conformational transitions of Escherichia coli dihydrofolate reductase (DHFR) is investigated theoretically by applying a newly developed coarse-grained model. Functional forms of interaction potentials in the model depend on the local structural environments around those interactions to represent the many-residue effects due to atomic packing in each local region, and hence, this model is called "the chameleon model". The chameleon model consistently describes the free-energy landscape of two conformational transitions in the catalytic cycle of DHFR, which we call conformational transition 1 (CT1) and conformational transition 2 (CT2); CT1 is accompanied by the hydride transfer reaction, and CT2 is accompanied by the product ligand release. The transition state of CT1 is entropically stabilized by the disordering of loops at the peripheral regions of the protein, which enhances the positively correlated fluctuations at the center part of the protein, showing that the allosteric communication between distant regions through the central region is intrinsically associated with the entropic stabilization of the transition state. The transition state of CT2 is entropically stabilized through the mechanism that enhances the breathing motion of two domains, showing that the difference in the distribution of interactions brings about the difference in the transition mechanism between CT1 and CT2. The chameleon model opens a way to consistently describe the dynamical energy landscape of enzymatic reactions. PMID:23705773

  2. Conformational transitions of glycine induced by vibrational excitation of the O-H stretch.

    PubMed

    Shmilovits-Ofir, Michaela; Miller, Yifat; Gerber, R Benny

    2011-05-21

    Vibrational energy flow and conformational transitions following excitation of the OH stretching mode of the most stable conformer of glycine are studied by classical trajectories. "On the fly" simulations with the PM3 semiempirical electronic structure method for the potential surface are used. Initial conditions are selected to correspond to the ?=1 excitation of the OH stretch. The main findings are: (1) An an equilibrium-like ratio is established between the populations of the 3 lowest-lying conformers after about 10 picoseconds. (2) There is a high probability throughout the 150 ps of the simulations for finding the molecule in geometries far from the equilibrium structures of the lowest-energy conformers. (3) Energy from the initial excited OH (?=1) stretch flows preferentially to 5 other vibrational modes, including the bending motion of the H atom. (4) RRK theory yields conformational transition rates that deviate substantially from the classical trajectory results. Possible implication of these results for vibrational energy flow and conformational transitions in small biological molecules are discussed. PMID:20922237

  3. Modeling conformational transitions in kinases by molecular dynamics simulations: achievements, difficulties, and open challenges

    PubMed Central

    D'Abramo, Marco; Besker, Neva; Chillemi, Giovanni; Grottesi, Alessandro

    2014-01-01

    Protein kinases work because their flexibility allows to continuously switch from inactive to active form. Despite the large number of structures experimentally determined in such states, the mechanism of their conformational transitions as well as the transition pathways are not easily to capture. In this regard, computational methods can help to shed light on such an issue. However, due to the intrinsic sampling limitations, much efforts have been done to model in a realistic way the conformational changes occurring in protein kinases. In this review we will address the principal biological achievements and structural aspects in studying kinases conformational transitions and will focus on the main challenges related to computational approaches such as molecular modeling and MD simulations. PMID:24860596

  4. Investigation of the influence on conformational transition of DNA induced by cationic lipid vesicles

    NASA Astrophysics Data System (ADS)

    Zhang, Zheling; Huang, Weimin; Wang, Erkang; Dong, Shaojun

    2003-01-01

    Recent studies have focused on the structural features of DNA-lipid assemblies. In this paper we take nile blue A (NBA) as a probe molecule to study the influence of the conformational transition of DNA induced by didodecyldimethylammonium bromide (DDAB) cationic vesicles to the interaction between DNA and the probe molecules. We find that upon binding to DNA, a secondary conformational transition of DNA induced by the cationic liposome from the native B-form to the C-form resulted in the change of binding modes of NBA to DNA and different complexes are formed between DNA, DDAB and NBA.

  5. Asymmetric ligand binding facilitates conformational transitions in pentameric ligand-gated ion channels.

    PubMed

    Mowrey, David; Cheng, Mary Hongying; Liu, Lu Tian; Willenbring, Dan; Lu, Xinghua; Wymore, Troy; Xu, Yan; Tang, Pei

    2013-02-13

    The anesthetic propofol inhibits the currents of the homopentameric ligand-gated ion channel GLIC, yet the crystal structure of GLIC with five propofol molecules bound symmetrically shows an open-channel conformation. To address this dilemma and determine if the symmetry of propofol binding sites affects the channel conformational transition, we performed a total of 1.5 ?s of molecular dynamics simulations for different GLIC systems with propofol occupancies of 0, 1, 2, 3, and 5. GLIC without propofol binding or with five propofol molecules bound symmetrically, showed similar channel conformation and hydration status over multiple replicates of 100-ns simulations. In contrast, asymmetric binding to one, two or three equivalent sites in different subunits accelerated the channel dehydration, increased the conformational heterogeneity of the pore-lining TM2 helices, and shifted the lateral and radial tilting angles of TM2 toward a closed-channel conformation. The results differentiate two groups of systems based on the propofol binding symmetry. The difference between symmetric and asymmetric groups is correlated with the variance in the propofol-binding cavity adjacent to the hydrophobic gate and the force imposed by the bound propofol. Asymmetrically bound propofol produced greater variance in the cavity size that could further elevate the conformation heterogeneity. The force trajectory generated by propofol in each subunit over the course of a simulation exhibits an ellipsoidal shape, which has the larger component tangential to the pore. Asymmetric propofol binding creates an unbalanced force that expedites the channel conformation transitions. The findings from this study not only suggest that asymmetric binding underlies the propofol functional inhibition of GLIC, but also advocate for the role of symmetry breaking in facilitating channel conformational transitions. PMID:23339564

  6. Asymmetric Ligand Binding Facilitates Conformational Transitions in Pentameric Ligand-Gated Ion Channels

    PubMed Central

    Mowrey, David; Cheng, Mary Hongying; Liu, Lu Tian; Willenbring, Dan; Lu, Xinghua; Wymore, Troy; Xu, Yan; Tang, Pei

    2013-01-01

    The anesthetic propofol inhibits the currents of the homo-pentameric ligand-gated ion channel GLIC, yet the crystal structure of GLIC with five propofol molecules bound symmetrically shows an open-channel conformation. To address this dilemma and determine if symmetry of propofol binding sites affects the channel conformational transition, we performed a total of 1.5 As of molecular dynamics simulations for different GLIC systems with propofol occupancies of 0, 1, 2, 3, and 5. GLIC without propofol binding or with five propofol molecules bound symmetrically showed similar channel conformation and hydration status over multiple replicates of 100-ns simulations. In contrast, asymmetric binding to one, two or three equivalent sites in different subunits accelerated the channel dehydration, which was accompanied by increased conformational heterogeneity of the pore and shifted the lateral and radial tilting angles of the pore-lining TM2 towards a closed-channel conformation. The results differentiate two groups of systems based on the propofol binding symmetry. The difference between symmetric and asymmetric groups is correlated with the variance in the propofol-binding cavity adjacent to the hydrophobic gate and the force imposed by the bound propofol. Asymmetrically bound propofol produced greater variance in the cavity size that could further elevate the conformation heterogeneity. The force trajectory generated by propofol in each subunit over the course of a simulation exhibits an ellipsoidal shape, which has the larger component tangential to the pore. Asymmetric propofol binding creates an unbalanced force that expedites the channel conformation transitions. The findings from this study not only suggest that asymmetric binding underlies the propofol functional inhibition of GLIC, but also advocate for the role of symmetry breaking in facilitating channel conformational transitions. PMID:23339564

  7. Lithium Diisopropylamide-Mediated Enolizations: Solvent-Dependent Mixed Aggregation Effects

    E-print Network

    Collum, David B.

    Lithium Diisopropylamide-Mediated Enolizations: Solvent-Dependent Mixed Aggregation Effects Xiufeng spectroscopic investigations of lithium diisopropylamide-mediated ester enolization in THF, t-BuOMe, HMPA that the metalations by lithium diisopropylamide (LDA) homonuclear dimers proceed at nearly solvent-independent rates

  8. Molecular dynamics study of the weakly solvent dependent relaxation dynamics following chlorine dioxide photoexcitation

    E-print Network

    Molecular dynamics study of the weakly solvent dependent relaxation dynamics following chlorine The solvation dynamics following photoexcitation of chlorine dioxide OClO in different solvents are investigated chemistry.1­3 Representative of this group of compounds, chlorine dioxide OClO has been the subject of much

  9. Conformations Conformations

    E-print Network

    Fischer, Wolfgang

    59 Chapter 10 Conformations #12;60 Conformations · Identical Composition · Identical Connection Pattern · Different bond length · Different angles · Different dihedrals #12;61 Stochastic Conformational Search The Stochastic Conformational Search algorithm proceeds as follows: 1. Initialize the conformer

  10. Modeling Conformational Transitions and Energetics of Ligand Binding with the Glutamate Receptor Ligand Binding Domain

    NASA Astrophysics Data System (ADS)

    Kurnikova, Maria

    2009-03-01

    Understanding of protein motion and energetics of conformational transitions is crucial to understanding protein function. The glutamate receptor ligand binding domain (GluR2 S1S2) is a two lobe protein, which binds ligand at the interface of two lobes and undergoes conformational transition. The cleft closure conformational transition of S1S2 has been implicated in gating of the ion channel formed by the transmembrane domain of the receptor. In this study we present a composite multi-faceted theoretical analysis of the detailed mechanism of this conformational transition based on rigid cluster decomposition of the protein structure [1] and identifying hydrogen bonds that are responsible for stabilizing the closed conformation [2]. Free energy of the protein reorganization upon ligand binding was calculated using combined Thermodynamic Integration (TI) and Umbrella Sampling (US) simulations [3]. Ligand -- protein interactions in the binding cleft were analyzed using Molecular Dynamics, continuum electrostatics and QM/MM models [4]. All model calculations compare well with corresponding experimental measurements. [4pt] [1] Protein Flexibility using Constraints from Molecular Dynamics Simulations T. Mamonova, B. Hespenheide, R. Straub, M. F. Thorpe, M. G. Kurnikova , Phys. Biol., 2, S137 (2005)[0pt] [2] Theoretical Study of the Glutamate Receptor Ligand Binding Domain Flexibility and Conformational Reorganization T. Mamonova, K. Speranskiy, and M. Kurnikova , Prot.: Struct., Func., Bioinf., 73,656 (2008)[0pt] [3] Energetics of the cleft closing transition and glutamate binding in the Glutamate Receptor ligand Binding Domain T. Mamonova, M. Yonkunas, and M. Kurnikova Biochemistry 47, 11077 (2008)[0pt] [4] On the Binding Determinants of the Glutamate Agonist with the Glutamate Receptor Ligand Binding Domain K. Speranskiy and M. Kurnikova Biochemistry 44, 11208 (2005)

  11. Conformal Dynamics and Thermal/Bulk Phase Transition in Lattice Gauge Theory with Many Fermion Species

    NASA Astrophysics Data System (ADS)

    Miura, Kohtaroh; Lombardo, Maria Paola; Pallante, Elisabetta; da Silva, Tiago Nunes; Deuzeman, Albert

    We summarize our recent results1,2 which investigate the conformal dynamics associated with the infra-red fixed point in colour SU(Nc = 3) gauge theory with a variable number (Nf) of fundamental fermions by using lattice Monte-Carlo simulations. We evaluate the thermal chiral phase transition as a function of Nf, and investigate the vanishing of the chiral dynamics in the large Nf region. Then, three independent analyses consistently indicate the onset of the conformal phase for Nf ? N*f ˜ 9.2 - 14.1. Furthermore, we study the bulk transition in Nf = 12 system with a focus on the interplay between the transition property and the improvements for the lattice action. We show that the bulk transition observed in the case of the naive action evolves into two rapid crossovers due to the improvement for the fermion sector.

  12. Structural Plasticity and Conformational Transitions of HIV Envelope Glycoprotein gp120

    PubMed Central

    Korkut, Anil; Hendrickson, Wayne A.

    2012-01-01

    HIV envelope glycoproteins undergo large-scale conformational changes as they interact with cellular receptors to cause the fusion of viral and cellular membranes that permits viral entry to infect targeted cells. Conformational dynamics in HIV gp120 are also important in masking conserved receptor epitopes from being detected for effective neutralization by the human immune system. Crystal structures of HIV gp120 and its complexes with receptors and antibody fragments provide high-resolution pictures of selected conformational states accessible to gp120. Here we describe systematic computational analyses of HIV gp120 plasticity in such complexes with CD4 binding fragments, CD4 mimetic proteins, and various antibody fragments. We used three computational approaches: an isotropic elastic network analysis of conformational plasticity, a full atomic normal mode analysis, and simulation of conformational transitions with our coarse-grained virtual atom molecular mechanics (VAMM) potential function. We observe collective sub-domain motions about hinge points that coordinate those motions, correlated local fluctuations at the interfacial cavity formed when gp120 binds to CD4, and concerted changes in structural elements that form at the CD4 interface during large-scale conformational transitions to the CD4-bound state from the deformed states of gp120 in certain antibody complexes. PMID:23300605

  13. Transition Networks for the Comprehensive Characterization of Complex Conformational Change in proteins

    SciTech Connect

    Noe, F; Krachtus, D; Smith, Jeremy C; Fischer, S.

    2006-03-01

    Functionally relevant transitions between native conformations of a protein can be complex, involving, for example, the reorganization of parts of the backbone fold, and may occur via a multitude of pathways. Such transitions can be characterized by a transition network (TN), in which the experimentally determined end state structures are connected by a dense network of subtransitions via low-energy intermediates. We show here how the computation of a TN can be achieved for a complex protein transition. First, an efficient hierarchical procedure is used to uniformly sample the conformational subspace relevant to the transition. Then, the best path which connects the end states is determined as well as the rate-limiting ridge on the energy surface which separates them. Graph-theoretical algorithms permit this to be achieved by computing the barriers of only a small number out of the many subtransitions in the TN. These barriers are computed using the Conjugate Peak Refinement method. The approach is illustrated on the conformational switch of Ras p21. The best and the 12 next-best transition pathways, having rate-limiting barriers within a range of 10 kcal/mol, were identified. Two main energy ridges, which respectively involve rearrangements of the switch I and switch II loops, show that switch I must rearrange by threading Tyr32 underneath the protein backbone before the rate-limiting switch II rearrangement can occur, while the details of the switch II rearrangement differ significantly among the low-energy pathways.

  14. The role of the 132–160 region in prion protein conformational transitions

    PubMed Central

    Torrent, Joan; Alvarez-Martinez, Maria Teresa; Liautard, Jean-Pierre; Balny, Claude; Lange, Reinhard

    2005-01-01

    The native conformation of host-encoded cellular prion protein (PrPC) is metastable. As a result of a post-translational event, PrPC can convert to the scrapie form (PrPSc), which emerges as the essential constituent of infectious prions. Despite thorough research, the mechanism underlying this conformational transition remains unknown. However, several studies have highlighted the importance of the N-terminal region spanning residues 90–154 in PrP folding. In order to understand why PrP folds into two different conformational states exhibiting distinct secondary and tertiary structure, and to gain insight into the involvement of this particular region in PrP transconformation, we studied the pressure-induced unfolding/ refolding of recombinant Syrian hamster PrP expanding from residues 90–231, and compared it with heat unfolding. By using two intrinsic fluorescent variants of this protein (Y150W and F141W), conformational changes confined to the 132–160 segment were monitored. Multiple conformational states of the Trp variants, characterized by their spectroscopic properties (fluorescence and UV absorbance in the fourth derivative mode), were achieved by tuning the experimental conditions of pressure and temperature. Further insight into unexplored conformational states of the prion protein, likely to mimic the in vivo structural change, was obtained from pressure-assisted cold unfolding. Furthermore, salt-induced conformational changes suggested a structural stabilizing role of Tyr150 and Phe141 residues, slowing down the conversion to a ?-sheet form. PMID:15772306

  15. Reaction paths and free energy profiles for conformational transitions: An internal coordinate approach

    E-print Network

    Lazaridis, Themis

    Reaction paths and free energy profiles for conformational transitions: An internal coordinate to study in Cartesian space. A procedure to obtain reaction paths and free energy profiles in solution is also proposed. The free energy profile along the path in solution is calculated utilizing a free energy

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

    PubMed

    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-LC interfaces. PMID:25856793

  17. The Atomistic Mechanism of Conformational Transition of Adenylate Kinase Investigated by Lorentzian Structure-Based Potential.

    PubMed

    Lee, Juyong; Joo, Keehyoung; Brooks, Bernard R; Lee, Jooyoung

    2015-07-14

    We present a new all-atom structure-based method to study protein conformational transitions using Lorentzian attractive interactions based on native structures. The variability of each native contact is estimated based on evolutionary information using a machine learning method. To test the validity of this approach, we have investigated the conformational transition of adenylate kinase (ADK). The intrinsic boundedness of the Lorentzian attractive interactions facilitated frequent conformational transitions, and consequently we were able to observe more than 1000 structural interconversions between the open and closed states of ADK out of a total of 6 ?s MD simulations. ADK has three domains: the nucleoside monophosphate (NMP) binding domain, the LID-domain, and the CORE domain, which catalyze the interconversion between ATP and ADP. We identified two transition states: a more frequent LID-closed-NMP-open (TS1) state and a less frequent LID-open-NMP-closed (TS2) state. The transition was found to be symmetric in both directions via TS1. We also obtained an off-pathway metastable state that was previously observed with physics-based all-atom simulations but not with coarse-grained models. In the metastable state, the LID domain was slightly twisted and formed contacts with the NMP domain. Our model correctly identified a total of 14 out of the top 16 residues with highest fluctuation by NMR experiment, thus showing excellent agreement with experimental NMR relaxation data and overwhelmingly better results than existing models. PMID:26575758

  18. The impact of N-terminal phosphorylation on LHCII conformation in state transition

    NASA Astrophysics Data System (ADS)

    Ding, Jin-Hong; Li, Ning; Wang, Man-Liu; Zhang, Yan; Lü, Shou-Qin; Long, Mian

    2014-06-01

    State transition is an important protection mechanism of plants for maintaining optimal efficiency through redistributing unbalanced excitation energy between photo-system II (PSII) and photosystem I (PSI). This process depends on the reversible phosphorylation/dephosphorylation of the major light-harvesting complex II (LHCII) and its bi-directional migration between PSII and PSI. But it remains unclear how phosphorylation/dephosphorylation modulates the LHCII conformation and further regulates its reversible migration. Here molecular dynamics simulations (MDS) were employed to elucidate the impact of phosphorylation on LHCII conformation. The results indicated that N-terminal phosphorylation loosened LHCII trimer with decreased hydrogen bond (H-bond) interactions and extended the distances between neighboring monomers, which stemmed from the conformational adjustment of each monomer itself. Global conformational change of LHCII monomer started from its stromal Nterminal (including the phosphorylation sites) by enhancing its interaction to lipid membrane and by adjusting the interaction network with surrounded inter-monomer and intra-monomer transmembrane helixes of B, C, and A, and finally triggered the reorientation of transmembrane helixes and transferred the conformational change to luminal side helixes and loops. These results further our understanding in molecular mechanism of LHCII migration during state transition from the phosphorylation-induced microstructural feature of LHCII.

  19. Solvent-dependent optical limiting response of platinum nanoparticles stabilized by [60] fullerene derivative

    NASA Astrophysics Data System (ADS)

    Gao, Y. C.; He, C. Y.

    2015-05-01

    The optical limiting performance of platinum nanoparticle protected by C60 derivative in chloroform, ethanol and dimethylformamide (DMF) was measured with 532nm, 8ns duration laser pulses. Experiments showed that the optical limiting is solvent-dependent. The origins and solvent effect of the optical limiting were analyzed. It was proposed that the absorption-induced scattering is the main mechanism causing the optical limiting behavior and solvent effect.

  20. Features of Large Hinge-Bending Conformational Transitions. Prediction of Closed Structure from Open State

    PubMed Central

    Uyar, Arzu; Kantarci-Carsibasi, Nigar; Haliloglu, Turkan; Doruker, Pemra

    2014-01-01

    We performed a detailed analysis of conformational transition pathways for a set of 10 proteins, which undergo large hinge-bending-type motions with 4–12 Å RMSD (root mean-square distance) between open and closed crystal structures. Anisotropic network model-Monte Carlo (ANM-MC) algorithm generates a targeted pathway between two conformations, where the collective modes from the ANM are used for deformation at each iteration and the conformational energy of the deformed structure is minimized via an MC algorithm. The target structure was approached successfully with an RMSD of 0.9–4.1 Å when a relatively low cutoff radius of 10 Å was used in ANM. Even though one predominant mode (first or second) directed the open-to-closed conformational transition, changes in the dominant mode character were observed for most cases along the transition. By imposing radius of gyration constraint during mode selection, it was possible to predict the closed structure for eight out of 10 proteins (with initial 4.1–7.1 Å and final 1.7–2.9 Å RMSD to target). Deforming along a single mode leads to most successful predictions. Based on the previously reported free energy surface of adenylate kinase, deformations along the first mode produced an energetically favorable path, which was interestingly facilitated by a change in mode shape (resembling second and third modes) at key points. Pathway intermediates are provided in our database of conformational transitions (http://safir.prc.boun.edu.tr/anmmc/method/1). PMID:24940783

  1. Finite-Size Conformational Transitions: A Unifying Concept Underlying Chromosome Dynamics

    NASA Astrophysics Data System (ADS)

    Bertrand, R. Caré; Pascal, Carrivain; Thierry, Forné; Jean-Marc, Victor; Annick, Lesne

    2014-10-01

    Investigating average thermodynamic quantities is not sufficient to understand conformational transitions of a finite-size polymer. We propose that such transitions are better described in terms of the probability distribution of some finite-size order parameter, and the evolution of this distribution as a control parameter varies. We demonstrate this claim for the coil-globule transition of a linear polymer and its mapping onto a two-state model. In a biological context, polymer models delineate the physical constraints experienced by the genome at different levels of organization, from DNA to chromatin to chromosome. We apply our finite-size approach to the formation of plectonemes in a DNA segment submitted to an applied torque and the ensuing helix-coil transition that can be numerically observed, with a coexistence of the helix and coil states in a range of parameters. Polymer models are also essential to analyze recent in vivo experiments providing the frequency of pairwise contacts between genomic loci. The probability distribution of these contacts yields quantitative information on the conformational fluctuations of chromosome regions. The changes observed in the shape of the distribution when the cell type or the physiological conditions vary may reveal an epigenetic modulation of the conformational constraints experienced by the chromosomes.

  2. Mechanistic picture for conformational transition of a membrane transporter at atomic resolution.

    PubMed

    Moradi, Mahmoud; Tajkhorshid, Emad

    2013-11-19

    During their transport cycle, ATP-binding cassette (ABC) transporters undergo large-scale conformational changes between inward- and outward-facing states. Using an approach based on designing system-specific reaction coordinates and using nonequilibrium work relations, we have performed extensive all-atom molecular dynamics simulations in the presence of explicit membrane/solvent to sample a large number of mechanistically distinct pathways for the conformational transition of MsbA, a bacterial ABC exporter whose structure has been solved in multiple functional states. The computational approach developed here is based on (i) extensive exploration of system-specific biasing protocols (e.g., using collective variables designed based on available low-resolution crystal structures) and (ii) using nonequilibrium work relations for comparing the relevance of the transition pathways. The most relevant transition pathway identified using this approach involves several distinct stages reflecting the complex nature of the structural changes associated with the function of the protein. The opening of the cytoplasmic gate during the outward- to inward-facing transition of apo MsbA is found to be disfavored when the periplasmic gate is open and facilitated by a twisting motion of the nucleotide-binding domains that involves a dramatic change in their relative orientation. These results highlight the cooperativity between the transmembrane and the nucleotide-binding domains in the conformational transition of ABC exporters. The approach introduced here provides a framework to study large-scale conformational changes of other membrane transporters whose computational investigation at an atomic resolution may not be currently feasible using conventional methods. PMID:24191018

  3. The kinetics of effector binding to phosphofructokinase. The influence of effectors on the allosteric conformational transition.

    PubMed Central

    Roberts, D; Kellett, G L

    1980-01-01

    1. The extent of the allosteric transition from the R into the T conformation of rabbit skeletal muscle phosphofructokinase induced by Mg2+-1,N6-etheno-ATP was determined by stopped-flow fluorimetry from the amplitude of the slow phase of the Mg2+-1,N6-etheno-ATP fluorescence enhancement [Roberts & Kellet (1979) Biochem. J. 183, 349--360]. 2. The amplitude of the slow phase was decreased by low concentrations of the activators cyclic AMP and fructose 1,6-bisphosphate, but increased in a complex manner by the inhibitor citrate. 3. Mg2+-1,N6-etheno-ATP and Mg2+-ATP are unable to induce the T conformation to a detectable extent in the presence of saturating cyclic AMP, but can do so readily in the presence of saturating fructose 1,6-bisphosphate. 4. The conformational transitions induced in enzyme alone by different ligands were observed by changes in intrinsic protein fluorescence. In general, an R-type conformation has diminished protein fluorescence compared with a T-type conformation. 5. Mg2+-ATP exerts a complex effect on protein fluorescence; both the enhancement at low concentrations and the quenching at high concentrations of Mg2+-ATP result from the binding of Mg2+-ATP to the inhibitory site and the ensuing allosteric transition. Enhancement reflects the extent of the allosteric transition and involves both tyrosine and tryptophan, probably in the region of the active site; quenching reflects occupation of the inhibitory site and involves tyrosine at the inhibitory site. 6. The mechanism of the allosteric transition from the R into the T conformation induced by Mg2+-1,N6-etheno-ATP at low concentrations occurs predominantly by a 'prior-isomerization' pathway; at higher concentrations a limited contribution from a 'substrate-guided' pathway occurs. 7. The allosteric behaviour of phosphofructokinase with respect to Mg2+-ATP and Mg2+-1,N6-ethenol-ATP binding may be accounted for in terms of the simple, concerted model. Images Fig. 1. Fig. 5. Fig. 6. PMID:6260084

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

    DOEpatents

    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.

  5. Solvent effects on the conformational transition of a model polyalanine peptide

    PubMed Central

    Nguyen, Hung D.; Marchut, Alexander J.; Hall, Carol K.

    2004-01-01

    We have investigated the folding of polyalanine by combining discontinuous molecular dynamics simulation with our newly developed off-lattice intermediate-resolution protein model. The thermodynamics of a system containing a single Ac-KA14K-NH2 molecule has been explored by using the replica exchange simulation method to map out the conformational transitions as a function of temperature. We have also explored the influence of solvent type on the folding process by varying the relative strength of the side-chain’s hydrophobic interactions and backbone hydrogen bonding interactions. The peptide in our simulations tends to mimic real polyalanine in that it can exist in three distinct structural states: ?-helix, ?-structures (including ?-hairpin and ?-sheet–like structures), and random coil, depending upon the solvent conditions. At low values of the hydrophobic interaction strength between nonpolar side-chains, the polyalanine peptide undergoes a relatively sharp transition between an ?-helical conformation at low temperatures and a random-coil conformation at high temperatures. As the hydrophobic interaction strength increases, this transition shifts to higher temperatures. Increasing the hydrophobic interaction strength even further induces a second transition to a ?-hairpin, resulting in an ?-helical conformation at low temperatures, a ?-hairpin at intermediate temperatures, and a random coil at high temperatures. At very high values of the hydrophobic interaction strength, polyalanines become ?-hairpins and ?-sheet–like structures at low temperatures and random coils at high temperatures. This study of the folding of a single polyalanine-based peptide sets the stage for a study of polyalanine aggregation in a forthcoming paper. PMID:15498937

  6. On the Phase Transition of Conformal Field Theories with Holographic Duals

    E-print Network

    Cappiello, L

    2001-01-01

    We study the thermodynamic relations of conformal field theories (CFTs), which are holographically dual to anti-de Sitter-Schwarzschild bulk space-times. A Cardy-Verlinde formula is derived thermodynamically for CFTs living on S^n x R with S^n having an arbitrary radius. The Hawking-Page phase transition of the CFT is described using Landau's theory of phase transitions, and an alternative derivation of the Cardy-Verlinde formula is presented. The condensate in the high temperature phase is identified as being composed of radiational matter.

  7. On the Phase Transition of Conformal Field Theories with Holographic Duals

    E-print Network

    L. Cappiello; W. Mueck

    2001-10-24

    We study the thermodynamic relations of conformal field theories (CFTs), which are holographically dual to anti-de Sitter-Schwarzschild bulk space-times. A Cardy-Verlinde formula is derived thermodynamically for CFTs living on S^n x R with S^n having an arbitrary radius. The Hawking-Page phase transition of the CFT is described using Landau's theory of phase transitions, and an alternative derivation of the Cardy-Verlinde formula is presented. The condensate in the high temperature phase is identified as being composed of radiational matter.

  8. Equilibrium transitions between side-chain conformations in leucine and isoleucine.

    PubMed

    Caballero, Diego; Smith, W Wendell; O'Hern, Corey S; Regan, Lynne

    2015-08-01

    Despite recent improvements in computational methods for protein design, we still lack a quantitative, predictive understanding of the intrinsic probabilities for amino acids to adopt particular side-chain conformations. Surprisingly, this question has remained unsettled for many years, in part because of inconsistent results from different experimental approaches. To explicitly determine the relative populations of different side-chain dihedral angles, we performed all-atom hard-sphere Langevin Dynamics simulations of leucine (Leu) and isoleucine (Ile) dipeptide mimetics with stereo-chemical constraints and repulsive-only steric interactions between non-bonded atoms. We determine the relative populations of the different ?(1) and ?(2) dihedral angle combinations as a function of the backbone dihedral angles ? and ?. We also propose, and test, a mechanism for inter-conversion between the different side-chain conformations. Specifically, we discover that some of the transitions between side-chain dihedral angle combinations are very frequent, whereas others are orders of magnitude less frequent, because they require rare coordinated motions to avoid steric clashes. For example, to transition between different values of ?(2), the Leu side-chain bond angles ?(1) and ?(2) must increase, whereas to transition in ?(1), the Ile bond angles ?(1) and ?(2) must increase. These results emphasize the importance of computational approaches in stimulating further experimental studies of the conformations of side-chains in proteins. Moreover, our studies emphasize the power of simple steric models to inform our understanding of protein structure, dynamics, and design. PMID:26018846

  9. Mean field theory for the intermolecular and intramolecular conformational transitions of a single flexible polyelectrolyte chain

    NASA Astrophysics Data System (ADS)

    Shew, Chwen-Yang; Yoshikawa, Kenichi

    2007-04-01

    The diMarzio theory has been extended to elucidate the intermolecular and intramolecular phase segregations of a single flexible chain polyelectrolyte in dilute salt-free solutions. At the long chain limit, this theory yields the formalism obtained from the more sophisticated Edward Hamiltonian for polyelectrolyte problems. The calculated phase diagram exhibits the features of a first-order phase transition, with continuous and discontinuous transitions separated by a critical point. Under the discontinuous transition, the polyelectrolyte chain exhibits coexistent expanded and collapsed conformational states, same as intermolecular phase segregation. For a limiting long chain, the mean chain size at critical point is roughly 90% of the size of an ideal chain. Such a result implies that partial contraction within a chain molecule is required to collapse a flexible polyelectrolyte chain. Moreover, the theory predicts that for a longer chain, intramolecular segregated conformations differ significantly from intermolecular segregated conformations, but the difference becomes small for shorter chains. Besides, the charge needed to induce intramolecular segregation is smaller than that of intermolecular segregation for a given chain length. These findings are consistent with previous literature results.

  10. Mean field theory for the intermolecular and intramolecular conformational transitions of a single flexible polyelectrolyte chain.

    PubMed

    Shew, Chwen-Yang; Yoshikawa, Kenichi

    2007-04-14

    The diMarzio theory has been extended to elucidate the intermolecular and intramolecular phase segregations of a single flexible chain polyelectrolyte in dilute salt-free solutions. At the long chain limit, this theory yields the formalism obtained from the more sophisticated Edward Hamiltonian for polyelectrolyte problems. The calculated phase diagram exhibits the features of a first-order phase transition, with continuous and discontinuous transitions separated by a critical point. Under the discontinuous transition, the polyelectrolyte chain exhibits coexistent expanded and collapsed conformational states, same as intermolecular phase segregation. For a limiting long chain, the mean chain size at critical point is roughly 90% of the size of an ideal chain. Such a result implies that partial contraction within a chain molecule is required to collapse a flexible polyelectrolyte chain. Moreover, the theory predicts that for a longer chain, intramolecular segregated conformations differ significantly from intermolecular segregated conformations, but the difference becomes small for shorter chains. Besides, the charge needed to induce intramolecular segregation is smaller than that of intermolecular segregation for a given chain length. These findings are consistent with previous literature results. PMID:17444749

  11. The solvent dependent shift of the amide I band of a fully solvated peptide in methanol/water mixtures as a local probe for the solvent composition in the peptide/solvent interface

    SciTech Connect

    Gnanakaran, S

    2008-01-01

    We determine the shift and line-shape of the amide I band of a model AK-peptide from molecular dynamics (MD) simulations of the peptide dissolved in methanol/water mixtures with varying composition. The IR-spectra are determined from a transition dipole coupling exciton model. A simplified empirical model Hamiltonian is employed, taking both the effect of hydrogen bonding, as well as intramolecular vibrational coupling into account. We consider a single isolated AK-peptide in a mostly helical conformation, while the solvent is represented by 2600 methanol or water molecules, simulated for a pressure of 1 bar and a temperature of 300 K. Over the course of the simulations minor reversible conformational changes at the termini are observed, which are found to only slightly affect the calculated spectral properties. Over the entire composition range, varying from pure water to the pure methanol solvent, a monotonous blue-shift of the IR amide I band of about 8 wavenumbers is observed. The shift is found to be caused by two counter-compensating effects: An intramolecular red-shift of about 1.2 wavenumbers, due to stronger intramolecular hydrogen-bonding in a methanol-rich environment. Dominating, however, is the intermolecular solvent-dependent blue-shift of about 10 wavenumbers, being attributed to the less effective hydrogen bond donor capabilities of methanol compared to water. The importance of solvent-contribution to the IR-shift, as well as the significantly different hydrogen formation capabilities of water and methanol make the amide I band sensitive to composition changes in the local environment close the peptide/solvent interface. This allows, in principle, an experimental determination of the composition of the solvent in close proximity to the peptide surface. For the AK-peptide case they observe at low methanol concentrations a significantly enhanced methanol concentration at the peptide/solvent-interface, supposedly promoted by the partially hydrophobic character of the AK-peptide's solvent accessible surface.

  12. EB1 Accelerates Two Conformational Transitions Important for Microtubule Maturation and Dynamics

    PubMed Central

    Maurer, Sebastian P.; Cade, Nicholas I.; Bohner, Gerg?; Gustafsson, Nils; Boutant, Emmanuel; Surrey, Thomas

    2014-01-01

    Summary Background The dynamic properties of microtubules depend on complex nanoscale structural rearrangements in their end regions. Members of the EB1 and XMAP215 protein families interact autonomously with microtubule ends. EB1 recruits several other proteins to growing microtubule ends and has seemingly antagonistic effects on microtubule dynamics: it induces catastrophes, and it increases growth velocity, as does the polymerase XMAP215. Results Using a combination of in vitro reconstitution, time-lapse fluorescence microscopy, and subpixel-precision image analysis and convolved model fitting, we have studied the effects of EB1 on conformational transitions in growing microtubule ends and on the time course of catastrophes. EB1 density distributions at growing microtubule ends reveal two consecutive conformational transitions in the microtubule end region, which have growth-velocity-independent kinetics. EB1 binds to the microtubule after the first and before the second conformational transition has occurred, positioning it several tens of nanometers behind XMAP215, which binds to the extreme microtubule end. EB1 binding accelerates conformational maturation in the microtubule, most likely by promoting lateral protofilament interactions and by accelerating reactions of the guanosine triphosphate (GTP) hydrolysis cycle. The microtubule maturation time is directly linked to the duration of a growth pause just before microtubule depolymerization, indicating an important role of the maturation time for the control of dynamic instability. Conclusions These activities establish EB1 as a microtubule maturation factor and provide a mechanistic explanation for its effects on microtubule growth and catastrophe frequency, which cause microtubules to be more dynamic. PMID:24508171

  13. Solvent-Dependent Divergent Functions of Sc(OTf)3 in Stereoselective Epoxide-Opening Spiroketalizations

    PubMed Central

    2015-01-01

    A stereocontrolled synthesis of benzannulated spiroketals has been developed using solvent-dependent Sc(OTf)3-mediated spirocyclizations of exo-glycal epoxides having alcohol side chains. In THF, the reaction proceeds via Lewis acid catalysis under kinetic control with inversion of configuration at the anomeric carbon. In contrast, in CH2Cl2, Brønsted acid catalysis under thermodynamic control leads to retention of configuration. The reactions accommodate a variety of aryl substituents and ring sizes and provide stereochemically diverse spiroketals. PMID:24742081

  14. The 'order-to-disorder' conformational transition in CD44 protein: an umbrella sampling analysis.

    PubMed

    Plazinski, Wojciech; Knys-Dzieciuch, Agnieszka

    2013-09-01

    The molecule of CD44, a membrane protein being the major cell surface receptor for hyaluronan, is postulated to undergo the conformational rearrangement called the 'order-to-disorder' transition. The experimental studies suggest that the Tyr161 residue is crucial for maintaining the equilibrium between the 'ordered' (O) and 'partially disordered' (PD) forms of CD44. The molecular modeling study based on the umbrella sampling protocol was carried out separately for the wild-type CD44 and Tyr161Ala mutant in order to gain more insight into the molecular mechanism of the O-PD transition and to clarify the role of the Tyr161 amino acid residue. The calculated free energy profiles associated with the initial stages of the O-PD conformational transition allow to identify the crucial steps of this process and their molecular details. The differences between the wild-type CD44 and the Tyr161Ala mutant are very insignificant which allows for speculating that, surprisingly, the role of Tyr161 in the O-PD transition is not connected with disrupting the attractive Glu48-Tyr161 and Leu52-Tyr161 interactions but with other types of (unknown yet) interactions located outside the ?7-?8 loop or with the existence of the PD-like structure in which the terminal lobe remains located under the ?7-?8 loop. PMID:24012974

  15. The temperature and pH dependence of conformational transitions of the chromatin subunit.

    PubMed

    Gordon, V C; Schumaker, V N; Olins, D E; Knobler, C M; Horwitz, J

    1979-08-24

    Hydrodynamic, spectroscopic, and chemical crosslinking studies on monomer chromatin subnits are reported as a function of ionic strength, pH, and temperature. In earlier studies, two salt-dependent conformational transitions were described (Gordon et al., Proceedings of the National Academy of Science, 75, 660, 1978). Transition one occurred between 0.7 and 2.0 mM ionic strength and transition two occurred between 5.0 and 11.0 mM ionic strength. Crosslinking at 11 mM ionic strength with formaldehyde suppressed both transitions. In this communication we report that the second transition was characterized by changes in the circular dichroism spectra in the 260--320 nm region as well as by changes in the hydrodynamic properties. As the ionic strength was increased from 5.0 to 11.0 mM, [theta]282 decreased from 2000 TO 1500 DEG CM2/DMOLE AND [THETA]295 decreased from 0 to -400 deg cm2/dmole. Both transitions occurred in the pH range from pH 6.0 to 9.2. At pH 5.0, the two ionic strength-dependent transitions were no longer observed and the characteristic changes in the circular dichroism spectra were suppressed. The spectra of the monomer subunits at pH 5.0 showed only small changes with ionic strength and resembled the spectra of the subunits at 11 mM ionic strength above pH 6.0. In order to characterize the transitions in thermodynamic terms an ionic strength near the midpoint of each transition was selected. Then, changes in s20,w and D20,w were measured as a function of temperature. These data allow an estimation to be made of the enthalpies and entropies of the transitions. PMID:40207

  16. Application of Conformal Invariance to the Investigation of Second Order Surface Phase Transitions.

    NASA Astrophysics Data System (ADS)

    Hentschke, Reinhard

    Using the consequences of conformal invariance of critical correlation functions, the effects of finite size, shape and boundary conditions on scattering functions S(vec{rm K}), susceptibilities, correlation lengths and specific heat correction terms for 2D Ising systems at criticality were investigated (Hentschke, Kleban and Akinci, 1986; Kleban, Akinci, Hentschke and Brownstein, 1986). Very good agreement was found with specific model calculations using Monte Carlo and transfer matrix resutls (Bartelt and Einstein, 1986) for the scattering functions and susceptibilities of fully finite, two dimensional rectangular and circular geometries as well as for the infinite strip with periodic boundary conditions. The decay of S(vec{rm K}) according to the power law 1/k ^{2-eta_{rm app} } with an apparent exponent eta _{rm app} not= eta in the intermediate k-regime is discussed and modeled analytically for the circular geometry (Kleban and Hentschke, 1986). The concepts of conformal invariance are reviewed, and a dynamical LEED (low energy electron diffraction) theory at the critical point is proposed for adsorbates or reconstructing undergoing a second order phase transition. The method employed combines conformal invariance with the standard dynamical LEED theory as found in Pendry (1974). An explicit expression for the scattering intensity at the bulk (infinite system) critical temperature is given for transitions belonging to the Ising universality class. The formulas are evaluated in s-wave approximation using the (1 times 1)Leftrightarrow p(2 times 1) transition on a simple cubic substrate as an example. In addition the extension of this method to other universality classes is discussed in some detail. These results are of interest for several reasons. (i) They are directly applicable to the experiment, allowing a test of some fundamental aspects of the conformal principle. (ii) The predictions are universal, in the sense that they do not depend on the details of the forces responsible for the transition. They are determined by the universality class of the transition, which is generally specified by easily observable symmetry breaking. (iii) The predicted intimate relation between finite size and the detailed dependence of the scattering on experimental parameters (incoming energy, angles, etc.) may prove useful for surface characterization.

  17. Conformational transitions of plasmid ds-DNA on ultrathin films of alkylamines on graphite

    NASA Astrophysics Data System (ADS)

    Falk, Caroline; Liang, Hua; Severin, Nikolai; Zhuang, Wei; Zauscher, Stefan; Rabe, Jürgen P.

    2015-03-01

    DNA replication is an important process in the human body. Replication of double-stranded (ds)-DNA requires its local melting into two single strands. DNA, when stretched in solution, overwinds and melts. This was argued to give insight onto the replication mechanism. It is difficult, however, to access the direct conformational changes during stretching in solution. Recent work demonstrated that this transition can be imaged with scanning force microscopy on a graphite surface that is coated with an alkylamine layer. ds-DNA can be controlled by an amphiphilic layer, since the DNA conformation depends on the amphiphile concentration. In particular we analyzed different DNA lengths on the same surface, and we found that at a specific concentration of octadecylamine the ds-DNA pUC19 plasmid ring splits into two single strands at one position. We will discuss methods to mark the DNA to determine the exact location at which the plasmid ring splits.

  18. Modeling protein conformational transitions by a combination of coarse-grained normal mode analysis and robotics-inspired methods

    PubMed Central

    2013-01-01

    Background Obtaining atomic-scale information about large-amplitude conformational transitions in proteins is a challenging problem for both experimental and computational methods. Such information is, however, important for understanding the mechanisms of interaction of many proteins. Methods This paper presents a computationally efficient approach, combining methods originating from robotics and computational biophysics, to model protein conformational transitions. The ability of normal mode analysis to predict directions of collective, large-amplitude motions is applied to bias the conformational exploration performed by a motion planning algorithm. To reduce the dimension of the problem, normal modes are computed for a coarse-grained elastic network model built on short fragments of three residues. Nevertheless, the validity of intermediate conformations is checked using the all-atom model, which is accurately reconstructed from the coarse-grained one using closed-form inverse kinematics. Results Tests on a set of ten proteins demonstrate the ability of the method to model conformational transitions of proteins within a few hours of computing time on a single processor. These results also show that the computing time scales linearly with the protein size, independently of the protein topology. Further experiments on adenylate kinase show that main features of the transition between the open and closed conformations of this protein are well captured in the computed path. Conclusions The proposed method enables the simulation of large-amplitude conformational transitions in proteins using very few computational resources. The resulting paths are a first approximation that can directly provide important information on the molecular mechanisms involved in the conformational transition. This approximation can be subsequently refined and analyzed using state-of-the-art energy models and molecular modeling methods. PMID:24564964

  19. Solvent dependent assembly of lanthanide metallacrowns using building blocks with incompatible symmetry preferences.

    PubMed

    Jankolovits, Joseph; Kampf, Jeff W; Pecoraro, Vincent L

    2014-07-21

    Solvent dependence in the assembly of coordination driven macrocycles is a poorly understood phenomenon. This work presents the solvent dependent assembly of 8 lanthanide metallacrowns (LnMCs) in solution using picoline hydroxamic acid (picHA), Zn(II), and Ln(III) ions. ESI-MS and single-crystal X-ray crystallography reveal the selective assembly of LnZn4(picHA)4(3+), LnZn5(picHA)5(3+), LnZn8(picHA)8(3+), LnZn12(picHA)12(3+), LnZn16(picHA)16(3+), Ln2Zn3(picHA)4(4+), Ln2Zn7-9(picHA)8-10, and Ln4Zn4-5(picHA)8-9 complexes in five different solvents. The coordination preferences of the hard Ln(III) ion and relatively soft Zn(II) ion dictate the solvent selectivity in this system. The LnMCs assemble with open or closed Zn(II) and/or Ln(III) coordination sites based on the behavior of the solvent as an ancillary ligand. This structural promiscuity is attributed to the symmetry incompatible building blocks, which generate assemblies with substantial geometric strain such that no clear thermodynamic minimum exists between the different LnMCs. These LnMCs assemble from a Zn5(picHA)4(2+) intermediate, which is monitored using (1)H NMR and ESI-MS to assess the stability of the complexes and possible assembly pathways based on kinetic considerations. LnMC assemblies that can be generated through central metal substitution reactions such as the LnZn4(picHA)4(3+), LnZn5(picHA)5(3+), and LnZn8(picHA)8(3+) effectively reach equilibrium after 24 h at room temperature. In contrast, LnMCs that must disrupt the Zn5L4(2+) structure to assemble, such as the LnZn16L16(3+), reach equilibrium after heating for 24 h at 65 °C. A pathway for LnMC assembly is presented where the Zn5L4(2+) is the key intermediate based on these reaction data and shared structural motifs in the complexes. These results correlate solvent dependent assembly to the building block geometry, highlighting synthetic approaches for generating novel complexes. PMID:24956137

  20. Distinguishing Unfolding and Functional Conformational Transitions of Calmodulin Using Ultraviolet Resonance Raman Spectroscopy

    SciTech Connect

    Jones, Eric M.; Balakrishnan, G.; Squier, Thomas C.; Spiro, Thomas

    2014-06-14

    Calmodulin (CaM) is a ubiquitous moderator protein for calcium signaling in all eukaryotic cells. This small calcium-binding protein exhibits a broad range of structural transitions, including domain opening and folding-unfolding, that allow it to recognize a wide variety of binding partners in vivo. While the static structures of CaM associated with its various binding activities are fairly well known, it has been challenging to examine the dynamics of transition between these structures in real-time, due to a lack of suitable spectroscopic probes of CaM structure. In this paper, we examine the potential of ultraviolet resonance Raman (UVRR) spectroscopy for clarifying the nature of structural transitions in CaM. We find that the UVRR spectral change (with 229 nm excitation) due to thermal unfolding of CaM is qualitatively different from that associated with opening of the C-terminal domain in response to Ca2+ binding. This spectral difference is entirely due to differences in teritary contacts at the inter-domain tyrosine residue Tyr138, toward which other spectroscopic methods are not sensitive. We conclude that UVRR is ideally suited to identifying the different types of structural transitions in CaM and other proteins with conformation-sensitive tyrosine residues, opening a path to time-resolved studies of CaM dynamics using Raman spectroscopy.

  1. The kinetics of effector binding to phosphofructokinase. The allosteric conformational transition induced by 1,N6-ethenoadenosine triphosphate.

    PubMed Central

    Roberts, D; Kellett, G L

    1979-01-01

    1. The fluorescent ATP analogue 1,N6-etheno-ATP is a good substrate and an efficient allosteric inhibitor of rabbit skeletal-muscle phosphofructokinase. 2. Fluorescence energy transfer occurs between bound 1,N6-etheno-ATP and phosphofructokinase. 1,N6-Etheno-ATP fluorescence is enhanced, intrinsic protein fluorescence is quenched, and the excitation spectrum of 1,N6-etheno-ATP fluorescence is characteristic of protein absorption. 3. The binding reaction of 1,N6-etheno-ATP observed by stopped-flow fluorimetry is biphasic. The fast phase results from binding to the catalytic site alone. The slow phase results from the allosteric transition of the R conformation into the T conformation induced by the binding of 1,N6-etheno-ATP to the regulatory site. 4. The fluorescence signal that allows the transition of the R conformation into the T conformation to be observed does not arise from 1,N6-etheno-ATP bound to the regulatory site. It arises instead from 1,N6-etheno-ATP bound to the catalytic site as a consequence of changes at the catalytic site caused by the transition of the R conformation into the T conformation. 5. In the presence of excess of Mg2+, the affinity of 1,N6-etheno-ATP for the regulatory site is very much greater in the T state than in the R state. Images Fig. 5. Fig. 8. PMID:160791

  2. Inherent flexibility and protein function: The open/closed conformational transition in the N-terminal domain of calmodulin

    NASA Astrophysics Data System (ADS)

    Tripathi, Swarnendu; Portman, John J.

    2008-05-01

    The key to understand a protein's function often lies in its conformational dynamics. We develop a coarse-grained variational model to investigate the interplay between structural transitions, conformational flexibility, and function of the N-terminal calmodulin domain (nCaM). In this model, two energy basins corresponding to the ``closed'' apo conformation and ``open'' holo conformation of nCaM are coupled by a uniform interpolation parameter. The resulting detailed transition route from our model is largely consistent with the recently proposed EF?-scaffold mechanism in EF-hand family proteins. We find that the N-terminal parts of the calcium binding loops shows higher flexibility than the C-terminal parts which form this EF?-scaffold structure. The structural transition of binding loops I and II are compared in detail. Our model predicts that binding loop II, with higher flexibility and earlier structural change than binding loop I, dominates the open/closed conformational transition in nCaM.

  3. Particular behavior of the adenine and guanine ring-breathing modes upon the DNA conformational transitions.

    PubMed

    Ghomi, M; Letellier, R; Taillandier, E

    1988-06-01

    Harmonic dynamics calculations performed on the deoxyguanosine (dG) and deoxyadenosine (dA) residues, based on a reliable force field, show that the breathing motions of both guanine and adenine residues are involved in two different vibration modes (750-500 cm-1 spectral region). The calculated results reveal a strong coupling of these modes with the sugar pucker motions. This effect has been verified for the dG residue by the Raman spectra of polyd(G-C). As far as the dA residue is concerned, the particular behavior of the adenine residue breathing mode predicted by these calculations, has been confirmed by Raman spectra of polyd(A-T) undergoing a B----Z conformational transition. PMID:3139101

  4. The conformational transitions in organic solution on the cress seed gum nanoparticles production.

    PubMed

    Taheri, Afsaneh; Razavi, Seyed M A

    2015-09-01

    The seeds of Lepidium sativum (garden cress) were selected as a new hydrocolloid source to fabricate cress seed gum nanoparticles (CSGN) by the desolvation method. The intrinsic viscosity of the CSGN solutions was measured to evaluate the conformational differences of the CSG resulted by the various production conditions. The intrinsic viscosity of CSGN solutions was estimated by using various models, i.e. Huggins, Kraemer, Tanglertpaibul-Rao and Higiro, and then the intrinsic viscosity was an objective function aimed at optimizing the conditions for the solubilization of CSG nanoparticles by the response surface method. The results indicated that among the conditions for the preparation of nanoparticles, acetone and gum concentrations had significant effects on the intrinsic viscosity of nanoparticles. Hereby, CSG served as a source of anionic polyelectrolyte molecules in dilute solutions with acetone-water mixtures. This compound goes on to display a coil-globule transition above a certain threshold of acetone. PMID:26143122

  5. Conformational transitions of macromolecules in an eluent flow and their manifestation in the chromatography of polymers

    NASA Astrophysics Data System (ADS)

    Kurganov, A. A.; Kanateva, A. Yu; Orekhov, V. A.

    2014-07-01

    The behaviour of macromolecules in a free eluent flow, in a confined space, and in a flow passing through a pore system is considered. It is shown that the behaviour of macromolecules can be described by different theories such as the De Gennes theory and the theory of A DiMarzio and C M Guttman. Specific features of chromatographic fractionation and separation processes with the use of membranes formed from ultrahigh-molecular-mass polymers, which are widely used as constructional materials, are discussed. To account for these features, theoretical models considering conformational transitions of macromolecules in the eluent flow and taking into account possible degradation of macromolecules under the influence of the flow are applied. The current state of theoretical and experimental studies of the behaviour of macromolecules in a fluid flow is surveyed. The bibliography includes 152 references.

  6. Solvent-dependent dual-mode photochromism between T- and P-types in a dipyrrinone derivative.

    PubMed

    Sakata, Yoko; Fukushima, Satomi; Akine, Shigehisa; Setsune, Jun-Ichiro

    2016-01-01

    A newly synthesized dipyrrinone derivative bearing an ethoxycarbonyl group at the pyrrolic-? position exhibited solvent-dependent dual-mode photochromism between T- and P-types. While this molecule underwent thermally reversible (T-type) photoresponsive reaction in chloroform, it became a thermally irreversible (P-type) system in methanol. PMID:26615770

  7. Colloids and Surfaces B: Biointerfaces 59 (2007) 184193 Effects of poly (ethylene glycol) chains conformational transition on the

    E-print Network

    2007-01-01

    Available online 16 May 2007 Abstract Foam thin liquid films (TLF) and monolayers at the air­water interface-to-brush conformational transition and (ii) of the liposome/micelle ratio in the film-forming dispersions, on the interfacial properties of mixed DMPC/DMPE-PEG films was compared. Foam film studies demonstrated that DMPE

  8. Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase

    PubMed Central

    Korkut, Anil; Hendrickson, Wayne A.

    2009-01-01

    Many proteins function through conformational transitions between structurally disparate states, and there is a need to explore transition pathways between experimentally accessible states by computation. The sizes of systems of interest and the scale of conformational changes are often beyond the scope of full atomic models, but appropriate coarse-grained approaches can capture significant features. We have designed a comprehensive knowledge-based potential function based on a C? representation for proteins that we call the virtual atom molecular mechanics (VAMM) force field. Here, we describe an algorithm for using the VAMM potential to describe conformational transitions, and we validate this algorithm in application to a transition between open and closed states of adenylate kinase (ADK). The VAMM algorithm computes normal modes for each state and iteratively moves each structure toward the other through a series of intermediates. The move from each side at each step is taken along that normal mode showing greatest engagement with the other state. The process continues to convergence of terminal intermediates to within a defined limit—here, a root-mean-square deviation of 1 ?. Validations show that the VAMM algorithm is highly effective, and the transition pathways examined for ADK are compatible with other structural and biophysical information. We expect that the VAMM algorithm can address many biological systems. PMID:19706894

  9. An allolactose trapped at the lacZ ?-galactosidase active site with its galactosyl moiety in a (4)H3 conformation provides insights into the formation, conformation, and stabilization of the transition state.

    PubMed

    Wheatley, Robert W; Huber, Reuben E

    2015-12-01

    When lactose was incubated with G794A-?-galactosidase (a variant with a "closed" active site loop that binds transition state analogs well) an allolactose was trapped with its Gal moiety in a (4)H3 conformation, similar to the oxocarbenium ion-like conformation expected of the transition state. The numerous interactions formed between the (4)H3 structure and ?-galactosidase indicate that this structure is representative of the transition state. This conformation is also very similar to that of d-galactono-1,5-lactone, a good transition state analog. Evidence indicates that substrates take up the (4)H3 conformation during migration from the shallow to the deep mode. Steric forces utilizing His418 and other residues are important for positioning the O1 leaving group into a quasi-axial position. An electrostatic interaction between the O5 of the distorted Gal and Tyr503 as well as C-H-? bonds with Trp568 are also significant. Computational studies of the energy of sugar ring distortion show that the ?-galactosidase reaction itinerary is driven by energetic considerations in utilization of a (4)H3 transition state with a novel (4)C1-(4)H3-(4)C1 conformation itinerary. To our knowledge, this is the first X-ray crystallographic structural demonstration that the transition state of a natural substrate of a glycosidase has a (4)H3 conformation. PMID:26291713

  10. Large scale conformational transitions in ?-structural motif of gramicidin A: kinetic analysis based on CD and FT-IR data.

    PubMed

    Sychev, Sergei V; Ivanov, Vadim T

    2014-08-01

    Gramicidin A (gA) is a polypeptide antibiotic, which forms dimeric channels specific for monovalent cations in artificial and biological membranes. It is a polymorphic molecule that adopts a unique variety of helical conformations, including antiparallel double-stranded ???5.6 or ???7.2 helices (number of residues per turn) and a single-stranded ?6.3 helix (the 'channel form'). The behavior of gA-Cs(+) complex in the micelles of TX-100 was studied in this work. Transfer of the complex into the micelles activates a cascade of sequential conformational transitions monitored by CD and FT-IR spectroscopy: [Formula: see text] At the first step after Cs(+) removal, the RH ???5.6 helix is formed, which has been discussed so far only hypothetically. Kinetics of the transitions was measured, and the activation parameters were determined. The activation energies of the ???5.6????-helical monomer transition in dioxane and dioxane/water solutions were also measured for comparison. The presence of water raises the transition rate constant ~10(3) times but does not lead to crucial fall of the activation energy. All activation energies were found in the 20-25?kcal/mol range, i.e. much lower than would be expected for unwinding of the double helix (when 28 H-bonds are broken simultaneously). These results can be accounted for in the light of local unfolding (or 'cracking') model for large scale conformational transitions developed by the P.?G.Wolynes team [Miyashita O, Onuchic JN, Wolynes PG. Proc. Natl. Acad. Sci. USA 2003; 100: 12570-12575.]. PMID:24788525

  11. Ghrelin receptor conformational dynamics regulate the transition from a preassembled to an active receptor:Gq complex

    PubMed Central

    Damian, Marjorie; Mary, Sophie; Maingot, Mathieu; M'Kadmi, Céline; Gagne, Didier; Leyris, Jean-Philippe; Denoyelle, Séverine; Gaibelet, Gérald; Gavara, Laurent; Garcia de Souza Costa, Mauricio; Perahia, David; Trinquet, Eric; Mouillac, Bernard; Galandrin, Ségolène; Galès, Céline; Fehrentz, Jean-Alain; Floquet, Nicolas; Martinez, Jean; Marie, Jacky; Banères, Jean-Louis

    2015-01-01

    How G protein-coupled receptor conformational dynamics control G protein coupling to trigger signaling is a key but still open question. We addressed this question with a model system composed of the purified ghrelin receptor assembled into lipid discs. Combining receptor labeling through genetic incorporation of unnatural amino acids, lanthanide resonance energy transfer, and normal mode analyses, we directly demonstrate the occurrence of two distinct receptor:Gq assemblies with different geometries whose relative populations parallel the activation state of the receptor. The first of these assemblies is a preassembled complex with the receptor in its basal conformation. This complex is specific of Gq and is not observed with Gi. The second one is an active assembly in which the receptor in its active conformation triggers G protein activation. The active complex is present even in the absence of agonist, in a direct relationship with the high constitutive activity of the ghrelin receptor. These data provide direct evidence of a mechanism for ghrelin receptor-mediated Gq signaling in which transition of the receptor from an inactive to an active conformation is accompanied by a rearrangement of a preassembled receptor:G protein complex, ultimately leading to G protein activation and signaling. PMID:25605885

  12. ?-Fluorophosphonates reveal how a phosphomutase conserves transition state conformation over hexose recognition in its two-step reaction

    PubMed Central

    Jin, Yi; Bhattasali, Debabrata; Pellegrini, Erika; Forget, Stephanie M.; Baxter, Nicola J.; Cliff, Matthew J.; Bowler, Matthew W.; Jakeman, David L.; Blackburn, G. Michael; Waltho, Jonathan P.

    2014-01-01

    ?-Phosphoglucomutase (?PGM) catalyzes isomerization of ?-d-glucose 1-phosphate (?G1P) into d-glucose 6-phosphate (G6P) via sequential phosphoryl transfer steps using a ?-d-glucose 1,6-bisphosphate (?G16BP) intermediate. Synthetic fluoromethylenephosphonate and methylenephosphonate analogs of ?G1P deliver novel step 1 transition state analog (TSA) complexes for ?PGM, incorporating trifluoromagnesate and tetrafluoroaluminate surrogates of the phosphoryl group. Within an invariant protein conformation, the ?-d-glucopyranose ring in the ?G1P TSA complexes (step 1) is flipped over and shifted relative to the G6P TSA complexes (step 2). Its equatorial hydroxyl groups are hydrogen-bonded directly to the enzyme rather than indirectly via water molecules as in step 2. The (C)O–P bond orientation for binding the phosphate in the inert phosphate site differs by ?30° between steps 1 and 2. By contrast, the orientations for the axial O–Mg–O alignment for the TSA of the phosphoryl group in the catalytic site differ by only ?5°, and the atoms representing the five phosphorus-bonded oxygens in the two transition states (TSs) are virtually superimposable. The conformation of ?G16BP in step 1 does not fit into the same invariant active site for step 2 by simple positional interchange of the phosphates: the TS alignment is achieved by conformational change of the hexose rather than the protein. PMID:25104750

  13. Transition Networks for the Comprehensive Characterization of Complex Conformational Change in

    E-print Network

    the lever-arm motion in myosin during muscle contraction,2 and the molecular switch in Ras p21 (see Figure 2) that signals cell division.3,4 Such functional changes in conformation are often complex, involving

  14. Role of the Subunits Interactions in the Conformational Transitions in Adult Human Hemoglobin: an Explicit Solvent Molecular Dynamics Study

    E-print Network

    Yusuff, Olaniyi K; Bussi, Giovanni; Raugei, Simone

    2012-01-01

    Hemoglobin exhibits allosteric structural changes upon ligand binding due to the dynamic interactions between the ligand binding sites, the amino acids residues and some other solutes present under physiological conditions. In the present study, the dynamical and quaternary structural changes occurring in two unligated (deoxy-) T structures, and two fully ligated (oxy-) R, R2 structures of adult human hemoglobin were investigated with molecular dynamics. It is shown that, in the sub-microsecond time scale, there is no marked difference in the global dynamics of the amino acids residues in both the oxy- and the deoxy- forms of the individual structures. In addition, the R, R2 are relatively stable and do not present quaternary conformational changes within the time scale of our simulations while the T structure is dynamically more flexible and exhibited the T\\rightarrow R quaternary conformational transition, which is propagated by the relative rotation of the residues at the {\\alpha}1{\\beta}2 and {\\alpha}2{\\b...

  15. Atomic layer deposition conformality and process optimization: Transitioning from 2-dimensional planar systems to 3-dimensional nanostructures

    NASA Astrophysics Data System (ADS)

    Robertson Cleveland, Erin Darcy

    Conformal coatings are becoming increasingly important as technology heads towards the nanoscale. The exceptional thickness control (atomic scale) and conformality (uniformity over nanoscale 3D features) of atomic layer deposition (ALD) has made it the process of choice for numerous applications found in microelectronics and nanotechnology with a wide variety of ALD processes and resulting materials. While its benefits derive from self-limited saturating surface reactions of alternating gas precursors, process optimization for ALD conformality is often difficult as process parameters, such as dosage, purge, temperature and pressure are often interdependent with one another, especially within the confines of an ultra-high aspect ratio nanopore. Therefore, processes must be optimized to achieve self-limiting saturated surfaces and avoid parasitic CVD-like reactions in order to maintain thickness control and achieve uniformity and conformality at the atomic level while preserving the desired materials' properties (electrical, optical, compositional, etc.). This work investigates novel approaches to optimize ALD conformality when transitioning from a 2D planar system to a 3D ultra-high aspect ratio nanopore in the context of a cross-flow wafer-scale reactor used to highlight deviations from ideal ALD behavior. Porous anodic alumina (PAA) is used as a versatile platform to analyze TiO2 ALD profiles via ex-situ SEM, EDS and TEM. Results of TiO2 ALD illustrate enhanced growth rates that can occur when the precursors titanium tetraisopropoxide and ozone were used at minimal saturation doses for ALD and for considerably higher doses. The results also demonstrate that ALD process recipes that achieve excellent across-wafer uniformity across full 100 mm wafers do not produce conformal films in ultra-high aspect ratio nanopores. The results further demonstrate that conformality is determined by precursor dose, surface residence time, and purge time, creating large depletion gradients down the length of the nanopore. Also, deposition of ALD films over sharp surface features are very uniform, and verified by profile evolution modeling. This behavior, in contrast to that in high aspect ratio structures, suggests strongly that detailed dynamics, local flow conditions (e.g. viscous vs molecular), surface residence time, and ALD surface reaction kinetics play a complex role in determining ALD profiles for high aspect ratio features.

  16. Two-Dimensional Electronic Spectroscopy of Chlorophyll a: Solvent Dependent Spectral Evolution.

    PubMed

    Moca, Roberta; Meech, Stephen R; Heisler, Ismael A

    2015-07-01

    The interaction of the monomeric chlorophyll Q-band electronic transition with solvents of differing physical-chemical properties is investigated through two-dimensional electronic spectroscopy (2DES). Chlorophyll constitutes the key chromophore molecule in light harvesting complexes. It is well-known that the surrounding protein in the light harvesting complex fine-tunes chlorophyll electronic transitions to optimize energy transfer. Therefore, an understanding of the influence of the environment on the monomeric chlorophyll electronic transitions is important. The Q-band 2DES is inhomogeneous at early times, particularly in hydrogen bonding polar solvents, but also in nonpolar solvents like cyclohexane. Interestingly this inhomogeneity persists for long times, even up to the nanosecond time scale in some solvents. The reshaping of the 2DES occurs over multiple time scales and was assigned mainly to spectral diffusion. At early times the reshaping is Gaussian-like, hinting at a strong solvent reorganization effect. The temporal evolution of the 2DES response was analyzed in terms of a Brownian oscillator model. The spectral densities underpinning the Brownian oscillator fitting were recovered for the different solvents. The absorption spectra and Stokes shift were also properly described by this model. The extent and nature of inhomogeneous broadening was a strong function of solvent, being larger in H-bonding and viscous media and smaller in nonpolar solvents. The fastest spectral reshaping components were assigned to solvent dynamics, modified by interactions with the solute. PMID:26087152

  17. Thermodynamic and spectroscopic analysis of the conformational transition of poly(vinyl alcohol) by temperature-dependent FTIR

    NASA Astrophysics Data System (ADS)

    Han, Shan; Luan, Ye-Mei; Pang, Shu-Feng; Zhang, Yun-Hong

    2015-03-01

    The conformational change of poly(vinyl alcohol) has been studied by Fourier transform infrared spectroscopy at various temperatures in the 4000-400 cm-1 region. The molecular motion and the trans/gauche content are sensitive to the Csbnd H, Csbnd C stretching modes. FTIR spectra show that the I2920/I2849 decreases from 1.84 to 1.0 with increasing temperature, companying the decrease in I1047/I1095 from 0.78 to 0.58, implying the conformational transition from trans to gauche in alkyl chain. Based on the van't Hoff relation, the enthalpies and entropies have been calculated in different temperatures, which are 4.61 kJ mol-1 and 15.23 J mol-1 K-1, respectively, in the region of 80-140 °C. From the Cdbnd O stretching mode and Osbnd H band, it can be concluded that the intermolecular hydrogen bonds decrease owing to elevating temperature, which leads to more gauche conformers.

  18. Mapping the conformational transition in Src activation by cumulating the information from

    E-print Network

    Yang, Sichun

    . conformational landscape connectivity map intermediate kinase inhibitor Non-receptor Src tyrosine kinases) The Src-family kinases are allosteric enzymes that play a key role in the regulation of cell growth processes. Uncontrolled Src kinase activa- tion is linked to a number of diseases, particularly cancer

  19. Steered Molecular Dynamics Simulations of a Type IV Pilus Probe Initial Stages of a Force-Induced Conformational Transition

    PubMed Central

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

    2013-01-01

    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 ?1 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 ?1 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. PMID:23592974

  20. Conformational Transitions and Stop-and-Go Nanopore Transport of Single Stranded DNA on Charged Graphene

    PubMed Central

    Shankla, Manish; Aksimentiev, Aleksei

    2014-01-01

    Control over interactions with biomolecules holds the key to applications of graphene in biotechnology. One such application is nanopore sequencing, where a DNA molecule is electrophoretically driven through a graphene nanopore. Here, we investigate how interactions of single-stranded DNA and a graphene membrane can be controlled by electrically biasing the membrane. The results of our molecular dynamics simulations suggest that electric charge on graphene can force a DNA homopolymer to adopt a range of strikingly different conformations. The conformational response is sensitive to even very subtle nucleotide modifications, such as DNA methylation. The speed of DNA motion through a graphene nanopore is strongly affected by the graphene charge: a positive charge accelerates the motion whereas a negative charge arrests it. As a possible application of the effect, we demonstrate stop-and-go transport of DNA controlled by the charge of graphene. Such on-demand transport of DNA is essential for realizing nanopore sequencing. PMID:25296960

  1. Direct visualization of flow-induced conformational transitions of single actin filaments in entangled solutions

    NASA Astrophysics Data System (ADS)

    Kirchenbuechler, Inka; Guu, Donald; Kurniawan, Nicholas A.; Koenderink, Gijsje H.; Lettinga, M. Paul

    2014-10-01

    While semi-flexible polymers and fibres are an important class of material due to their rich mechanical properties, it remains unclear how these properties relate to the microscopic conformation of the polymers. Actin filaments constitute an ideal model polymer system due to their micron-sized length and relatively high stiffness that allow imaging at the single filament level. Here we study the effect of entanglements on the conformational dynamics of actin filaments in shear flow. We directly measure the full three-dimensional conformation of single actin filaments, using confocal microscopy in combination with a counter-rotating cone-plate shear cell. We show that initially entangled filaments form disentangled orientationally ordered hairpins, confined in the flow-vorticity plane. In addition, shear flow causes stretching and shear alignment of the hairpin tails, while the filament length distribution remains unchanged. These observations explain the strain-softening and shear-thinning behaviour of entangled F-actin solutions, which aids the understanding of the flow behaviour of complex fluids containing semi-flexible polymers.

  2. A new solvent-dependent mechanism for a triazolinedione ene reaction.

    PubMed

    Acevedo, Orlando; Squillacote, Michael E

    2008-02-01

    The ene reaction between 4-phenyl-1,2,4-triazoline-3,5-dione (PTAD) and tetramethylethylene has been investigated using QM/MM calculations in water, methanol, DMSO, and acetonitrile. The effects of solvation on the mechanism and rates of reaction are elucidated using two-dimensional potentials of mean force (PMF) simulations utilizing free-energy perturbation theory and Monte Carlo statistical mechanics. A new mechanism is proposed where direct formation of an open dipolar intermediate following the addition of PTAD to the alkene is rate-limiting and the pathway toward ene product is significantly dependent on the reaction medium. In protic solvents, the open dipolar intermediate may proceed directly to the ene product or reversibly form an aziridinium imide (AI) intermediate that does not participate in the reaction. However, in aprotic solvents the open intermediate is short-lived (<10-11 s) and the ene product forms via the AI intermediate. The calculated free energies of activation are in close agreement with those derived from experiment, e.g., DeltaG of 14.9 kcal/mol compared to 15.0 kcal/mol in acetonitrile. Density functional theory calculations at the (U)B3LYP/6-311++G(2d,p) level using the CPCM continuum solvent model were also carried out and confirmed a zwitterionic, and not diradical, open intermediate present in the reaction. Only the QM/MM methodology was able to accurately reproduce the experimental rates and differentiate between the protic and aprotic solvents. Solute-solvent interaction energies, radial distribution functions, and charges are analyzed and show that the major factor dictating the changes in reaction path is hydrogen bond stabilization of the charge separations spanning 2 to 4 atoms in the intermediates and transition states. PMID:18161986

  3. Cyanide Single-Molecule Magnets Exhibiting Solvent Dependent Reversible "On" and "Off" Exchange Bias Behavior.

    PubMed

    Pinkowicz, Dawid; Southerland, Heather I; Avendaño, Carolina; Prosvirin, Andrey; Sanders, Codi; Wernsdorfer, Wolfgang; Pedersen, Kasper S; Dreiser, Jan; Clérac, Rodolphe; Nehrkorn, Joscha; Simeoni, Giovanna G; Schnegg, Alexander; Holldack, Karsten; Dunbar, Kim R

    2015-11-18

    The syntheses, structures, and magnetic properties of four new complex salts, (PPN){[Mn(III)(salphen)(MeOH)]2[M(III)(CN)6]}·7MeOH (Mn2M·7MeOH) (M = Fe, Ru, Os and Co; PPN(+) = bis(triphenylphosphoranylidene)ammonium cation; H2salphen = N,N'-bis(salicylidene)-1,2-diaminobenzene), and a mixed metal Co/Os analogue (PPN){[Mn(III)(salphen)(MeOH)]2[Co(III)0.92Os(III)0.08(CN)6]}·7MeOH were undertaken. It was found that all compounds exhibit switchable single-molecule magnet (SMM) and exchange-bias behavior depending on the interstitial methanol content. The pristine (PPN){[Mn(salphen)(MeOH)]2[Os(CN)6]}·7MeOH (Mn2Os·7MeOH) behaves as an SMM with an effective barrier for the magnetization reversal, (Ueff/kB), of 17.1 K. Upon desolvation, Mn2Os exhibits an increase of Ueff/kB to 42.0 K and an opening of the hysteresis loop observable at 1.8 K. Mn2Os·7MeOH shows also exchange-bias behavior with magnetic hysteresis loops exhibiting a shift in the quantum tunneling to 0.25 T from zero-field. The Fe(III) and Ru(III) analogues were prepared as reference compounds for assessing the effect of the 5d versus 4d and 3d metal ions on the SMM properties. These compounds are also SMMs and exhibit similar effects but with lower energy barriers. These findings underscore the importance of introducing heavy transition elements into SMMs to improve their slow relaxation of the magnetization properties. The (PPN){[Mn(III)(salphen)(MeOH)]2[Co(III)(CN)6]}·7MeOH (Mn2Co·7MeOH) analogue with a diamagnetic Co(III) central atom and the mixed Co/Os (PPN){[Mn(III)(salphen)(MeOH)]2[Co(III)0.92Os(III)0.08(CN)6]}·7MeOH (Mn2Co/Os·7MeOH) "magnetically diluted" system with a 9:1 Co/Os metal ratio were prepared in order to further probe the nature of the energy barrier increase upon desolvation of Mn2Os. In addition, inelastic neutron scattering and frequency-domain Fourier-transform THz electron paramagnetic resonance spectra obtained on Mn2Os·7MeOH and Mn2Os in combination with the magnetic data revealed the presence of anisotropic exchange interactions between Mn(III) and Os(III) ions. PMID:26542645

  4. Ionic liquid-induced all-? to ? + ? conformational transition in cytochrome c with improved peroxidase activity in aqueous medium.

    PubMed

    Bharmoria, Pankaj; Trivedi, Tushar J; Pabbathi, Ashok; Samanta, Anunay; Kumar, Arvind

    2015-04-21

    Choline dioctylsulfosuccinate [Cho][AOT] (a surface active ionic liquid) has been found to induce all-? to ? + ? conformational transition in the secondary structure of enzyme cytochrome c (Cyt c) with an enhanced peroxidase activity in its aqueous vesicular phase at pH 7.0. [Cho][AOT] interacted with Cyt c distinctly at three critical concentrations (aggregation C1, saturation C2 and vesicular C3) as detected from isothermal titration calorimetric analysis. Oxidation of heme iron was observed from the disappearance of the Q band in the UV-vis spectra of Cyt c upon [Cho][AOT] binding above C3. Circular dichroism analysis (CD) has shown the loss in both the secondary (190-240 nm) and tertiary (250-300 nm) structure of Cyt c in the monomeric regime until C1, followed by their stabilization until the pre-vesicular regime (C1 ? C3). Loss in both the secondary and tertiary structure has been observed in the post-vesicular regime with the change in Cyt c conformation from all-? to ? + ? which is similar to the conformational changes of Cyt c upon binding with mitochondrial membrane (Biochemistry 1998, 37, 6402-6409), thus citing the potential utility of [Cho][AOT] membranes as an artificial analog for in vitro bio-mimicking. Fluorescence correlation spectroscopy (FCS) measurements confirm the unfolding of Cyt c in the vesicular phase. Dynamic light scattering experiments have shown the contraction of [Cho][AOT] vesicles upon Cyt c binding driven by electrostatic interactions observed by charge neutralization from zeta potential measurements. [Cho][AOT] has been found to enhance the peroxidase activity of Cyt c with maximum activity at C3, observed using 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt as the substrate in the presence of hydrogen peroxide. This result shows the relevance of tuning ionic liquids to surfactants for bio-mimicking of specific membrane protein-lipid interactions. PMID:25798458

  5. Molecular dynamics simulation of phosphorylation-induced conformational transitions in the mycobacterium tuberculosis response regulator PrrA

    SciTech Connect

    Chen, Guo; Mcmahon, Benjamin H; Tung, Chang - Shung

    2008-01-01

    Phosphorylation-activated modulation of response regulators (RR) is predominantly used by bacteria as a strategy in regulating their two-component signaling (TCS) systems, the underlying molecular mechanisms are however far from fully understood. In this work we have conducted a molecular dynamics (MD) simulation of the phosphorylation-induced conformational transitions of RRs with the Mycobacterium Tuberculosis PrrA as a particular example. Starting from the full-length inactive structure of PrrA we introduced a local disturbance by phosphorylating the conserved aspartic acid residue, Asp-58, in the regulatory domain. A Go-model-type algorithm packaged with AMBER force fields was then applied to simulate the dynamics upon phosphorylation. The MD simulation shows that the phosphorylation of Asp-58 facilitates PrrA, whose inactive state has a compact conformation with a closed interdomain interface, to open up with its interdomain separation being increased by an average of about 1.5 {angstrom} for a simulation of 20 ns. The trans-activation loop, which is completely buried within the interdomain interface in the inactive PrrA, is found to become more exposed with the phosphorylated structure as well. These results provide more structural details of how the phosphorylation of a local aspartate activates PrrA to undergo a global conformational rearrangement toward its extended active state. This work also indicates that MD simulations can serve as a fast tool to unravel the regulation mechanisms of all RRs, which is especially valuable when the structures of full-length active RRs are currently unavailable.

  6. Conformation and dynamics of biopharmaceuticals: transition of mass spectrometry-based tools from academe to industry

    PubMed Central

    Kaltashov, Igor A.; Bobst, Cedric E.; Abzalimov, Rinat R.; Berkowitz, Steven A.; Houde, Damian

    2009-01-01

    Mass spectrometry plays a very visible role in biopharmaceutical industry, although its use in development, characterization and quality control of protein drugs is mostly limited to the analysis of covalent structure (amino acid sequence and post-translational modifications). Despite the centrality of protein conformation to biological activity, stability and safety of biopharmaceutical products, the expanding arsenal of mass spectrometry-based methods that are currently available to probe higher order structure and conformational dynamics of biopolymers did not enjoy until recently much attention in the industry. This is beginning to change as a result of recent work demonstrating the utility of these experimental tools for various aspects of biopharmaceutical product development and manufacturing. In this work we use a paradigmatic protein drug interferon ?-1a as an example to illustrate the utility of mass spectrometry as a powerful tool not only to assess the integrity of higher order structure of a protein drug, but also to predict consequences of its degradation at a variety of levels. PMID:19963397

  7. Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones

    PubMed Central

    Malinverni, Duccio; Marsili, Simone; Barducci, Alessandro; De Los Rios, Paolo

    2015-01-01

    Hsp70s are a class of ubiquitous and highly conserved molecular chaperones playing a central role in the regulation of proteostasis in the cell. Hsp70s assist a myriad of cellular processes by binding unfolded or misfolded substrates during a complex biochemical cycle involving large-scale structural rearrangements. Here we show that an analysis of coevolution at the residue level fully captures the characteristic large-scale conformational transitions of this protein family, and predicts an evolutionary conserved–and thus functional–homo-dimeric arrangement. Furthermore, we highlight that the features encoding the Hsp70 dimer are more conserved in bacterial than in eukaryotic sequences, suggesting that the known Hsp70/Hsp110 hetero-dimer is a eukaryotic specialization built on a pre-existing template. PMID:26046683

  8. Single-Molecule Analysis of Protein Large-Amplitude Conformational Transitions

    NASA Astrophysics Data System (ADS)

    Yang, Haw

    2011-03-01

    Proteins have evolved to harness thermal fluctuations, rather than frustrated by them, to carry out chemical transformations and mechanical work. What are, then, the operation and design principles of protein machines? To frame the problem in a tractable way, several basic questions have been formulated to guide the experimental design: (a) How many conformational states can a protein sample on the functionally important timescale? (b) What are the inter-conversion rates between states? (c) How do ligand binding or interactions with other proteins modulate the motions? (d) What are the structural basis of flexibility and its underlying molecular mechanics? Guided by this framework, we have studied protein tyrosine phosphatase B, PtpB, from M. tuberculosis (a virulence factor of tuberculosis and a potential drug target) and adenylate kinase, AK, from E. coli (a ubiquitous energy-balancing enzyme in cells). These domain movements have been followed in real time on their respective catalytic timescales using high-resolution single-molecule Förster resonance energy transfer (FRET) spectroscopy. It is shown quantitatively that both PtpB and AK are capable of dynamically sampling two distinct states that correlate well with those observed by x-ray crystallography. Integrating these microscopic dynamics into macroscopic kinetics allows us to place the experimentally measured free-energy landscape in the context of enzymatic turnovers.

  9. The nicotinic acetylcholine receptor and its prokaryotic homologues: Structure, conformational transitions & allosteric modulation.

    PubMed

    Cecchini, Marco; Changeux, Jean-Pierre

    2015-09-01

    Pentameric ligand-gated ion channels (pLGICs) play a central role in intercellular communications in the nervous system by converting the binding of a chemical messenger - a neurotransmitter - into an ion flux through the postsynaptic membrane. Here, we present an overview of the most recent advances on the signal transduction mechanism boosted by X-ray crystallography of both prokaryotic and eukaryotic homologues of the nicotinic acetylcholine receptor (nAChR) in conjunction with time-resolved analyses based on single-channel electrophysiology and Molecular Dynamics simulations. The available data consistently point to a global mechanism of gating that involves a large reorganization of the receptor mediated by two distinct quaternary transitions: a global twisting and a radial expansion/contraction of the extracellular domain. These transitions profoundly modify the organization of the interface between subunits, which host several sites for orthosteric and allosteric modulatory ligands. The same mechanism may thus mediate both positive and negative allosteric modulations of pLGICs ligand binding at topographically distinct sites. The emerging picture of signal transduction is expected to pave the way to new pharmacological strategies for the development of allosteric modulators of nAChR and pLGICs in general. This article is part of the Special Issue entitled 'The Nicotinic Acetylcholine Receptor: From Molecular Biology to Cognition'. PMID:25529272

  10. Conformational Transitions that Enable Histidine Kinase Autophosphorylation and Receptor Array Integration.

    PubMed

    Greenswag, Anna R; Muok, Alise; Li, Xiaoxiao; Crane, Brian R

    2015-12-01

    During bacterial chemotaxis, transmembrane chemoreceptor arrays regulate autophosphorylation of the dimeric histidine kinase CheA. The five domains of CheA (P1-P5) each play a specific role in coupling receptor stimulation to CheA activity. Biochemical and X-ray scattering studies of thermostable CheA from Thermotoga maritima determine that the His-containing substrate domain (P1) is sequestered by interactions that depend upon P1 of the adjacent subunit. Non-hydrolyzable ATP analogs (but not ATP or ADP) release P1 from the protein core (domains P3P4P5) and increase its mobility. Detachment of both P1 domains or removal of one within a dimer increases net autophosphorylation substantially at physiological temperature (55°C). However, nearly all activity is lost without the dimerization domain (P3). The linker length between P1 and P3 dictates intersubunit (trans) versus intrasubunit (cis) autophosphorylation, with the trans reaction requiring a minimum length of 47 residues. A new crystal structure of the most active dimerization-plus-kinase unit (P3P4) reveals trans directing interactions between the tether connecting P3 to P2-P1 and the adjacent ATP-binding (P4) domain. The orientation of P4 relative to P3 in the P3P4 structure supports a planar CheA conformation that is required by membrane array models, and it suggests that the ATP lid of CheA may be poised to interact with receptors and coupling proteins. Collectively, these data suggest that the P1 domains are restrained in the off-state as a result of cross-subunit interactions. Perturbations at the nucleotide-binding pocket increase P1 mobility and access of the substrate His to P4-bound ATP. PMID:26522934

  11. Network representation of conformational transitions between hidden intermediates of Rd-apocytochrome b562

    NASA Astrophysics Data System (ADS)

    Duan, Mojie; Liu, Hanzhong; Li, Minghai; Huo, Shuanghong

    2015-10-01

    The folding kinetics of Rd-apocytochrome b562 is two-state, but native-state hydrogen exchange experiments show that there are discrete partially unfolded (PUF) structures in equilibrium with the native state. These PUF structures are called hidden intermediates because they are not detected in kinetic experiments and they exist after the rate-limiting step. Structures of the mimics of hidden intermediates of Rd-apocytochrome b562 are resolved by NMR. Based upon their relative stability and structural features, the folding mechanism was proposed to follow a specific pathway (unfolded ? rate-limiting transition state ? PUF1 ? PUF2 ? native). Investigating the roles of equilibrium PUF structures in folding kinetics and their interrelationship not only deepens our understanding of the details of folding mechanism but also provides guides in protein design and prevention of misfolding. We performed molecular dynamics simulations starting from a hidden intermediate and the native state of Rd-apocytochrome b562 in explicit solvent, for a total of 37.18 ?s mainly with Anton. We validated our simulations by detailed comparison with experimental data and other computations. We have verified that we sampled the post rate-limiting transition state region only. Markov state model was used to analyze the simulation results. We replace the specific pathway model with a network model. Transition-path theory was employed to calculate the net effective flux from the most unfolded state towards the most folded state in the network. The proposed sequential folding pathway via PUF1 then more stable, more native-like PUF2 is one of the routes in our network, but it is not dominant. The dominant path visits PUF2 without going through PUF1. There is also a route from PUF1 directly to the most folded state in the network without visiting PUF2. Our results indicate that the PUF states are not necessarily sequential in the folding. The major routes predicted in our network are testable by future experiments such as single molecule experiment.

  12. Conformality Lost

    E-print Network

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

    2009-07-22

    We consider zero-temperature transitions from conformal to non-conformal 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 non-relativistic 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, xi ~ 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.

  13. Unusual solvent-dependent photophysical and self-assembly properties of NO2 substituted T-shaped phenazines.

    PubMed

    Lee, Dong-Chan; Brownell, Lacie V; Jang, Kyoungmi; Han, Seung Ju; Robins, Kathleen A

    2015-01-28

    This paper investigates the importance of substituent placement when designing low-molecular mass ?-organogelators. The electron-deficient NO2 substituent was systematically added to novel T-shaped phenazines to examine electronic as well as assembly properties. This T-shaped molecular platform promotes selective electronic tuning, which can be theoretically analyzed by examining the system's frontier molecular orbitals. Electronic properties were characterized by UV-vis spectroscopy and cyclic voltammetry, and comparisons were made based on number and placement of the NO2 group. Computational chemistry (B3LYP/6-31G*) was employed for geometry optimizations, and to generate molecular orbital diagrams for all systems. The most noticeable influence of NO2 position was found for two molecules with four NO2 groups placed at different locations about the molecule (T-34dNT and T-35dNT). A 0.13 eV difference in ELUMO was observed while EHOMO was not significantly impacted by this change only in NO2 placement. Interestingly and unexpectedly, the photophysical properties and solvent-dependent gelation properties were considerably different for T-34dNT and T-35dNT. T-34dNT exhibited a unique fluorescence (FL) solvatochromism, with FL intensity and maxima dependent on solvent polarity. This result is indicative of intramolecular charge transfer. In addition, long tailing at the solid-state absorption of T-34dNT suggests the presence of intermolecular charge transfer. The gelation of T-34dNT produced chromism ranging from red to orange to yellow when the solvents changed from acetonitrile to ethyl acetate to cyclohexane, respectively. T-35dNT gels in these solvents did not exhibit any of the same properties. Xerogel morphology characterizations were carried out using three different solvents for both T-34dNT and T-35dNT. In the case of T-34dNT, striking differences in the morphology were detected by field-emission scanning electron microscopy (FE-SEM). We conclude that numbers of substituents are not the only consideration in effective molecular design for organogelators, but that substituent position plays a critical role in certain fundamental properties of these systems. PMID:25491727

  14. Unique Optical Oxygen-Sensing Performance of [Ru(IP)2(HNAIP)](2+) during the Groove-Binding-Induced B-to-Z DNA Conformational Transition.

    PubMed

    Chen, Linlin; Chao, Hui; Zhao, Qianwen; Li, Hong

    2015-09-01

    The oxygen-sensing performance of [Ru(IP)2(HNAIP)](2+) (Ru1, IP = imidazo[4,5-f][1,10]phenanthroline and HNAIP = 2-(2-hydroxy-1-naphthyl)imidazo [4,5-f][1,10]phenanthroline) in the presence of DNA conformational transition has been investigated by means of absorption spectroscopy, steady-state and time-resolved fluorescence spectroscopies, and circular dichroism spectroscopy. Ru1 shows a good linear response toward oxygen between pure nitrogen and pure oxygen with an on-off emission intensity ratio (I0/I100) of up to 9.3 via a dynamic quenching mechanism. Compared with [Ru(IP)2(DHPIP)](2+) (Ru2, DHPIP = 2-(2,4-dihydroxyphenyl)imidazo[4,5-f][1,10]phenanthroline, I0/I100 = 5.8), the HNAIP ligand endows Ru1 with favorable oxygen binding sites to achieve larger energy and electron transfer rates. Simultaneously, Ru1 can induce the B-to-Z DNA conformational transition via a groove interaction with an intrinsic binding constant (K(b)) of 7.9 × 10(4) M(-1), whereas there is no same phenomenon for Ru2 intercalated into DNA (Kb = 3.3 × 10(5) M(-1)). Furthermore, the B-to-Z DNA conformational transition is interestingly found to decrease the Ru1-based oxygen-sensing rate by about 33%. PMID:26280304

  15. Accounting for conformational flexibility and torsional anharmonicity in the H + CH3CH2OH hydrogen abstraction reactions: a multi-path variational transition state theory study.

    PubMed

    Meana-Pañeda, Rubén; Fernández-Ramos, Antonio

    2014-05-01

    This work reports a detailed theoretical study of the hydrogen abstraction reactions from ethanol by atomic hydrogen. The calculated thermal rate constants take into account torsional anharmonicity and conformational flexibility, in addition to the variational and tunneling effects. Specifically, the kinetics calculations were performed by using multi-path canonical variational transition state theory with least-action path tunneling corrections, to which we have added the two-dimensional non-separable method to take into account torsional anharmonicity. The multi-path thermal rate constant is expressed as a sum over conformational reaction channels. Each of these channels includes all the transition states that can be reached by internal rotations. The results show that, in the interval of temperatures between 250 and 2500 K, the account for multiple paths leads to higher thermal rate constants with respect to the single path approach, mainly at low and at high temperatures. In addition, torsional anharmonicity enhances the slope of the Arrhenius plot in this range of temperatures. Finally, we show that the incorporation of tunneling into the hydrogen abstraction reactions substantially changes the contribution of each of the transition states to the conformational reaction channel. PMID:24811637

  16. Accounting for conformational flexibility and torsional anharmonicity in the H + CH3CH2OH hydrogen abstraction reactions: A multi-path variational transition state theory study

    NASA Astrophysics Data System (ADS)

    Meana-Pañeda, Rubén; Fernández-Ramos, Antonio

    2014-05-01

    This work reports a detailed theoretical study of the hydrogen abstraction reactions from ethanol by atomic hydrogen. The calculated thermal rate constants take into account torsional anharmonicity and conformational flexibility, in addition to the variational and tunneling effects. Specifically, the kinetics calculations were performed by using multi-path canonical variational transition state theory with least-action path tunneling corrections, to which we have added the two-dimensional non-separable method to take into account torsional anharmonicity. The multi-path thermal rate constant is expressed as a sum over conformational reaction channels. Each of these channels includes all the transition states that can be reached by internal rotations. The results show that, in the interval of temperatures between 250 and 2500 K, the account for multiple paths leads to higher thermal rate constants with respect to the single path approach, mainly at low and at high temperatures. In addition, torsional anharmonicity enhances the slope of the Arrhenius plot in this range of temperatures. Finally, we show that the incorporation of tunneling into the hydrogen abstraction reactions substantially changes the contribution of each of the transition states to the conformational reaction channel.

  17. Tight Conformational Coupling between the Domains of the Enterotoxigenic Escherichia coli Fimbrial Adhesin CfaE Regulates Binding State Transition*

    PubMed Central

    Liu, Yang; Esser, Lothar; Interlandi, Gianluca; Kisiela, Dagmara I.; Tchesnokova, Veronika; Thomas, Wendy E.; Sokurenko, Evgeni; Xia, Di; Savarino, Stephen J.

    2013-01-01

    CfaE, the tip adhesin of enterotoxigenic Escherichia coli colonization factor antigen I fimbriae, initiates binding of this enteropathogen to the small intestine. It comprises stacked ?-sandwich adhesin (AD) and pilin (PD) domains, with the putative receptor-binding pocket at one pole and an equatorial interdomain interface. CfaE binding to erythrocytes is enhanced by application of moderate shear stress. A G168D replacement along the AD facing the CfaE interdomain region was previously shown to decrease the dependence on shear by increasing binding at lower shear forces. To elucidate the structural basis for this functional change, we studied the properties of CfaE G168D (with a self-complemented donor strand) and solved its crystal structure at 2.6 ? resolution. Compared with native CfaE, CfaE G168D showed a downward shift in peak erythrocyte binding under shear stress and greater binding under static conditions. The thermal melting transition of CfaE G168D occurred 10 °C below that of CfaE. Compared with CfaE, the atomic structure of CfaE G168D revealed a 36% reduction in the buried surface area at the interdomain interface. Despite the location of this single modification in the AD, CfaE G168D exhibited structural derangements only in the adjoining PD compared with CfaE. In molecular dynamics simulations, the G168D mutation was associated with weakened interdomain interactions under tensile force. Taken together, these findings indicate that the AD and PD of CfaE are conformationally tightly coupled and support the hypothesis that opening of the interface plays a critical modulatory role in the allosteric activation of CfaE. PMID:23393133

  18. Electronic transitions in conformationally controlled tetrasilanes with a wide range of SiSiSiSi dihedral angles.

    PubMed

    Tsuji, Hayato; Fogarty, Heather A; Ehara, Masahiro; Fukuda, Ryoichi; Casher, Deborah L; Tamao, Kohei; Nakatsuji, Hiroshi; Michl, Josef

    2014-07-21

    Unlike ?-electron chromophores, the peralkylated n-tetrasilane ?-electron chromophore resembles a chameleon in that its electronic spectrum changes dramatically as its silicon backbone is twisted almost effortlessly from the syn to the anti conformation (changing the SiSiSiSi dihedral angle ? from 0 to 180°). A combination of UV absorption, magnetic circular dichroism (MCD), and linear dichroism (LD) spectroscopy on conformationally controlled tetrasilanes 1-9, which cover fairly evenly the full range of angles ?, permitted a construction of an experimental correlation diagram for three to four lowest valence electronic states. The free chain tetrasilane n-Si4 Me10 (10), normally present as a mixture of three enantiomeric conformer pairs of widely different angles ?, has also been included in our study. The spectral trends are interpreted in terms of avoided crossings of 1B with 2B and 2A with 3A states, in agreement with SAC-CI calculations on the excited states of 1-7 and conformers of 10. PMID:25043859

  19. A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution

    SciTech Connect

    Pallan, Pradeep S.; Prakash, Thazha P.; Li, Feng; Eoff, Robert L.; Manoharan, Muthiah; Egli, Martin

    2009-06-17

    Crystal structures of A-form and B-form DNA duplexes containing 2'-S-methyl-uridines reveal that the modified residues adopt a RNA-like C3'-endo pucker, illustrating that the replacement of electronegative oxygen at the 2'-carbon of RNA by sulfur does not appear to fundamentally alter the conformational preference of the sugar in the oligonucleotide context and sterics trump stereoelectronics.

  20. Effects of poly (ethylene glycol) chains conformational transition on the properties of mixed DMPC/DMPE-PEG thin liquid films and monolayers.

    PubMed

    Georgiev, Georgi As; Sarker, Dipak K; Al-Hanbali, Othman; Georgiev, Georgi D; Lalchev, Zdravko

    2007-10-01

    Foam thin liquid films (TLF) and monolayers at the air-water interface formed by DMPC mixed with DMPE-bonded poly (ethylene glycol)s (DMPE-PEG(550), DMPE-PEG(2000) and DMPE-PEG(5000)) were obtained. The influence of both (i) PEG chain size (evaluated in terms of Mw) and mushroom-to-brush conformational transition and (ii) of the liposome/micelle ratio in the film-forming dispersions, on the interfacial properties of mixed DMPC/DMPE-PEG films was compared. Foam film studies demonstrated that DMPE-PEG addition to foam TLFs caused (i) delayed kinetics of film thinning and black spot expansion and (ii) film stabilization. At the mushroom-to-brush transition, due to steric repulsion increased DMPE-PEG films thickness reached 25 nm while pure DMPC films were only 8 nm thick Newton black films. It was possible to differentiate DMPE-PEG(2000/5000) from DMPE-PEG(550) by the ability to change foam TLF formation mechanism, which could be of great importance for "stealth" liposome design. Monolayer studies showed improved formation kinetics and equilibrium surface tension decrease for DMPE-PEG monolayers compared with DMPC pure films. SEM observations revealed "smoothing" and "sealing" of the defects in the solid-supported layer surface by DMPE-PEGs adsorption, which could explain DMPE-PEGs ability to stabilize TLFs and to decrease monolayer surface tension. All effects in monolayers, foam TLFs and solid-supported layers increased with the increase of PEG Mw and DMPE-PEG concentration. However, at the critical DMPE-PEG concentration (where mushroom-to-brush conformational transition occurred) maximal magnitude of the effects was reached, which only slightly changed at further DMPE-PEG content and micelle/liposome ratio increase. PMID:17587556

  1. FTIR/PCA study of propanol in argon matrix: The initial stage of clustering and conformational transitions

    NASA Astrophysics Data System (ADS)

    Doroshenko, Iryna; Balevicius, Vytautas; Pitsevich, George; Aidas, Kestutis; Sablinskas, Valdas; Pogorelov, Valeriy

    2014-12-01

    FTIR spectra of 1-propanol in an argon matrix were studied in the range 11-30 K. Principal component analysis of dynamic FTIR spectra and nonlinear band shape fitting has been carried out. The peaks of monomer, open dimer, mixed propanol-water dimer and those of higher H-bond clusters have been resolved and analyzed. The attribution of certain FTIR peaks has been supported by proper density functional theory calculations. Analyzing dependences of the integral band intensities of various aggregates on temperature it has been deduced that in the initial stage of clustering monomers and dimers are the basic building blocks forming higher H-bond clusters. The peaks assigned to two conformers of monomers and mixed propanol-water dimers were investigated processing the temperature dependences of their integral intensities in Arrhenius plot. The obtained values of 0.18 kJ.mol-1 for propanol monomer and 0.26 kJ.mol-1 for mixed dimer are well comparable with the energy differences between the global minimum conformation of 1-propanol (Gt) and some other energetically higher structures (Tt or Tg).

  2. Cytomegalovirus UL131-128 Products Promote gB Conformational Transition and gB-gH Interaction during Entry into Endothelial Cells?

    PubMed Central

    Patrone, Marco; Secchi, Massimiliano; Bonaparte, Eleonora; Milanesi, Gabriele; Gallina, Andrea

    2007-01-01

    Herpesviruses use gB and gH-gL glycoproteins to execute fusion. Other virus-specific glycoproteins are required for receptor binding and fusion activation. The human cytomegalovirus (HCMV) UL131-128 proteins are essential for the infection of leukocytes, endothelial cells (ECs), and many epithelial cell lines. Here we show that UL131-128 play a role in a chain of events involving gB and gH during HCMV entry into ECs. An HCMV strain bearing the wild-type (wt) UL131-128 locus exhibited a gB transition from a protease-resistant to protease-sensitive form, a conformational change that was suppressed by a thiourea inhibitor of fusion (WY1768); in contrast, gH was susceptible to proteolysis throughout entry. Moreover, gB and gH transiently interacted, and a lipid mixing assay showed that the wt strain had carried out fusion by 60 min postinfection. However, these events were greatly altered when UL131-128-defective strains were used for infection or when there was an excess of soluble pUL128 during wt infection: the gB conformational change became WY1768 resistant, the gB-gH complex was no longer observed, and fusion was prevented. Both gB and gH in this case showed late protease resistance, related to their endocytic uptake. Our data point to the involvement of UL131-128 proteins in driving gB through a WY1768-sensitive fold transition, thus promoting a short-lived gB-gH complex and fusion; they also suggest that HCMV fuses with the EC plasma membrane and that endocytosis ensues only when the virus cannot trigger UL131-128-dependent steps. PMID:17686875

  3. Structural basis of conformational transitions in the active site and 80?s loop in the FK506-binding protein FKBP12

    PubMed Central

    Mustafi, Sourajit M.; Brecher, Matthew; Zhang, Jing; Li, Hongmin; Lemaster, David M.; Hernández, Griselda

    2014-01-01

    The extensive set of NMR doublings exhibited by the immunophilin FKBP12 (FK506-binding protein 12) arose from a slow transition to the cis-peptide configuration at Gly89 near the tip of the 80?s loop, the site for numerous protein-recognition interactions for both FKBP12 and other FKBP domain proteins. The 80?s loop also exhibited linebroadening, indicative of microsecond to millisecond conformational dynamics, but only in the trans-peptide state. The G89A variant shifted the trans–cis peptide equilibrium from 88:12 to 33:67, whereas a proline residue substitution induced fully the cis-peptide configuration. The 80?s loop conformation in the G89P crystal structure at 1.50 Å resolution differed from wild-type FKBP12 primarily at residues 88, 89 and 90, and it closely resembled that reported for FKBP52. Structure-based chemical-shift predictions indicated that the microsecond to millisecond dynamics in the 80?s loop probably arose from a concerted main chain (?88 and ?89) torsion angle transition. The indole side chain of Trp59 at the base of the active-site cleft was reoriented ~90o and the adjacent backbone was shifted in the G89P crystal structure. NOE analysis of wild-type FKBP12 demonstrated that this indole populates the perpendicular orientation at 20%. The 15N relaxation analysis was consistent with the indole reorientation occurring in the nanosecond timeframe. Recollection of the G89P crystal data at 1.20 Å resolution revealed a weaker wild-type-like orientation for the indole ring. Differences in the residues that underlie the Trp59 indole ring and altered interactions linking the 50?s loop to the active site suggested that reorientation of this ring may be disfavoured in the other six members of the FKBP domain family that bear this active-site tryptophan residue. PMID:24405377

  4. Structure Analysis and Conformational Transitions of the Cell Penetrating Peptide Transportan 10 in the Membrane-Bound State

    PubMed Central

    Strandberg, Erik; Verdurmen, Wouter P. R.; Bürck, Jochen; Ehni, Sebastian; Mykhailiuk, Pavel K.; Afonin, Sergii; Gerthsen, Dagmar; Komarov, Igor V.; Brock, Roland; Ulrich, Anne S.

    2014-01-01

    Structure analysis of the cell-penetrating peptide transportan 10 (TP10) revealed an exemplary range of different conformations in the membrane-bound state. The bipartite peptide (derived N-terminally from galanin and C-terminally from mastoparan) was found to exhibit prominent characteristics of (i) amphiphilic ?-helices, (ii) intrinsically disordered peptides, as well as (iii) ?-pleated amyloid fibrils, and these conformational states become interconverted as a function of concentration. We used a complementary approach of solid-state 19F-NMR and circular dichroism in oriented membrane samples to characterize the structural and dynamical behaviour of TP10 in its monomeric and aggregated forms. Nine different positions in the peptide were selectively substituted with either the L- or D-enantiomer of 3-(trifluoromethyl)-bicyclopent-[1.1.1]-1-ylglycine (CF3-Bpg) as a reporter group for 19F-NMR. Using the L-epimeric analogs, a comprehensive three-dimensional structure analysis was carried out in lipid bilayers at low peptide concentration, where TP10 is monomeric. While the N-terminal region is flexible and intrinsically unstructured within the plane of the lipid bilayer, the C-terminal ?-helix is embedded in the membrane with an oblique tilt angle of ?55° and in accordance with its amphiphilic profile. Incorporation of the sterically obstructive D-CF3-Bpg reporter group into the helical region leads to a local unfolding of the membrane-bound peptide. At high concentration, these helix-destabilizing C-terminal substitutions promote aggregation into immobile ?-sheets, which resemble amyloid fibrils. On the other hand, the obstructive D-CF3-Bpg substitutions can be accommodated in the flexible N-terminus of TP10 where they do not promote aggregation at high concentration. The cross-talk between the two regions of TP10 thus exerts a delicate balance on its conformational switch, as the presence of the ?-helix counteracts the tendency of the unfolded N-terminus to self-assemble into ?-pleated fibrils. PMID:24937132

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

    PubMed

    Fanghänel, Susanne; Wadhwani, Parvesh; Strandberg, Erik; Verdurmen, Wouter P R; Bürck, Jochen; Ehni, Sebastian; Mykhailiuk, Pavel K; Afonin, Sergii; Gerthsen, Dagmar; Komarov, Igor V; Brock, Roland; Ulrich, Anne S

    2014-01-01

    Structure analysis of the cell-penetrating peptide transportan 10 (TP10) revealed an exemplary range of different conformations in the membrane-bound state. The bipartite peptide (derived N-terminally from galanin and C-terminally from mastoparan) was found to exhibit prominent characteristics of (i) amphiphilic ?-helices, (ii) intrinsically disordered peptides, as well as (iii) ?-pleated amyloid fibrils, and these conformational states become interconverted as a function of concentration. We used a complementary approach of solid-state (19)F-NMR and circular dichroism in oriented membrane samples to characterize the structural and dynamical behaviour of TP10 in its monomeric and aggregated forms. Nine different positions in the peptide were selectively substituted with either the L- or D-enantiomer of 3-(trifluoromethyl)-bicyclopent-[1.1.1]-1-ylglycine (CF3-Bpg) as a reporter group for (19)F-NMR. Using the L-epimeric analogs, a comprehensive three-dimensional structure analysis was carried out in lipid bilayers at low peptide concentration, where TP10 is monomeric. While the N-terminal region is flexible and intrinsically unstructured within the plane of the lipid bilayer, the C-terminal ?-helix is embedded in the membrane with an oblique tilt angle of ? 55° and in accordance with its amphiphilic profile. Incorporation of the sterically obstructive D-CF3-Bpg reporter group into the helical region leads to a local unfolding of the membrane-bound peptide. At high concentration, these helix-destabilizing C-terminal substitutions promote aggregation into immobile ?-sheets, which resemble amyloid fibrils. On the other hand, the obstructive D-CF3-Bpg substitutions can be accommodated in the flexible N-terminus of TP10 where they do not promote aggregation at high concentration. The cross-talk between the two regions of TP10 thus exerts a delicate balance on its conformational switch, as the presence of the ?-helix counteracts the tendency of the unfolded N-terminus to self-assemble into ?-pleated fibrils. PMID:24937132

  6. Trifluoroethanol-induced conformational transitions of proteins: insights gained from the differences between alpha-lactalbumin and ribonuclease A.

    PubMed Central

    Gast, K.; Zirwer, D.; Müller-Frohne, M.; Damaschun, G.

    1999-01-01

    The trifluoroethanol (TFE)-induced structural changes of two proteins widely used in folding experiments, bovine alpha-lactalbumin, and bovine pancreatic ribonuclease A, have been investigated. The experiments were performed using circular dichroism spectroscopy in the far- and near-UV region to monitor changes in the secondary and tertiary structures, respectively, and dynamic light scattering to measure the hydrodynamic dimensions and the intermolecular interactions of the proteins in different conformational states. Both proteins behave rather differently under the influence of TFE: alpha-lactalbumin exhibits a molten globule state at low TFE concentrations before it reaches the so-called TFE state, whereas ribonuclease A is directly transformed into the TFE state at TFE concentrations above 40% (v/v). The properties of the TFE-induced states are compared with those of equilibrium and kinetic intermediate states known from previous work to rationalize the use of TFE in yielding information about the folding of proteins. Additionally, we report on the properties of TFE/water and TFE/buffer mixtures derived from dynamic light scattering investigations under conditions used in our experiments. PMID:10091665

  7. Transitions.

    ERIC Educational Resources Information Center

    Field, David; And Others

    1992-01-01

    Includes four articles: "Career Aspirations" (Field); "Making the Transition to a New Curriculum" (Baker, Householder); "How about a 'Work to School' Transition?" (Glasberg); and "Technological Improvisation: Bringing CNC to Woodworking" (Charles, McDuffie). (SK)

  8. Accounting for conformational flexibility and torsional anharmonicity in the H + CH{sub 3}CH{sub 2}OH hydrogen abstraction reactions: A multi-path variational transition state theory study

    SciTech Connect

    Meana-Pañeda, Rubén; Fernández-Ramos, Antonio

    2014-05-07

    This work reports a detailed theoretical study of the hydrogen abstraction reactions from ethanol by atomic hydrogen. The calculated thermal rate constants take into account torsional anharmonicity and conformational flexibility, in addition to the variational and tunneling effects. Specifically, the kinetics calculations were performed by using multi-path canonical variational transition state theory with least-action path tunneling corrections, to which we have added the two-dimensional non-separable method to take into account torsional anharmonicity. The multi-path thermal rate constant is expressed as a sum over conformational reaction channels. Each of these channels includes all the transition states that can be reached by internal rotations. The results show that, in the interval of temperatures between 250 and 2500 K, the account for multiple paths leads to higher thermal rate constants with respect to the single path approach, mainly at low and at high temperatures. In addition, torsional anharmonicity enhances the slope of the Arrhenius plot in this range of temperatures. Finally, we show that the incorporation of tunneling into the hydrogen abstraction reactions substantially changes the contribution of each of the transition states to the conformational reaction channel.

  9. The transition from closed to open conformation of Treponema pallidum outer membrane-associated lipoprotein TP0453 involves membrane sensing and integration by two amphipathic helices.

    PubMed

    Luthra, Amit; Zhu, Guangyu; Desrosiers, Daniel C; Eggers, Christian H; Mulay, Vishwaroop; Anand, Arvind; McArthur, Fiona A; Romano, Fabian B; Caimano, Melissa J; Heuck, Alejandro P; Malkowski, Michael G; Radolf, Justin D

    2011-12-01

    The molecular architecture and composition of the outer membrane (OM) of Treponema pallidum (Tp), the noncultivable agent of venereal syphilis, differ considerably from those of typical Gram-negative bacteria. Several years ago we described TP0453, the only lipoprotein associated with the inner leaflet of the Tp OM. Whereas polypeptides of other treponemal lipoproteins are hydrophilic, non-lipidated TP0453 can integrate into membranes, a property attributed to its multiple amphipathic helices (AHs). Furthermore, membrane integration of the TP0453 polypeptide was found to increase membrane permeability, suggesting the molecule functions in a porin-like manner. To better understand the mechanism of membrane integration of TP0453 and its physiological role in Tp OM biogenesis, we solved its crystal structure and used mutagenesis to identify membrane insertion elements. The crystal structure of TP0453 consists of an ?/?/?-fold and includes five stably folded AHs. In high concentrations of detergent, TP0453 transitions from a closed to open conformation by lateral movement of two groups of AHs, exposing a large hydrophobic cavity. Triton X-114 phase partitioning, liposome floatation assay, and bis-1-anilino-8-naphthalenesulfonate binding revealed that two adjacent AHs are critical for membrane sensing/integration. Using terbium-dipicolinic acid complex-loaded large unilamellar vesicles, we found that TP0453 increased efflux of fluorophore only at acidic pH. Gel filtration and cross-linking experiments demonstrated that one AH critical for membrane sensing/insertion also forms a dimeric interface. Based on structural dynamics and comparison with Mycobacterium tuberculosis lipoproteins LprG and LppX, we propose that TP0453 functions as a carrier of lipids, glycolipids, and/or derivatives during OM biogenesis. PMID:21965687

  10. Calcium binding domains and calcium-induced conformational transition of SPARC/BM-40/osteonectin, an extracellular glycoprotein expressed in mineralized and nonmineralized tissues

    SciTech Connect

    Engel, J.; Taylor, W.; Paulsson, M.; Sage, H.; Hogan, B.

    1987-11-03

    PSARC, BM-40, and osteonectin are identical or very closely related extracellular proteins of apparent M/sub r/ 43,000 (M/sub r/ 33,000 predicted from sequence). They were originally isolated from parietal endoderm cells, basement membrane producing tumors, and bone, respectively, but are rather widely distributed in various tissues. In view of the calcium binding activity reported for osteonectin, the authors analyzed the SPARC sequence and found two putative calcium binding domains. One is an N-terminal acid region with clusters of glutamic acid residues. This region, although neither ..gamma..-carboxylated nor homologous, resembles the ..gamma..-carboxyglutamic acid (Gla) domain of vitamin K dependent proteins of the blood clotting system in charge density, size of negatively charged clusters, and linkage to the rest of the molecule by a cysteine-rich domain. The other region is an EF-hand calcium binding domain located near the C-terminus. A disulfide bond between the E and F helix is predicted from modeling the EF-hand structure with the known coordinates of intestinal calcium binding protein. The disulfide bridge apparently serves to stabilize the isolated calcium loop in the extracellular protein. As observed for cytoplasmic EF-hand-containing proteins and for Gla domain containing proteins, a major conformational transition is induced in BM-40 upon binding of several Ca/sup 2 +/ ions. This is accompanied by a 35% increase in ..cap alpha..-helicity. A pronounced sigmoidicity of the dependence of the circular dichroism signal at 220 nm on calcium concentration indicates that the process is cooperative. In view of its properties, abundance, and wide distribution, it is proposed that SPARC/BM-40/osteonectin has a rather general regulatory function in calcium-dependent processes of the extra-cellular matrix.

  11. Conformal Infinity

    NASA Astrophysics Data System (ADS)

    Frauendiener, Jörg

    2004-02-01

    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.

  12. Conformal Infinity

    NASA Astrophysics Data System (ADS)

    Frauendiener, Jörg

    2000-08-01

    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 conceptgradually 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.

  13. Conformal House

    E-print Network

    Thomas A Ryttov; Francesco Sannino

    2009-06-01

    We investigate the gauge dynamics of nonsupersymmetric SU(N) gauge theories featuring the simultaneous presence of fermionic matter transforming according to two distinct representations of the underlying gauge group. We bound the regions of flavors and colors which can yield a physical infrared fixed point. As a consistency check we recover the previously investigated conformal windows bounds 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.

  14. New insights into the geometry of resorc[4]arenes: solvent-mediated supramolecular conformational and chiroptical control.

    PubMed

    Schiel, Christian; Hembury, Guy A; Borovkov, Victor V; Klaes, Michael; Agena, Ceno; Wada, Takehiko; Grimme, Stefan; Inoue, Yoshihisa; Mattay, Jochen

    2006-02-01

    The conformations of inherently chiral resorc[4]arenes were studied by circular dichroism (CD) spectroscopy. Whereas in aprotic solvents the crown conformation (C4) is preferred, protic solvents favor the boat conformation (C2). As a result of electronic coupling of the lowest L(b) state of the resorcinol unit in the resorc[4]arene, the CD spectra show a strong dependence on the conformation of the macrocycle. For the first time the solvent dependence of the CD spectra was qualitatively analyzed and simulated by using theoretical methods. We have thus demonstrated not only that the conformation of the calixarene is dramatically manipulated by the solvent but also that the joint use of chiroptical measurements and theoretical calculations is a powerful and versatile tool for elucidating structural variations in supramolecular chemistry. PMID:16438509

  15. Redox-dependent conformational transition of catalytic domain of protein disulfide isomerase indicated by crystal structure-based molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Inagaki, Koya; Satoh, Tadashi; Itoh, Satoru G.; Okumura, Hisashi; Kato, Koichi

    2015-01-01

    Protein disulfide isomerase is a multidomain protein operating as an essential folding catalyst. The b? and a? domains of this enzyme exhibit a domain rearrangement depending on the redox states of the a? domain, which is coupled with an open-closed conformational change of substrate-binding hydrophobic surface. Here we performed crystallographic analysis along with molecular dynamics simulations to study the structural mechanisms underlying this domain rearrangement. Based on our data, we propose that oxidization of the a? active site induces conformational changes in its b?-interacting segments, which is concealed by crystal packing, resulting in segregation of these two domains.

  16. Conformation analysis and computation of energy barrier to rotation about Csbnd N bond in para-methylphenyl carbamate and its solvent dependence in comparison with tertiary carbamates and tertiary amides

    NASA Astrophysics Data System (ADS)

    Modarresi-Alam, Ali Reza; Nowroozi, Alireza; Najafi, Parisa; Movahedifar, Fahimeh; Hajiabadi, Hossein

    2014-11-01

    Barrier to rotation about conjugated Csbnd N bond in p-Methyl phenyl carbamate (PMPC) was computed 14-16 kcal/mol at three levels of HF, B3LYP and MP2 using 6-311++G?? basis set. The solvent effect and energy barriers about Csbnd N bond in PMPC were compared to the case of tertiary carbamates and tertiary amides. Moreover, it is shown that in primary carbamates such as PMPC and tertiary amides isomerisation process passes through TS2 and TS1 respectively, while in tertiary carbamates goes through a combination of both TSs. Furthermore, X-ray analysis which is reported for the first time for primary aryl carbamates demonstrated that the inclusive plane of carbamate functional group is perpendicular to the plane of phenyl ring. The results of computations are completely in agreement with the X-ray data.

  17. Modeling conformational changes in cyclosporin A.

    PubMed Central

    O'Donohue, M. F.; Burgess, A. W.; Walkinshaw, M. D.; Treutlein, H. R.

    1995-01-01

    NMR and X-ray structures for the immunosuppressant cyclosporin A (CsA) reveal a remarkable difference between the unbound (free) conformation in organic solvents and the conformation bound to cyclophilin. We have performed computer simulations of the molecular dynamics of CsA under a variety of conditions and confirmed the stability of these two conformations at room temperature in water and in vacuum. However, when the free conformation was modeled in vacuum at 600 K, a transition pathway leading to the bound conformation was observed. This involved a change in the cis MeLeu-9 peptide bond to a trans conformation and the movement of the side chains forming the dominant hydrophobic cluster (residues MeBmt-1, MeLeu-4, MeLeu-6, and MeLeu-10) to the opposite side of the plane formed by the backbone atoms in the molecular ring. The final conformation had a backbone RMS deviation from the bound conformation of 0.53 A and was as stable in dynamics simulations as the bound conformation. Our calculations allowed us to make a detailed analysis of a transition pathway between the free and the bound conformations of CsA and to identify two distinct regions of coordinated movement in CsA, both of which underwent transitions independently. PMID:8535256

  18. Kinetics of binding of [3H]acetylcholine and [3H]carbamoylcholine to Torpedo postsynaptic membranes: slow conformational transitions of the cholinergic receptor.

    PubMed

    Boyd, N D; Cohen, J B

    1980-11-11

    The kinetics of binding of [3H]acetylcholine (AcCh) and [3H]carbamoylcholine (Carb) to membrane-bound nicotinic receptor from Torpedo electric tissue have been measured on the second time scale by rapid mixing and ultrafiltration. The concentration dependence of the association kinetics of agonist binding and the kinetics of ligand dissociation and receptor reisomerization following the removal of agonist are analyzed in terms of a model in which the observed binding is by a single population of receptors that exists in the absence of agonist in two interconvertible conformations, one binding agonist weakly (R1) and the other binding with high affinity (R2). A computer simulation has been used to determine values of rate and equilibrium constants characterizing the ligand interactions with the two conformations and for the conformational equilibrium in the presence and absence of agonist. At 4 degrees C, R1/R2 - 4.5, and the half-time for isomerization for low to high affinity of unliganded receptor is equal to 200 s, while for receptors occupied by either AcCh of Carb the half-time is reduced to approximately 4 s. For AcCh the apparent dissociation constants of the low- and high-affinity conformations re 800 nM and 2 nM, respectively (Keq = 8 nM), and for Carb the values are 30 microM and 25 nM (Keq = 100 nM). The dissociation rate constant of [3H]AcCh from R2 is equal to 0.04 s-1. The results are further discussed in terms of alternate less satisfactory reaction models and are compared with the receptor conformational equilibria deduced by the use of other kinetic techniques. PMID:7448173

  19. Conformational selection in protein binding and function

    PubMed Central

    Weikl, Thomas R; Paul, Fabian

    2014-01-01

    Protein binding and function often involves conformational changes. Advanced nuclear magnetic resonance (NMR) experiments indicate that these conformational changes can occur in the absence of ligand molecules (or with bound ligands), and that the ligands may “select” protein conformations for binding (or unbinding). In this review, we argue that this conformational selection requires transition times for ligand binding and unbinding that are small compared to the dwell times of proteins in different conformations, which is plausible for small ligand molecules. Such a separation of timescales leads to a decoupling and temporal ordering of binding/unbinding events and conformational changes. We propose that conformational-selection and induced-change processes (such as induced fit) are two sides of the same coin, because the temporal ordering is reversed in binding and unbinding direction. Conformational-selection processes can be characterized by a conformational excitation that occurs prior to a binding or unbinding event, while induced-change processes exhibit a characteristic conformational relaxation that occurs after a binding or unbinding event. We discuss how the ordering of events can be determined from relaxation rates and effective on- and off-rates determined in mixing experiments, and from the conformational exchange rates measured in advanced NMR or single-molecule fluorescence resonance energy transfer experiments. For larger ligand molecules such as peptides, conformational changes and binding events can be intricately coupled and exhibit aspects of conformational-selection and induced-change processes in both binding and unbinding direction. PMID:25155241

  20. Geometrie conforme infinitesimale Geometrie conforme microscopique

    E-print Network

    Pansu, Pierre

    G´eom´etrie conforme infinit´esimale G´eom´etrie conforme microscopique G´eom´etrie conforme m´esoscopique G´eom´etrie conforme `a grande ´echelle Qu'est ce que la g´eom´etrie conforme m´etrique ? Pierre Pansu 25 septembre 2014 Pierre Pansu Qu'est ce que la g´eom´etrie conforme m´etrique ? #12;G

  1. Effect of pH and copper(II) on the conformation transitions of silk fibroin based on EPR, NMR, and Raman spectroscopy.

    PubMed

    Zong, Xiao-Hong; Zhou, Ping; Shao, Zheng-Zhong; Chen, Shi-Ming; Chen, Xin; Hu, Bing-Wen; Deng, Feng; Yao, Wen-Hua

    2004-09-28

    Much attention has been paid to the natural mechanism of silkworm spinning due to the impressive mechanical properties of the natural fibers. Our results in the present work show that the fractional changes of the conformational components in regenerated silk fibroin (SF) extracted from Bombyx mori fibers is remarkably pH- and Cu(II)-dependent as demonstrated by Cu(II) EPR, (13)C NMR, and Raman spectroscopy. Cu(II) coordination atoms in SF are changed from four nitrogens to two nitrogens and two oxygens as well as to one nitrogen and three oxygens when the pH is lowered from 8.0 to 4.0. The addition of a given amount of Cu(II) into a SF solution could induce efficiently the SF conformational fractional change from silk I, a soluble helical conformation, to silk II, an insoluble beta-sheet conformation. This behavior is strikingly similar to that seen in prion protein and amyloid beta-peptide. On the basis of the similarity in the relevant sequence in SF to the octapeptide PHGGGWGQ in PrP, we suggest that at basic and neutral pH polypeptide AHGGYSGY in SF may form a 1:1 complex with Cu(II) by coordination of imidazole N(pi) of His together with two deprotonated main-chain nitrogens from two glycine residues and one nitrogen or oxygen from serine. Such a type of coordination may make the interaction between two adjacent beta-form polypeptide chains more difficult, thereby leading to an amorphous structure. Under weakly acidic conditions, however, Cu(II)-amide linkages may be broken and Cu(II) may switch to bind two N(tau) from two histidines in adjacent peptide chains, forming an intermolecular His(N(tau))-Cu(II)-His(N(tau)) bridge. This type of coordination may induce beta-sheet formation and aggregation, leading to a crystalline structure. PMID:15379533

  2. Conformable seal

    DOEpatents

    Neef, W.S.; Lambert, D.R.

    1982-08-10

    Sealing apparatus and method, comprising first and second surfaces or membranes, at least one of which surfaces is deformable, placed in proximity to one another. Urging means cause these surfaces to contact one another in a manner such that the deformable surface deforms to conform to the geometry of the other surface, thereby creating a seal. The seal is capable of undergoing multiple cycles of sealing and unsealing.

  3. A quantitative measure for protein conformational heterogeneity

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  4. Solvent-dependent reactions for the synthesis of ?-keto-benzo-?-sultone scaffolds via DBU-catalyzed O-sulfonylation/intramolecular Baylis-Hillman/1,3-H shift or dehydration tandem sequences.

    PubMed

    Ghandi, Mehdi; Bozcheloei, Abolfazl Hasani; Nazari, Seyed Hadi; Sadeghzadeh, Masoud

    2011-12-16

    We have developed a solvent-dependent method for the synthesis of novel benzo-?-sultone scaffolds. A variety of benzylbenzo[e][1,2]oxathiin-4(3H)-one-2,2-dioxides were obtained in high yields in DMF using a one-pot, DBU-catalyzed condensation of 2-hydroxybenzaldehydes with a number of (E)-2-phenylethenesulfonyl chlorides. On the other hand, the initially prepared 2-formylphenyl-(E)-2-phenylethenesulfonate derivatives underwent DBU-catalyzed reactions to a series of 3-[methoxy(phenyl)methyl]benzo[e][1,2]oxathiine-2,2-dioxides in moderate to good yields in MeOH. These reactions presumably proceed via DBU-catalyzed O-sulfonylation/intramolecular Baylis-Hillman/1,3-H shift or dehydration tandem sequences, respectively. PMID:22053779

  5. Eukaryotic translation initiation factor eIF5 promotes the accuracy of start codon recognition by regulating Pi release and conformational transitions of the preinitiation complex.

    PubMed

    Saini, Adesh K; Nanda, Jagpreet S; Martin-Marcos, Pilar; Dong, Jinsheng; Zhang, Fan; Bhardwaj, Monika; Lorsch, Jon R; Hinnebusch, Alan G

    2014-09-01

    eIF5 is the GTPase activating protein (GAP) for the eIF2 · GTP · Met-tRNAi (Met) ternary complex with a critical role in initiation codon selection. Previous work suggested that the eIF5 mutation G31R/SUI5 elevates initiation at UUG codons by increasing GAP function. Subsequent work implicated eIF5 in rearrangement of the preinitiation complex (PIC) from an open, scanning conformation to a closed state at AUG codons, from which Pi is released from eIF2 · GDP · Pi. To identify eIF5 functions crucial for accurate initiation, we investigated the consequences of G31R on GTP hydrolysis and Pi release, and the effects of intragenic G31R suppressors on these reactions, and on the partitioning of PICs between open and closed states. eIF5-G31R altered regulation of Pi release, accelerating it at UUG while decreasing it at AUG codons, consistent with its ability to stabilize the closed complex at UUG. Suppressor G62S mitigates both defects of G31R, accounting for its efficient suppression of UUG initiation in G31R,G62S cells; however suppressor M18V impairs GTP hydrolysis with little effect on PIC conformation. The strong defect in GTP hydrolysis conferred by M18V likely explains its broad suppression of Sui(-) mutations in numerous factors. We conclude that both of eIF5's functions, regulating Pi release and stabilizing the closed PIC conformation, contribute to stringent AUG selection in vivo. PMID:25114053

  6. Solvent dependent branching between C-I and C-Br bond cleavage following 266 nm excitation of CH2BrI

    NASA Astrophysics Data System (ADS)

    Anderson, Christopher P.; Spears, Kenneth G.; Wilson, Kaitlynn R.; Sension, Roseanne J.

    2013-11-01

    It is well known that ultraviolet photoexcitation of halomethanes results in halogen-carbon bond cleavage. Each halogen-carbon bond has a dominant ultraviolet (UV) absorption that promotes an electron from a nonbonding halogen orbital (nX) to a carbon-halogen antibonding orbital (?*C-X). UV absorption into specific transitions in the gas phase results primarily in selective cleavage of the corresponding carbon-halogen bond. In the present work, broadband ultrafast UV-visible transient absorption studies of CH2BrI reveal a more complex photochemistry in solution. Transient absorption spectra are reported spanning the range from 275 nm to 750 nm and 300 fs to 3 ns following excitation of CH2BrI at 266 nm in acetonitrile, 2-butanol, and cyclohexane. Channels involving formation of CH2Br + I radical pairs, iso-CH2Br-I, and iso-CH2I-Br are identified. The solvent environment has a significant influence on the branching ratios, and on the formation and stability of iso-CH2Br-I. Both iso-CH2Br-I and iso-CH2I-Br are observed in cyclohexane with a ratio of ˜2.8:1. In acetonitrile this ratio is 7:1 or larger. The observation of formation of iso-CH2I-Br photoproduct as well as iso-CH2Br-I following 266 nm excitation is a novel result that suggests complexity in the dissociation mechanism. We also report a solvent and concentration dependent lifetime of iso-CH2Br-I. At low concentrations the lifetime is >4 ns in acetonitrile, 1.9 ns in 2-butanol and ˜1.4 ns in cyclohexane. These lifetimes decrease with higher initial concentrations of CH2BrI. The concentration dependence highlights the role that intermolecular interactions can play in the quenching of unstable isomers of dihalomethanes.

  7. Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: Explicit treatment of the vibronic transitions

    SciTech Connect

    D’Abramo, Marco; Dipartimento di Chimica, Universitá Sapienza, P.le Aldo Moro, 5, 00185, Rome ; Aschi, Massimiliano; Amadei, Andrea

    2014-04-28

    Here, we extend a recently introduced theoretical-computational procedure [M. D’Alessandro, M. Aschi, C. Mazzuca, A. Palleschi, and A. Amadei, J. Chem. Phys. 139, 114102 (2013)] to include quantum vibrational transitions in modelling electronic spectra of atomic molecular systems in condensed phase. The method is based on the combination of Molecular Dynamics simulations and quantum chemical calculations within the Perturbed Matrix Method approach. The main aim of the presented approach is to reproduce as much as possible the spectral line shape which results from a subtle combination of environmental and intrinsic (chromophore) mechanical-dynamical features. As a case study, we were able to model the low energy UV-vis transitions of pyrene in liquid acetonitrile in good agreement with the experimental data.

  8. Attitudinal Conformity and Anonymity

    ERIC Educational Resources Information Center

    Tyson, Herbert; Kaplowitz, Stan

    1977-01-01

    Tested college students for conformity when conditions contributing to conformity were absent. Found that social pressures (responding in public, being surveyed by fellow group members) are necessary to produce conformity. (RL)

  9. Fake conformal symmetry in conformal cosmological models

    E-print Network

    Pi, So-Young

    We examine the local conformal invariance (Weyl invariance) in tensor-scalar theories used in recently proposed conformal cosmological models. We show that the Noether currents associated with Weyl invariance in these ...

  10. Geometrie conforme Empilements

    E-print Network

    Pansu, Pierre

    G´eom´etrie conforme Empilements Plongements conformes `a grande ´echelle Cohomologie Lp et g´eom´etrie conforme `a grande ´echelle Pierre Pansu 19 d´ecembre 2013 Pierre Pansu Cohomologie Lp et g´eom´etrie conforme `a grande ´echelle #12;G´eom´etrie conforme Empilements Plongements conformes `a grande ´echelle

  11. Holographic multiverse and conformal invariance

    SciTech Connect

    Garriga, Jaume; Vilenkin, Alexander E-mail: vilenkin@cosmos.phy.tufts.edu

    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.

  12. Holographic multiverse and conformal invariance

    E-print Network

    Jaume Garriga; Alexander Vilenkin

    2009-10-15

    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.

  13. Solvent dependent photophysical properties of dimethoxy curcumin

    NASA Astrophysics Data System (ADS)

    Barik, Atanu; Indira Priyadarsini, K.

    2013-03-01

    Dimethoxy curcumin (DMC) is a methylated derivative of curcumin. In order to know the effect of ring substitution on photophysical properties of curcumin, steady state absorption and fluorescence spectra of DMC were recorded in organic solvents with different polarity and compared with those of curcumin. The absorption and fluorescence spectra of DMC, like curcumin, are strongly dependent on solvent polarity and the maxima of DMC showed red shift with increase in solvent polarity function (?f), but the above effect is prominently observed in case of fluorescence maxima. From the dependence of Stokes' shift on solvent polarity function the difference between the excited state and ground state dipole moment was estimated as 4.9 D. Fluorescence quantum yield (?f) and fluorescence lifetime (?f) of DMC were also measured in different solvents at room temperature. The results indicated that with increasing solvent polarity, ?f increased linearly, which has been accounted for the decrease in non-radiative rate by intersystem crossing (ISC) processes.

  14. Viscoelasticity, Conformational Transition and Ultrastructure of Kappa-Carrageenan in the Presence of Potassium Ion around the Critical Total Ion Concentration

    NASA Astrophysics Data System (ADS)

    Núñez-Santiago, María C.; Tecante, Alberto; Durand, Sylvie; Garnier, Catherine; Doublier, Jean L.

    2008-07-01

    Rheology, microDSC, and confocal laser scanning microscopy were used to study the effect of potassium ion on the viscoelastic behavior, disorder-order transition and the ultrastructure, respectively, of kappa-carrageenan in aqueous medium in the vicinity of the critical total ionic concentration (C*). The rheological tests showed a "weak" gel behavior, with G'>G? and both moduli dependent on frequency. However, during heating, microDSC showed two zones: one attributed to the presence of ordered double helices without aggregation, and another to the fusion of aggregated double helices. Microscopy showed a three-dimensional network whose continuity depends of the concentration of added potassium ions. For a gel to be formed, a sufficient amount of potassium ion is necessary to promote complete aggregation of double helices so they can form a continuous three-dimensional network.

  15. Conformational Templates for Rational Drug Design: Flexibility of cyclo(D-Pro1

    E-print Network

    Marshall, Garland R.

    Conformational Templates for Rational Drug Design: Flexibility of cyclo(D-Pro1 -Ala2 -Ala3 -Ala4-AA and AMBER03 force fields. Simulations revealed conformational transitions between two main conformers, a predominant one (population 93-99%) and a minor conformer (population 0.4-6.7%). These results

  16. Spinning Conformal Blocks

    E-print Network

    Miguel S. Costa; Joao Penedones; David Poland; Slava Rychkov

    2011-09-28

    For conformal field theories in arbitrary dimensions, we introduce a method to derive the conformal blocks corresponding to the exchange of a traceless symmetric tensor appearing in four point functions of operators with spin. Using the embedding space formalism, we show that one can express all such conformal blocks in terms of simple differential operators acting on the basic scalar conformal blocks. This method gives all conformal blocks for conformal field theories in three dimensions. We demonstrate how this formalism can be applied in a few simple examples.

  17. Conformal symmetry superalgebras

    E-print Network

    Paul de Medeiros; Stefan Hollands

    2013-06-03

    We show how the rigid conformal supersymmetries associated with a certain class of pseudo-Riemannian spin manifolds define a Lie superalgebra. The even part of this superalgebra contains conformal isometries and constant R-symmetries. The odd part is generated by twistor spinors valued in a particular R-symmetry representation. We prove that any manifold which admits a conformal symmetry superalgebra of this type must generically have dimension less than seven. Moreover, in dimensions three, four, five and six, we provide the generic data from which the conformal symmetry superalgebra is prescribed. For conformally flat metrics in these dimensions, and compact R-symmetry, we identify each of the associated conformal symmetry superalgebras with one of the conformal superalgebras classified by Nahm. We also describe several examples for Lorentzian metrics that are not conformally flat.

  18. CREATIVITY AND CONFORMITY.

    ERIC Educational Resources Information Center

    ALLEN, VERNON L.; LEVINE, JOHN M.

    USING THREE FIFTH-GRADE CLASSES IN RACINE, WISCONSIN, AS AN EXPERIMENTAL GROUP AND THREE FIFTH-GRADE CLASSES AS A CONTROL GROUP, CONFORMITY TO GROUP PRESSURE WAS COMPARED FOR 76 SUBJECTS RECEIVING A FOUR-WEEK PROGRAM OF CREATIVITY TRAINING AND FOR 88 MATCHED CONTROLS. EFFECT OF CREATIVITY TRAINING ON CONFORMITY WAS QUITE SPECIFIC, WITH CONFORMITY

  19. Solvent dependence of the kinetic isotope effect in the reaction of ascorbate with the 2,2,6,6-tetramethylpiperidine-1-oxyl radical: tunnelling in a small molecule reaction.

    PubMed

    Sajenko, Ivana; Pilepi?, Viktor; Brala, Cvijeta Jakobusi?; Ursi?, Stanko

    2010-03-18

    The oxidation of ascorbate with the 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) radical in water and water-dioxane mixed solvent has been demonstrated to be a proton-coupled electron transfer (PCET) process, involving hydrogen tunnelling at room temperature. The magnitude of the kinetic isotope effect (KIE) k(H)/k(D) in the reaction increases with decrease of the solvent polarity. The evidence comprise: (a) the spectroscopic and kinetic evidence for the interaction of ascorbate and TEMPO; (b) the observation of KIEs k(H)/k(D) of 24.2(0.6) in water and 31.1(1.1) in 1:1 v/v water-diox. (diox = dioxane), at 298 K; (c) the observation of isotope effect on the Arrhenius prefactor, A(H)/A(D) of 0.6(0.2) in the reaction in water and 1.2(0.2) in 1:1 v/v water-diox solvent; (d) the observation of isotope differences in the enthalpies of activation in water and D(2)O, Delta(r)H(double dagger) (in H(2)O) = 31.0(0.4) kJ/mol, Delta(r)H(double dagger) (in D(2)O) = 40.0 (0.5) kJ/mol; in 1:1 v/v water-diox and 1:1 v/v D(2)O-diox, Delta(r)H(double dagger) (in H(2)O/diox) = 23.9(0.2) kJ/mol, Delta(r)H(double dagger) (in D(2)O/diox) = 32.1(0.3) kJ/mol; (e) the temperature dependence of the KIEs in water and 1:1 v/v water-dioxane; these KIEs range from 27.3 at 285.4 K to 19.1 at 317.4 K in water and from 34.3 to 24.6 at the corresponding temperatures in 1:1 v/v water-diox, respectively; (f) the observation of an increase of the KIE in 10-40% v/v dioxane-water solvents relative to the KIE in water alone. There is a weak solvent dependence of the rate constant on going from water to 1:1 v/v water-diox. solvent, from 2.20(0.03) mol(-1) dm(3) s(-1) to 5.50(0.14) mol(-1) dm(3) s(-1), respectively, which originates from the mutual compensation of the enthalpy and entropy of activation. PMID:20151699

  20. Conformally Dual to Inflation

    E-print Network

    Piao, Yun-Song

    2011-01-01

    It is showed by a conformal rescaling that the inflationary background can be dual to a slowly expanding background, which is almost Minkowski and described by a conformal field theory conformally coupled to gravity. It is proved that the primordial curvature perturbation and tensor perturbation generated during these two conformally equivalent backgrounds are completely equal, and the scale invariance of perturbations is determined by the conformal invariance of field theory in slowly expanding background. In dual slowly expanding scenario, the primordial universe is asymptotical to a static state in infinite past. We discuss the implication of the results obtained.

  1. Conformally Dual to Inflation

    E-print Network

    Yun-Song Piao

    2011-12-16

    It is showed by a conformal rescaling that the inflationary background can be dual to a slowly expanding background, which is almost Minkowski and described by a conformal field theory conformally coupled to gravity. It is proved that the primordial curvature perturbation and tensor perturbation generated during these two conformally equivalent backgrounds are completely equal, and the scale invariance of perturbations is determined by the conformal invariance of field theory in slowly expanding background. In dual slowly expanding scenario, the primordial universe is asymptotical to a static state in infinite past. We discuss the implication of the results obtained.

  2. Multiple conformational states of riboswitches fine-tune gene regulation.

    PubMed

    Fürtig, Boris; Nozinovic, Senada; Reining, Anke; Schwalbe, Harald

    2015-02-01

    Riboswitches are structured regions of mRNAs that modulate gene expression in response to specific binding of low molecular-weight ligands. They function by induced transitions between different functional conformations. The standard model assumed that the two functional states, the ligand-bound and ligand-free state, populated only two stable conformations. Recent discoveries of multiple conformations for the apo-state and holo-state of riboswitches challenge this model. Moreover, it becomes evident that detected conformational heterogeneity--mostly in the apo-state--provides sensitivity to multiple environmental inputs for riboswitch-based gene-regulation. PMID:25727496

  3. Galilean Conformal Electrodynamics

    E-print Network

    Arjun Bagchi; Rudranil Basu; Aditya Mehra

    2014-11-24

    Maxwell's Electrodynamics admits two distinct Galilean limits called the Electric and Magnetic limits. We show that the equations of motion in both these limits are invariant under the Galilean Conformal Algebra in D=4, thereby exhibiting non-relativistic conformal symmetries. Remarkably, the symmetries are infinite dimensional and thus Galilean Electrodynamics give us the first example of an infinitely extended Galilean Conformal Field Theory in D>2. We examine details of the theory by looking at purely non-relativistic conformal methods and also use input from the limit of the relativistic theory.

  4. Conformational Selection or Induced Fit? A Critical Appraisal of the Kinetic Mechanism

    E-print Network

    Di Cera, Enrico

    Conformational Selection or Induced Fit? A Critical Appraisal of the Kinetic Mechanism Austin D, two competing mechanisms of ligand recognition, conformational selection and induced fit, have-dissociation events are fast compared to conformational transitions, the rate of approach to equilibrium, kobs

  5. Dynamics and Conformational Energetics of a Peptide Hormone: Vasopressin

    NASA Astrophysics Data System (ADS)

    Hagler, A. T.; Osguthorpe, D. J.; Dauber-Osguthorpe, P.; Hempel, J. C.

    1985-03-01

    A theoretical methodology for use in conjunction with experiment was applied to the neurohypophyseal hormone lysine vasopressin for elucidation of its accessible molecular conformations and associated flexibility, conformational transitions, and dynamics. Molecular dynamics and energy minimization techniques make possible a description of the conformational properties of a peptide in terms of the precise positions of atoms, their fluctuations in time, and the interatomic forces acting on them. Analysis of the dynamic trajectory of lysine vasopressin shows the ability of a flexible peptide hormone to undergo spontaneous conformational transitions. The excursions of an individual phenylalanine residue exemplify the dynamic flexibility and multiple conformational states available to small peptide hormones and their component residues, even within constraints imposed by a cyclic hexapeptide ring.

  6. CONFORMALLY COVARIANT OPERATORS AND CONFORMAL INVARIANTS ON WEIGHTED GRAPHS

    E-print Network

    Jakobson, Dmitry

    CONFORMALLY COVARIANT OPERATORS AND CONFORMAL INVARIANTS ON WEIGHTED GRAPHS DMITRY JAKOBSON, THOMAS define the moduli space of conformal structures on G. We propose a definition of conformally covariant operators on graphs, motivated by [23]. We provide examples of conformally covariant operators, which

  7. Discovering conformational sub-states relevant to protein function

    SciTech Connect

    Agarwal, Pratul K; Ramanathan, Arvind

    2011-01-01

    Internal motions enable proteins to explore a range of conformations, even in the vicinity of native state. The role of conformational fluctuations in the designated function of a protein is widely debated. Emerging evidence suggests that sub-groups within the range of conformations (or sub-states) contain properties that may be functionally relevant. However, low populations in these sub-states and the transient nature of conformational transitions between these sub-states present significant challenges for their identification and characterization. To overcome these challenges we have developed a new computational technique, quasi-anharmonic analysis (QAA). QAA utilizes higher-order statistics of protein motions to identify sub-states in the conformational landscape. Further, the focus on anharmonicity allows identification of conformational fluctuations that enable transitions between sub-states. QAA applied to equilibrium simulations of human ubiquitin and T4 lysozyme reveals functionally relevant sub-states and protein motions involved in molecular recognition. In combination with a reaction pathway sampling method, QAA characterizes conformational sub-states associated with cis/trans peptidyl-prolyl isomerization catalyzed by the enzyme cyclophilin A. In these three proteins, QAA allows identification of conformational sub-states, with critical structural and dynamical features relevant to protein function. Overall, QAA provides a novel framework to intuitively understand the biophysical basis of conformational diversity and its relevance to protein function.

  8. Conformal Radii for Conformal Loop Ensembles

    NASA Astrophysics Data System (ADS)

    Schramm, Oded; Sheffield, Scott; Wilson, David B.

    2009-05-01

    The conformal loop ensembles CLE ? , defined for 8/3 ? ? ? 8, are random collections of loops in a planar domain which are conjectured scaling limits of the O( n) loop models. We calculate the distribution of the conformal radii of the nested loops surrounding a deterministic point. Our results agree with predictions made by Cardy and Ziff and by Kenyon and Wilson for the O( n) model. We also compute the expectation dimension of the CLE ? gasket, which consists of points not surrounded by any loop, to be 2 - {(8 - kappa)(3kappa - 8)}/{32kappa} , which agrees with the fractal dimension given by Duplantier for the O( n) model gasket.

  9. Conformations of Substituted Ethanes.

    ERIC Educational Resources Information Center

    Kingsbury, Charles A.

    1979-01-01

    Reviews state-of-the-art of conformational analysis and factors which affect it. Emphasizes sp-3 hybridized acrylic molecules. Provides examples on the importance of certain factors in determining conformation. Purpose, is to provide examples for examination questions. (Author/SA)

  10. Metamaterials with conformational nonlinearity

    E-print Network

    , in the same direction. This dual conformational feedback leads to exotic nonlinear behaviour. SpiralsMetamaterials with conformational nonlinearity Mikhail Lapine1,2 , Ilya V. Shadrivov1,2 , David A. Powell1 & Yuri S. Kivshar1,2 1 Nonlinear Physics Center, Research School of Physics and Engineering

  11. Conformity index: A review

    SciTech Connect

    Feuvret, Loic . E-mail: loic.feuvret@cpo.curie.net; Noel, Georges; Mazeron, Jean-Jacques; Bey, Pierre

    2006-02-01

    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.

  12. Unitarity of conformal supergravity

    NASA Astrophysics Data System (ADS)

    Binegar, B.

    1985-05-01

    The possibility of unitarizing the conformal supergravity of Kaku, Townsend, and van Nieuwenhuizen is investigated by examining the representation content of its linearized equations. Conformal (Weyl) gravitons are seen to correspond to a pair of helicity-conjugate, irreducible, and nonunitary representations of so(4,2). The solutions of the linearized gravitino field equation are seen to carry both unitary and nonunitary representations of so(4,2). The linearized constraint equation of Kaku et al., however, removes the unitary content from the gravitino field equation. The solution space of the linearized constraint and field equations of conformal supergravity is seen to carry a direct sum of two nonunitary and irreducible representations of the superalgebra su(2,2/1). These results imply that current models of conformal supergravity cannot be unitarized without breaking both su(2,2/1) and so(4,2) symmetries. A suggestion as to how one might construct a unitary model of conformal supergravity is made.

  13. Unitarity of conformal supergravity

    SciTech Connect

    Binegar, B.

    1985-05-15

    The possibility of unitarizing the conformal supergravity of Kaku, Townsend, and van Nieuwenhuizen is investigated by examining the representation content of its linearized equations. Conformal (Weyl) gravitons are seen to correspond to a pair of helicity-conjugate, irreducible, and nonunitary representations of so(4,2). The solutions of the linearized gravitino field equation are seen to carry both unitary and nonunitary representations of so(4,2). The linearized constraint equation of Kaku et al., however, removes the unitary content from the gravitino field equation. The solution space of the linearized constraint and field equations of conformal supergravity is seen to carry a direct sum of two nonunitary and irreducible representations of the superalgebra su(2,2/1). These results imply that current models of conformal supergravity cannot be unitarized without breaking both su(2,2/1) and so(4,2) symmetries. A suggestion as to how one might construct a unitary model of conformal supergravity is made.

  14. Standards and Conformity Assessment Training

    E-print Network

    Standards and Conformity Assessment Training Workshops for Government Agencies Visit http and Conformity Assessment Training for all levels of government NIST offers interactive workshops and seminars for federal, state, and local government agencies on the fundamentals of standards, conformity assessment

  15. Conformal Invariance in Inverse Turbulent Cascades

    E-print Network

    G. Falkovich; S. Musacchio

    2010-12-17

    We study statistical properties of turbulent inverse cascades in a class of nonlinear models describing a scalar field transported by a two-dimensional incompressible flow. The class is characterized by a linear relation between the transported field and the velocity, and include several cases of physical interest, such as Navier-Stokes, surface quasi-geostrophic and Charney-Hasegawa-Mima equations. We find that some statistical properties of the inverse turbulent cascades in such systems are conformal invariant. In particular, the zero-isolines of the scalar field are statistically equivalent to conformal invariant curves within the resolution of our numerics. We show that the choice of the conformal class is determined by the properties of a transporting velocity rather than those of a transported field and discover a phase transition when the velocity turns from a large-scale field to a small-scale one.

  16. Conformal Carroll groups

    E-print Network

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

    2014-07-02

    Conformal extensions of Levy-Leblond's Carroll group, based on geometric properties analogous to those of Newton-Cartan space-time are proposed. The extensions are labelled by an integer $k$. This framework includes and extends our recent study of the Bondi-Metzner-Sachs (BMS) and Newman-Unti (NU) groups. The relation to Conformal Galilei groups is clarified. Conformal Carroll symmetry is illustrated by "Carrollian photons". Motion both in the Newton-Cartan and Carroll spaces may be related to that of strings in the Bargmann space.

  17. Logarithmic conformal field theory

    NASA Astrophysics Data System (ADS)

    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 complicated non-rational theories. Examples include critical percolation, supersymmetric string backgrounds, disordered electronic systems, sandpile models describing avalanche processes, and so on. In each case, the non-rationality and non-unitarity of the CFT suggested that a more general theoretical framework was needed. Driven by the desire to better understand these applications, the mid-1990s saw significant theoretical advances aiming to generalise the constructs of rational CFT to a more general class. In 1994, Nahm introduced an algorithm for computing the fusion product of representations which was significantly generalised two years later by Gaberdiel and Kausch who applied it to explicitly construct (chiral) representations upon which the energy operator acts non-diagonalisably. Their work made it clear that underlying the physically relevant correlation functions are classes of reducible but indecomposable representations that can be investigated mathematically to the benefit of applications. In another direction, Flohr had meanwhile initiated the study of modular properties of the characters of logarithmic CFTs, a topic which had already evoked much mathematical interest in the rational case. Since these seminal theoretical papers appeared, the field has undergone rapid development, both theoretically and with regard to applications. Logarithmic CFTs are now known to describe non-local observables in the scaling limit of critical lattice models, for example percolation and polymers, and are an integral part of our understanding of quantum strings propagating on supermanifolds. They are also believed to arise as duals of three-dimensional chiral gravity models, fill out hidden sectors in non-rational theories with non-compact target spaces, and describe certain transitions in various incarnations of the quantum Hall effect. Other physical applications range from two-dimensional turbulence and non-equilibrium systems to aspects of the AdS/CFT correspondence and describing supersymmetric sigma models beyond the topological sector. We refer the reader to the

  18. Characterizing Protein Conformation Space

    E-print Network

    Nigham, Anshul

    In this work, we propose a radical approach for exploring the space of all possible protein structures. We present techniques to explore the clash-free conformation space, which comprises all protein structures whose atoms ...

  19. Quantum conformal mechanics

    E-print Network

    K. Andrzejewski

    2015-06-18

    The quantum mechanics of one degree of freedom exhibiting the exact conformal SL(2,R) symmetry is presented. The starting point is the classification of the unitary irreducible representations of the SL(2,R) group (or, to some extent, its universal covering). The coordinate representation is defined as the basis diagonalizing the special conformal generator K. It is indicated how the resulting theory emerges from the canonical/geometric quantization of the Hamiltonian dynamics on the relevant coadjoint orbits.

  20. Quantum conformal mechanics

    E-print Network

    Andrzejewski, K

    2015-01-01

    The quantum mechanics of one degree of freedom exhibiting the exact conformal SL(2,R) symmetry is presented. The starting point is the classification of the unitary irreducible representations of the SL(2,R) group (or, to some extent, its universal covering). The coordinate representation is defined as the basis diagonalizing the special conformal generator K. It is indicated how the resulting theory emerges from the canonical/geometric quantization of the Hamiltonian dynamics on the relevant coadjoint orbits.

  1. Air Quality Conformity Trip Generation

    E-print Network

    Handy, Susan L.

    Air Quality Conformity TTP220 S. Handy 4/30/14 #12;Trip Generation Trip Distribution Mode Split/graphics/Figure1.gif Ozone "On-Road Mobile Sources" #12;CONFORMITY DEFINED #12;Federal State Regional Local #12;Transportation Conformity Reference Guide Revised 2010 Transportation conformity is a way

  2. Protein Conformational Populations and Functionally Relevant Sub-states

    SciTech Connect

    Agarwal, Pratul K; Burger, Virginia; Savol, Andrej; Ramanathan, Arvind; Chennubhotla, Chakra

    2013-01-01

    Functioning proteins do not remain fixed in a unique structure, but instead they sample a range of conformations facilitated by motions within the protein. Even in the native state, a protein exists as a collection of interconverting conformations driven by thermodynamic fluctuations. Motions on the fast time scale allow a protein to sample conformations in the nearby area of its conformational landscape, while motions on slower time scales give it access to conformations in distal areas of the landscape. Emerging evidence indicates that protein landscapes contain conformational substates with dynamic and structural features that support the designated function of the protein. Nuclear magnetic resonance (NMR) experiments provide information about conformational ensembles of proteins. X-ray crystallography allows researchers to identify the most populated states along the landscape, and computational simulations give atom-level information about the conformational substates of different proteins. This ability to characterize and obtain quantitative information about the conformational substates and the populations of proteins within them is allowing researchers to better understand the relationship between protein structure and dynamics and the mechanisms of protein function. In this Account, we discuss recent developments and challenges in the characterization of functionally relevant conformational populations and substates of proteins. In some enzymes, the sampling of functionally relevant conformational substates is connected to promoting the overall mechanism of catalysis. For example, the conformational landscape of the enzyme dihydrofolate reductase has multiple substates, which facilitate the binding and the release of the cofactor and substrate and catalyze the hydride transfer. For the enzyme cyclophilin A, computational simulations reveal that the long time scale conformational fluctuations enable the enzyme to access conformational substates that allow it to attain the transition state, therefore promoting the reaction mechanism. In the long term, this emerging view of proteins with conformational substates has broad implications for improving our understanding of enzymes, enzyme engineering, and better drug design. Researchers have already used photoactivation to modulate protein conformations as a strategy to develop a hypercatalytic enzyme. In addition, the alteration of the conformational substates through binding of ligands at locations other than the active site provides the basis for the design of new medicines through allosteric modulation.

  3. Targeting the Conformal Window: Scalars on the Lattice

    E-print Network

    Evan Weinberg; Rich Brower; Anna Hasenfratz; Claudio Rebbi; Oliver Witzel

    2014-12-05

    The light Higgs boson of the Standard Model could arise as the consequence of the weakly broken conformal symmetry in a strongly interacting gauge theory. Here we present a novel idea to study the transition from conformal to confining behavior using an SU(3) gauge theory with four light and eight heavy flavors. This system interpolates between the 12-flavor conformal and the 4 flavor chirally broken theory as the mass of the heavy flavors are varied. We show first results on our determination of the iso-singlet 0++ state.

  4. Targeting the Conformal Window: Scalars on the Lattice

    NASA Astrophysics Data System (ADS)

    Weinberg, Evan; Brower, Rich; Hasenfratz, Anna; Rebbi, Claudio; Witzel, Oliver

    2015-09-01

    The light Higgs boson of the Standard Model could arise as the consequence of the weakly broken conformal symmetry in a strongly interacting gauge theory. Here we present a novel idea to study the transition from conformal to confining behavior using an SU(3) gauge theory with four light and eight heavy flavors. This system interpolates between the 12-flavor conformal and the 4 flavor chirally broken theory as the mass of the heavy flavors are varied. We show first results on our determination of the iso-singlet 0++ state.

  5. Conformal Random Geometry

    E-print Network

    Bertrand Duplantier

    2006-08-23

    In these Notes, a comprehensive description of the universal fractal geometry of conformally-invariant scaling curves or interfaces, in the plane or half-plane, is given. The present approach focuses on deriving critical exponents associated with interacting random paths, by exploiting their underlying quantum gravity structure. The latter relates exponents in the plane to those on a random lattice, i.e., in a fluctuating metric, using the so-called Knizhnik, Polyakov and Zamolodchikov (KPZ) map. This is accomplished within the framework of random matrix theory and conformal field theory, with applications to geometrical critical models, like Brownian paths, self-avoiding walks, percolation, and more generally, the O(N) or Q-state Potts models and, last but not least, Schramm's Stochastic Loewner Evolution (SLE_kappa). These Notes can be considered as complementary to those by Wendelin Werner (2006 Fields Medalist!), ``Some Recent Aspects of Random Conformally Invariant Systems,'' arXiv:math.PR/0511268.

  6. Conformal symmetry and unification

    SciTech Connect

    Pawlowski, Marek

    1998-12-15

    The Weyl-Weinberg-Salam model is presented. It is based on the local conformal gauge symmetry. The model identifies the Higgs scalar field in SM with the Penrose-Chernikov-Tagirov scalar field of the conformal theory of gravity. Higgs mechanism for generation of particle masses is replaced by the originated in Weyl's ideas conformal gauge scale fixing. Scalar field is no longer a dynamical field of the model and does not lead to quantum particle-like excitations that could be observed in HE experiments. Cosmological constant is naturally generated by the scalar quadric term. Weyl vector bosons can be present in the theory and can mix with photon--Z-boson system.

  7. Random Conformal Weldings

    E-print Network

    K. Astala; P. Jones; A. Kupiainen; E. Saksman

    2009-09-07

    We construct a conformally invariant random family of closed curves in the plane by welding of random homeomorphisms of the unit circle. The homeomorphism is constructed using the exponential of $\\beta X$ where $X$ is the restriction of the two dimensional free field on the circle and the parameter $\\beta$ is in the "high temperature" regime $\\betawelding problem is solved by studying a non-uniformly elliptic Beltrami equation with a random complex dilatation. For the existence a method of Lehto is used. This requires sharp probabilistic estimates to control conformal moduli of annuli and they are proven by decomposing the free field as a sum of independent fixed scale fields and controlling the correlations of the complex dilation restricted to dyadic cells of various scales. For uniqueness we invoke a result by Jones and Smirnov on conformal removability of H\\"older curves. We conjecture that our curves are locally related to SLE$(\\kappa)$ for $\\kappa<4$.

  8. Conformal General Relativity

    E-print Network

    V. Pervushin; D. Proskurin

    2001-06-03

    The inflation-free solution of problems of the modern cosmology (horizon, cosmic initial data, Planck era, arrow of time, singularity,homogeneity, and so on) is considered in the conformal-invariant unified theory given in the space with geometry of similarity where we can measure only the conformal-invariant ratio of all quantities. Conformal General Relativity is defined as the $SU_c(3)\\times SU(2)\\times U(1)$-Standard Model where the dimensional parameter in the Higgs potential is replaced by a dilaton scalar field described by the negative Penrose-Chernikov-Tagirov action. Spontaneous SU(2) symmetry breaking is made on the level of the conformal-invariant angle of the dilaton-Higgs mixing, and it allows us to keep the structure of Einstein's theory with the equivalence principle. We show that the lowest order of the linearized equations of motion solves the problems mentioned above and describes the Cold Universe Scenario with the constant temperature T and z-history of all masses with respect to an observable conformal time. A new fact is the intensive cosmic creation of $W,Z$-vector bosons due to their mass singularity. In the rigid state, this effect is determined by the integral of motion $(m_w^2H_{\\rm hubble})^{1/3}=2.7 K k_B$ that coincides with the CMB temperature and has the meaning of the primordial Hubble parameter. The created bosons are enough to consider their decay as an origin of the CMB radiation and all observational matter with the observational element abundances and the baryon asymmetry. Recent Supernova data on the relation between the luminosity distance and redshift (including the point $z=1.7$) do not contradict the dominance of the rigid state of the dark matter in the Conformal Cosmology.

  9. Galilean conformal and superconformal symmetries

    SciTech Connect

    Lukierski, J.

    2012-10-15

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

  10. Connections on conformal blocks

    E-print Network

    Rozenblyum, Nikita

    2011-01-01

    For an algebraic group G and a projective curve X, we study the category of D-modules on the moduli space Bung of principal G-bundles on X using ideas from conformal field theory. We describe this category in terms of the ...

  11. Conformal cloak for waves

    SciTech Connect

    Chen Huanyang; Leonhardt, Ulf; Tyc, Tomas

    2011-05-15

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

  12. Atomic cranks and levers control sugar ring conformations

    NASA Astrophysics Data System (ADS)

    Zhang, Qingmin; Lee, Gwangrog; Marszalek, Piotr E.

    2005-05-01

    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 ?-1\\to 4 -linked D-glucose, and amylose, composed of ?-1\\to 4 -linked D-glucose. In contrast to ?-glucose rings, which are mechanically stable and produce simple entropic elasticity of the chain, ?-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 \\to 6 -linked polysaccharides: pustulan, a ?-1\\to 6 -linked glucan, and dextran, a ?-1\\to 6 -linked glucan. Forced rotations about the C5-C6 bonds govern the elasticity of pustulan, and complex conformational transitions that involve simultaneous C5-C6 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.

  13. Conformation of Oligo(Ethylene Glycol) grafted Poly(Norbornene) in solutions: A Small Angle Neutron Scattering Study

    SciTech Connect

    Cheng, Gang; Melnichenko, Yuri B; Hua, Fengjun; Hong, Kunlun; Wignall, George D; Hammouda, B.; Mays, Jimmy

    2008-01-01

    The structure of thermo sensitive poly(methoxyoligo(ethylene glycol) norbornenyl esters) homopolymers in dilute solution was investigated by Small Angle Neutron Scattering (SANS). The homopolymers consist of a polynorbornene (PNB) backbone with a degree of polymerization (DP) of 50, and each backbone monomer has a grafted Ethylene Glycol (EG) side chain with an average DP of 6.6. The hydrophobic backbone and hydrophilic side chains interact differently with solvents depending on their polarity, which makes the conformation very sensitive to the solvent quality. The polymer conformation was studied in two solvents, d-toluene and D2O, with the aim of understanding the influence of solvent/polymer interactions on the resulting structures. It was found that in a 0.5 wt. % solution in d-toluene the polymers assume wormlike chains and gradually contract with increasing polymer concentration. In a 0.5 wt. % solution in D2O, the polymers are partially contracted at room temperature and their conformation can be described by the form factor of a rigid cylinder. The volume of the cylinder shows no concentration dependence. Furthermore, the polymers in D2O collapse at higher temperatures due to decreasing solubility of the side chains in water.

  14. A Conformal Extension Theorem based on Null Conformal Geodesics

    E-print Network

    Christian Lübbe

    2009-11-19

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

  15. Conformational properties of isolated polyelectrolytes in poor solvents

    NASA Astrophysics Data System (ADS)

    Shew, Chwen-Yang; Yethiraj, Arun

    1999-01-01

    The conformational behavior of isolated polyelectrolytes in poor solvents is investigated using theory and computer simulation. DiMarzio's approach for the collapse transition in neutral polymers is extended to uniformly charged polymers [E. A. diMarzio, Macromolecules 17, 969 (1984)]. The theory predicts a discontinuous collapse transition with decreasing solvent quality in highly charged polymers. A discontinuous collapse transition is also observed when the charge fraction is decreased in very poor solvents. Monte Carlo simulations are reported for the collapse transition in a lattice model of polyelectrolytes. Under some conditions the distribution of polymer size is bimodal, consistent with the theory.

  16. Diffeomorphism group and conformal fields

    E-print Network

    T. A. Larsson

    1992-08-15

    Conformal fields are a new class of $Vect(N)$ modules which are more general than tensor fields. The corresponding diffeomorphism group action is constructed. Conformal fields are thus invariantly defined.

  17. Relaxation time of non-conformal plasma

    E-print Network

    Alex Buchel

    2009-11-27

    We study effective relaxation time of viscous hydrodynamics of strongly coupled non-conformal gauge theory plasma using gauge theory/string theory correspondence. We compute leading corrections to the conformal plasma relaxation time from the relevant deformations due to dim-2 and dim-3 operators. We discuss in details the relaxation time tau_eff of N=2^* plasma. For a certain choice of masses this theory undergoes a phase transition with divergent specific heat c_V ~ |1-T_c/T|^(-1/2). Although the bulk viscosity remains finite all the way to the critical temperature, we find that tau_eff diverges near the critical point as tau_eff ~ |1-T_c/T|^(-1/2).

  18. Theory for the conformational changes of double-stranded chain molecules

    NASA Astrophysics Data System (ADS)

    Chen, Shi-Jie; Dill, Ken A.

    1998-09-01

    We develop statistical mechanical theory to predict the thermodynamic properties of chain molecules having noncovalent double-stranded conformations, as in RNA molecules and ?-sheets in proteins. Sequence dependence and excluded volume interactions are explicitly taken into account. We classify conformations by their polymer graphs and enumerate all the conformations corresponding to each graph by a recently developed matrix method [S-J. Chen and K. A. Dill, J. Chem. Phys. 103, 5802 (1995)]. All such graphs are summed by a recursive method. Tests against exact computer enumeration for short chains on a 2D lattice show that the density of states and partition function are given quite accurately. So far, we have explored two classes of conformations; hairpins, which model small ?-sheets, and RNA secondary structures. The main folding transition is predicted to be quite different for these two conformational classes: the hairpin transition is two-state while the RNA secondary structure transition is one-state for homopolymeric chains.

  19. On Conformally Invariant CLE Explorations

    NASA Astrophysics Data System (ADS)

    Werner, Wendelin; Wu, Hao

    2013-06-01

    We study some conformally invariant dynamic ways to construct the Conformal Loop Ensembles with simple loops introduced in earlier papers by Sheffield, and by Sheffield and Werner. One outcome is a conformally invariant way to measure a distance of a CLE4 loop to the boundary "within" the CLE4, when one identifies all points of each loop.

  20. Movement of elongation factor G between compact and extended conformations.

    PubMed

    Salsi, Enea; Farah, Elie; Netter, Zoe; Dann, Jillian; Ermolenko, Dmitri N

    2015-01-30

    Previous structural studies suggested that ribosomal translocation is accompanied by large interdomain rearrangements of elongation factor G (EF-G). Here, we follow the movement of domain IV of EF-G relative to domain II of EF-G using ensemble and single-molecule Förster resonance energy transfer. Our results indicate that ribosome-free EF-G predominantly adopts a compact conformation that can also, albeit infrequently, transition into a more extended conformation in which domain IV moves away from domain II. By contrast, ribosome-bound EF-G predominantly adopts an extended conformation regardless of whether it is interacting with pretranslocation ribosomes or with posttranslocation ribosomes. Our data suggest that ribosome-bound EF-G may also occasionally sample at least one more compact conformation. GTP hydrolysis catalyzed by EF-G does not affect the relative stability of the observed conformations in ribosome-free and ribosome-bound EF-G. Our data support a model suggesting that, upon binding to a pretranslocation ribosome, EF-G moves from a compact to a more extended conformation. This transition is not coupled to but likely precedes both GTP hydrolysis and mRNA/tRNA translocation. PMID:25463439

  1. Conformational ensembles and sampled energy landscapes: Analysis and comparison.

    PubMed

    Cazals, Frédéric; Dreyfus, Tom; Mazauric, Dorian; Roth, Christine-Andrea; Robert, Charles H

    2015-06-15

    We present novel algorithms and software addressing four core problems in computational structural biology, namely analyzing a conformational ensemble, comparing two conformational ensembles, analyzing a sampled energy landscape, and comparing two sampled energy landscapes. Using recent developments in computational topology, graph theory, and combinatorial optimization, we make two notable contributions. First, we present a generic algorithm analyzing height fields. We then use this algorithm to perform density-based clustering of conformations, and to analyze a sampled energy landscape in terms of basins and transitions between them. In both cases, topological persistence is used to manage (geometric) frustration. Second, we introduce two algorithms to compare transition graphs. The first is the classical earth mover distance metric which depends only on local minimum energy configurations along with their statistical weights, while the second incorporates topological constraints inherent to conformational transitions. Illustrations are provided on a simplified protein model (BLN69), whose frustrated potential energy landscape has been thoroughly studied. The software implementing our tools is also made available, and should prove valuable wherever conformational ensembles and energy landscapes are used. PMID:25994596

  2. Evaluation of conformal integrals

    E-print Network

    Bzowski, Adam; Skenderis, Kostas

    2015-01-01

    We present a comprehensive method for the evaluation of a vast class of integrals representing 3-point functions of conformal field theories in momentum space. The method leads to analytic, closed-form expressions for all scalar and tensorial 3-point functions of operators with integer dimensions in any spacetime dimension. In particular, this encompasses all 3-point functions of the stress tensor, conserved currents and marginal scalar operators.

  3. Conformal scalar field wormholes

    NASA Technical Reports Server (NTRS)

    Halliwell, Jonathan J.; Laflamme, Raymond

    1989-01-01

    The Euclidian Einstein equations with a cosmological constant and a conformally coupled scalar field are solved, taking the metric to be of the Robertson-Walker type. In the case Lambda = 0, solutions are found which represent a wormhole connecting two asymptotically flat Euclidian regions. In the case Lambda greater than 0, the solutions represent tunneling from a small Tolman-like universe to a large Robertson-Walker universe.

  4. Conformations of organophosphine oxides

    DOE PAGESBeta

    De Silva, Nuwan; Zahariev, Federico; Hay, Benjamin P.; Gordon, Mark S.; Windus, Theresa L.

    2015-07-17

    The conformations of a series of organophosphine oxides, OP(CH3)2R, where R = methyl, ethyl, isopropyl, tert-butyl, vinyl, and phenyl, are predicted using the MP2/cc-pVTZ level of theory. Comparison of potential energy surfaces for rotation about P–C bonds with crystal structure data reveals a strong correlation between predicted location and energetics of minima and histograms of dihedral angle distributions observed in the solid state. In addition, the most stable conformers are those that minimize the extent of steric repulsion between adjacent rotor substituents, and the torsional barriers tend to increase with the steric bulk of the rotating alkyl group. MM3 forcemore »field parameters were adjusted to fit the MP2 results, providing a fast and accurate model for predicting organophosphine oxides shapes—an essential part of understanding the chemistry of these compounds. As a result, the predictive power of the modified MM3 model was tested against MP2/cc-pVTZ conformations for triethylphosphine oxide, OP(CH2CH3)3, and triphenylphosphine oxide, OP(Ph)3.« less

  5. Conformations of organophosphine oxides

    SciTech Connect

    De Silva, Nuwan; Zahariev, Federico; Hay, Benjamin P.; Gordon, Mark S.; Windus, Theresa L.

    2015-07-17

    The conformations of a series of organophosphine oxides, OP(CH3)2R, where R = methyl, ethyl, isopropyl, tert-butyl, vinyl, and phenyl, are predicted using the MP2/cc-pVTZ level of theory. Comparison of potential energy surfaces for rotation about P–C bonds with crystal structure data reveals a strong correlation between predicted location and energetics of minima and histograms of dihedral angle distributions observed in the solid state. In addition, the most stable conformers are those that minimize the extent of steric repulsion between adjacent rotor substituents, and the torsional barriers tend to increase with the steric bulk of the rotating alkyl group. MM3 force field parameters were adjusted to fit the MP2 results, providing a fast and accurate model for predicting organophosphine oxides shapes—an essential part of understanding the chemistry of these compounds. As a result, the predictive power of the modified MM3 model was tested against MP2/cc-pVTZ conformations for triethylphosphine oxide, OP(CH2CH3)3, and triphenylphosphine oxide, OP(Ph)3.

  6. Conformal symmetries of spherical spacetimes

    E-print Network

    S. Moopanar; S. D. Maharaj

    2011-08-20

    We investigate the conformal geometry of spherically symmetric spacetimes in general without specifying the form of the matter distribution. The general conformal Killing symmetry is obtained subject to a number of integrability conditions. Previous results relating to static spacetimes are shown to be a special case of our solution. The general inheriting conformal symmetry vector, which maps fluid flow lines conformally onto fluid flow lines, is generated and the integrability conditions are shown to be satisfied. We show that there exists a hypersurface orthogonal conformal Killing vector in an exact solution of Einstein's equations for a relativistic fluid which is expanding, accelerating and shearing.

  7. Dissecting conformational contributions to glycosidase catalysis and inhibition

    PubMed Central

    Speciale, Gaetano; Thompson, Andrew J; Davies, Gideon J; Williams, Spencer J

    2014-01-01

    Glycoside hydrolases (GHs) are classified into >100 sequence-based families. These enzymes process a wide variety of complex carbohydrates with varying stereochemistry at the anomeric and other ring positions. The shapes that these sugars adopt upon binding to their cognate GHs, and the conformational changes that occur along the catalysis reaction coordinate is termed the conformational itinerary. Efforts to define the conformational itineraries of GHs have focussed upon the critical points of the reaction: substrate-bound (Michaelis), transition state, intermediate (if relevant) and product-bound. Recent approaches to defining conformational itineraries that marry X-ray crystallography of enzymes bound to ligands that mimic the critical points, along with advanced computational methods and kinetic isotope effects are discussed. PMID:25016573

  8. Conformal profiles in the Hilhorst-van Leeuwen model

    NASA Astrophysics Data System (ADS)

    Karevski, D.; Turban, L.; Iglói, F.

    2000-04-01

    We study the critical energy and magnetization profiles for the Ising quantum chain with a marginal extended surface perturbation of the form A /y , y being the distance from the surface (Hilhorst-van Leeuwen model). For weak local couplings, A transition with A -dependent exponents, whereas, for A >A c , there is surface order at the bulk critical point. If conformal invariance is assumed to hold with such marginal perturbations, it predicts conformal profiles with the same scaling form as for the unperturbed quantum chain, with marginal surface exponents replacing the unperturbed ones. The results of direct analytical and numerical calculations of the profiles confirm the validity of the conformal expressions in the regimes of second- and first-order surface transitions.

  9. Study of the conformal region of the SU(3) gauge theory with domain-wall fermions

    E-print Network

    J. Noaki; G. Cossu; K-I. Ishikawa; Y. Iwasaki; T. Yoshie

    2015-11-20

    We investigate the phase structure of the SU(3) gauge theory with $N_f=8$ by numerical simulations employing the massless Domain-Wall fermions.Our aim is to study directly the massless quark region, since it is the most important region to clarify the properties of conformal theories. When the number of flavor is within the conformal window, it is claimed recently with Wilson quarks that there is the conformal region at the small quark mass region in the parameter space in addition to the confining phase and the deconfining phase. We study the properties of the conformal region investing the spatial Polyakov loops and the temporal meson propagators. Our data imply that there is the conformal region, and a phase transition between the confining phase and the conformal region takes place. These results are consistent with the claim that the conformal window is between $7$ and $16$. Progress reports on other related studies are also presented.

  10. Study of the conformal region of the SU(3) gauge theory with domain-wall fermions

    E-print Network

    Noaki, J; Ishikawa, K-I; Iwasaki, Y; Yoshie, T

    2015-01-01

    We investigate the phase structure of the SU(3) gauge theory with $N_f=8$ by numerical simulations employing the massless Domain-Wall fermions.Our aim is to study directly the massless quark region, since it is the most important region to clarify the properties of conformal theories. When the number of flavor is within the conformal window, it is claimed recently with Wilson quarks that there is the conformal region at the small quark mass region in the parameter space in addition to the confining phase and the deconfining phase. We study the properties of the conformal region investing the spatial Polyakov loops and the temporal meson propagators. Our data imply that there is the conformal region, and a phase transition between the confining phase and the conformal region takes place. These results are consistent with the claim that the conformal window is between $7$ and $16$. Progress reports on other related studies are also presented.

  11. The Observation and Study of ELP V5-120 Conformational Changes 

    E-print Network

    Zhou, Qian

    2012-10-24

    and secondary/tertiary structure formation. In this thesis, the collapse process of ELP was studied with differential scanning calorimetry (DSC). In DSC thermal cycling, a clear conformational transition was observed. Also, a transiently stable state of ELP V5...

  12. Conformal superalgebras via tractor calculus

    NASA Astrophysics Data System (ADS)

    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.

  13. Conformations of amphiphilic polyelectrolyte stars with diblock copolymer arms

    E-print Network

    Alexey A. Polotsky; Tatiana M. Birshtein; Mohamed Daoud; Oleg V. Borisov

    2012-05-12

    We consider conformations and intra-molecular conformational transitions in amphiphilic starlike polymers formed by diblock copolymer arms with inner hydrophobic and outer polyelectrolyte blocks. A combination of an analytical mean-field theory with the assumption-free numerical self-consistent field (SCF) modeling approach is applied. It is demonstrated that unimolecular micelles with collapsed hydrophobic cores and swollen polyelectrolyte coronae are formed in dilute aqueous solutions at high ionic strength or/and low degree of ionization of the outer hydrophilic block. An intra-molecular conformational transition related to the unfolding of the hydrophobic core of the unimolecular micelles can be triggered by a decrease in the ionic strength of the solution or/and increase in the degree of ionization of the coronal blocks. In the stars with large number of diblock copolymer arms the transition between conformations with collapsed or stretched core-forming blocks occurs continuously by progressive unfolding of the core domain. By contrast, in the stars with relatively small number of arms the continuous unfolding of the core is interrupted by an abrupt unravelling transition. A detailed SCF analysis indicates that under both unfolding scenario the arms of the star are extended fairly equally, i.e., no intra-molecular disproportionation occurs.

  14. Parafermionic conformal field theory on the lattice

    E-print Network

    Roger S. K. Mong; David J. Clarke; Jason Alicea; Netanel H. Lindner; Paul Fendley

    2014-09-18

    Finding the precise correspondence between lattice operators and the continuum fields that describe their long-distance properties is a largely open problem for strongly interacting critical points. Here we solve this problem essentially completely in the case of the three-state Potts model, which exhibits a phase transition described by a strongly interacting 'parafermion' conformal field theory. Using symmetry arguments, insights from integrability, and extensive simulations, we construct lattice analogues of nearly all the relevant and marginal physical fields governing this transition. This construction includes chiral fields such as the parafermion. Along the way we also clarify the structure of operator product expansions between order and disorder fields, which we confirm numerically. Our results both suggest a systematic methodology for attacking non-free field theories on the lattice and find broader applications in the pursuit of exotic topologically ordered phases of matter.

  15. Conformational Properties of Charged Polymers in Poor Solvents

    NASA Astrophysics Data System (ADS)

    Shew, Chwen-Yang; Yethiraj, Arun

    1997-03-01

    A simple theory is presented for the conformational properties of charged polymers in poor solvents. The theory extends an approach pioneered by diMarzio for neutral polymers to charged polymers. The starting point is an expression for the free energy in terms of the average polymer size, which is minimized with respect to the size to obtain the equilibrium conformations. For poor enough solvents the theory predicts a discontinuous transition from an extended to a collapsed state as the solvent quality is decreased. For high enough charge fractions the theory predicts a discontinuous transition from an extended to a collapsed as the solvent quality is decreased. The chain size probability distribution function is bimodal in the neighborhood of these transitions. These predictions are verified via computer simulations.

  16. Eikonalization of conformal blocks

    SciTech Connect

    Fitzpatrick, A. Liam; Kaplan, Jared; Walters, Matthew T.; Wang, Junpu

    2015-09-03

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

  17. Conformally symmetric traversable wormholes

    SciTech Connect

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

    2007-10-15

    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.

  18. Eikonalization of conformal blocks

    DOE PAGESBeta

    Fitzpatrick, A. Liam; Kaplan, Jared; Walters, Matthew T.; Wang, Junpu

    2015-09-03

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

  19. Fermion-Scalar Conformal Blocks

    E-print Network

    Luca Iliesiu; Filip Kos; David Poland; Silviu S. Pufu; David Simmons-Duffin; Ran Yacoby

    2015-11-04

    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.

  20. Fermion-Scalar Conformal Blocks

    E-print Network

    Iliesiu, Luca; Poland, David; Pufu, Silviu S; Simmons-Duffin, David; Yacoby, Ran

    2015-01-01

    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.

  1. Synthesis, molecular conformation, vibrational and electronic transition, isometric chemical shift, polarizability and hyperpolarizability analysis of 3-(4-methoxy-phenyl)-2-(4-nitro-phenyl)-acrylonitrile: a combined experimental and theoretical analysis.

    PubMed

    Asiri, Abdullah Mohamed; Karabacak, Mehmet; Kurt, Mustafa; Alamry, Khalid A

    2011-11-01

    This work presents the synthesis and characterization of a novel compound, 3-(4-methoxy-phenyl)-2-(4-nitro-phenyl)-acrylonitrile (abbreviated as 3-(4MP)-2-(4-NP)-AN, C(16)H(12)N(2)O(3)). The spectroscopic properties of the compound were examined by FT-IR, UV-vis and NMR ((1)H and (13)C) techniques. FT-IR spectrum in solid state was observed in the region 4000-400 cm(-1). The UV-vis absorption spectrum of the compound which dissolved in chloroform was recorded in the range of 200-800 nm. The (1)H and (13)C NMR spectra were recorded in CDCl(3) solution. To determine lowest-energy molecular conformation of the title molecule, the selected torsion angle is varied every 10° and molecular energy profile is calculated from 0° to 360°. The structural and spectroscopic data of the molecule in the ground state were calculated using density functional theory (DFT) employing B3LYP/6-31G(d,p) basis set. The dipole moment, linear polarizability and first hyperpolarizability values were also computed using the same basis set. A study on the electronic properties, such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. The HOMO and LUMO analysis were used to elucidate information regarding charge transfer within the molecule. The vibrational wavenumbers were calculated and scaled values were compared with experimental FT-IR spectrum. The complete assignments were performed on the basis of the experimental results and total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. Isotropic chemical shifts were calculated using the gauge-invariant atomic orbital (GIAO) method. Comparison of the calculated frequencies, NMR chemical shifts, absorption wavelengths with the experimental values revealed that DFT and TD-DFT method produce good results. The linear polarizabilities and first hyperpolarizabilities of the studied molecule indicate that the title compound can be used as a good nonlinear optical material. The thermodynamic properties of the studied compound at different temperatures were calculated, revealing the correlations between standard heat capacity, standard entropy, standard enthalpy changes and temperatures. PMID:21856218

  2. Synthesis, molecular conformation, vibrational and electronic transition, isometric chemical shift, polarizability and hyperpolarizability analysis of 3-(4-Methoxy-phenyl)-2-(4-nitro-phenyl)-acrylonitrile: A combined experimental and theoretical analysis

    NASA Astrophysics Data System (ADS)

    Asiri, Abdullah Mohamed; Karabacak, Mehmet; Kurt, Mustafa; Alamry, Khalid A.

    2011-11-01

    This work presents the synthesis and characterization of a novel compound, 3-(4-Methoxy-phenyl)-2-(4-nitro-phenyl)-acrylonitrile (abbreviated as 3-(4MP)-2-(4-NP)-AN, C 16H 12N 2O 3). The spectroscopic properties of the compound were examined by FT-IR, UV-vis and NMR ( 1H and 13C) techniques. FT-IR spectrum in solid state was observed in the region 4000-400 cm -1. The UV-vis absorption spectrum of the compound which dissolved in chloroform was recorded in the range of 200-800 nm. The 1H and 13C NMR spectra were recorded in CDCl 3 solution. To determine lowest-energy molecular conformation of the title molecule, the selected torsion angle is varied every 10° and molecular energy profile is calculated from 0° to 360°. The structural and spectroscopic data of the molecule in the ground state were calculated using density functional theory (DFT) employing B3LYP/6-31G(d,p) basis set. The dipole moment, linear polarizability and first hyperpolarizability values were also computed using the same basis set. A study on the electronic properties, such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. The HOMO and LUMO analysis were used to elucidate information regarding charge transfer within the molecule. The vibrational wavenumbers were calculated and scaled values were compared with experimental FT-IR spectrum. The complete assignments were performed on the basis of the experimental results and total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. Isotropic chemical shifts were calculated using the gauge-invariant atomic orbital (GIAO) method. Comparison of the calculated frequencies, NMR chemical shifts, absorption wavelengths with the experimental values revealed that DFT and TD-DFT method produce good results. The linear polarizabilities and first hyperpolarizabilities of the studied molecule indicate that the title compound can be used as a good nonlinear optical material. The thermodynamic properties of the studied compound at different temperatures were calculated, revealing the correlations between standard heat capacity, standard entropy, standard enthalpy changes and temperatures.

  3. Holographic dual of a boundary conformal field theory.

    PubMed

    Takayanagi, Tadashi

    2011-09-01

    We propose a holographic dual of a conformal field theory defined on a manifold with boundaries, i.e., boundary conformal field theory (BCFT). Our new holography, which may be called anti-de Sitter BCFT, successfully calculates the boundary entropy or g function in two-dimensional BCFTs and it agrees with the finite part of the holographic entanglement entropy. Moreover, we can naturally derive a holographic g theorem. We also analyze the holographic dual of an interval at finite temperature and show that there is a first order phase transition. PMID:21981491

  4. Holographic Dual of a Boundary Conformal Field Theory

    SciTech Connect

    Takayanagi, Tadashi

    2011-09-02

    We propose a holographic dual of a conformal field theory defined on a manifold with boundaries, i.e., boundary conformal field theory (BCFT). Our new holography, which may be called anti-de Sitter BCFT, successfully calculates the boundary entropy or g function in two-dimensional BCFTs and it agrees with the finite part of the holographic entanglement entropy. Moreover, we can naturally derive a holographic g theorem. We also analyze the holographic dual of an interval at finite temperature and show that there is a first order phase transition.

  5. Replacement between conformity and counter-conformity in consumption decisions.

    PubMed

    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. PMID:23654033

  6. Screening of solvent dependent antibacterial activity of Prunus domestica.

    PubMed

    Yaqeen, Zahra; Naqvi, Naim-ul-Hasan; Sohail, Tehmina; Rehman, Zakir-ur; Fatima, Nudrat; Imran, Hina; Rehman, Atiqur

    2013-03-01

    Fruit of Prunus domestica was extracted in ethanol. The ethanol extract was further extracted with two solvents ethyl acetate and chloroform. The crude ethanol extract and two fractions (ethyl acetate and chloroform) were screened for their antibacterial activity using the agar well diffusion method .They were tested against nine bacteria; five Gram positive bacteria (Staphylococcus aureus, Streptococcuc intermedius, Bacillus cereus, Bacillus pumilus) and four Gram negative bacteria (Eschrichia coli, Proteus mirabilis Shigella flexneri, Salmonella typhi and Klebsiela pneumoniae). The susceptibility of microorganisms to all three fractions was compared with each other and with standard antibiotic (Ampicillin) Among all fractions ethyl acetate exhibited highest antibacterial activity (average zone of inhibition 34.57mm ± 1.3) while ethyl alcohol exhibited least antibacterial activity (average zone of inhibition 17.42mm ± 3.3). Minimum inhibitory concentration of ethanol, ethyl acetate and chloroform fractions was found in the range of 78 ? g/ml to 2500 ? gl/ml against gram positive and gram negative bacteria. PMID:23455215

  7. Reflections on Conformal Spectra

    E-print Network

    Hyungrok Kim; Petr Kravchuk; Hirosi Ooguri

    2015-10-29

    We use modular invariance and crossing symmetry of conformal field theory to reveal approximate reflection symmetries in the spectral decompositions of the partition function in two dimensions in the limit of large central charge and of the four-point function in any dimension in the limit of large scaling dimensions $\\Delta_0$ of external operators. We use these symmetries to motivate universal upper bounds on the spectrum and the operator product expansion coefficients, which we then derive by independent techniques. Some of the bounds for four-point functions are valid for finite $\\Delta_0$ as well as for large $\\Delta_0$. We discuss a similar symmetry in a large spacetime dimension limit. Finally, we comment on the analogue of the Cardy formula and sparse light spectrum condition for the four-point function.

  8. Capturing Chromosome Conformation

    NASA Astrophysics Data System (ADS)

    Dekker, Job; Rippe, Karsten; Dekker, Martijn; Kleckner, Nancy

    2002-02-01

    We describe an approach to detect the frequency of interaction between any two genomic loci. Generation of a matrix of interaction frequencies between sites on the same or different chromosomes reveals their relative spatial disposition and provides information about the physical properties of the chromatin fiber. This methodology can be applied to the spatial organization of entire genomes in organisms from bacteria to human. Using the yeast Saccharomyces cerevisiae, we could confirm known qualitative features of chromosome organization within the nucleus and dynamic changes in that organization during meiosis. We also analyzed yeast chromosome III at the G1 stage of the cell cycle. We found that chromatin is highly flexible throughout. Furthermore, functionally distinct AT- and GC-rich domains were found to exhibit different conformations, and a population-average 3D model of chromosome III could be determined. Chromosome III emerges as a contorted ring.

  9. Reflections on Conformal Spectra

    E-print Network

    Kim, Hyungrok; Ooguri, Hirosi

    2015-01-01

    We use modular invariance and crossing symmetry of conformal field theory to reveal approximate reflection symmetries in the spectral decompositions of the partition function in two dimensions in the limit of large central charge and of the four-point function in any dimension in the limit of large scaling dimensions $\\Delta_0$ of external operators. We use these symmetries to motivate universal upper bounds on the spectrum and the operator product expansion coefficients, which we then derive by independent techniques. Some of the bounds for four-point functions are valid for finite $\\Delta_0$ as well as for large $\\Delta_0$. We discuss a similar symmetry in a large spacetime dimension limit. Finally, we comment on the analogue of the Cardy formula and sparse light spectrum condition for the four-point function.

  10. Conformally symmetric relativistic star

    E-print Network

    Rahaman, Farook; Sardar, Iftikar Hossain; Chakraborty, Koushik

    2015-01-01

    We investigate whether compact stars having Tolman-like interior geometry admit conformal symmetry. Taking anisotropic pressure along the two principal directions within the compact object, we obtain physically relevant quantities such as transverse and radial pressure, density and redshift function. We study the equation of state for the matter distribution inside the star. From the relation between pressure and density function of the constituent matter, we explore the nature and properties of the interior matter. The red shift function, compactness parameter are found to be physically reasonable. The matter inside the star satisfies the null, weak and strong energy conditions. Finally, we compare the masses and radii predicted from the model with corresponding values in some observed stars.

  11. Conformally symmetric relativistic star

    E-print Network

    Farook Rahaman; Sunil D. Maharaj; Iftikar Hossain Sardar; Koushik Chakraborty

    2015-08-03

    We investigate whether compact stars having Tolman-like interior geometry admit conformal symmetry. Taking anisotropic pressure along the two principal directions within the compact object, we obtain physically relevant quantities such as transverse and radial pressure, density and redshift function. We study the equation of state for the matter distribution inside the star. From the relation between pressure and density function of the constituent matter, we explore the nature and properties of the interior matter. The red shift function, compactness parameter are found to be physically reasonable. The matter inside the star satisfies the null, weak and strong energy conditions. Finally, we compare the masses and radii predicted from the model with corresponding values in some observed stars.

  12. The Principle of Maximum Conformality

    SciTech Connect

    Brodsky, Stanley J; Giustino, Di; /SLAC

    2011-04-05

    A key problem in making precise perturbative QCD predictions is the uncertainty in determining the renormalization scale of the running coupling {alpha}{sub s}({mu}{sup 2}). It is common practice to guess a physical scale {mu} = Q which is of order of a typical momentum transfer Q in the process, and then vary the scale over a range Q/2 and 2Q. This procedure is clearly problematic since the resulting fixed-order pQCD prediction will depend on the renormalization scheme, and it can even predict negative QCD cross sections at next-to-leading-order. Other heuristic methods to set the renormalization scale, such as the 'principle of minimal sensitivity', give unphysical results for jet physics, sum physics into the running coupling not associated with renormalization, and violate the transitivity property of the renormalization group. Such scale-setting methods also give incorrect results when applied to Abelian QED. Note that the factorization scale in QCD is introduced to match nonperturbative and perturbative aspects of the parton distributions in hadrons; it is present even in conformal theory and thus is a completely separate issue from renormalization scale setting. The PMC provides a consistent method for determining the renormalization scale in pQCD. The PMC scale-fixed prediction is independent of the choice of renormalization scheme, a key requirement of renormalization group invariance. The results avoid renormalon resummation and agree with QED scale-setting in the Abelian limit. The PMC global scale can be derived efficiently at NLO from basic properties of the PQCD cross section. The elimination of the renormalization scheme ambiguity using the PMC will not only increases the precision of QCD tests, but it will also increase the sensitivity of colliders to new physics beyond the Standard Model.

  13. Conformal Technicolor: From the Weak Scale

    E-print Network

    Weaver, Harold A. "Hal"

    Conformal Technicolor: From the Weak Scale To the Planck Scale Markus Luty UC Davis with J. Evans: Technicolor: Conformal/Walking Technicolor: Want Requires strong conformal (scale invariant) dynamics! #12;QCD Conformal Window QCD is scale invariant (conformal) for 5 0 50 100 150 200 2 4 6 8 10 12 Tcr[Mev] N f FIG. 3

  14. Classical Virasoro irregular conformal block

    E-print Network

    Chaiho Rim; Hong Zhang

    2015-06-24

    Virasoro irregular conformal block with arbitrary rank is obtained for the classical limit or equivalently Nekrasov-Shatashvili limit using the beta-deformed irregular matrix model (Penner-type matrix model for the irregular conformal block). The same result is derived using the generalized Mathieu equation which is equivalent to the loop equation of the irregular matrix model.

  15. Counselor Identity: Conformity or Distinction?

    ERIC Educational Resources Information Center

    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.

  16. Methods to differentiate protein conformers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Discrimination and quantitation of protein conformers is an unsolved scientific problem. Many proteins are known to exist in two or more conformations (e.g. PrPc and PrPsc in CJD, CWD, BSE, TME, scrapies; sup35 and ure2p in yeast; CPEB in long term memory formation; huntington and A-beta in neurolog...

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

    SciTech Connect

    Chang, Shan-Yan; Liu, Fu-Feng E-mail: ysun@tju.edu.cn; Dong, Xiao-Yan; Sun, Yan E-mail: ysun@tju.edu.cn; Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 300072

    2013-12-14

    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 ?-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.

  18. Recursion Relations for Conformal Blocks

    E-print Network

    João Penedones; Emilio Trevisani; Masahito Yamazaki

    2015-09-01

    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.

  19. 40 CFR 93.154 - Conformity analysis.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...2010-07-01 2010-07-01 false Conformity analysis. 93.154 Section...PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR...IMPLEMENTATION PLANS Determining Conformity of General Federal Actions...

  20. 40 CFR 52.938 - General conformity.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...2010-07-01 2010-07-01 false General conformity. 52.938 Section 52.938 Protection...IMPLEMENTATION PLANS Kentucky § 52.938 General conformity. The General Conformity regulations were submitted on November...

  1. 40 CFR 52.799 - Transportation conformity.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...2014-07-01 false Transportation conformity. 52.799 Section 52.799 ...Indiana § 52.799 Transportation conformity. On June 4, 2010, Indiana submitted the Transportation Conformity Consultation SIP consisting...

  2. 40 CFR 52.2133 - General conformity.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...2011-07-01 2011-07-01 false General conformity. 52.2133 Section 52.2133 Protection...CONTINUED) South Carolina § 52.2133 General conformity. The General Conformity regulations adopted into the South...

  3. 40 CFR 52.799 - Transportation conformity.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...2012-07-01 false Transportation conformity. 52.799 Section 52.799 ...Indiana § 52.799 Transportation conformity. On June 4, 2010, Indiana submitted the Transportation Conformity Consultation SIP consisting...

  4. 40 CFR 52.938 - General conformity.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...2014-07-01 2014-07-01 false General conformity. 52.938 Section 52.938 Protection...IMPLEMENTATION PLANS Kentucky § 52.938 General conformity. The General Conformity regulations were submitted on November...

  5. 40 CFR 52.2133 - General conformity.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...2010-07-01 2010-07-01 false General conformity. 52.2133 Section 52.2133 Protection...CONTINUED) South Carolina § 52.2133 General conformity. The General Conformity regulations adopted into the South...

  6. 40 CFR 52.799 - Transportation conformity.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...2011-07-01 false Transportation conformity. 52.799 Section 52.799 ...Indiana § 52.799 Transportation conformity. On June 4, 2010, Indiana submitted the Transportation Conformity Consultation SIP consisting...

  7. 40 CFR 52.2133 - General conformity.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...2012-07-01 2012-07-01 false General conformity. 52.2133 Section 52.2133 Protection...CONTINUED) South Carolina § 52.2133 General conformity. The General Conformity regulations adopted into the South...

  8. 40 CFR 52.938 - General conformity.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...2012-07-01 2012-07-01 false General conformity. 52.938 Section 52.938 Protection...IMPLEMENTATION PLANS Kentucky § 52.938 General conformity. The General Conformity regulations were submitted on November...

  9. 40 CFR 51.854 - Conformity analysis.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...2010-07-01 2010-07-01 false Conformity analysis. 51.854 Section 51...OF IMPLEMENTATION PLANS Determining Conformity of General Federal Actions to State...Implementation Plans § 51.854 Conformity analysis. Link to an amendment...

  10. 40 CFR 52.799 - Transportation conformity.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...2013-07-01 false Transportation conformity. 52.799 Section 52.799 ...Indiana § 52.799 Transportation conformity. On June 4, 2010, Indiana submitted the Transportation Conformity Consultation SIP consisting...

  11. 40 CFR 52.938 - General conformity.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...2011-07-01 2011-07-01 false General conformity. 52.938 Section 52.938 Protection...IMPLEMENTATION PLANS Kentucky § 52.938 General conformity. The General Conformity regulations were submitted on November...

  12. 40 CFR 52.2133 - General conformity.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...2013-07-01 2013-07-01 false General conformity. 52.2133 Section 52.2133 Protection...CONTINUED) South Carolina § 52.2133 General conformity. The General Conformity regulations adopted into the South...

  13. 40 CFR 52.938 - General conformity.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...2013-07-01 2013-07-01 false General conformity. 52.938 Section 52.938 Protection...IMPLEMENTATION PLANS Kentucky § 52.938 General conformity. The General Conformity regulations were submitted on November...

  14. 40 CFR 52.2133 - General conformity.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...2014-07-01 2014-07-01 false General conformity. 52.2133 Section 52.2133 Protection...CONTINUED) South Carolina § 52.2133 General conformity. The General Conformity regulations adopted into the South...

  15. Conformational activation of visual rhodopsin in native disc membranes.

    PubMed

    Malmerberg, Erik; M Bovee-Geurts, Petra H; Katona, Gergely; Deupi, Xavier; Arnlund, David; Wickstrand, Cecilia; Johansson, Linda C; Westenhoff, Sebastian; Nazarenko, Elena; Schertler, Gebhard F X; Menzel, Andreas; de Grip, Willem J; Neutze, Richard

    2015-03-10

    Rhodopsin is the G protein-coupled receptor (GPCR) that serves as a dim-light receptor for vision in vertebrates. We probed light-induced conformational changes in rhodopsin in its native membrane environment at room temperature using time-resolved wide-angle x-ray scattering. We observed a rapid conformational transition that is consistent with an outward tilt of the cytoplasmic portion of transmembrane helix 6 concomitant with an inward movement of the cytoplasmic portion of transmembrane helix 5. These movements were considerably larger than those reported from the basis of crystal structures of activated rhodopsin, implying that light activation of rhodopsin involves a more extended conformational change than was previously suggested. PMID:25759477

  16. Conformal Magnifier: A Focus+Context Technique with Minimal Distortion

    PubMed Central

    Zhao, Xin; Zeng, Wei; Gu, Xianfeng; Kaufman, Arie; Xu, Wei; Mueller, Klaus

    2010-01-01

    We present the conformal magnifier, a novel interactive Focus+Context visualization technique to magnify a region of interest (ROI) using conformal mapping. Our framework allows the user to design an arbitrary magnifier to enlarge the features of interest while deforming part of the remaining areas without any cropping. By using conformal mapping, the ROI is magnified with minimal distortion, while the transition region is a smooth and continuous deformation between the focus and context regions. An interactive interface is designed for the user to select important features, design focus models of arbitrary shape and set deformation constraints to satisfy his/her specified requirements. We demonstrate the effectiveness, robustness and efficiency of our method using several applications: texts, maps, geographic images, data structures and multi-media visualization. PMID:26279613

  17. Elucidation of Conformational Hysteresis on a Giant DNA

    E-print Network

    Chwen-Yang Shew; Yuji Higuchi; Kenichi Yoshikawa

    2007-05-04

    The conformational behavior of a giant DNA mediated by condensing agents in the bulk solution has been investigated through experimental and theoretical approaches. Experimentally, a pronounced conformational hysteresis is observed for folding and unfolding processes, by increasing and decreasing the concentration of condensing agent PEG (Polyethylene glycol), respectively. To elucidate the observed hysteresis, a semiflexible chain model is studied by using Monte Carlo simulations for the coil-globule transition. In the simulations, the hysteresis loop emerges for stiff enough chains, indicating distinct pathways for folding and unfolding processes. Also, our results show that globular state is thermodynamically more stable than coiled state in the hysteresis loop. Our findings suggest that increasing chain stiffness may reduce the chain conformations relevant to the folding pathway, which impedes the folding process.

  18. Conformal Fermi Coordinates

    NASA Astrophysics Data System (ADS)

    Dai, Liang; Pajer, Enrico; Schmidt, Fabian

    2015-11-01

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

  19. Dynamics of protein conformations

    NASA Astrophysics Data System (ADS)

    Stepanova, Maria

    2010-10-01

    A novel theoretical methodology is introduced to identify dynamic structural domains and analyze local flexibility in proteins. The methodology employs a multiscale approach combining identification of essential collective coordinates based on the covariance analysis of molecular dynamics trajectories, construction of the Mori projection operator with these essential coordinates, and analysis of the corresponding generalized Langevin equations [M.Stepanova, Phys.Rev.E 76(2007)051918]. Because the approach employs a rigorous theory, the outcomes are physically transparent: the dynamic domains are associated with regions of relative rigidity in the protein, whereas off-domain regions are relatively soft. This also allows scoring the flexibility in the macromolecule with atomic-level resolution [N.Blinov, M.Berjanskii, D.S.Wishart, and M.Stepanova, Biochemistry, 48(2009)1488]. The applications include the domain coarse-graining and characterization of conformational stability in protein G and prion proteins. The results are compared with published NMR experiments. Potential applications for structural biology, bioinformatics, and drug design are discussed.

  20. Conformational changes of adsorbed proteins

    NASA Astrophysics Data System (ADS)

    Allen, Scott

    2005-03-01

    The adsorption of bovine serum albumin (BSA) and pepsin to gold surfaces has been studied using surface plasmon resonance (SPR). Proteins are adsorbed from solution onto a gold surface and changes in the conformation of the adsorbed proteins are induced by changing the buffer solution. We selected pH and ionic strength values for the buffer solutions that are known from our circular dichroism measurements to cause conformational changes of the proteins in bulk solution. We find that for both BSA and pepsin the changes in conformation are impeded by the interaction of the protein with the gold surface.

  1. Local conformity induced global oscillation

    NASA Astrophysics Data System (ADS)

    Li, Dong; Li, Wei; Hu, Gang; Zheng, Zhigang

    2009-04-01

    The game ‘rock-paper-scissors’ model, with the consideration of the effect of the psychology of conformity, is investigated. The interaction between each two agents is global, but the strategy of the conformity is local for individuals. In the statistical opinion, the probability of the appearance of each strategy is uniform. The dynamical analysis of this model indicates that the equilibrium state may lose its stability at a threshold and is replaced by a globally oscillating state. The global oscillation is induced by the local conformity, which is originated from the synchronization of individual strategies.

  2. Entanglement constant for conformal families

    NASA Astrophysics Data System (ADS)

    Caputa, Pawe?; Veliz-Osorio, Alvaro

    2015-09-01

    We show that in 1 +1 dimensional conformal field theories, exciting a state with a local operator increases the Rényi entanglement entropies by a constant which is the same for every member of the conformal family. Hence, it is an intrinsic parameter that characterizes local operators from the perspective of quantum entanglement. In rational conformal field theories this constant corresponds to the logarithm of the quantum dimension of the primary operator. We provide several detailed examples for the second Rényi entropies and a general derivation.

  3. Hunting for the Conformal Window

    E-print Network

    A. Deuzeman; M. P. Lombardo; E. Pallante

    2008-10-17

    Undeniably, the imminent activity of LHC and the quest for the nature of physics beyond the standard model have raised renewed interest in the conformal and quasi-conformal behaviour of gauge field theories with matter content. Theoretically driven questions seem to now acquire a strong experimental appeal and might guide us towards a more realistic string theory to field theory connection, originally inspired by the AdS/CFT conjecture. In this brief report, we discuss the state of the art of our search for the conformal window in the SU(3) colour-gauge theory with fermions in the fundamental representation.

  4. 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.

    PubMed

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

    2015-08-20

    The conformers of ?-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. PMID:26201050

  5. Conformational Landscape of Nicotinoids: Solving the "conformational - Rity" of Anabasine

    NASA Astrophysics Data System (ADS)

    Lesarri, Alberto; Cocinero, Emilio J.; Evangelisti, Luca; Suenram, Richard D.; Caminati, Walther; Grabow, Jens-Uwe

    2010-06-01

    The conformational landscape of the alkaloid anabasine (neonicotine) has been investigated using rotational spectroscopy and ab initio calculations. The results allow a detailed comparison of the structural properties of the prototype piperidinic and pyrrolidinic nicotinoids (anabasine vs. nicotine). Anabasine adopts two most stable conformations in isolation conditions, for which we determined accurate rotational and nuclear quadrupole coupling parameters. The preferred conformations are characterized by an equatorial pyridine moiety and additional N-H equatorial stereochemistry at the piperidine ring (Eq-Eq). The two rings of anabasine are close to a bisecting arrangement, with the observed conformations differing in a ca. 180° rotation of the pyridine subunit, denoted either Syn or Anti. The preference of anabasine for the Eq-Eq-Syn conformation has been established by relative intensity measurements (Syn/Anti˜5(2)). The conformational preferences of free anabasine are directed by a N\\cdot\\cdot\\cdotH-C weak hydrogen bond interaction between the nitrogen lone pair at piperidine and the closest hydrogen bond in pyridine, with N\\cdot\\cdot\\cdotN distances ranging from 4.750 Å (Syn) to 4.233 Å (Anti). R. J. Lavrich, R. D. Suenram, D. F. Plusquellic and S. Davis, 58^th OSU Int. Symp. on Mol. Spectrosc., Columbus, OH, 2003, Comm. RH13.

  6. Protein-dependent conformational behavior of DNA in chromatin.

    PubMed

    Riehm, M R; Harrington, R E

    1987-05-19

    Information from circular dichroism (CD) and DNA thermal denaturation has been used in concert to study the conformational behavior of DNA in the extended 11-nm fiber of chromatin isolated from HeLa nuclei. The histone-dependent conformational states of the system were investigated by selectively removing the hydrophilic histone domains with trypsin. These were compared to acetylated chromatin from the same source. The integrated intensity of the positive CD band for DNA above 260 nm is found to increase with the content of relatively unstressed B-form DNA. This same increase is observed along the series of whole, H1-stripped, and trypsinized chromatin samples as protein is removed. Hence, the ratio of percent hyperchromicity to integrated CD band intensity of the respective melting transitions provides useful information on the conformational state of DNA in the three principal regions of the chromatin fiber: the central loop and flanking nucleosomal regions and the linker. Results from this study suggest that central loop DNA in both hyperacetylated and control chromatin relaxes as protein is removed. However, hyperacetylated chromatin shows significantly less dependence than control chromatin upon core histone hydrophilic domains in the flanking and linker regions. Thus, histone hyperacetylation evidently relaxes DNA in chromatin with no major overall conformational changes. A possible role of histone hyperacetylation may therefore be to reduce cooperativity in the unfolding transition in chromatin and thus provide for greater localized control of unfolding during transcription. PMID:3606996

  7. Conformal Lorentz geometry revisited

    NASA Astrophysics Data System (ADS)

    Teleman, Kostake

    1996-02-01

    The group U(2,2) and its subgroup SU(2,2) were considered by Penrose in his study of the conformal compactification M of the Minkowski space M [R. Penrose and W. Rindler, Spinors and Space-Time (Cambridge University, Cambridge, 1986) and R. O. Wells, Jr., Bull. Am. Math. Soc. I, 2 (1979)]. The standard representation of SU(2,2) in C4 and in M are the corner stones of twistor theory, which was created by Penrose to the double purpose of obtaining new solutions of Einstein equations and new insights on gravitational radiation. We think that other representations of SU(2,2) or U(2,2) could also bring some information in relativity [see also, Barut O. Asjim, in Noncompact Lie Groups and some of their Applications, edited by E. A. Tanner and R. Wilson (Kluwer Academic, Dordrecht, 1994), p. 103] and, accordingly, we propose an extension of Penrose twistor program. In this paper we deal with a new U(2,2)-space, which we denote by W. We show first that the SU(2,2)-space M introduced by Penrose is isomorphic to U(2), endowed with an action of SU(2,2) given by non-Abelian homographic transformations. These transformations keep invariant the equation det(u-v)=0, characterizing the pairs (u,v)?U(2)×U(2) such that ``u lies on the light-cone of v.'' By definition, our space W consists of all pairs (u,v)?U(2)×U(2) satisfying the condition det(u-v)?0. The starting point of this article is the observation that W carries an SU(2,2)-invariant pseudo-Riemannian metric L:=Tr[(u-v)-1u? ×(u-v)-1v?], of signature (4,4). (W,L) is in fact an irreducible symmetric space in Cartan's sense, which is isomorphic to the quotient SO(2,4)/S[O(1,1)×O(1,3)]. As an irreducible symmetric space, it is an 8-dimensional Einstein space, whose Ricci tensor is proportional to the metric tensor. We study the geodesic paths of this space giving the general solutions in terms of initial data and studying the constants of motion. In particular we determine the geodesic paths which exhibit two periods. We also show that Mach's principle on inertial motions receives an explanation in our theory by considering the particular geodesic paths, for which one of the partners of an interacting pair is fixed and sent to infinity. In fact we study a dynamical system (W,L) which presents some formal and topological similarities with a system of two particles interacting gravitationally. (W,L) is the only conformally invariant relativistic two-point dynamical system. At the end we show that W can be naturally regarded as the base of a principal GL(2,C)-bundle which comes with a natural connection. We study this bundle from differential geometric point of view. Physical interpretations will be discussed in a future paper. This text is an improvement of a previous version, which was submitted under the title ``Hypertwistor Geometry.'' [See, K. Teleman, ``Hypertwistor Geometry (abstract),'' 14th International Conference on General Relativity and Gravitation, Florence, Italy, 1995.] The change of the title and many other improvements are due to the valuable comments of the referee, who also suggested the author to avoid hazardous interpretations.

  8. CONFORMANCE IMPROVEMENT USING GELS

    SciTech Connect

    Randall S. Seright

    2002-02-28

    This technical progress report describes work performed from June 20 through December 19, 2001, for the project, ''Conformance Improvement Using Gels''. Interest has increased in some new polymeric products that purport to substantially reduce permeability to water while causing minimum permeability reduction to oil. In view of this interest, we are currently studying BJ's Aqua Con. Results from six corefloods revealed that the Aqua Con gelant consistently reduced permeability to water more than that to oil. However, the magnitude of the disproportionate permeability reduction varied significantly for the various experiments. Thus, as with most materials tested to date, the issue of reproducibility and control of the disproportionate permeability remains to be resolved. Concern exists about the ability of gels to resist washout after placement in fractures. We examined whether a width constriction in the middle of a fracture would cause different gel washout behavior upstream versus downstream of the constriction. Tests were performed using a formed Cr(III)-acetate-HPAM gel in a 48-in.-long fracture with three sections of equal length, but with widths of 0.08-, 0.02-, and 0.08-in., respectively. The pressure gradients during gel extrusion (i.e., placement) were similar in the two 0.08-in.-wide fracture sections, even though they were separated by a 0.02-in.-wide fracture section. The constriction associated with the middle fracture section may have inhibited gel washout during the first pulse of brine injection after gel placement. However, during subsequent phases of brine injection, the constriction did not inhibit washout in the upstream fracture section any more than in the downstream section.

  9. Radial Coordinates for Conformal Blocks

    E-print Network

    Matthijs Hogervorst; Slava Rychkov

    2013-03-21

    We develop the theory of conformal blocks in CFT_d expressing them as power series with Gegenbauer polynomial coefficients. Such series have a clear physical meaning when the conformal block is analyzed in radial quantization: individual terms describe contributions of descendants of a given spin. Convergence of these series can be optimized by a judicious choice of the radial quantization origin. We argue that the best choice is to insert the operators symmetrically. We analyze in detail the resulting "rho-series" and show that it converges much more rapidly than for the commonly used variable z. We discuss how these conformal block representations can be used in the conformal bootstrap. In particular, we use them to derive analytically some bootstrap bounds whose existence was previously found numerically.

  10. Conformation Distributions in Adsorbed Proteins.

    NASA Astrophysics Data System (ADS)

    Meuse, Curtis W.; Hubbard, Joseph B.; Vrettos, John S.; Smith, Jackson R.; Cicerone, Marcus T.

    2007-03-01

    While the structural basis of protein function is well understood in the biopharmaceutical and biotechnology industries, few methods for the characterization and comparison of protein conformation distributions are available. New methods capable of measuring the stability of protein conformations and the integrity of protein-protein, protein-ligand and protein-surface interactions both in solution and on surfaces are needed to help the development of protein-based products. We are developing infrared spectroscopy methods for the characterization and comparison of molecular conformation distributions in monolayers and in solutions. We have extracted an order parameter describing the orientational and conformational variations of protein functional groups around the average molecular values from a single polarized spectrum. We will discuss the development of these methods and compare them to amide hydrogen/deuterium exchange methods for albumin in solution and on different polymer surfaces to show that our order parameter is related to protein stability.

  11. Conformally rescaled noncommutative Andrzej Sitarz

    E-print Network

    Sitarz, Andrzej

    of space (or space-time) as a differentiable man- ifold should break down. Still, is not clear whether of conformally rescaled and curved spectral triples, which are obtained from a real spectral triple by a non

  12. Lattice Simulations and Infrared Conformality

    DOE PAGESBeta

    Appelquist, Thomas; Fleming, George T.; Lin, Meifeng; Neil, Ethan T.; Schaich, David A

    2011-09-01

    We examine several recent lattice-simulation data sets, asking whether they are consistent with infrared conformality. We observe, in particular, that for an SU(3) gauge theory with 12 Dirac fermions in the fundamental representation, recent simulation data can be described assuming infrared conformality. Lattice simulations include a fermion mass m which is then extrapolated to zero, and we note that this data can be fit by a small-m expansion, allowing a controlled extrapolation. We also note that the conformal hypothesis does not work well for two theories that are known or expected to be confining and chirally broken, and that itmore »does work well for another theory expected to be infrared conformal.« less

  13. Lattice Simulations and Infrared Conformality

    SciTech Connect

    Appelquist, Thomas; Fleming, George T.; Lin, Meifeng; Neil, Ethan T.; Schaich, David A

    2011-09-01

    We examine several recent lattice-simulation data sets, asking whether they are consistent with infrared conformality. We observe, in particular, that for an SU(3) gauge theory with 12 Dirac fermions in the fundamental representation, recent simulation data can be described assuming infrared conformality. Lattice simulations include a fermion mass m which is then extrapolated to zero, and we note that this data can be fit by a small-m expansion, allowing a controlled extrapolation. We also note that the conformal hypothesis does not work well for two theories that are known or expected to be confining and chirally broken, and that it does work well for another theory expected to be infrared conformal.

  14. Einstein Gravity from Conformal Gravity

    E-print Network

    Juan Maldacena

    2011-06-09

    We show that that four dimensional conformal gravity plus a simple Neumann boundary condition can be used to get the semiclassical (or tree level) wavefunction of the universe of four dimensional asymptotically de-Sitter or Euclidean anti-de Sitter spacetimes. This simple Neumann boundary condition selects the Einstein solution out of the more numerous solutions of conformal gravity. It thus removes the ghosts of conformal gravity from this computation. In the case of a five dimensional pure gravity theory with a positive cosmological constant we show that the late time superhorizon tree level probability measure, $|\\Psi [ g ]|^2$, for its four dimensional spatial slices is given by the action of Euclidean four dimensional conformal gravity.

  15. Allosteric transitions of Torpedo acetylcholine receptor in lipids, detergent and amphipols

    E-print Network

    Allosteric transitions of Torpedo acetylcholine receptor in lipids, detergent and amphipols, in the detergent CHAPS, and after complexation by amphipathic polymers (`amphipols'). Binding kinetics was similar: Nicotinic acetylcholine receptor; Conformational transition; Membrane protein; Detergent; Amphipol 1

  16. From residue coevolution to protein conformational ensembles and functional dynamics

    PubMed Central

    Sutto, Ludovico; Marsili, Simone; Valencia, Alfonso; Gervasio, Francesco Luigi

    2015-01-01

    The analysis of evolutionary amino acid correlations has recently attracted a surge of renewed interest, also due to their successful use in de novo protein native structure prediction. However, many aspects of protein function, such as substrate binding and product release in enzymatic activity, can be fully understood only in terms of an equilibrium ensemble of alternative structures, rather than a single static structure. In this paper we combine coevolutionary data and molecular dynamics simulations to study protein conformational heterogeneity. To that end, we adapt the Boltzmann-learning algorithm to the analysis of homologous protein sequences and develop a coarse-grained protein model specifically tailored to convert the resulting contact predictions to a protein structural ensemble. By means of exhaustive sampling simulations, we analyze the set of conformations that are consistent with the observed residue correlations for a set of representative protein domains, showing that (i) the most representative structure is consistent with the experimental fold and (ii) the various regions of the sequence display different stability, related to multiple biologically relevant conformations and to the cooperativity of the coevolving pairs. Moreover, we show that the proposed protocol is able to reproduce the essential features of a protein folding mechanism as well as to account for regions involved in conformational transitions through the correct sampling of the involved conformers. PMID:26487681

  17. Conformational Entropies and Order Parameters: Convergence, Reproducibility, and Transferability.

    PubMed

    Genheden, Samuel; Akke, Mikael; Ryde, Ulf

    2014-01-14

    Conformational entropy provides major contributions to protein folding and functions, such as ligand binding, making it a potentially important driver of biologically relevant processes. NMR spectroscopy is a unique technique to estimate conformational entropy changes at atomic resolution, an approach that can be favorably augmented by comparisons with results from molecular dynamics (MD) simulations, for example, by generating an order-parameter-to-entropy dictionary. Here, we address critical issues pertaining to such an approach, including reproducibility, convergence, and transferability by analyzing long (380 ns -1 ms) MD trajectories obtained for five different proteins. We observe that order parameters and conformational entropies calculated over 10-100 ns windows are typically well converged among individual MD trajectories and reproducible between pairs of independent trajectories, when calculated on a per-residue level. However, significant discrepancies sometimes arise for the total conformational entropy evaluated as the sum of the residue-specific entropies, especially in cases that involve rare transitions to alternative conformational states. Furthermore, we find that the order-parameter-to-entropy dictionary depends strongly on the protein and the sampling frequency, but much less so on the molecular dynamics force field. Thus, the transferability of the dictionary is poor between proteins but relatively good between different states (e.g., different ligand-bound complexes) of the same protein, provided that a protein-specific dictionary has been derived. PMID:26579922

  18. Extensive Conformational Heterogeneity within Protein Cores

    PubMed Central

    2015-01-01

    Basic principles of statistical mechanics require that proteins sample an ensemble of conformations at any nonzero temperature. However, it is still common to treat the crystallographic structure of a protein as the structure of its native state, largely because high-resolution structural characterization of protein flexibility remains a profound challenge. To assess the typical degree of conformational heterogeneity within folded proteins, we construct Markov state models describing the thermodynamics and kinetics of proteins ranging from 72 to 263 residues in length. Each of these models is built from hundreds of microseconds of atomically detailed molecular dynamics simulations. Examination of the side-chain degrees of freedom reveals that almost every residue visits at least two rotameric states over this time frame, with rotamer transition rates spanning a wide range of time scales (from nanoseconds to tens of microseconds). We also report substantial backbone dynamics on time scales longer than are typically addressed by experimental measures of protein flexibility, such as NMR order parameters. Finally, we demonstrate that these extensive rearrangements are consistent with NMR and crystallographic data, which supports the validity of our models. Altogether, these results depict the interior of proteins not as well-ordered solids, as is often imagined, but instead as dense fluids, which undergo substantial structural fluctuations despite their high packing fraction. PMID:24564338

  19. Chameleonic dilaton and conformal transformations

    E-print Network

    Andrea Zanzi

    2012-06-20

    We recently proposed a chameleonic solution to the cosmological constant problem - Phys. Rev. D82 (2010) 044006. One of the results of that paper is a non-equivalence of different conformal frames at the quantum level. In this letter we further discuss our proposal focusing our attention on the conformal transformation. Moreover, we point out that a different choice of parameters is necessary in the model.

  20. Conformal Properties in High Temperature QCD

    E-print Network

    K. -I. Ishikawa; Y. Iwasaki; Yu Nakayama; T. Yoshie

    2015-11-11

    We investigate the properties of quarks and gluons above the chiral phase transition temperature $T_c,$ using the RG improved gauge action and the Wilson quark action with two degenerate quarks mainly on a $32^3\\times 16$ lattice. In the one-loop perturbation theory, the thermal ensemble is dominated by the gauge configurations with effectively $Z(3)$ center twisted boundary conditions, making the thermal expectation value of the spatial Polyakov loop take a non-trivial $Z(3)$ center. This is in agreement with our lattice simulation of high temperature QCD. We further observe that the temporal propagator of massless quarks at extremely high temperature $\\beta=100.0 \\, (T \\simeq10^{58} T_c)$ remarkably agrees with the temporal propagator of free quarks with the $Z(3)$ twisted boundary condition for $t/L_t \\geq 0.2$, but differs from that with the $Z(3)$ trivial boundary condition. As we increase the mass of quarks $m_q$, we find that the thermal ensemble continues to be dominated by the $Z(3)$ twisted gauge field configurations as long as $m_q \\le 3.0 \\, T$ and above that the $Z(3)$ trivial configurations come in. The transition is essentially identical to what we found in the departure from the conformal region in the zero-temperature many-flavor conformal QCD on a finite lattice by increasing the mass of quarks. We argue that the behavior is consistent with the renormalization group analysis at finite temperature.

  1. Transition Planning

    ERIC Educational Resources Information Center

    Statfeld, Jenna L.

    2011-01-01

    Post-school transition is the movement of a child with disabilities from school to activities that occur after the completion of school. This paper provides information about: (1) post-school transition; (2) transition plan; (3) transition services; (4) transition planning; (5) vocational rehabilitation services; (6) services that are available…

  2. Polyethylene glycol binding alters human telomere G-quadruplex structure by conformational selection

    PubMed Central

    Buscaglia, Robert; Miller, M. Clarke; Dean, William L.; Gray, Robert D.; Lane, Andrew N.; Trent, John O.; Chaires, Jonathan B.

    2013-01-01

    Polyethylene glycols (PEGs) are widely used to perturb the conformations of nucleic acids, including G-quadruplexes. The mechanism by which PEG alters G-quadruplex conformation is poorly understood. We describe here studies designed to determine how PEG and other co-solutes affect the conformation of the human telomeric quadruplex. Osmotic stress studies using acetonitrile and ethylene glycol show that conversion of the ‘hybrid’ conformation to an all-parallel ‘propeller’ conformation is accompanied by the release of about 17 water molecules per quadruplex and is energetically unfavorable in pure aqueous solutions. Sedimentation velocity experiments show that the propeller form is hydrodynamically larger than hybrid forms, ruling out a crowding mechanism for the conversion by PEG. PEGs do not alter water activity sufficiently to perturb quadruplex hydration by osmotic stress. PEG titration experiments are most consistent with a conformational selection mechanism in which PEG binds more strongly to the propeller conformation, and binding is coupled to the conformational transition between forms. Molecular dynamics simulations show that PEG binding to the propeller form is sterically feasible and energetically favorable. We conclude that PEG does not act by crowding and is a poor mimic of the intranuclear environment, keeping open the question of the physiologically relevant quadruplex conformation. PMID:23804761

  3. CONFORMANCE IMPROVEMENT USING GELS

    SciTech Connect

    Randall S. Seright

    2004-09-30

    This report describes work performed during the third and final year of the project, ''Conformance Improvement Using Gels.'' Corefloods revealed throughput dependencies of permeability reduction by polymers and gels that were much more prolonged during oil flow than water flow. This behavior was explained using simple mobility ratio arguments. A model was developed that quantitatively fits the results and predicts ''clean up'' times for oil productivity when production wells are returned to service after application of a polymer or gel treatment. X-ray computed microtomography studies of gels in strongly water-wet Berea sandstone and strongly oil-wet porous polyethylene suggested that oil penetration through gel-filled pores occurs by a gel-dehydration mechanism, rather than gel-ripping or gel-displacement mechanisms. In contrast, analysis of data from the University of Kansas suggests that the gel-ripping or displacement mechanisms are more important in more permeable, strongly water-wet sandpacks. These findings help to explain why aqueous gels can reduce permeability to water more than to oil under different conditions. Since cement is the most commonly used material for water shutoff, we considered when gels are preferred over cements. Our analysis and experimental results indicated that cement cannot be expected to completely fill (top to bottom) a vertical fracture of any width, except near the wellbore. For vertical fractures with apertures less than 4 mm, the cement slurry will simply not penetrate very far into the fracture. For vertical fractures with apertures greater than 4 mm, the slurry may penetrate a substantial distance into the bottom part of the fracture. However, except near the wellbore, the upper part of the fracture will remain open due to gravity segregation. We compared various approaches to plugging fractures using gels, including (1) varying polymer content, (2) varying placement (extrusion) rate, (3) using partially formed gels, (4) using combinations of high and low molecular weight (Mw) polymers, (5) using secondary crosslinking reactions, (6) injecting un-hydrated polymer particles, and (7) incorporating particulates. All of these methods showed promise in some aspects, but required performance improvements in other aspects. All materials investigated to date showed significant performance variations with fracture width. High pressure gradients and limited distance of penetration are common problems in tight fractures. Gravity segregation and low resistance to breaching are common problems in wide fractures. These will be key issues to address in future work. Although gels can exhibit disproportionate permeability reduction in fractures, the levels of permeability reduction for oil flow are too high to allow practical exploitation in most circumstances. In contrast, disproportionate permeability reduction provided by gels that form in porous rock (adjacent to the fractures) has considerable potential in fractured systems.

  4. Combined inhibitor free-energy landscape and structural analysis reports on the mannosidase conformational coordinate.

    PubMed

    Williams, Rohan J; Iglesias-Fernández, Javier; Stepper, Judith; Jackson, Adam; Thompson, Andrew J; Lowe, Elisabeth C; White, Jonathan M; Gilbert, Harry J; Rovira, Carme; Davies, Gideon J; Williams, Spencer J

    2014-01-20

    Mannosidases catalyze the hydrolysis of a diverse range of polysaccharides and glycoconjugates, and the various sequence-based mannosidase families have evolved ingenious strategies to overcome the stereoelectronic challenges of mannoside chemistry. Using a combination of computational chemistry, inhibitor design and synthesis, and X-ray crystallography of inhibitor/enzyme complexes, it is demonstrated that mannoimidazole-type inhibitors are energetically poised to report faithfully on mannosidase transition-state conformation, and provide direct evidence for the conformational itinerary used by diverse mannosidases, including ?-mannanases from families GH26 and GH113. Isofagomine-type inhibitors are poor mimics of transition-state conformation, owing to the high energy barriers that must be crossed to attain mechanistically relevant conformations, however, these sugar-shaped heterocycles allow the acquisition of ternary complexes that span the active site, thus providing valuable insight into active-site residues involved in substrate recognition. PMID:24339341

  5. CONFORMAL GEOMETRY AND FULLY NONLINEAR JEFF VIACLOVSKY

    E-print Network

    Viaclovsky, Jeff

    CONFORMAL GEOMETRY AND FULLY NONLINEAR EQUATIONS JEFF VIACLOVSKY To the memory of Professor S.S. Chern Abstract. This article is a survey of results involving conformal deformation of Riemannian in conformal geometry is the Yamabe Prob- lem, which is to determine whether there exists a conformal metric

  6. Conformal motions in plane symmetric static spacetimes

    E-print Network

    K. Saifullah; Shair-e-Yazdan

    2009-04-22

    In this paper, conformal motions are studied in plane symmetric static spacetimes. The general solution of conformal Killing equations and the general form of the conformal Killing vector for these spacetimes are presented. All possibilities for the existence of conformal motions in these spacetimes are exhausted.

  7. Conformal decomposition in canonical general relativity

    E-print Network

    Charles H. -T. Wang

    2006-03-15

    A new canonical transformation is found that enables the direct canonical treatment of the conformal factor in general relativity. The resulting formulation significantly simplifies the previously presented conformal geometrodynamics. It provides a further theoretical basis for the conformal approach to loop quantum gravity and offers a generic framework for the conformal analysis of spacetime dynamics.

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

    PubMed

    Yu, Rongjun; Sun, Sai

    2013-01-01

    When people have different opinions in a group, they often adjust their own attitudes and behaviors to match the group opinion, known as social conformity. The affiliation account of normative conformity states that people conform to norms in order to 'fit in', whereas the accuracy account of informative conformity posits that the motive to learn from others produces herding. Here, we test another possibility that following the crowd reduces the experienced negative emotion when the group decision turns out to be a bad one. Using event related potential (ERP) combined with a novel group gambling task, we found that participants were more likely to choose the option that was predominately chosen by other players in previous trials, although there was little explicit normative pressure at the decision stage and group choices were not informative. When individuals' choices were different from others, the feedback related negativity (FRN), an ERP component sensitive to losses and errors, was enhanced, suggesting that being independent is aversive. At the outcome stage, the losses minus wins FRN effect was significantly reduced following conformity choices than following independent choices. Analyses of the P300 revealed similar patterns both in the response and outcome period. Our study suggests that social conformity serves as an emotional buffer that protects individuals from experiencing strong negative emotion when the outcomes are bad. PMID:23691242

  9. To Conform or Not to Conform: Spontaneous Conformity Diminishes the Sensitivity to Monetary Outcomes

    PubMed Central

    2013-01-01

    When people have different opinions in a group, they often adjust their own attitudes and behaviors to match the group opinion, known as social conformity. The affiliation account of normative conformity states that people conform to norms in order to ‘fit in’, whereas the accuracy account of informative conformity posits that the motive to learn from others produces herding. Here, we test another possibility that following the crowd reduces the experienced negative emotion when the group decision turns out to be a bad one. Using event related potential (ERP) combined with a novel group gambling task, we found that participants were more likely to choose the option that was predominately chosen by other players in previous trials, although there was little explicit normative pressure at the decision stage and group choices were not informative. When individuals' choices were different from others, the feedback related negativity (FRN), an ERP component sensitive to losses and errors, was enhanced, suggesting that being independent is aversive. At the outcome stage, the losses minus wins FRN effect was significantly reduced following conformity choices than following independent choices. Analyses of the P300 revealed similar patterns both in the response and outcome period. Our study suggests that social conformity serves as an emotional buffer that protects individuals from experiencing strong negative emotion when the outcomes are bad. PMID:23691242

  10. Deconstructing Conformal Blocks in 4D CFT

    E-print Network

    Alejandro Castedo Echeverri; Emtinan Elkhidir; Denis Karateev; Marco Serone

    2015-08-19

    We show how conformal partial waves (or conformal blocks) of spinor/tensor correlators can be related to each other by means of differential operators in four dimensional conformal field theories. We explicitly construct such differential operators for all possible conformal partial waves associated to four-point functions of arbitrary traceless symmetric operators. Our method allows any conformal partial wave to be extracted from a few "seed" correlators, simplifying dramatically the computation needed to bootstrap tensor correlators.

  11. Conformation of viroids.

    PubMed Central

    Henco, K; Riesner, D; Sanger, H L

    1977-01-01

    Viroids are uncoated infectious RNA molecules (MW 107 000-127 000) known as pathogens of certain higher plants. Thermodynamic and kinetic studies were carried out on highly purified viroid preparations by applying UV-absorption melting analysis and temperature jump methods. The thermal denaturation of viroids is characterized by high thermal stability, high cooperativity and a high degree of base pairing. Two relaxation processes could be resolved; a process in the sec range could be evaluated as an independent all-or-none-transition with the following properties: reaction enthalpy= 550 kcal/mol, activation enthalpy of the dissociation = 470 kcal/mol; G : C content = 72 %. These data indicate the existence of an uninterrupted double helix of 52 base pairs. A process in the msec range involves 15 - 25 base pairs which are most probably distributed over several short double helical stretches. A tentative model for the secondary structure of viroids isproposed and the possible functional implications of their physicochemical properties are discussed. PMID:866174

  12. Chair-boat transitions in single polysaccharide molecules observed with force-ramp AFM

    E-print Network

    Fernandez, Julio M.

    Chair-boat transitions in single polysaccharide molecules observed with force-ramp AFM Piotr E of polysaccharide molecules switches from the chair to the boat-like or inverted chair conforma- tion transitions of the glucose monomers from their chair conformation to the boat-like conformation (4). Similarly

  13. CONFORMANCE IMPROVEMENT USING GELS

    SciTech Connect

    Randall S. Seright

    2003-09-01

    This report describes work performed during the second year of the project, ''Conformance Improvement Using Gels.'' The project has two objectives. The first objective is to identify gel compositions and conditions that substantially reduce flow through fractures that allow direct channeling between wells, while leaving secondary fractures open so that high fluid injection and production rates can be maintained. The second objective is to optimize treatments in fractured production wells, where the gel must reduce permeability to water much more than that to oil. Pore-level images from X-ray computed microtomography were re-examined for Berea sandstone and porous polyethylene. This analysis suggests that oil penetration through gel-filled pores occurs by a gel-dehydration mechanism, rather than a gel-ripping mechanism. This finding helps to explain why aqueous gels can reduce permeability to water more than to oil. We analyzed a Cr(III)-acetate-HPAM gel treatment in a production well in the Arbuckle formation. The availability of accurate pressure data before, during, and after the treatment was critical for the analysis. After the gel treatment, water productivity was fairly constant at about 20% of the pre-treatment value. However, oil productivity was stimulated by a factor of 18 immediately after the treatment. During the six months after the treatment, oil productivity gradually decreased to approach the pre-treatment value. To explain this behavior, we proposed that the fracture area open to oil flow was increased substantially by the gel treatment, followed by a gradual closing of the fractures during subsequent production. For a conventional Cr(III)-acetate-HPAM gel, the delay between gelant preparation and injection into a fracture impacts the placement, leakoff, and permeability reduction behavior. Formulations placed as partially formed gels showed relatively low pressure gradients during placement, and yet substantially reduced the flow capacity of fractures (with widths from 1 to 4 mm) during brine and oil flow after placement. Regardless of gel age before placement, very little gel washed out from the fractures during brine or oil flow. However, increased brine or oil flow rate and cyclic injection of oil and water significantly decreased the level of permeability reduction. A particular need exists for gels that can plug large apertures (e.g., wide fractures and vugs). Improved mechanical strength and stability were demonstrated (in 1- to 4-mm-wide fractures) for a gel that contained a combination of high- and low-molecular weight polymers. This gel reduced the flow capacity of 2- and 4-mm-wide fractures by 260,000. In a 1-mm-wide fracture, it withstood 26 psi/ft without allowing any brine flow through the fracture. Cr(III)-acetate-HPAM gels exhibited disproportionate permeability reduction in fractures. The effect was most pronounced when the gel was placed as gelant or partially formed gels. The effect occurred to a modest extent with concentrated gels and with gels that were ''fully formed'' when placed. The effect was not evident in tubes. We explored swelling polymers for plugging fractures. Polymer suspensions were quickly prepared and injected. In concept, the partially dissolved polymer would lodge and swell to plug the fracture. For three types of swelling polymers, behavior was promising. However, additional development is needed before their performance will be superior to that of conventional gels.

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

    PubMed

    Mohammad Hosseini Naveh, Zeynab; Malliavin, Therese E; Maragliano, Luca; Cottone, Grazia; Ciccotti, Giovanni

    2014-01-01

    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. PMID:24551117

  15. Conformal Gauge Transformations in Thermodynamics

    E-print Network

    A. Bravetti; C. S. Lopez-Monsalvo; F. Nettel

    2015-06-23

    In this work we consider conformal gauge transformations of the geometric structure of thermodynamic fluctuation theory. In particular, we show that the Thermodynamic Phase Space is naturally endowed with a non-integrable connection, defined by all those processes that annihilate the Gibbs 1-form, i.e. reversible processes. Therefore the geometry of reversible processes is invariant under re-scalings, that is, it has a conformal gauge freedom. Interestingly, as a consequence of the non-integrability of the connection, its curvature is not invariant under conformal gauge transformations and, therefore, neither is the associated pseudo-Riemannian geometry. We argue that this is not surprising, since these two objects are associated with irreversible processes. Moreover, we provide the explicit form in which all the elements of the geometric structure of the Thermodynamic Phase Space change under a conformal gauge transformation. As an example, we revisit the change of the thermodynamic representation and consider the resulting change between the two metrics on the Thermodynamic Phase Space which induce Weinhold's energy metric and Ruppeiner's entropy metric. As a by-product we obtain a proof of the well-known conformal relation between Weinhold's and Ruppeiner's metrics along the equilibrium directions. Finally, we find interesting properties of the almost para-contact structure and of its eigenvectors which may be of physical interest.

  16. Patterns and conformations in molecularly thin films

    NASA Astrophysics Data System (ADS)

    Basnet, Prem B.

    Molecularly thin films have been a subject of great interest for the last several years because of their large variety of industrial applications ranging from micro-electronics to bio-medicine. Additionally, molecularly thin films can be used as good models for biomembrane and other systems where surfaces are critical. Many different kinds of molecules can make stable films. My research has considered three such molecules: a polymerizable phospholipid, a bent-core molecules, and a polymer. One common theme of these three molecules is chirality. The phospolipid molecules studied here are strongly chiral, which can be due to intrinsically chiral centers on the molecules and also due to chiral conformations. We find that these molecules give rise to chiral patterns. Bent-core molecules are not intrinsically chiral, but individual molecules and groups of molecules can show chiral structures, which can be changed by surface interactions. One major, unconfirmed hypothesis for the polymer conformation at surface is that it forms helices, which would be chiral. Most experiments were carried out at the air/water interface, in what are called Langmuir films. Our major tools for studying these films are Brewster Angle Microscopy (BAM) coupled with the thermodynamic information that can be deduced from surface pressure isotherms. Phospholipids are one of the important constituents of liposomes -- a spherical vesicle com-posed of a bilayer membrane, typically composed of a phospholipid and cholesterol bilayer. The application of liposomes in drug delivery is well-known. Crumpling of vesicles of polymerizable phospholipids has been observed. With BAM, on Langmuir films of such phospholipids, we see novel spiral/target patterns during compression. We have found that both the patterns and the critical pressure at which they formed depend on temperature (below the transition to a i¬‘uid layer). Bent-core liquid crystals, sometimes knows as banana liquid crystals, have drawn increasing attention because of the richness in phases that they exhibit. Due to the unique coupling between dipole properties and the packing constraints placed by the bent shape, these molecules are emerging as strong candidates in electromechanical devices. However, most applications require that the molecules be aligned, which has proved difficult. Our group has tested such molecules both as Langmuir layers and, when transferred to a solid, as alignment layers with some limited success. However, these molecules do not behave well with the surfaces and the domains at the air/water interface tend to form ill-controlled multilayer structures since attraction with the surfaces is relatively weak. New bent-core molecules obtained from Prof. Dr. C. Tsehiemke from Department of Chemistry Institute of Organic Chemistry, Martin-Luther-University, Germany, have a hydrophilic group at one end. We expect this molecule to behave better on the surface because of the stronger attraction of the hydrophilic group towards the surface than for the bent-core molecules without the hydrophilic group. Polydimethylsiloxane (PDMS) is a polymer which finds many applications in modifying surface properties. It is used in manufacturing lubricants, protective coatings, hair conditioner and glass-coating. However its properties are not well understood. This polymer has been proposed to follow either helical or caterpillar conformations on a surface. The orientational order of CH3 side groups can test for these conformations (they would be predominantly up/down for the caterpillar conformation, but rotating through the entire 360 degree for the helical one). Thus previous work on the Langmuir polymer films at the air/water interface were complemented by deuterium NMR studies to probe their conformations at a surface. These experiments were performed using humid porous solids, in order to provide sufficient surface area for the technique. Previous tests in this group at room temperature were suggestive but inconclusive because of the rapid averaging motion of the molecules. Here, we attempt t

  17. Double resonance spectroscopy of different conformers of the neurotransmitter amphetamine and its clusters with water

    NASA Astrophysics Data System (ADS)

    Brause, R.; Fricke, H.; Gerhards, M.; Weinkauf, R.; Kleinermanns, K.

    2006-08-01

    In this paper the conformational landscape of amphetamine in the neutral ground state is examined by both spectroscopy and theory. Several spectroscopic methods are used: laser-induced fluorescence (LIF), resonance-enhanced two-photon ionization (R2PI), dispersed fluorescence and IR/R2PI hole burning spectroscopy. The latter two methods provide for the first time vibrationally resolved spectra of the neutral ground state of dl-amphetamine and the amphetamine-(H 2O) 1,2 complexes. Nine stable conformers of the monomer were found by DFT (B3LYP/6-311++G(d,p)) and ab initio (MP2/6-311++G(d,p)) calculations. For conformer analysis the vibrations observed in the IR/R2PI hole burning and dispersed fluorescence spectra obtained from single vibronic levels (SVLF) of a selected conformer were compared with the results of an ab initio normal mode analysis. By this procedure three S 0 ? S 1 transitions in the R2PI spectrum were assigned to three different conformer structures. Another weak transition earlier attributed to another conformer could be assigned to a vibronic band of one of the three conformers. Furthermore spectra of amphetamine-(H 2O) 1,2 are tentatively assigned.

  18. Geometry-Based Sampling of Conformational Transitions in Proteins

    E-print Network

    de Groot, Bert

    , are the biologically relevant ones. The method rests on a reliable es- timate of the stability of interactions observed-protein dock- ing (Bonvin, 2006; Mustard and Ritchie, 2005; Ehrlich et al., 2005) and structure-based drug

  19. Equilibrium transitions between side chain conformations in leucine and isoleucine

    E-print Network

    Regan, Lynne

    of proteins, protein-protein interactions, protein folding April 30, 2015 Research Article Proteins: Structure John Wiley & Sons, Inc. PROTEINS: Structure, Function, and Bioinformatics This article is protected; 5 Department of Molecular Biophysics & Biochemistry, Yale University; 6 Department of Chemistry

  20. Conformational Transitions in Silver Nanoparticals: DNA and Photoirradiation

    E-print Network

    Bregadze, Vasil G; Giorgadze, Tamar G

    2012-01-01

    Photoirradiation of silver nanoparticles in water solution of NaNO3 (0.01M) and in dissolved DNA was investigated by spectrophotometric and thermodynamic kinetic approaches. It is shown that only the irradiated complexes AgNPs-DNA have distinctly expressed isosbestic point. The test with the free AgNPs demonstrates that as a result of photo-irradiation desorption of silver atoms and their oxidation takes place. We have also observed that at photo-irradiation of the complexes by AgNPs-DNA desorption of silver atoms from the surface of AgNPs takes place. Kinetic study of photo-desorption of silver atoms has allowed to estimate desorption rate constant and the heat of adsorption for free AgNPs and AgNPs bound with DNA. On DNA example toxicity of AgNPs at their application to photo-chemo and photo-thermo therapy of cancer is discussed.

  1. Universality class in conformal inflation

    SciTech Connect

    Kallosh, Renata; Linde, Andrei E-mail: alinde@stanford.edu

    2013-07-01

    We develop a new class of chaotic inflation models with spontaneously broken conformal invariance. Observational consequences of a broad class of such models are stable with respect to strong deformations of the scalar potential. This universality is a critical phenomenon near the point of enhanced symmetry, SO(1,1), in case of conformal inflation. It appears because of the exponential stretching of the moduli space and the resulting exponential flattening of scalar potentials upon switching from the Jordan frame to the Einstein frame in this class of models. This result resembles stretching and flattening of inhomogeneities during inflationary expansion. It has a simple interpretation in terms of velocity versus rapidity near the Kähler cone in the moduli space, similar to the light cone of special theory of relativity. This effect makes inflation possible even in the models with very steep potentials. We describe conformal and superconformal versions of this cosmological attractor mechanism.

  2. Conformally Invariant Equations for Graviton

    E-print Network

    Mohsen Fathi

    2012-11-12

    Recent astrophysical data indicate that our universe might currently be in a de Sitter (dS) phase. The importance of dS space has been primarily ignited by the study of the inflationary model of the universe and the quantum gravity. As we know Einstein's theory of gravitation (with a nonzero cosmological constant) can be interpreted as a theory of a metric field; that is, a symmetric tensor field of rank-2 on a fixed de Sitter background. It has been shown that the massless spin-2 Fierz-Pauli wave equation (or the linearized Einstein equation) is not conformally invariant. This result is in contrary with what we used to expect for massless theories. In this thesis we obtain conformally invariant wave equation for the massless spin-2 in the dS space. This study is motivated by the belief that conformal invariance may be the key to a future theory of quantum gravity.

  3. Conformal Mapping for Multiple Terminals

    E-print Network

    Wang, Weimin; Wang, Qiang; Ren, Hao

    2015-01-01

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

  4. Lectures on Conformal Field Theory

    E-print Network

    Qualls, Joshua D

    2015-01-01

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

  5. Lectures on Conformal Field Theory

    E-print Network

    Joshua D. Qualls

    2015-11-12

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

  6. Quantum cosmology and conformal invariance.

    PubMed

    Pioline, B; Waldron, A

    2003-01-24

    According to Belinsky, Khalatnikov, and Lifshitz, gravity near a spacelike singularity reduces to a set of decoupled one-dimensional mechanical models at each point in space. We point out that these models fall into a class of conformal mechanical models first introduced by de Alfaro, Fubini, and Furlan (DFF). The deformation used by DFF to render the spectrum discrete corresponds to a negative cosmological constant. The wave function of the Universe is the zero-energy eigenmode of the Hamiltonian, or the spherical vector of the representation of the conformal group SO(1,2). A new class of conformal quantum mechanical models with enhanced ADE symmetry is constructed, based on the quantization of nilpotent coadjoint orbits. PMID:12570480

  7. Stochastic Ensembles, Conformationally Adaptive Teamwork and Enzymatic Detoxification

    PubMed Central

    Atkins, William M.; Qian, Hong

    2011-01-01

    It has been appreciated for a long time that enzymes exist as conformational ensembles throughout multiple stages of the reactions they catalyze, but there is renewed interest in the functional implications. The energy landscape that results from conformationlly diverse poteins is a complex surface with an energetic topography in multiple dimensions, even at the transition state(s) leading to product formation, and this represents a new paradigm. Nearly simultaneous with the renewed interest in conformational ensembles, a new paradigm concerning enzyme function has grown, wherein catalytic promiscuity has clear biological advantages in some cases. ‘Useful’, or biologically functional, promiscuity or the related behavior of ‘multifunctionality’, can be found in the immune system, enzymatic detoxification, signal transduction, and in the evolution of new function from an existing pool of folded protein scaffolds. Experimental evidence supports the widely held assumption that conformational heterogeneity promotes functional promiscuity. The common link between these co-evolving paradigms is the inherent structural plasticity and conformational dynamics of proteins that, on one hand, leads to complex but evolutionarily selected energy landscapes, and on the other hand promotes functional promiscuity. Here we consider a logical extension of the overlap between these two nascent paradigms: functionally promiscuous and multifunctional enzymes such as detoxification enzymes are expected to have an ensemble landscape with a greater number of states accessible on multiple time scales than substrate specific enzymes. Two attributes of detoxification enzymes become important in the context of conformational ensembles: these enzymes metabolize multiple substrates, often in substrate mixtures, and they can form multiple products from a single substrate. These properties, combined with complex conformational landscapes, lead to the possibility of interesting time-dependent, or emergent, properties. Here we demonstrate these properties with kinetic simulations of non-equilibrium steady state (NESS) behavior resulting from energy landscapes expected for detoxification enzymes. Analogous scenarios with other promiscuous enzymes may be worthy of consideration. PMID:21473615

  8. On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase

    PubMed Central

    Brokaw, Jason B.; Chu, Jhih-Wei

    2010-01-01

    We characterized the conformational change of adenylate kinase (AK) between open and closed forms by conducting five all-atom molecular-dynamics simulations, each of 100 ns duration. Different initial structures and substrate binding configurations were used to probe the pathways of AK conformational change in explicit solvent, and no bias potential was applied. A complete closed-to-open and a partial open-to-closed transition were observed, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available x-ray structures and earlier works of coarse-grained modeling. The trajectories of the all-atom molecular-dynamics simulations revealed the complexity of protein dynamics and the coupling between different domains during conformational change. Calculations of solvent density and density fluctuations surrounding AK did not show prominent variation during the transition between closed and open forms. Finally, we characterized the effects of local unfolding of an important hinge near Pro177 on the closed-to-open transition of AK and identified a novel mechanism by which hinge unfolding modulates protein conformational change. The local unfolding of Pro177 hinge induces alternative tertiary contacts that stabilize the closed structure and prevent the opening transition. PMID:21081091

  9. On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase

    SciTech Connect

    Brokaw, Jason B.; Chu, Jhih-wei

    2010-11-17

    We characterized the conformational change of adenylate kinase (AK) between open and closed forms by conducting five all-atom molecular-dynamics simulations, each of 100 ns duration. Different initial structures and substrate binding configurations were used to probe the pathways of AK conformational change in explicit solvent, and no bias potential was applied. A complete closed-to-open and a partial open-to-closed transition were observed, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available x-ray structures and earlier works of coarse-grained modeling. The trajectories of the all-atom molecular-dynamics simulations revealed the complexity of protein dynamics and the coupling between different domains during conformational change. Calculations of solvent density and density fluctuations surrounding AK did not show prominent variation during the transition between closed and open forms. Finally, we characterized the effects of local unfolding of an important hinge near Pro177 on the closed-to-open transition of AK and identified a novel mechanism by which hinge unfolding modulates protein conformational change. The local unfolding of Pro177 hinge induces alternative tertiary contacts that stabilize the closed structure and prevent the opening transition.

  10. The conformational analysis of 2-halocyclooctanones

    NASA Astrophysics Data System (ADS)

    Rozada, Thiago C.; Gauze, Gisele F.; Rosa, Fernanda A.; Favaro, Denize C.; Rittner, Roberto; Pontes, Rodrigo M.; Basso, Ernani A.

    2015-02-01

    The establishment of the most stable structures of eight membered rings is a challenging task to the field of conformational analysis. In this work, a series of 2-halocyclooctanones were synthesized (including fluorine, chlorine, bromine and iodine derivatives) and submitted to conformational studies using a combination of theoretical calculation and infrared spectroscopy. For each compound, four conformations were identified as the most important ones. These conformations are derived from the chair-boat conformation of cyclooctanone. The pseudo-equatorial (with respect to the halogen) conformer is preferred in vacuum and in low polarity solvents for chlorine, bromine and iodine derivatives. For 2-fluorocyclooctanone, the preferred conformation in vacuum is pseudo-axial. In acetonitrile, the pseudo-axial conformer becomes the most stable for the chlorine derivative. According to NBO calculations, the conformational preference is not dictated by electron delocalization, but by classical electrostatic repulsions.

  11. Conformal blocks and equivariant cohomology

    E-print Network

    R. Rimányi; V. Schechtman; A. Varchenko

    2011-02-19

    We show that the conformal blocks constructed in the previous article by the first and the third author may be described as certain integrals in equivariant cohomology. When the bundles of conformal blocks have rank one, this construction may be compared with the old integral formulas of the second and the third author. The proportionality coefficients are some Selberg type integrals which are computed. Finally, a geometric construction of the tensor products of vector representations of the Lie algebra $\\frak{gl}(m)$ is proposed.

  12. SUSY Unparticle and Conformal Sequestering

    SciTech Connect

    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.

  13. Epigenetic Dominance of Prion Conformers

    PubMed Central

    Saijo, Eri; Kang, Hae-Eun; Bian, Jifeng; Bowling, Kristi G.; Browning, Shawn; Kim, Sehun; Hunter, Nora; Telling, Glenn C.

    2013-01-01

    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 the otherwise unfavorable U conformer. This epigenetic mechanism thus expands the range of selectable conformations that can be adopted by PrP, and therefore the variety of options for strain propagation. PMID:24204258

  14. The Conformal Universe II: Conformal Symmetry, its Spontaneous Breakdown and Higgs Fields in Conformally Flat Spacetime

    E-print Network

    Renato Nobili

    2014-12-22

    This is the second of three papers on Conformal General Relativity (CGR). The conformal group is here introduced as the invariance group of the partial ordering of causal events in nD spacetime. Its general structure and field-theoretical representations are described with particular emphasis on the remarkable properties of orthochronous inversions. Discrete symmetries and field representations in flat 4D spacetime are described in details. The spontaneous breakdown of conformal symmetry is then discussed and the roles played in this regard by the dilation field and one or more physical scalar fields are evidenced. Hyperbolic and conformal-hyperbolic coordinates are introduced in 4D de Sitter spacetime for the purpose of providing different but equivalent mathematical representations of CGR. These are respectively the Riemann and the Cartan representations. The first of these is manifestly conformal invariant and the second is not, but, in compensation, preserves the formal structure of standard General Relativity (GR) with local quantities multiplied by suitable dilation field powers. The equivalence of these representations in regard to scale relativity is also discussed. In the end, in view of the detailed study of Higgs-field dynamics carried out in the third paper, the action integrals, the motion equations and the total energy-momentum tensors of the Higgs field interacting with the dilation field are described in the two above-mentioned representations.

  15. CONFORMAL TILINGS II: LOCAL ISOMORPHISM, HIERARCHY, AND CONFORMAL TYPE

    E-print Network

    over the last decade and a half. In the first paper of the series [4], the authors laid out a general of [4] are reviewed, repackaged, and expanded in the first section of this paper, so that this paper STEPHENSON Abstract. This is the second in a series of papers on conformal tilings. The overriding themes

  16. 1,3-Propanediol millimeter wave spectrum: Conformers I and II

    NASA Astrophysics Data System (ADS)

    Smirnov, I. A.; Alekseev, E. A.; Piddyachiy, V. I.; Ilyushin, V. V.; Motiyenko, R. A.

    2013-11-01

    We present a new study of the millimeter wave spectrum of the lowest two conformers of the 1,3-propanediol (CH2OHCH2CH2OH) molecule. The new measurements involving rotational transitions with J up to 65 and Ka up to 30 for conformer I and J up to 59 and Ka up to 29 for conformer II have been carried out between 49 and 237 GHz using the Kharkov millimeter wave spectrometer. The new data were combined with previously published measurements and fitted using a model that assumes a symmetric potential energy surface with two minima between which the system tunnels. The final fit included 19 parameters for conformer I and 23 parameters for conformer II with weighted root-mean-square deviations of 0.81 and 0.73 achieved for datasets consisting of 3384 and 2947 line frequencies belonging to the ground states of conformer I and conformer II, respectively. The millimeter wave spectra of both conformers reveal a rather strong influence of the Coriolis type perturbation, which previously was not taken into account in the analysis of the 1,3-propanediol spectrum.

  17. Impact of mutations on the allosteric conformational equilibrium

    PubMed Central

    Weinkam, Patrick; Chen, Yao Chi; Pons, Jaume; Sali, Andrej

    2012-01-01

    Allostery in a protein involves effector binding at an allosteric site that changes the structure and/or dynamics at a distant, functional site. In addition to the chemical equilibrium of ligand binding, allostery involves a conformational equilibrium between one protein substate that binds the effector and a second substate that less strongly binds the effector. We run molecular dynamics simulations using simple, smooth energy landscapes to sample specific ligand-induced conformational transitions, as defined by the effector-bound and unbound protein structures. These simulations can be performed using our web server: http://salilab.org/allosmod/. We then develop a set of features to analyze the simulations and capture the relevant thermodynamic properties of the allosteric conformational equilibrium. These features are based on molecular mechanics energy functions, stereochemical effects, and structural/dynamic coupling between sites. Using a machine-learning algorithm on a dataset of 10 proteins and 179 mutations, we predict both the magnitude and sign of the allosteric conformational equilibrium shift by the mutation; the impact of a large identifiable fraction of the mutations can be predicted with an average unsigned error of 1 kBT. With similar accuracy, we predict the mutation effects for an 11th protein that was omitted from the initial training and testing of the machine-learning algorithm. We also assess which calculated thermodynamic properties contribute most to the accuracy of the prediction. PMID:23228330

  18. Electron-conformational model of ryanodine receptor lattice dynamics.

    PubMed

    Moskvin, A S; Philipiev, M P; Solovyova, O E; Kohl, P; Markhasin, V S

    2006-01-01

    We propose a simple, physically reasonable electron-conformational model for the ryanodine receptor (RyR) and, on that basis, present a theory to describe RyR lattice responses to L-type channel triggering as an induced non-equilibrium phase transition. Each RyR is modelled with a single open and a single closed (electronic) state only, described utilizing a s=12 pseudospin approach. In addition to the fast electronic degree of freedom, the RyR channel is characterized by a slow classical conformational coordinate, Q, which specifies the RyR channel calcium conductance and provides a multimodal continuum of possible RyR states. The cooperativity in the RyR lattice is assumed to be determined by inter-channel conformational coupling. Given a threshold sarcoplasmic reticulum (SR) calcium load, the RyR lattice fires due to a nucleation process with a step-by-step domino-like opening of a fraction of lattice channels, providing for a sufficient release to generate calcium sparks. The optimal mode of RyR lattice functioning during calcium-induced calcium release implies a fractional release with a robust termination due to a decrease in SR calcium load, accompanied by a respective change in effective conformational strain of the lattice. SR calcium overload is shown to result in excitation of RyR lattice auto-oscillations with spontaneous RyR channel opening and closure. PMID:16061275

  19. Electrochemical evidence on the molten globule conformation of cytochrome c.

    PubMed

    Pineda, T; Sevilla, J M; Román, A J; Blázquez, M

    1997-12-01

    To explore a new approach for characterizing the molten globule conformation, cyclic voltammetric studies of salt induced transitions at acidic pH of cyt c have been carried out. The use of modified electrodes has made the observation of direct electrochemistry in native cyt c possible. However, most of these electrodes do not show reversible responses at acidic pH, due to the fact that, for this system, a deprotonated electrode surface is needed. In these studies, we have used a 6-mercaptopurine and cysteine-modified gold electrodes which are effective for direct rapid electron transfer to cyt c, even in acid solutions. The change in the absorption bands of cyt c are used to monitor the conformational states and, hence, to compare the voltammetric results. Under the experimental conditions where the A state of cyt c is obtained, a reversible voltammetric signal is observed. The midpoint peak potentials are found to be very close to the formal potential of native cyt c. Results are discussed in terms of a cooperative two-state transition between the acid unfolded and the globular acidic states of cyt c. This finding establishes, for the first time, the similarity of both the native and the molten globule-like conformations in terms of its redox properties. PMID:9434113

  20. Boundary and Interface CFTs from the Conformal Bootstrap

    E-print Network

    F. Gliozzi; P. Liendo; M. Meineri; A. Rago

    2015-05-12

    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-epsilon dimensions the renormalization group interface between the O(N) model and the free theory and check numerically the results in 3d.

  1. Conformational Changes in Two Inter-Helical Loops of Mhp1 Membrane Transporter

    PubMed Central

    Song, Hyun Deok; Zhu, Fangqiang

    2015-01-01

    Mhp1 is a bacterial secondary transporter with high-resolution crystal structures available for both the outward- and inward-facing conformations. Through molecular dynamics simulations of the ligand-free Mhp1 as well as analysis of its crystal structures, here we show that two inter-helical loops, respectively located at the extra- and intracellular ends of the “hash motif” in the protein, play important roles in the conformational transition. In the outward- and inward-facing states of the protein, the loops adopt different secondary structures, either wrapped to the end of an alpha-helix, or unwrapped to extended conformations. In equilibrium simulations of 100 ns with Mhp1 in explicit lipids and water, the loop conformations remain largely stable. In targeted molecular dynamics simulations with the protein structure driven from one state to the other, the loops exhibit resistance and only undergo abrupt changes when other parts of the protein already approach the target conformation. Free energy calculations on the isolated loops further confirm that the wrapping/unwrapping transitions are associated with substantial energetic barriers, and consist of multiple sequential steps involving the rotation of certain backbone torsion angles. Furthermore, in simulations with the loops driven from one state to the other, a large part of the protein follows the loops to the target conformation. Taken together, our simulations suggest that changes of the loop secondary structures would be among the slow degrees of freedom in the conformational transition of the entire protein. Incorporation of detailed loop structures into the reaction coordinate, therefore, should improve the convergence and relevance of the resulting conformational free energy. PMID:26186341

  2. Direct measurement of the energy thresholds to conformational isomerization in Tryptamine: Experiment and theory

    NASA Astrophysics Data System (ADS)

    Clarkson, Jasper R.; Dian, Brian C.; Moriggi, Loïck; DeFusco, Albert; McCarthy, Valerie; Jordan, Kenneth D.; Zwier, Timothy S.

    2005-06-01

    The methods of stimulated emission pumping-hole filling spectroscopy (SEP-HFS) and stimulated emission pumping population transfer spectroscopy (SEP-PTS) were applied to the conformation-specific study of conformational isomerization in tryptamine [TRA, 3-(2-aminoethyl)indole]. These experimental methods employ stimulated emission pumping to selectively excite a fraction of the population of a single conformation of TRA to well-defined ground-state vibrational levels. This produces single conformations with well-defined internal energy, tunable over a range of energies from near the zero-point level to well above the lowest barriers to conformational isomerization. When the SEP step overcomes a barrier to isomerization, a fraction of the excited population isomerizes to form that product. By carrying out SEP excitation early in a supersonic expansion, these product molecules are subsequently cooled to their zero-point vibrational levels, where they can be detected downstream with a third tunable laser that probes the ground-state population of a particular product conformer via a unique ultraviolet transition using laser-induced fluorescence. The population transfer spectra (recorded by tuning the SEP dump laser while holding the pump and probe lasers fixed) exhibit sharp onsets that directly determine the energy thresholds for conformational isomerization in a given reactant-product conformer pair. In the absence of tunneling effects, the first observed transition in a given X -Y PTS constitutes an upper bound to the energy barrier to conformational isomerization, while the last transition not observed constitutes a lower bound. The bounds for isomerizing conformer A of tryptamine to B(688-748cm-1), C(1)(860-1000cm-1), C(2)(1219-1316cm-1), D(1219-1282cm-1), E(1219-1316cm-1), and F(688-748cm-1) are determined. In addition, thresholds for isomerizing from B to A(<1562cm-1), B to F(562-688cm-1), and out of C(2) to B(<747cm-1) are also determined. The A ?B and B ?A transitions are used to place bounds on the relative energies of minima B relative to A, with B lying at least 126cm-1 above A. The corresponding barriers have been computed using both density functional and second-order many-body perturbation theory methods in order to establish the level of theory needed to reproduce experimental results. While most of the computed barriers match experiment well, the barriers for the A-F and B-F transitions are too high by almost a factor of 2. Possible reasons for this discrepancy are discussed.

  3. Quasilocal rotating conformal Killing horizons

    NASA Astrophysics Data System (ADS)

    Chatterjee, Ayan; Ghosh, Avirup

    2015-08-01

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

  4. Correct Representation of Conformational Equilibria.

    ERIC Educational Resources Information Center

    Fulop, F.; And Others

    1983-01-01

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

  5. Critical point and conformal anomaly

    E-print Network

    G. A. Kozlov

    2015-03-17

    We study the critical point (CP) phenomenon through the increase of fluctuations related to characteristic critical mode. CP would also be identified through the production of primary photons induced by conformal anomaly of strong and electromagnetic interactions. The novel approach to an approximate scale symmetry breaking is developed for this.

  6. Psychological Androgyny and Social Conformity.

    ERIC Educational Resources Information Center

    Brehony, Kathleen; And Others

    The decisions and attitudes of sex-stereotyped and androgynous individuals (as defined by the Bem Sex Role Inventory) were compared in a social conformity paradigm. On each of 160 trials subjects predicted one of two possible stimuli after hearing predictions of two other "subjects." No effects of physical sex were observed. On trials when the…

  7. Random Curves by Conformal Welding

    E-print Network

    Astala, K; Kupiainen, A; Saksman, E

    2009-01-01

    We construct a conformally invariant random family of closed curves in the plane by welding of random homeomorphisms of the unit circle given in terms of the exponential of Gaussian Free Field. We conjecture that our curves are locally related to SLE$(\\kappa)$ for $\\kappa<4$.

  8. Random Curves by Conformal Welding

    E-print Network

    K. Astala; P. Jones; A. Kupiainen; E. Saksman

    2009-12-17

    We construct a conformally invariant random family of closed curves in the plane by welding of random homeomorphisms of the unit circle given in terms of the exponential of Gaussian Free Field. We conjecture that our curves are locally related to SLE$(\\kappa)$ for $\\kappa<4$.

  9. Parsimony in Protein Conformational Change.

    PubMed

    Chapman, Brynmor K; Davulcu, Omar; Skalicky, Jack J; Brüschweiler, Rafael P; Chapman, Michael S

    2015-07-01

    Protein conformational change is analyzed by finding the minimalist backbone torsion angle rotations that superpose crystal structures within experimental error. Of several approaches for enforcing parsimony during flexible least-squares superposition, an ?(1)-norm restraint provided greatest consistency with independent indications of flexibility from nuclear magnetic resonance relaxation dispersion and chemical shift perturbation in arginine kinase and four previously studied systems. Crystallographic cross-validation shows that the dihedral parameterization describes conformational change more accurately than rigid-group approaches. The rotations that superpose the principal elements of structure constitute a small fraction of the raw (?, ?) differences that also reflect local conformation and experimental error. Substantial long-range displacements can be mediated by modest dihedral rotations, accommodated even within ? helices and ? sheets without disruption of hydrogen bonding at the hinges. Consistency between ligand-associated and intrinsic motions (in the unliganded state) implies that induced changes tend to follow low-barrier paths between conformational sub-states that are in intrinsic dynamic equilibrium. PMID:26095029

  10. Temperature: Human Regulating, Ants Conforming

    ERIC Educational Resources Information Center

    Clopton, Joe R.

    2007-01-01

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

  11. Phase transition in the Sznajd model with independence

    E-print Network

    Sznajd-Weron, K; Timpanaro, A M

    2011-01-01

    We propose a model of opinion dynamics which describes two major types of social influence -- conformity and independence. Conformity in our model is described by the so called outflow dynamics (known as Sznajd model). According to sociologists' suggestions, we introduce also a second type of social influence, known in social psychology as independence. Various social experiments have shown that the level of conformity depends on the society. We introduce this level as a parameter of the model and show that there is a continuous phase transition between conformity and independence.

  12. Phase transition in the Sznajd model with independence

    NASA Astrophysics Data System (ADS)

    Sznajd-Weron, K.; Tabiszewski, M.; Timpanaro, A. M.

    2011-11-01

    We propose a model of opinion dynamics which describes two major types of social influence —conformity and independence. Conformity in our model is described by the so-called outflow dynamics (known as Sznajd model). According to sociologists' suggestions, we introduce also a second type of social influence, known in social psychology as independence. Various social experiments have shown that the level of conformity depends on the society. We introduce this level as a parameter of the model and show that there is a continuous phase transition between conformity and independence.

  13. Myosin and tropomyosin stabilize the conformation of formin-nucleated actin filaments.

    PubMed

    Ujfalusi, Zoltán; Kovács, Mihály; Nagy, Nikolett T; Barkó, Szilvia; Hild, Gábor; Lukács, András; Nyitrai, Miklós; Bugyi, Beáta

    2012-09-14

    The conformational elasticity of the actin cytoskeleton is essential for its versatile biological functions. Increasing evidence supports that the interplay between the structural and functional properties of actin filaments is finely regulated by actin-binding proteins; however, the underlying mechanisms and biological consequences are not completely understood. Previous studies showed that the binding of formins to the barbed end induces conformational transitions in actin filaments by making them more flexible through long range allosteric interactions. These conformational changes are accompanied by altered functional properties of the filaments. To get insight into the conformational regulation of formin-nucleated actin structures, in the present work we investigated in detail how binding partners of formin-generated actin structures, myosin and tropomyosin, affect the conformation of the formin-nucleated actin filaments using fluorescence spectroscopic approaches. Time-dependent fluorescence anisotropy and temperature-dependent Förster-type resonance energy transfer measurements revealed that heavy meromyosin, similarly to tropomyosin, restores the formin-induced effects and stabilizes the conformation of actin filaments. The stabilizing effect of heavy meromyosin is cooperative. The kinetic analysis revealed that despite the qualitatively similar effects of heavy meromyosin and tropomyosin on the conformational dynamics of actin filaments the mechanisms of the conformational transition are different for the two proteins. Heavy meromyosin stabilizes the formin-nucleated actin filaments in an apparently single step reaction upon binding, whereas the stabilization by tropomyosin occurs after complex formation. These observations support the idea that actin-binding proteins are key elements of the molecular mechanisms that regulate the conformational and functional diversity of actin filaments in living cells. PMID:22753415

  14. Myosin and Tropomyosin Stabilize the Conformation of Formin-nucleated Actin Filaments*

    PubMed Central

    Ujfalusi, Zoltán; Kovács, Mihály; Nagy, Nikolett T.; Barkó, Szilvia; Hild, Gábor; Lukács, András; Nyitrai, Miklós; Bugyi, Beáta

    2012-01-01

    The conformational elasticity of the actin cytoskeleton is essential for its versatile biological functions. Increasing evidence supports that the interplay between the structural and functional properties of actin filaments is finely regulated by actin-binding proteins; however, the underlying mechanisms and biological consequences are not completely understood. Previous studies showed that the binding of formins to the barbed end induces conformational transitions in actin filaments by making them more flexible through long range allosteric interactions. These conformational changes are accompanied by altered functional properties of the filaments. To get insight into the conformational regulation of formin-nucleated actin structures, in the present work we investigated in detail how binding partners of formin-generated actin structures, myosin and tropomyosin, affect the conformation of the formin-nucleated actin filaments using fluorescence spectroscopic approaches. Time-dependent fluorescence anisotropy and temperature-dependent Förster-type resonance energy transfer measurements revealed that heavy meromyosin, similarly to tropomyosin, restores the formin-induced effects and stabilizes the conformation of actin filaments. The stabilizing effect of heavy meromyosin is cooperative. The kinetic analysis revealed that despite the qualitatively similar effects of heavy meromyosin and tropomyosin on the conformational dynamics of actin filaments the mechanisms of the conformational transition are different for the two proteins. Heavy meromyosin stabilizes the formin-nucleated actin filaments in an apparently single step reaction upon binding, whereas the stabilization by tropomyosin occurs after complex formation. These observations support the idea that actin-binding proteins are key elements of the molecular mechanisms that regulate the conformational and functional diversity of actin filaments in living cells. PMID:22753415

  15. 47 CFR 68.324 - Supplier's Declaration of Conformity requirements.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... false Supplier's Declaration of Conformity requirements. 68.324...68.324 Supplier's Declaration of Conformity requirements. (a...include in the Supplier's Declaration of Conformity, the following...

  16. Conformal Triality of the Kepler problem

    E-print Network

    Marco Cariglia

    2015-10-02

    We show that the Kepler problem is projectively equivalent to null geodesic motion on the conformal compactification of Minkowski-4 space. This space realises the conformal triality of Minkwoski, dS and AdS spaces.

  17. Gauge natural formulation of conformal gravity

    NASA Astrophysics Data System (ADS)

    Campigotto, M.; Fatibene, L.

    2015-03-01

    We consider conformal gravity as a gauge natural theory. We study its conservation laws and superpotentials. We also consider the Mannheim and Kazanas spherically symmetric vacuum solution and discuss conserved quantities associated to conformal and diffeomorphism symmetries.

  18. Gravity Duals for Nonrelativistic Conformal Field Theories

    E-print Network

    McGreevy, John

    We attempt to generalize the anti–de Sitter/conformal field theory correspondence to nonrelativistic conformal field theories which are invariant under Galilean transformations. Such systems govern ultracold atoms at ...

  19. Measuring chromosome conformation with degenerate labels

    E-print Network

    Ross, Brian Christopher

    Although DNA conformation plays an integral role in all genetic processes from transcription to chromosome segregation, there is as yet no tractable method for capturing the in vivo conformation of a chromosome at high ...

  20. Conformal Killing forms on Riemannian manifolds Habilitationsschrift

    E-print Network

    Semmelmann, Uwe

    Conformal Killing forms on Riemannian manifolds Habilitationsschrift zur Feststellung der Lehrbef Conformal Killing Forms 9 1.1 Definition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 1.2 Killing tensors and first integrals . . . . . . . . . . . . . . . . . . . . . . . . 14 2

  1. Systematic conformational search with constraint satisfaction

    E-print Network

    Tucker-Kellogg, Lisa, 1969-

    2002-01-01

    Determining the conformations of biological molecules is a high scientific priority for biochemists and for the pharmaceutical industry. This thesis describes a systematic method for conformational search, an application ...

  2. Conformational Variety of Polyanionic Peptides At Low Salt Concentrations

    NASA Astrophysics Data System (ADS)

    Bertrand, Marylène; Brack, André

    1997-12-01

    Cordially dedicated to Dr. Leslie Orgel on the occasion of his 70th birthday. Sequential oligo- and polypeptides based on glutamic acid and leucine residues have been synthesized. In pure water, they exhibit a random coil conformation. Addition of very small amounts of divalent metallic cations induces the formation of ordered structure in the peptides which remain in solution. Higher salt concentrations precipitate the peptides. Polypeptides with alternating glutamic acid and leucine residues undergo a coil to ?-sheet transition in the presence of Ca^2+, Ba^2+, Mn^2+, Co^2+, Zn^2+ and Hg^2+. Addition of Cu^2+ or Fe^3+ induces the formation of an ?-helix. Solid amorphous CdS generates water soluble ?-sheets, as well. Sequential poly(Leu-Glu-Glu-Leu) adopts an ?-helix in the presence of divalent cations. The sequence-dependent conformational diversity was extended to poly(Asp-Leu) and poly(Leu-Asp-Asp-Leu).

  3. Conformal holonomy of bi-invariant metrics

    NASA Astrophysics Data System (ADS)

    Leitner, Felipe

    We discuss in this paper the conformal geometry of bi-invariant metrics on compact semisimple Lie groups. For this purpose, we develop an invariant Cartan calculus. Our main goal is to derive an iterative formula for the holonomy algebra of the normal conformal Cartan connection of a bi-invariant metric. As an example, we demonstrate the application of our invariant calculus to the computation of the conformal holonomy of SO(4) . Its conformal holonomy algebra is so(7) .

  4. China's urban transition.

    PubMed

    Pannell, C

    1995-01-01

    This article describes recent changes in urban patterns in Shanghai-Nanjing, Beijing-Tianjin-Tangshan, Canton-Hong Kong, and Dalian-Shenyang. The urban patterns in these metropolitan areas are viewed as part of an urban transition that is responding to population growth, a structural shift in employment, relaxed rules on migration and household registration, and foreign investment and trade. It is argued that these metropolitan coastal areas will form the key growth centers and will lead China's economic development. Urban transition is defined as the shift from rural to urban and from agricultural employment to industrial, commercial, or service employment. China's large cities always dominated as important centers of politics and trade. The recent shift is from interior to coastal cities due to a new world view and a movement away from the isolationism of prior centuries. It is assumed that cities are formed to take advantage of economies of scale in production, consumption, and distribution and to conform to regional specialization. Governments can intervene in growth processes. China's development of cities reflects state controls and market forces. The size and scale of China's population influenced the development process, which resulted in differences in the shape and process of the urban transition. It was under Chinese communism that cities became more than a set of discrete regional urban systems. Reference is made to Oshima's model of change that is specific to monsoon countries. Oshima argues that monsoon agricultural conditions require a distinct strategy based on full employment in order to achieve industrial transition. Rice cultivation requires a large and disciplined labor force. The discussion focuses on other models as well, such as the McGee's model of the extended metropolis and its extension by Zhou Yixing to China. China's changes may not follow Skeldon's models of urbanization in developing countries, because of state control of migration. However, the longer migrants remain in cities the more likely Skeldon's models of early European transitions apply to China's urban transition. PMID:12178548

  5. Conformal Blocks in the Large D Limit

    E-print Network

    A. Liam Fitzpatrick; Jared Kaplan; David Poland

    2013-04-30

    We derive conformal blocks in an inverse spacetime dimension expansion. In this large D limit, the blocks are naturally written in terms of a new combination of conformal cross-ratios. We comment on the implications for the conformal bootstrap at large D.

  6. Conformance for DecSerFlow Constraints

    E-print Network

    California at Santa Barbara, University of

    Conformance for DecSerFlow Constraints Yutian (James) Sun University of California, Santa Barbara Jianwen Su #12;DecSerFlow and Conformance ·(Dental) scaling and root planning process October 29, 2014 Conformance for DecSerFlow Constraints a.k.a., DECLARE [van der Aalst-Pesic, 2006] Open account Appointment

  7. CONFORMAL TILINGS I: FOUNDATIONS, THEORY, AND PRACTICE

    E-print Network

    CONFORMAL TILINGS I: FOUNDATIONS, THEORY, AND PRACTICE PHILIP L. BOWERS AND KENNETH STEPHENSON Abstract. This paper opens a new chapter in the study of planar tilings by introducing conformal tilings as concrete patterns of geometric shapes, the tiles. In the conformal case, however, these geometric tiles

  8. Simplicity of quadratic Lie conformal algebras

    E-print Network

    Yanyong Hong; Zhixiang Wu

    2015-07-07

    In this paper, simplicity of quadratic Lie conformal algebras are investigated. From the point view of the corresponding Gel'fand-Dorfman bialgebras, some sufficient conditions and necessary conditions to ensure simplicity of quadratic Lie conformal algebras are presented. By these observations, we present several classes of new infinite simple Lie conformal algebras. These results will be useful for classification purposes.

  9. 40 CFR 52.799 - Transportation conformity.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 3 2014-07-01 2014-07-01 false Transportation conformity. 52.799... (CONTINUED) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS Indiana § 52.799 Transportation conformity. On June 4, 2010, Indiana submitted the Transportation Conformity Consultation SIP consisting...

  10. 40 CFR 52.799 - Transportation conformity.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 3 2013-07-01 2013-07-01 false Transportation conformity. 52.799... (CONTINUED) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS Indiana § 52.799 Transportation conformity. On June 4, 2010, Indiana submitted the Transportation Conformity Consultation SIP consisting...

  11. 40 CFR 52.799 - Transportation conformity.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 3 2011-07-01 2011-07-01 false Transportation conformity. 52.799... (CONTINUED) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS Indiana § 52.799 Transportation conformity. On June 4, 2010, Indiana submitted the Transportation Conformity Consultation SIP consisting...

  12. 40 CFR 52.799 - Transportation conformity.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 3 2012-07-01 2012-07-01 false Transportation conformity. 52.799... (CONTINUED) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS Indiana § 52.799 Transportation conformity. On June 4, 2010, Indiana submitted the Transportation Conformity Consultation SIP consisting...

  13. An extension theorem for conformal gauge singularities

    SciTech Connect

    Luebbe, Christian; Tod, Paul

    2009-11-15

    We analyze conformal gauge, or isotropic, singularities in cosmological models in general relativity. Using the calculus of tractors, we find conditions in terms of tractor curvature for a local extension of the conformal structure through a cosmological singularity and prove a local extension theorem along a congruence of timelike conformal geodesics.

  14. Conformational Proofreading: The Impact of Conformational Changes on the Specificity of Molecular

    E-print Network

    Tlusty, Tsvi

    Conformational Proofreading: The Impact of Conformational Changes on the Specificity of Molecular the induced-fit mechanism, are known to involve conformational changes. This raises a basic question: Does molecular recognition gain any advantage by such conformational changes? By introducing a simple statistical

  15. Ionization Spectroscopy of Conformational Isomers of Propanal: The Origin of the Conformational Preference

    E-print Network

    Kim, Sang Kyu

    Ionization Spectroscopy of Conformational Isomers of Propanal: The Origin of the Conformational conformational isomers of propanal, cis and gauche, are investigated by the vacuum-UV mass- analyzed thresholdV and 9.9516 ( 0.0006 eV, respectively. cis-Propanal, which is the more stable conformer in the neutral

  16. Conformational Properties of Helical Protein Polymers with Varying Densities of Chemically Reactive Groups

    PubMed Central

    Farmer, Robin S.; Argust, Lindsey M.; Sharp, Jared D.; Kiick, Kristi L.

    2008-01-01

    Protein engineering strategies have proven valuable for the production of a variety of well-defined macromolecular materials with controlled properties that have enabled their use in a range of materials and biological applications. In this work, such biosynthetic strategies have been employed in the production of monodisperse alanine-rich, helical protein polymers with the sequences [AAAQEAAAAQAAAQAEAAQAAQ]3 and [AAAQAAQAQAAAEAAAQAAQAQ]6. The composition of these protein polymers is similar to that of a previously reported family of alanine-rich protein polymers, but the density and placement of chemically reactive residues has been varied to facilitate the future use of these macromolecules in elucidating polymeric structure-function relationships in biological recognition events. Both protein polymers are readily expressed from E. coli and purified to homogeneity; characterization of their conformational behavior via circular dichroic spectroscopy (CD) indicates that they adopt highly helical conformations under a range of solution conditions. Differential scanning calorimetry, in concert with CD, demonstrates that the conformational transition from helix to coil in these macromolecules can be well-defined, with helicity, conformational transitions, Tm values, and calorimetric enthalpies that vary with the molecular weight of the protein polymers. A combination of infrared spectroscopy and CD also reveals that the macromolecules can adopt ?-sheet structures at elevated temperatures and concentrations and that the existence and kinetics of this conformational transition appear to be related to the density of charged groups on the protein polymer. PMID:19180254

  17. Nontargeted Parallel Cascade Selection Molecular Dynamics for Enhancing the Conformational Sampling of Proteins.

    PubMed

    Harada, Ryuhei; Kitao, Akio

    2015-11-10

    Nontargeted parallel cascade selection molecular dynamics (nt-PaCS-MD) is proposed as an efficient conformational sampling method to enhance the conformational transitions of proteins, which is an extension of the original targeted PaCS-MD (t-PaCS-MD). The original PaCS-MD comprises cycles of (i) selection of initial structures for multiple independent MD simulations toward a predetermined target and (ii) conformational sampling by the independent MDs. In nt-PaCS-MD, structures that significantly deviate from an average are regarded as candidates that have high potential to address other metastable states and are chosen as the initial structures in the selection. To select significantly deviated structures, we examine the root-mean-square deviation (RMSD) of snapshots generated from the average structure based on Gram-Schmidt orthogonalization. nt-PaCS-MD was applied to the folding of the mini-protein chignolin in implicit solvent and to the open-closed conformational transitions of T4 lysozyme (T4L) and glutamine binding protein (QBP) in explicit solvent. We show that nt-PaCS-MD can reach chignolin's native state and can also cause the open-closed transition of T4L and QBP on a nanosecond time scale, which are very efficient in terms of conformational sampling and comparable to that with t-PaCS-MD. PMID:26574337

  18. Conformal Window and Correlation Functions in Lattice Conformal QCD

    E-print Network

    Y. Iwasaki

    2013-07-23

    We discuss various aspects of Conformal Field Theories on the Lattice. We mainly investigate the SU(3) gauge theory with N_f degenerate fermions in the fundamental representation, employing the one-plaquette gauge action and the Wilson fermion action. First we make a brief review of our previous works and thereby clarify the reason why we conjecture that the conformal window is 7 le N_f le 16. Secondly, we introduce a new concept, "conformal theories with an IR cutoff" and point out that any numerical simulation on a lattice is bounded by an IR cutoff Lambda_{IR}. Then we make predictions that when N_f is within the conformal window, the propagator of a meson G(t) behaves at large t, as G(t) = c exp(-m_H t)/t^alpha, that is, a modified Yukawa-type decay form, instead of the usual exponential decay form in the small quark mass region. This holds on an any lattice for any coupling constant g, as far as g is between 0 and g^*, where g^* is the IR fixed point. We verify that numerical results really satisfy the predictions for the N_f=7 case and the N_f=16 case. Thirdly, we discuss small number of flavors (N_f=2 sim 6) QCD at finite temperatures. We point out theoretically and verify numerically that the correlation functions at T/T_c > 1 exhibit the characteristics of the conformal function with IR cutoff, an exponential decay with power correction. Further, we observe our data are consistent with the picture that the N_f=7 case and the N_f=2 at T sim 2 T_c case are close to the meson unparticle model, and we estimate gamma^* = 1.2(1). On the other hand, the N_f=16 case and the N_f=2 at T= 10^2 sim 10^5 Tc cases are close to a free state in the Z(3) twisted vacuum. The results give clues for long standing issues such as slow approach of the free energy to the Stefan-Boltzmann ideal gas limit.

  19. Conformation and intramolecular relaxation dynamics of semiflexible randomly hyperbranched polymers

    NASA Astrophysics Data System (ADS)

    Kumar, Amit; Rai, Gobind Ji; Biswas, Parbati

    2013-03-01

    The conformational and dynamic properties of semiflexible randomly hyperbranched polymers are investigated in dilute solutions within the framework of optimized Rouse-Zimm formalism. Semiflexibility is incorporated by restricting the directions and orientations of the respective bond vectors, while hydrodynamic interactions are modeled through the preaveraged Oseen tensor. The effect of semiflexibility is typically reflected in the intermediate frequency regime of the viscoelastic relaxation moduli where the bond orientation angle restores the characteristic power-law scaling in fractal structures, as in randomly hyperbranched polymers. Despite the absence of this power-law scaling regime in flexible randomly hyperbranched polymers and in earlier models of semiflexible randomly branched polymers due to weak disorder [C. von Ferber and A. Blumen, J. Chem. Phys. 116, 8616 (2002)], 10.1063/1.1470198, this power-law behavior may be reinstated by explicitly modeling hyperbranched polymers as a Vicsek fractals. The length of this power-law zone in the intermediate frequency region is a combined function of the number of monomers and the degree of semiflexibility. A clear conformational transition from compact to open structures is facilitated by changing the bond orientation angle, where the compressed conformations are compact, while the expanded ones are relatively non-compact. The extent of compactness in the compressed conformations are much less compared to the semiflexible dendrimers, which resemble hard spheres. The fractal dimensions of the compressed and expanded conformations calculated from the Porod's scaling law vary as a function of the bond orientation angle, spanning the entire range of three distinct scaling regimes of linear polymers in three-dimensions. The results confirm that semiflexibility exactly accounts for the excluded volume interactions which are expected to be significant for such polymers with complex topologies.

  20. Conformal theories including conformal gravity as gauge theories on the hypercone

    E-print Network

    Par Arvidsson; Robert Marnelius

    2006-12-07

    Conformal theories in a d dimensional spacetime may be expressed as manifestly conformal theories in a d+2 dimensional conformal space as first proposed by Dirac. The reduction to d dimensions goes via the d+1 dimensional hypercone in the conformal space. Here we give a rather extensive expose of such theories. We review and extend the theory of spinning conformal particles. We give a precise and geometrical formulation of manifestly conformal fields for which we give a consistent action principle. The requirement of invariance under special gauge transformations off the hypercone plays a fundamental role here. Maxwell's theory and linear conformal gravity are derived in the conformal space and are treated in detail. Finally, we propose a consistent coordinate invariant action principle in the conformal space and give an action that should correspond to conformal gravity.

  1. Boundary terms of conformal anomaly

    NASA Astrophysics Data System (ADS)

    Solodukhin, Sergey N.

    2016-01-01

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

  2. Conformal theory of galactic halos

    NASA Astrophysics Data System (ADS)

    Nesbet, Robert K.

    2011-11-01

    In current cosmology, an observed galaxy is considered to be surrounded by a large spherical halo attributed to dark matter. Galaxy formation by condensation of mass-energy necessarily depletes the original uniform cosmic background. This must leave a scar, in the form of a gravitational field halo, as observed in anomalous galactic rotation and in gravitational lensing. Without invoking dark matter, conformal theory accounts for the otherwise counterintuitive centripetal effect.

  3. Theories conformes parafermioniques et combinatoire

    NASA Astrophysics Data System (ADS)

    Jacob, Patrick

    Along the lines of this thesis, we were trying to achieve two main goals: firstly to obtain a deeper understanding of parafermionic conformal theories in general and secondly to unravel some of the links existing between combinatorics and conformal field theory. By developing an original approach to freely generated bases and to singular vectors structures, we obtained the bosonic character formulas for the Zk parafermionic models and the graded parafermionic models. Through this analysis, using different technics proper to associativity calculus, we revealed a new classification of parafermionic theories linked to a number of WZW cosets. For each of these cosets featuring an underlying parafermionic description, we now have a different access to the construction of the bosonic character formulas and to the calculation of correlation functions. In conformal field theory, the quasi-particle bases are combinatorial object at the root of the fermionic description of the character formulas. These objects are difficult to identify. We showed how the quasi-particle bases followed naturally from simple and neat principles, for the Zk parafermionic models, the graded parafermionic models and the SM (2, 4k) supersymmetric models. For the last two sequences, a new combinatorial object, the set of jagged partitions, forms the bulk of the quasi-particle bases. From this point, we constructed a sequence of combinatorial identities between infinite sums and infinite products. This work could be the starting point for many generalizations leading to an infinite number of new identities of this kind, or even Rogers-Ramanujan type identities.

  4. The Conformational Landscape of Serinol

    NASA Astrophysics Data System (ADS)

    Sanz, M. Eugenia; Loru, Donatella; Peña, Isabel; Alonso, José L.

    2014-06-01

    The rotational spectrum of the amino alcohol serinol CH_2OH--CH(NH_2)--CH_2OH, which constitutes the hydrophilic head of the lipid sphingosine, has been investigated using chirped-pulsed Fourier transform microwave spectroscopy in combination with laser ablation Five different forms of serinol have been observed and conclusively identified by the comparison between the experimental values of their rotational and 14N quadrupole coupling constants and those predicted by ab initio calculations. In all observed conformers several hydrogen bonds are established between the two hydroxyl groups and the amino groups in a chain or circular arrangement. The most abundant conformer is stabilised by O--H···N and N--H···O hydrogen bonds forming a chain rather than a cycle. One of the detected conformers presents a tunnelling motion of the hydrogen atoms of the functional groups similar to that observed in glycerol. S. Mata, I. Peña, C. Cabezas, J. C. López, J. L. Alonso, J. Mol. Spectrosc. 2012, 280, 91 V. V. Ilyushin, R. A. Motiyenko, F. J. Lovas, D. F. Plusquellic, J. Mol. Spectrosc. 2008, 251, 129.

  5. Rényi entropy and conformal defects

    E-print Network

    Lorenzo Bianchi; Marco Meineri; Robert C. Myers; Michael Smolkin

    2015-11-20

    We propose a field theoretic framework for calculating the dependence of R\\'enyi 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 conjecture a simple relation between the coefficient defining the two-point function of the displacement operator and the conformal weight of the twist operator. With this approach, we are able to consolidate a number of apparently distinct conjectures found in the literature about the R\\'enyi entropy. In particular, 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 R\\'enyi entropy arising from small deformations of a spherical entangling surface, extending Mezei's results for the entanglement entropy.

  6. Conformation and chirality in liquid crystals

    NASA Astrophysics Data System (ADS)

    West, John L.; Zhao, Lei

    2013-09-01

    High helical twisting powerchiral additives are required for an expanding variety of liquid crystal displays and devices. Molecular conformation plays a critical role in determining the helical twisting power, HTP, of chiral additives. We studied additives based on an isosorbide benzoate ester core. Molecular modeling revealed two low energy states with very different conformations for this core The ultra-violet absorption and NMR spectra show two stable isosorbide conformers These spectra reveal how the relative populations of these two conformations change with temperature and how this is related to the helical twisting power. Conformation changes can explain many of the observed anomalous responses of HPT to temperature.

  7. Exchanging conformations of a hydroformylation catalyst structurally characterized using two-dimensional vibrational spectroscopy.

    PubMed

    Panman, Matthijs R; Vos, Jannie; Bocoki?, Vladica; Bellini, Rosalba; de Bruin, Bas; Reek, Joost H N; Woutersen, Sander

    2013-12-16

    Catalytic transition-metal complexes often occur in several conformations that exchange rapidly (conformations of the hydroformylation catalyst (xantphos)Rh(CO)2H using two-dimensional vibrational spectroscopy, a method that can be applied to any catalyst provided that the exchange between its conformers occurs on a time scale of a few picoseconds or slower. We find that, in one of the conformations, the OC-Rh-CO angle deviates significantly from the canonical value in a trigonal-bipyramidal structure. On the basis of complementary density functional calculations, we ascribe this effect to attractive van der Waals interaction between the CO and the xantphos ligand. PMID:24256078

  8. Conformational Substates of Myoglobin Intermediate Resolved by Picosecond X-ray Solution Scattering.

    PubMed

    Oang, Key Young; Kim, Jong Goo; Yang, Cheolhee; Kim, Tae Wu; Kim, Youngmin; Kim, Kyung Hwan; Kim, Jeongho; Ihee, Hyotcherl

    2014-03-01

    Conformational substates of proteins are generally considered to play important roles in regulating protein functions, but an understanding of how they influence the structural dynamics and functions of the proteins has been elusive. Here, we investigate the structural dynamics of sperm whale myoglobin associated with the conformational substates using picosecond X-ray solution scattering. By applying kinetic analysis considering all of the plausible candidate models, we establish a kinetic model for the entire cycle of the protein transition in a wide time range from 100 ps to 10 ms. Four structurally distinct intermediates are formed during the cycle, and most importantly, the transition from the first intermediate to the second one (B ? C) occurs biphasically. We attribute the biphasic kinetics to the involvement of two conformational substates of the first intermediate, which are generated by the interplay between the distal histidine and the photodissociated CO. PMID:24761190

  9. Conformally equivariant quantization for spinning particles

    E-print Network

    Jean-Philippe Michel

    2015-01-06

    This work takes place over a conformally flat spin manifold (M,g). We prove existence and uniqueness of the conformally equivariant quantization valued in spinor differential operators, and provide an explicit formula for it when restricted to first order operators. The Poisson algebra of symbols is realized as a space of functions on the supercotangent bundle, endowed with a symplectic form depending on the metric g. It admits two different actions of the conformal Lie algebra, one tensorial and one Hamiltonian. They are intertwined by the uniquely defined conformally equivariant superization, for which an explicit formula is given. This map allows us to classify all the conformal supercharges of the spinning particle in terms of conformal Killing tensors with mixed symmetry, generated by the totally symmetric and skew-symmetric ones. Higher symmetries of the Dirac operator are obtained by quantization of the conformal supercharges.

  10. STUDY OF LIQUID CRYSTAL CONFORMATION BY MULTIPLE QUANTUM NMR: n-PENTYL CYANOBIPHENYL

    SciTech Connect

    Sinton, S.; Pines, A.

    1980-09-01

    The multiple quantum NMR spectrum of 4-cyano-4'-n-pentyl-d{sub 11}-biphenyl in the nematic phase is presented. The sub-spectra of the higher quantum transitions are easier to interpret than the single quantum spectrum. A preliminary analysis of the biphenyl conformation indicates that the dihedral angle is 32° ± 1°.

  11. Entanglement in Quantum Spin Chains, Symmetry Classes of Random Matrices, and Conformal Field Theory

    E-print Network

    Mezzadri, Francesco

    Entanglement in Quantum Spin Chains, Symmetry Classes of Random Matrices, and Conformal Field and exponential decay away from it. Entanglement plays a fundamental role in the quantum phase transitions. We compute the entropy of entanglement between the first N spins and the rest of the system

  12. Identifying and correcting non-Markov states in peptide conformational Dmitry Nerukh,a

    E-print Network

    Nerukh, Dmitry

    Identifying and correcting non-Markov states in peptide conformational dynamics Dmitry Nerukh their biological activity and can be investigated in detail using the Markov state model. The fundamental assumption on the transitions between the states, their Markov property, is critical in this framework. We

  13. Gramicidin conformational studies with mixed-chain unsaturated phospholipid bilayer systems

    SciTech Connect

    Cox, K.J.; Ho, Cojen; Lombardi, J.V.; Stubbs, C.D. )

    1992-02-04

    The transition of gramicidin from a nonchannel to a channel form was investigated using mixed-chain phosphatidylcholine lipid bilayers. Gramicidin and phospholipids were codispersed, after removal of the solvents chloroform/methanol or trifluoroethanol which resulted in nonchannel and channel conformations, respectively, as confirmed using circular dichroism (CD). The fluorescence emission maxima of the nonchannel form were shifted toward shorter wavelengths by heating at 60C (for 0-12 h), which converted it to a channel form, again as confirmed by CD. The channel form did not respond to heat treatment. Heat treatment also increased the fluorescence anisotropy of the nonchannel gramicidin tryptophans. The rate of transition from the nonchannel to channel conformation was found to be faster is phosphatidylethanolamine was present in combination with phosphatidylcholine compared to phosphatidylcholine alone. Using the fluorescence anisotropy of the membrane lipid probe, 1,6-diphenyl-1,3,5-hexatriene, it was also shown that the motional properties of the surrounding lipid acyl chains differed for the channel and nonchannel gramicidin conformations. The possibility that lipids tending to favor the hexagonal phase (H{sub II}) would enhance the rate of the nonchannel to channel transition was supported by {sup 31}P NMR which revealed the presence of some H{sub II} lipids in the channel preparations. The results of this study suggest that gramicidin may serve as a useful model for similar conformational transitions in other more complex membrane proteins.

  14. Parity Doubling and the S Parameter Below the Conformal Window

    SciTech Connect

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

    2011-10-21

    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{sub 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{sub f} is increased from 2 to 6, motivating study of these trends as N{sub f} is increased further, toward the critical value for transition from confinement to infrared conformality.

  15. The catalytic transition state in ATP synthase.

    PubMed

    Senior, A E; Weber, J; Nadanaciva, S

    2000-10-01

    The catalytic transition state of ATP synthase has been characterized and modeled by combined use of (1) Mg-ADP-fluoroaluminate, Mg-ADP-fluoroscandium, and corresponding Mg-IDP-fluorometals as transition-state analogs; (2) fluorescence signals of beta-Trp331 and beta-Trp148 as optical probes to assess formation of the transition state; (3) mutations of critical catalytic residues to determine side-chain ligands required to stabilize the transition state. Rate acceleration by positive catalytic site cooperativity is explained as due to mobility of alpha-Arg376, acting as an "arginine finger" residue, which interacts with nucleotide specifically at the transition state step of catalysis, not with Mg-ATP- or Mg-ADP-bound ground states. We speculate that formation and collapse of the transition state may engender catalytic site alpha/beta subunit-interface conformational movement, which is linked to gamma-subunit rotation. PMID:15254388

  16. Conformance Testing: Measurement Decision Rules

    NASA Technical Reports Server (NTRS)

    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 decisions rules.

  17. En route Descent Advisor Concept for Efficient Arrival Metering Conformance

    NASA Technical Reports Server (NTRS)

    Green, Steven; Vivona, Robert; Coppenbarger, Richard

    2001-01-01

    The En-route Descent Advisor (EDA) is a suite of decision support tool (DST) capabilities for en route sector subject to metering restrictions such as those generated by the Center TRACON Automation System (CTAS) Traffic Management Advisor. EDA assists controllers with high-density arrival metering by providing fuel-efficient metering-conformance advisories, integrated with conflict detection and resolution (CD&R) capabilities, to minimize deviations from the user s preferred trajectory. These DST capabilities will enable controllers to change their procedures from ones that are oriented towards sector management to procedures oriented towards trajectory management. Although adaptable to current procedures and airspace structure, EDA is intended as a tool for transitioning traffic from a Free Flight environment to an efficiently organized flow into terminal airspace. This paper describes the transition airspace problem and EDA concept, defines the key benefit mechanisms that will be enabled by EDA capabilities, and presents a traffic scenario to illustrate the use of the tool.

  18. Scale Invariance + Unitarity => Conformal Invariance?

    E-print Network

    Dorigoni, Daniele

    2009-01-01

    We revisit the long-standing conjecture that in unitary field theories, scale invariance implies conformality. We explain why the Zamolodchikov-Polchinski proof in D=2 does not work in higher dimensions. We speculate which new ideas might be helpful in a future proof. We also search for possible counterexamples. We consider a general multi-field scalar-fermion theory with quartic and Yukawa interactions. We show that there are no counterexamples among fixed points of such models in 4-epsilon dimensions. We also discuss fake counterexamples, which exist among theories without a stress tensor.

  19. Conformational Diversity of the Helix 12 of the Ligand Binding Domain of PPAR? and Functional Implications.

    PubMed

    Batista, Mariana R B; Martínez, Leandro

    2015-12-17

    Nuclear hormone receptors (NR) are transcription factors that activate gene expression in response to ligands. Structural and functional studies of the ligand binding domains (LBD) of NRs revealed that the dynamics of their C-terminal helix (H12) is fundamental for NR activity. H12 is rigid and facilitates binding of coactivator proteins in the agonist-bound LBD. In the absence of ligand, H12 exhibits increased flexibility. To provide a comprehensive picture of the H12 conformational equilibrium, extensive molecular dynamics simulations of the LBD of the PPAR? receptor in the presence or absence of ligand, and of coactivators and corepressor peptides, were performed. Free-energy profiles of the conformational variability of the H12 were obtained from more than four microseconds of simulations using adaptive biasing-force calculations. Our results demonstrate that, without ligand, multiple conformations of the H12 are accessible, including agonist-like conformations. We also confirm that extended H12 conformations are not accessible at ordinary temperatures. Ligand binding stabilizes the agonist H12 conformation relative to other structures, promoting a conformational selection. Similar effects are observed with coactivator association. The presence of corepressor peptides stabilizes conformations not allowed in the ligand-free, Rosiglitazone-bound or coactivator-bound LBDs. Corepressor binding, therefore, induces a conformational transition in the protein. Nevertheless, initial stages of corepressor dissociation could be induced by the ligand as it stabilizes the H12 in agonist form. Therefore, the present results provide a comprehensive picture of the H12 motions and their functional implications, with molecular resolution. PMID:26598113

  20. Conformational Dynamics of o-Fluoro-Substituted Z-Azobenzene.

    PubMed

    Rastogi, S K; Rogers, R A; Shi, J; Gao, C; Rinaldi, P L; Brittain, W J

    2015-11-20

    A conformational analysis of o-fluoro Z-azobenzene reveals a slight preference for aromatic C-F/? interaction. Density functional theory (DFT) indicates that the conformation with a C-F/? interaction is preferred by approximately 0.3-0.5 kcal/mol. Ground-state conformations were corroborated with X-ray crystallography. (Z)-Azobenzene (Z-AB) with at least one o-fluoro per ring displays (19)F-(19)F through-space (TS) coupling. 2D J-resolved NMR was used to distinguish through-bond from TS coupling ((TS)JFF). (TS)JFF decreases as the temperature is lowered and the multiplets coalesce into broad singlets. We hypothesize that the coalescence temperature (Tc) corresponds to the barrier for phenyl rotation. The experimentally determined barrier of 8-10 kcal/mol has been qualitatively verified by DFT where transition states with a bisected geometry were identified with zero-point energies of 6-9 kcal/mol relative to ground state. These values are significantly higher that values estimated from previous theoretical studies but lie within a reasonable range for phenyl rotation in hydrocarbon systems. PMID:26505924

  1. Measuring the mechanical properties of molecular conformers

    NASA Astrophysics Data System (ADS)

    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.

  2. Magnetically-conformed, Variable Area Discharge Chamber for Hall Thruster, and Method

    NASA Technical Reports Server (NTRS)

    Hofer, Richard R. (Inventor)

    2013-01-01

    The invention is a Hall thruster that incorporates a discharge chamber having a variable area channel including an ionization zone, a transition region, and an acceleration zone. The variable area channel is wider through the acceleration zone than through the ionization zone. An anode is located in a vicinity of the ionization zone and a cathode is located in a vicinity of the acceleration zone. The Hall thruster includes a magnetic circuit which is capable of forming a local magnetic field having a curvature within the transition region of the variable area channel whereby the transition region conforms to the curvature of the local magnetic field. The Hall thruster optimizes the ionization and acceleration efficiencies by the combined effects of the variable area channel and magnetic conformity.

  3. Conformal inflation coupled to matter

    SciTech Connect

    Brax, Philippe

    2014-05-01

    We formulate new conformal models of inflation and dark energy which generalise the Higgs-Dilaton scenario. We embed these models in unimodular gravity whose effect is to break scale invariance in the late time Universe. In the early Universe, inflation occurs close to a maximum of both the scalar potential and the scalar coupling to the Ricci scalar in the Jordan frame. At late times, the dilaton, which decouples from the dynamics during inflation, receives a potential term from unimodular gravity and leads to the acceleration of the Universe. We address two central issues in this scenario. First we show that the Damour-Polyalov mechanism, when non-relativistic matter is present prior to the start of inflation, sets the initial conditions for inflation at the maximum of the scalar potential. We then show that conformal invariance implies that matter particles are not coupled to the dilaton in the late Universe at the classical level. When fermions acquire masses at low energy, scale invariance is broken and quantum corrections induce a coupling between the dilaton and matter which is still small enough to evade the gravitational constraints in the solar system.

  4. Conformational gating of DNA conductance.

    PubMed

    Artés, Juan Manuel; Li, Yuanhui; Qi, Jianqing; Anantram, M P; Hihath, Joshua

    2015-01-01

    DNA is a promising molecule for applications in molecular electronics because of its unique electronic and self-assembly properties. Here we report that the conductance of DNA duplexes increases by approximately one order of magnitude when its conformation is changed from the B-form to the A-form. This large conductance increase is fully reversible, and by controlling the chemical environment, the conductance can be repeatedly switched between the two values. The conductance of the two conformations displays weak length dependencies, as is expected for guanine-rich sequences, and can be fit with a coherence-corrected hopping model. These results are supported by ab initio electronic structure calculations that indicate that the highest occupied molecular orbital is more disperse in the A-form DNA case. These results demonstrate that DNA can behave as a promising molecular switch for molecular electronics applications and also provide additional insights into the huge dispersion of DNA conductance values found in the literature. PMID:26648400

  5. Conformational gating of DNA conductance

    PubMed Central

    Artés, Juan Manuel; Li, Yuanhui; Qi, Jianqing; Anantram, M. P.; Hihath, Joshua

    2015-01-01

    DNA is a promising molecule for applications in molecular electronics because of its unique electronic and self-assembly properties. Here we report that the conductance of DNA duplexes increases by approximately one order of magnitude when its conformation is changed from the B-form to the A-form. This large conductance increase is fully reversible, and by controlling the chemical environment, the conductance can be repeatedly switched between the two values. The conductance of the two conformations displays weak length dependencies, as is expected for guanine-rich sequences, and can be fit with a coherence-corrected hopping model. These results are supported by ab initio electronic structure calculations that indicate that the highest occupied molecular orbital is more disperse in the A-form DNA case. These results demonstrate that DNA can behave as a promising molecular switch for molecular electronics applications and also provide additional insights into the huge dispersion of DNA conductance values found in the literature. PMID:26648400

  6. BRST-BV approach to conformal fields

    E-print Network

    Metsaev, R R

    2015-01-01

    Using BRST-BV approach, we consider totally symmetric arbitrary spin conformal fields propagating in flat space. For such fields, we obtain ordinary-derivative BRST-BV Lagrangian which is invariant under gauge transformations. In our approach, the ordinary-derivative Lagrangian and gauge transformations are constructed in terms of traceless gauge fields and traceless gauge transformation parameters. Also we obtain the realization of conformal algebra symmetries on space of fields and antifields entering the BRST-BV formulation of conformal fields.

  7. Conformal totally symmetric arbitrary spin fermionic fields

    E-print Network

    R. R. Metsaev

    2012-11-19

    Conformal totally symmetric arbitrary spin fermionic fields in flat space-time of even dimension greater than or equal to four are studied. First-derivative formulation involving Fang-Fronsdal kinetic operator for such fields is developed. Gauge invariant Lagrangian and the corresponding gauge transformations are obtained. Gauge symmetries are realized by involving the Stueckelberg and auxiliary fields. Realization of conformal algebra symmetries on the space of conformal gauge fermionic fields is obtained. On-shell degrees of freedom of the arbitrary spin conformal fermionic field are also discussed.

  8. Test of conformal gravity with astrophysical observations

    NASA Astrophysics Data System (ADS)

    Yang, Rongjia; Chen, Bohai; Zhao, Haijun; Li, Jun; Liu, Yuan

    2013-11-01

    Since it can describe the rotation curves of galaxies without dark matter and can give rise to accelerated expansion, conformal gravity attracts much attention recently. As a theory of modified gravity, it is important to test conformal gravity with astrophysical observations. Here we constrain conformal gravity with SNIa and Hubble parameter data and investigate whether it suffers from an age problem with the age of APM 08279+5255. We find conformal gravity can accommodate the age of APM 08279+5255 at 3? deviation, unlike most of dark energy models which suffer from an age problem.

  9. Rotational Spectroscopy Unveils Eleven Conformers of Adrenaline

    NASA Astrophysics Data System (ADS)

    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.

  10. Conformal blocks for the four-point function in conformal quantum mechanics

    E-print Network

    Jackiw, Roman

    Extending previous work on two- and three-point functions, we study the four-point function and its conformal block structure in conformal quantum mechanics CFT[subscript 1], which realizes the SO(2,1) symmetry group. ...

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

    E-print Network

    Kim, Do-Nyun

    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 ...

  12. Rotational spectra, nuclear quadrupole hyperfine tensors, and conformational structures of the mustard gas simulent 2-chloroethyl ethyl sulfide

    NASA Astrophysics Data System (ADS)

    Tubergen, M. J.; Lesarri, A.; Suenram, R. D.; Samuels, A. C.; Jensen, J. O.; Ellzy, M. W.; Lochner, J. M.

    2005-10-01

    Rotational spectra have been recorded for both the 35Cl and 37Cl isotopic forms of two structural conformations of 2-chloroethyl ethyl sulfide (CEES). The rotational constants of the 35Cl and 37Cl isotopomers were used to identify the conformational isomers. A total of 236 hyperfine transitions have been assigned for 47 rotational transitions of the 35Cl isotope of a GGT conformer, and 146 hyperfine have been assigned for 37 rotational transitions of the 37Cl isotopomer. For the second conformer, a total of 128 (110) hyperfine and 30 (28) rotational transitions have also been assigned to the 35Cl ( 37Cl) isotopes of a TGT conformation. The extensive hyperfine splitting data, measured to high resolution with a compact Fourier transform microwave spectrometer, were used to determine both the diagonal and off-diagonal elements of the 35Cl and 37Cl nuclear quadrupole coupling tensors in the inertial tensor principal axis system. The experimental rotational constant data, as well as the 35Cl and 37Cl nuclear quadrupole coupling tensors, were compared to the results from 27 optimized ab initio (HF/6-311++G ?? and MP2/6-311++G ??) model structures.

  13. Generating Reservoir Conformations for Replica Exchange through the Use of the Conformational Space Annealing Method

    E-print Network

    Lee, Jooyoung

    Generating Reservoir Conformations for Replica Exchange through the Use of the Conformational Space of these is the Reservoir Replica Exchange Method (R-REM), in which the conformational search and temperature equilibration are separated by exchanging with a pre-existing reservoir of structures. This approach allows the integration

  14. Using Solutes and Kinetics to Probe Large Conformational Changes in the Steps of Transcription Initiation

    PubMed Central

    Ruff, Emily; Kontur, Wayne S.; Record, M. Thomas

    2014-01-01

    Summary Small solutes are useful probes of large conformational changes in RNA polymerase (RNAP)-promoter interactions and other biopolymer processes. In general, a large effect of a solute on an equilibrium constant (or rate constant) indicates a large change in water-accessible biopolymer surface area in the corresponding step (or transition state), resulting from conformational changes, interface formation, or both. Here, we describe nitrocellulose filter binding assays from series used to determine the urea dependence of open complex formation and dissociation with Escherichia coli RNAP and ?PR promoter DNA. Then, we describe the subsequent data analysis and interpretation of these solute effects. PMID:25665568

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

    PubMed

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

    2009-07-01

    The complete conformational space of monomeric 1,3-butanediol has been characterized theoretically, and 73 unique stable conformers were found at the MP2/6-311++G(d,p) level. These were classified into nine families whose members share the same heavy atom backbone configurations and differ in the hydrogen atom orientations. The first and third most populated backbone families are governed by the formation of an intramolecular hydrogen bond; however, the second precludes this type of interaction and was frequently overlooked in previous studies. Its stability is determined by the relatively high entropy of its main conformers. The hydrogen bonding of four of the most important conformers was characterized by means of atoms in molecules (AIM, also known as QTAIM) and natural bond orbital (NBO) analyses. Using appropriate isodesmic reactions, hydrogen bonding energy stabilizations of 12-14 kJ mol(-1) have been found. Experimentally, monomeric molecules of 1,3-butanediol were isolated in low-temperature inert matrixes, and their infrared spectra were analyzed from the viewpoint of the conformational distribution. All the relevant transition states for the conformational interconversion reaction paths were characterized at the same level of theory to interpret the conformational cooling dynamics observed in the low-temperature matrixes. The energy barriers for rotation of the OH groups were calculated to be very low (<3 kJ mol(-1)). These barriers were overcome in the experiments at 10 K (Ar matrix), in the process of matrix deposition, and population within each family was reduced to the most stable conformers. Further increase in the substrate temperature (up to 40 K, Xe matrix) resulted in conformational cooling where the medium-height barriers (approximately 13 kJ mol(-1)) could be surmounted and all conformational population converted to the ground conformational state. Remarkably, this state turned to consist of two forms of the most stable hydrogen bonded family, which were predicted by calculations to be accidentally degenerated and were found in the annealed matrix in equal amounts. All of these experimentally observed conformational cooling processes were analyzed and supported by full agreement with the theoretical calculations. PMID:19388693

  16. Assignment of side-chain conformation using adiabatic energy mapping, free energy perturbation, and molecular dynamic simulations.

    PubMed Central

    Frimurer, T. M.; Peters, G. H.; Sørensen, M. D.; Led, J. J.; Olsen, O. H.

    1999-01-01

    NMR spectroscopic analysis of the C-terminal Kunitz domain fragment (alpha3(VI)) from the human alpha3-chain of type VI collagen has revealed that the side chain of Trp21 exists in two unequally populated conformations. The major conformation (M) is identical to the conformation observed in the X-ray crystallographic structure, while the minor conformation (m) cannot structurally be resolved in detail by NMR due to insufficient NOE data. In the present study, we have applied: (1) rigid and adiabatic mapping, (2) free energy simulations, and (3) molecular dynamic simulations to elucidate the structure of the m conformer and to provide a possible pathway of the Trp21 side chain between the two conformers. Adiabatic energy mapping of conformations of the Trp21 side chain obtained by energy minimization identified two energy minima: One corresponding to the conformation of Trp21 observed in the X-ray crystallographic structure and solution structure of alpha3(VI) (the M conformation) and the second corresponding to the m conformation predicted by NMR spectroscopy. A transition pathway between the M and m conformation is suggested. The free-energy difference between the two conformers obtained by the thermodynamic integration method is calculated to 1.77+/-0.7 kcal/mol in favor of the M form, which is in good agreement with NMR results. Structural and dynamic properties of the major and minor conformers of the alpha3(VI) molecule were investigated by molecular dynamic. Essential dynamics analysis of the two resulting 800 ps trajectories reveals that when going from the M to the m conformation only small, localized changes in the protein structure are induced. However, notable differences are observed in the mobility of the binding loop (residues Thr13-Ile18), which is more flexible in the m conformation than in the M conformation. This suggests that the reorientation of Trp2 might influence the inhibitory activity against trypsin, despite the relative large distance between the binding loop and Trp21. PMID:10210180

  17. Electromagnetic characterization of conformal antennas

    NASA Technical Reports Server (NTRS)

    Volakis, John L.; Kempel, Leo C.; Alexanian, Angelos; Jin, J. M.; Yu, C. L.; Woo, Alex C.

    1992-01-01

    The ultimate objective of this project is to develop a new technique which permits an accurate simulation of microstrip patch antennas or arrays with various feed, superstrate and/or substrate configurations residing in a recessed cavity whose aperture is planar, cylindrical or otherwise conformed to the substructure. The technique combines the finite element and boundary integral methods to formulate a system suitable for solution via the conjugate gradient method in conjunction with the fast Fourier transform. The final code is intended to compute both scattering and radiation patterns of the structure with an affordable memory demand. With upgraded capabilities, the four included papers examined the radar cross section (RCS), input impedance, gain, and resonant frequency of several rectangular configurations using different loading and substrate/superstrate configurations.

  18. A mystery of conformal coupling

    E-print Network

    E. A. Tagirov

    2005-01-28

    An origin and necessity of so called conformal (or,Penrose-Chernikov-Tagirov) coupling of scalar field to the metric of n-dimensional Riemannian space-time is discussed in brief. The corresponding general-relativistic field equation implies a one-particle (quantum mechanical) Schrodinger Hamiltonian which depends on the space-time dimensionality n, contrary to the Hamiltonian constructed by quantization of geodesic motion, which is the same for any value of n. In general, the Hamiltonians can coincide only for n = 4, the dimensionality of the ordinarily observed Universe. In view of the fundamental role of a scalar field in various cosmological models, this fact may be of interest for models of brane worlds where n > 4 .

  19. Electrostatic imaging via conformal mapping

    NASA Astrophysics Data System (ADS)

    Akduman, Ibrahim; Kress, Rainer

    2002-12-01

    We present the solution of an inverse boundary value problem for harmonic functions arising in electrostatic imaging through conformal mapping techniques. The numerical method consists of two parts. In a first step, by successive approximations a nonlinear equation is solved to determine the boundary values of a holomorphic function on the outer boundary circle of an annulus. Then in a second step an ill-posed Cauchy problem is solved to determine the holomorphic function in the annulus. The method extends and modifies an earlier analysis of Idemen and Akduman (Idemen M and Akduman I 1988 SIAM J. Appl. Math. 48 703-18). We establish a convergence result for the iteration procedure and through numerical examples we illustrate the feasibility of the method.

  20. Approaching Conformality with Ten Flavors

    SciTech Connect

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

    2012-04-01

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

  1. Gravitomagnetic effects in conformal gravity

    E-print Network

    Jackson Levi Said; Joseph Sultana; Kristian Zarb Adami

    2014-01-10

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

  2. Electroweak phase transition in ultraminimal technicolor

    SciTech Connect

    Jaervinen, Matti; Sannino, Francesco; Ryttov, Thomas A.

    2009-05-01

    We unveil the temperature-dependent electroweak phase transition in new extensions of the standard model in which the electroweak symmetry is spontaneously broken via strongly coupled, nearly conformal dynamics achieved by the means of multiple matter representations. In particular, we focus on the low energy effective theory introduced to describe ultra minimal walking technicolor at the phase transition. Using the one-loop effective potential with ring improvement, we identify regions of parameter space, which yield a strong first-order transition. A striking feature of the model is the existence of a second phase transition associated to the electroweak-singlet sector. The interplay between these two transitions leads to an extremely rich phase diagram.

  3. On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

    NASA Astrophysics Data System (ADS)

    Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo; Roitberg, Adrian E.; Fernandez-Alberti, Sebastian

    2015-06-01

    The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data.

  4. Conformal Mapping in Wing Aerodynamics Thomas Johnson

    E-print Network

    Morrow, James A.

    Conformal Mapping in Wing Aerodynamics Thomas Johnson June 4, 2013 Contents 1 Introduction 1 2 the first complete treatment of conformal mapping in aerodynamics. Near the beginning of the twentieth and aerodynamics. The purpose of this exposition is to give the reader an elementary intro- duction to the use

  5. Conformal coordinates of a constant density star

    E-print Network

    Karthik Shankar; Bernard. F. Whiting

    2007-06-28

    It is well known that the interior of a constant density spherical star is conformally flat. In this paper we obtain the coordinate system in which the conformal flatness of the metric manifests itself. In a similar way, we also construct such coordinates for Robertson Walker metric.

  6. Regulatory Conformance Checking: Logic and Logical Form

    ERIC Educational Resources Information Center

    Dinesh, Nikhil

    2010-01-01

    We consider the problem of checking whether an organization conforms to a body of regulation. Conformance is studied in a runtime verification setting. The regulation is translated to a logic, from which we synthesize monitors. The monitors are evaluated as the state of an organization evolves over time, raising an alarm if a violation is…

  7. Conformational readout of RNA by small ligands.

    PubMed

    Kligun, Efrat; Mandel-Gutfreund, Yael

    2013-06-01

    RNA molecules have highly versatile structures that can fold into myriad conformations, providing many potential pockets for binding small molecules. The increasing number of available RNA structures, in complex with proteins, small ligands and in free form, enables the design of new therapeutically useful RNA-binding ligands. Here we studied RNA ligand complexes from 10 RNA groups extracted from the protein data bank (PDB), including adaptive and non-adaptive complexes. We analyzed the chemical, physical, structural and conformational properties of binding pockets around the ligand. Comparing the properties of ligand-binding pockets to the properties of computed pockets extracted from all available RNA structures and RNA-protein interfaces, revealed that ligand-binding pockets, mainly the adaptive pockets, are characterized by unique properties, specifically enriched in rare conformations of the nucleobase and the sugar pucker. Further, we demonstrate that nucleotides possessing the rare conformations are preferentially involved in direct interactions with the ligand. Overall, based on our comprehensive analysis of RNA-ligand complexes, we suggest that the unique conformations adopted by RNA nucleotides play an important role in RNA recognition by small ligands. We term the recognition of a binding site by a ligand via the unique RNA conformations "RNA conformational readout." We propose that "conformational readout" is a general way by which RNA binding pockets are recognized and selected from an ensemble of different RNA states. PMID:23618839

  8. Conformational analysis of thiophene analogs of propranolol

    NASA Astrophysics Data System (ADS)

    Corral, Carlos; Donoso, Rosa; Elguero, Jose; Goya, Pilar; Lissavetzky, Jaime; Rozas, Isabel

    1990-10-01

    Conformation of 3-tert-butylamino-1-thienyloxy-2-propanol, a thiophene analogue of propanolol, have been theoretically investigated by molecular mechanics and semiempirical calculations. The conformational minima obtained have been compared with those reported for propranolol using molecular graphics. The good "fit" obtained can account for the similar biological activity of these compounds.

  9. Logarithmic Conformal Null Vectors and SLE

    E-print Network

    S. Moghimi-Araghi; M. A. Rajabpour; S. Rouhani

    2004-08-10

    Formal Loewner evolution is connected to conformal field theory. In this letter we introduce an extension of Loewner evolution, which consists of two coupled equations and connect the martingales of these equations to the null vectors of logarithmic conformal field theory.

  10. Conformational Sampling of Peptides in Cellular Environments?

    PubMed Central

    Tanizaki, Seiichiro; Clifford, Jacob; Connelly, Brian D.; Feig, Michael

    2008-01-01

    Abstract Biological systems provide a complex environment that can be understood in terms of its dielectric properties. High concentrations of macromolecules and cosolvents effectively reduce the dielectric constant of cellular environments, thereby affecting the conformational sampling of biomolecules. To examine this effect in more detail, the conformational preference of alanine dipeptide, poly-alanine, and melittin in different dielectric environments is studied with computer simulations based on recently developed generalized Born methodology. Results from these simulations suggest that extended conformations are favored over ?-helical conformations at the dipeptide level at and below dielectric constants of 5–10. Furthermore, lower-dielectric environments begin to significantly stabilize helical structures in poly-alanine at ? = 20. In the more complex peptide melittin, different dielectric environments shift the equilibrium between two main conformations: a nearly fully extended helix that is most stable in low dielectrics and a compact, V-shaped conformation consisting of two helices that is preferred in higher dielectric environments. An additional conformation is only found to be significantly populated at intermediate dielectric constants. Good agreement with previous studies of different peptides in specific, less-polar solvent environments, suggest that helix stabilization and shifts in conformational preferences in such environments are primarily due to a reduced dielectric environment rather than specific molecular details. The findings presented here make predictions of how peptide sampling may be altered in dense cellular environments with reduced dielectric response. PMID:17905846

  11. Starkweather Social Conformity Test for Preschool Children.

    ERIC Educational Resources Information Center

    Starkweather, Elizabeth K.

    The Starkweather Social Conformity Test is a research instrument designed to measure conforming and nonconforming behavior by providing the young child with opportunities to make choices in a situation in which he can follow a model or respond freely according to his own preferences. The test discriminates between compulsive conformists or…

  12. Conformity to Peer Pressure in Preschool Children

    ERIC Educational Resources Information Center

    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…

  13. From Stability to Mobility: African Secondary School Aged Adolescents' Transition to Mainstream Schooling

    ERIC Educational Resources Information Center

    Gunasekera, Sashya; Houghton, Stephen; Glasgow, Kenneth; Boyle, Christopher

    2014-01-01

    Setting clear achievable goals that enhance reputational status has been shown to direct the energies of adolescents into socially conforming or non-conforming activities. It appears to be the case that following transition from Intensive English Centres (IECs) into mainstream schooling, students from African refugee backgrounds experience…

  14. Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes

    NASA Technical Reports Server (NTRS)

    Egli, M.; Usman, N.; Rich, A.

    1993-01-01

    We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.

  15. 76 FR 67534 - Federal Fiscal Year 2012 Annual List of Certifications and Assurances for Federal Transit...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-01

    ...as defined in the ``National ITS Architecture.'' The Applicant assures that...will] conform to the national architecture, applicable standards or provisional...FTA Notice, ``FTA National ITS Architecture Policy on Transit Projects,''...

  16. Observing the unfolding transition of [beta]-hairpin peptides with nonlinear infrared spectroscopy

    E-print Network

    Smith, Adam Wilcox, 1977-

    2008-01-01

    The biological function of a protein is in large measure determined by its three-dimensional structure. To date, however, the transition of the protein between the native and non-native conformations is not well-understood. ...

  17. Conformal Blocks for the 4-Point Function in Conformal Quantum Mechanics

    E-print Network

    R. Jackiw; S. -Y. Pi

    2012-10-11

    Extending previous work on 2 -- and 3 -- point functions, we study the 4 -- point function and its conformal block structure in conformal quantum mechanics CFT$_1$, which realizes the SO(2,1) symmetry group. Conformal covariance is preserved even though the operators with which we work need not be primary and the states are not conformally invariant. We find that only one conformal block contributes to the four-point function. We describe some further properties of the states that we use and we construct dynamical evolution generated by the compact generator of SO(2.1).

  18. Central extensions and conformal derivations of a class of Lie conformal algebras

    E-print Network

    Yanyong Hong

    2015-07-07

    A quadratic Lie conformal algebra corresponds to a Hamiltonian pair in \\cite{GD}, which plays fundamental roles in completely integrable systems. Moreover, it also corresponds to certain compatible pairs of a Lie algebra and a Novikov algebra which is called Gel'fand-Dorfman bialgebra by Xu in \\cite{X1}. In this paper, central extensions and conformal derivations of quadratic Lie conformal algebras are studied in terms of Gel'fand-Dorfman bialgebras. It is shown that central extensions and conformal derivations of a quadratic Lie conformal algebra are related with some bilinear forms and some operators of the corresponding Gel'fand-Dorfman bialgebra respectively.

  19. Conformal invariance in two-dimensional turbulence

    E-print Network

    D. Bernard; G. Boffetta; A. Celani; G. Falkovich

    2006-02-09

    Simplicity of fundamental physical laws manifests itself in fundamental symmetries. While systems with an infinity of strongly interacting degrees of freedom (in particle physics and critical phenomena) are hard to describe, they often demonstrate symmetries, in particular scale invariance. In two dimensions (2d) locality often promotes scale invariance to a wider class of conformal transformations which allow for nonuniform re-scaling. Conformal invariance allows a thorough classification of universality classes of critical phenomena in 2d. Is there conformal invariance in 2d turbulence, a paradigmatic example of strongly-interacting non-equilibrium system? Here, using numerical experiment, we show that some features of 2d inverse turbulent cascade display conformal invariance. We observe that the statistics of vorticity clusters is remarkably close to that of critical percolation, one of the simplest universality classes of critical phenomena. These results represent a new step in the unification of 2d physics within the framework of conformal symmetry.

  20. Dolastatin 11 conformations, analogues and pharmacophore.

    PubMed

    Ali, Md Ahad; Bates, Robert B; Crane, Zackary D; Dicus, Christopher W; Gramme, Michelle R; Hamel, Ernest; Marcischak, Jacob; Martinez, David S; McClure, Kelly J; Nakkiew, Pichaya; Pettit, George R; Stessman, Chad C; Sufi, Bilal A; Yarick, Gayle V

    2005-07-01

    Twenty analogues of the natural antitumor agent dolastatin 11, including majusculamide C, were synthesized and tested for cytotoxicity against human cancer cells and stimulation of actin polymerization. Only analogues containing the 30-membered ring were active. Molecular modeling and NMR evidence showed the low-energy conformations. The amide bonds are all trans except for the one between the Tyr and Val units, which is cis. Since an analogue restricted to negative 2-3-4-5 angles stimulated actin polymerization but was inactive in cells, the binding conformation (most likely the lowest-energy conformation in water) has a negative 2-3-4-5 angle, whereas a conformation with a positive 2-3-4-5 angle (most likely the lowest energy conformation in chloroform) goes through cell walls. The highly active R alcohol from borohydride reduction of dolastatin 11 is a candidate for conversion to prodrugs. PMID:15878670

  1. Performance of Conformable Ablators in Aerothermal Environments

    NASA Technical Reports Server (NTRS)

    Thornton, J.; Fan, W.; Skokova, K.; Stackpoole, M.; Beck, R.; Chavez-Garcia, J.

    2012-01-01

    Conformable Phenolic Impregnated Carbon Ablator, a cousin of Phenolic Impregnated Carbon Ablator (PICA), was developed at NASA Ames Research Center as a lightweight thermal protection system under the Fundamental Aeronautics Program. PICA is made using a brittle carbon substrate, which has a very low strain to failure. Conformable PICA is made using a flexible carbon substrate, a felt in this case. The flexible felt significantly increases the strain to failure of the ablator. PICA is limited by its thermal mechanical properties. Future NASA missions will require heatshields that are more fracture resistant than PICA and, as a result, NASA Ames is working to improve PICAs performance by developing conformable PICA to meet these needs. Research efforts include tailoring the chemistry of conformable PICA with varying amounts of additives to enhance mechanical properties and testing them in aerothermal environments. This poster shows the performance of conformable PICA variants in arc jets tests. Some mechanical and thermal properties will also be presented.

  2. On Combinatorial Expansions of Conformal Blocks

    E-print Network

    A. Marshakov; A. Mironov; A. Morozov

    2010-01-27

    In a recent paper (arXiv:0906.3219) the representation of Nekrasov partition function in terms of nontrivial two-dimensional conformal field theory has been suggested. For non-vanishing value of the deformation parameter \\epsilon=\\epsilon_1+\\epsilon_2 the instanton partition function is identified with a conformal block of Liouville theory with the central charge c = 1+ 6\\epsilon^2/\\epsilon_1\\epsilon_2. If reversed, this observation means that the universal part of conformal blocks, which is the same for all two-dimensional conformal theories with non-degenerate Virasoro representations, possesses a non-trivial decomposition into sum over sets of the Young diagrams, different from the natural decomposition studied in conformal field theory. We provide some details about this intriguing new development in the simplest case of the four-point correlation functions.

  3. Conformal nets III: fusion of defects

    E-print Network

    Arthur Bartels; Christopher L. Douglas; André Henriques

    2015-02-21

    Conformal nets provides a mathematical model for conformal field theory. We define a notion of defect between conformal nets, formalizing the idea of an interaction between two conformal field theories. We introduce an operation of fusion of defects, and prove that the fusion of two defects is again a defect, provided the fusion occurs over a conformal net of finite index. There is a notion of sector (or bimodule) between two defects, and operations of horizontal and vertical fusion of such sectors. Our most difficult technical result is that the horizontal fusion of the vacuum sectors of two defects is isomorphic to the vacuum sector of the fused defect. Equipped with this isomorphism, we construct the basic interchange isomorphism between the horizontal fusion of two vertical fusions and the vertical fusion of two horizontal fusions of sectors.

  4. 40 CFR 93.104 - Frequency of conformity determinations.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...2011-07-01 false Frequency of conformity determinations. 93.104 Section...PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR FEDERAL IMPLEMENTATION PLANS Conformity to State or Federal...

  5. Transportation Conformity: A Basic Guide for State and Local Officials

    E-print Network

    Handy, Susan L.

    Transportation Conformity: A Basic Guide for State and Local Officials Revised June 19, 2000 of Appeals for the District of Columbia Circuit which affected certain conformity provisions. #12;This page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Part One: The Basics of Transportation Conformity

  6. 40 CFR 93.104 - Frequency of conformity determinations.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...2012-07-01 false Frequency of conformity determinations. 93.104 Section...PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR FEDERAL IMPLEMENTATION PLANS Conformity to State or Federal...

  7. 47 CFR 68.324 - Supplier's Declaration of Conformity requirements.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... false Supplier's Declaration of Conformity requirements. 68.324 Section...324 Supplier's Declaration of Conformity requirements. (a) Each responsible...include in the Supplier's Declaration of Conformity, the following information:...

  8. 40 CFR 51.857 - Frequency of conformity determinations.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...2010-07-01 false Frequency of conformity determinations. 51.857 Section...OF IMPLEMENTATION PLANS Determining Conformity of General Federal Actions to State...Implementation Plans § 51.857 Frequency of conformity determinations. Link to an...

  9. 40 CFR 93.104 - Frequency of conformity determinations.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...2010-07-01 false Frequency of conformity determinations. 93.104 Section...PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR FEDERAL IMPLEMENTATION PLANS Conformity to State or Federal...

  10. 40 CFR 89.121 - Certificate of conformity effective dates.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...2013-07-01 true Certificate of conformity effective dates. 89.121 Section...Provisions § 89.121 Certificate of conformity effective dates. The certificate of conformity is valid from the date of issuance...

  11. 47 CFR 68.320 - Supplier's Declaration of Conformity.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ...2012-10-01 false Supplier's Declaration of Conformity. 68.320 Section 68.320 Telecommunication...68.320 Supplier's Declaration of Conformity. (a) Supplier's Declaration of Conformity is a procedure where the...

  12. 47 CFR 68.324 - Supplier's Declaration of Conformity requirements.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... false Supplier's Declaration of Conformity requirements. 68.324 Section...324 Supplier's Declaration of Conformity requirements. (a) Each responsible...include in the Supplier's Declaration of Conformity, the following information:...

  13. 47 CFR 2.1072 - Limitation on Declaration of Conformity.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... false Limitation on Declaration of Conformity. 2.1072 Section 2.1072 Telecommunication...Authorization Procedures Declaration of Conformity § 2.1072 Limitation on Declaration of Conformity. (a) The Declaration...

  14. 40 CFR 93.157 - Reevaluation of conformity.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...2011-07-01 false Reevaluation of conformity. 93.157 Section 93.157...PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR...IMPLEMENTATION PLANS Determining Conformity of General Federal Actions...

  15. 20 CFR 604.6 - Conformity and substantial compliance.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ...2014-04-01 2014-04-01 false Conformity and substantial compliance. 604...UNEMPLOYMENT COMPENSATION § 604.6 Conformity and substantial compliance. (a...program. (b) Resolving Issues of Conformity and Substantial Compliance. For...

  16. 40 CFR 93.154 - Federal agency conformity responsibility.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...2013-07-01 true Federal agency conformity responsibility. 93.154 ...PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR...IMPLEMENTATION PLANS Determining Conformity of General Federal Actions...

  17. 47 CFR 2.1072 - Limitation on Declaration of Conformity.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... false Limitation on Declaration of Conformity. 2.1072 Section 2.1072 Telecommunication...Authorization Procedures Declaration of Conformity § 2.1072 Limitation on Declaration of Conformity. (a) The Declaration...

  18. 40 CFR 89.121 - Certificate of conformity effective dates.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...2013-07-01 false Certificate of conformity effective dates. 89.121 Section...Provisions § 89.121 Certificate of conformity effective dates. The certificate of conformity is valid from the date of issuance...

  19. 20 CFR 604.6 - Conformity and substantial compliance.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ...2011-04-01 2011-04-01 false Conformity and substantial compliance. 604...UNEMPLOYMENT COMPENSATION § 604.6 Conformity and substantial compliance. (a...program. (b) Resolving Issues of Conformity and Substantial Compliance. For...

  20. 47 CFR 2.906 - Declaration of Conformity.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 2014-10-01 false Declaration of Conformity. 2.906 Section 2.906 Telecommunication...General Provisions § 2.906 Declaration of Conformity. (a) A Declaration of Conformity is a procedure where the...

  1. 20 CFR 604.6 - Conformity and substantial compliance.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ...2012-04-01 2012-04-01 false Conformity and substantial compliance. 604...UNEMPLOYMENT COMPENSATION § 604.6 Conformity and substantial compliance. (a...program. (b) Resolving Issues of Conformity and Substantial Compliance. For...

  2. 40 CFR 89.121 - Certificate of conformity effective dates.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...2011-07-01 false Certificate of conformity effective dates. 89.121 Section...Provisions § 89.121 Certificate of conformity effective dates. The certificate of conformity is valid from the date of issuance...

  3. 47 CFR 68.324 - Supplier's Declaration of Conformity requirements.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... false Supplier's Declaration of Conformity requirements. 68.324 Section...324 Supplier's Declaration of Conformity requirements. (a) Each responsible...include in the Supplier's Declaration of Conformity, the following information:...

  4. 40 CFR 93.104 - Frequency of conformity determinations.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...2013-07-01 true Frequency of conformity determinations. 93.104 Section...PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR FEDERAL IMPLEMENTATION PLANS Conformity to State or Federal...

  5. 40 CFR 93.154 - Federal agency conformity responsibility.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...2013-07-01 false Federal agency conformity responsibility. 93.154 ...PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR...IMPLEMENTATION PLANS Determining Conformity of General Federal Actions...

  6. 40 CFR 93.157 - Reevaluation of conformity.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...2013-07-01 true Reevaluation of conformity. 93.157 Section 93.157...PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR...IMPLEMENTATION PLANS Determining Conformity of General Federal Actions...

  7. 40 CFR 93.104 - Frequency of conformity determinations.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...2013-07-01 false Frequency of conformity determinations. 93.104 Section...PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR FEDERAL IMPLEMENTATION PLANS Conformity to State or Federal...

  8. 47 CFR 2.906 - Declaration of Conformity.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 2013-10-01 false Declaration of Conformity. 2.906 Section 2.906 Telecommunication...General Provisions § 2.906 Declaration of Conformity. (a) A Declaration of Conformity is a procedure where the...

  9. 47 CFR 68.320 - Supplier's Declaration of Conformity.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...2014-10-01 false Supplier's Declaration of Conformity. 68.320 Section 68.320 Telecommunication...68.320 Supplier's Declaration of Conformity. (a) Supplier's Declaration of Conformity is a procedure where the...

  10. 47 CFR 68.320 - Supplier's Declaration of Conformity.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...2013-10-01 false Supplier's Declaration of Conformity. 68.320 Section 68.320 Telecommunication...68.320 Supplier's Declaration of Conformity. (a) Supplier's Declaration of Conformity is a procedure where the...

  11. 20 CFR 604.6 - Conformity and substantial compliance.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ...2013-04-01 2013-04-01 false Conformity and substantial compliance. 604...UNEMPLOYMENT COMPENSATION § 604.6 Conformity and substantial compliance. (a...program. (b) Resolving Issues of Conformity and Substantial Compliance. For...

  12. 47 CFR 2.906 - Declaration of Conformity.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 2012-10-01 false Declaration of Conformity. 2.906 Section 2.906 Telecommunication...General Provisions § 2.906 Declaration of Conformity. (a) A Declaration of Conformity is a procedure where the...

  13. 40 CFR 93.157 - Frequency of conformity determinations.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...2010-07-01 false Frequency of conformity determinations. 93.157 ...PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR...IMPLEMENTATION PLANS Determining Conformity of General Federal Actions...

  14. 40 CFR 93.157 - Reevaluation of conformity.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...2012-07-01 false Reevaluation of conformity. 93.157 Section 93.157...PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR...IMPLEMENTATION PLANS Determining Conformity of General Federal Actions...

  15. 40 CFR 93.154 - Federal agency conformity responsibility.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...2011-07-01 false Federal agency conformity responsibility. 93.154 ...PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR...IMPLEMENTATION PLANS Determining Conformity of General Federal Actions...

  16. 40 CFR 89.121 - Certificate of conformity effective dates.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...2012-07-01 false Certificate of conformity effective dates. 89.121 Section...Provisions § 89.121 Certificate of conformity effective dates. The certificate of conformity is valid from the date of issuance...

  17. 40 CFR 93.157 - Reevaluation of conformity.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...2013-07-01 false Reevaluation of conformity. 93.157 Section 93.157...PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR...IMPLEMENTATION PLANS Determining Conformity of General Federal Actions...

  18. 40 CFR 89.121 - Certificate of conformity effective dates.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...2010-07-01 false Certificate of conformity effective dates. 89.121 Section...Provisions § 89.121 Certificate of conformity effective dates. The certificate of conformity is valid from the date of issuance...

  19. 40 CFR 93.154 - Federal agency conformity responsibility.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...2012-07-01 false Federal agency conformity responsibility. 93.154 ...PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR...IMPLEMENTATION PLANS Determining Conformity of General Federal Actions...

  20. 47 CFR 2.1072 - Limitation on Declaration of Conformity.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... false Limitation on Declaration of Conformity. 2.1072 Section 2.1072 Telecommunication...Authorization Procedures Declaration of Conformity § 2.1072 Limitation on Declaration of Conformity. (a) The Declaration...

  1. 77 FR 14979 - Transportation Conformity Rule Restructuring Amendments

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-14

    ...regional conformity tests. In Environmental Defense v. EPA, 467...for ozone conformity tests in its January 24...FR 4434). While the Environmental Defense case concerned...regional conformity tests described above,...

  2. 75 FR 49435 - Transportation Conformity Rule Restructuring Amendments

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-13

    ...regional conformity tests. In Environmental Defense v. EPA, 467...for ozone conformity tests in its January 24...FR 4434). While the Environmental Defense case concerned...regional conformity tests described above,...

  3. 47 CFR 2.1072 - Limitation on Declaration of Conformity.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...2010-10-01 false Limitation on Declaration of Conformity. 2.1072 Section 2.1072...Equipment Authorization Procedures Declaration of Conformity § 2.1072 Limitation on Declaration of Conformity. (a) The...

  4. 47 CFR 2.906 - Declaration of Conformity.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...2010-10-01 2010-10-01 false Declaration of Conformity. 2.906 Section 2.906 Telecommunication... General Provisions § 2.906 Declaration of Conformity. (a) A Declaration of Conformity is a procedure where the...

  5. 47 CFR 2.1072 - Limitation on Declaration of Conformity.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ...2011-10-01 false Limitation on Declaration of Conformity. 2.1072 Section 2.1072...Equipment Authorization Procedures Declaration of Conformity § 2.1072 Limitation on Declaration of Conformity. (a) The...

  6. 47 CFR 2.906 - Declaration of Conformity.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ...2011-10-01 2011-10-01 false Declaration of Conformity. 2.906 Section 2.906 Telecommunication... General Provisions § 2.906 Declaration of Conformity. (a) A Declaration of Conformity is a procedure where the...

  7. 47 CFR 68.320 - Supplier's Declaration of Conformity.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ...2011-10-01 false Supplier's Declaration of Conformity. 68.320 Section 68.320...Approval § 68.320 Supplier's Declaration of Conformity. (a) Supplier's Declaration of Conformity is a procedure where the...

  8. 20 CFR 604.6 - Conformity and substantial compliance.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ...Conformity and substantial compliance. 604.6 Section 604...Conformity and substantial compliance. (a) In general...against the Federal unemployment tax established by section 3301...Conformity and Substantial Compliance. For the purposes of...

  9. 21 CFR 26.70 - Conformity assessment bodies.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ...Conformity assessment bodies. 26.70 Section...DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ...MEDICAL DEVICE QUALITY SYSTEM AUDIT REPORTS, AND...Conformity assessment bodies. Each party recognizes...conformity assessment bodies (CAB's)...

  10. 21 CFR 26.70 - Conformity assessment bodies.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ...Conformity assessment bodies. 26.70 Section...DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ...MEDICAL DEVICE QUALITY SYSTEM AUDIT REPORTS, AND...Conformity assessment bodies. Each party recognizes...conformity assessment bodies (CAB's)...

  11. 21 CFR 26.70 - Conformity assessment bodies.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ...Conformity assessment bodies. 26.70 Section...DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ...MEDICAL DEVICE QUALITY SYSTEM AUDIT REPORTS, AND...Conformity assessment bodies. Each party recognizes...conformity assessment bodies (CAB's)...

  12. 21 CFR 26.70 - Conformity assessment bodies.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ...Conformity assessment bodies. 26.70 Section...DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ...MEDICAL DEVICE QUALITY SYSTEM AUDIT REPORTS, AND...Conformity assessment bodies. Each party recognizes...conformity assessment bodies (CAB's)...

  13. 21 CFR 26.70 - Conformity assessment bodies.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ...Conformity assessment bodies. 26.70 Section...DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ...MEDICAL DEVICE QUALITY SYSTEM AUDIT REPORTS, AND...Conformity assessment bodies. Each party recognizes...conformity assessment bodies (CAB's)...

  14. Calcineurin Undergoes a Conformational Switch Evoked via Peptidyl-Prolyl Isomerization

    PubMed Central

    Guasch, Alicia; Aranguren-Ibáñez, Álvaro; Pérez-Luque, Rosa; Aparicio, David; Martínez-Høyer, Sergio; Mulero, M. Carmen; Serrano-Candelas, Eva

    2015-01-01

    A limited repertoire of PPP family of serine/threonine phosphatases with a highly conserved catalytic domain acts on thousands of protein targets to orchestrate myriad central biological roles. A major structural reorganization of human calcineurin, a ubiquitous Ser/Thr PPP regulated by calcium and calmodulin and targeted by immunosuppressant drugs cyclosporin A and FK506, is unveiled here. The new conformation involves trans- to cis- isomerization of proline in the SAPNY sequence, highly conserved across PPPs, and remodels the main regulatory site where NFATc transcription factors bind. Transitions between cis- and trans- conformations may involve peptidyl prolyl isomerases such as cyclophilin A and FKBP12, which are known to physically interact with and modulate calcineurin even in the absence of immunosuppressant drugs. Alternative conformations in PPPs provide a new perspective on interactions with substrates and other protein partners and may foster development of more specific inhibitors as drug candidates. PMID:26248042

  15. Conformal boundary conditions in the critical O(n) model and dilute loop models

    E-print Network

    Jerome Dubail; Jesper Lykke Jacobsen; Hubert Saleur

    2009-05-09

    We study the conformal boundary conditions of the dilute O(n) model in two dimensions. A pair of mutually dual solutions to the boundary Yang-Baxter equations are found. They describe anisotropic special transitions, and can be interpreted in terms of symmetry breaking interactions in the O(n) model. We identify the corresponding boundary condition changing operators, Virasoro characters, and conformally invariant partition functions. We compute the entropies of the conformal boundary states, and organize the flows between the various boundary critical points in a consistent phase diagram. The operators responsible for the various flows are identified. Finally, we discuss the relation to open boundary conditions in the O(n) model, and present new crossing probabilities for Ising domain walls.

  16. Effect of stretching on the molecular conformation of oligo (ethylene oxide): a theoretical study

    NASA Astrophysics Data System (ADS)

    Kreuzer, H. J.; Wang, R. L. C.; Grunze, M.

    1999-11-01

    The force-extension measurements on simple poly(ethylene glycol) molecules by Oesterfelt et al in different solvents can be quantitatively explained based on ab initio quantum mechanical calculations of the potential energy surfaces of the polymer segments in vacuum and in the solvated form. The proper statistical mechanical calculations of the force-extension relation, both for isothermal-isochoric and isothermal-isobaric conditions (the latter appropriate to the experimental set-up), demonstrate, that in the low-force regime transitions from the amorphous to the helical conformers, and in the high-force regime stretching of the helical to the planar `all-trans' conformer occur. The presence of water affects all but the `all-trans' conformer by shortening and stiffening.

  17. Conformal Partial Waves: Further Mathematical Results

    E-print Network

    F. A. Dolan; H. Osborn

    2012-02-29

    Further results for conformal partial waves for four point functions for conformal primary scalar fields in conformally invariant theories are obtained. They are defined as eigenfunctions of the differential Casimir operators for the conformal group acting on two variable functions subject to appropriate boundary conditions. As well as the scale dimension $\\Delta$ and spin $\\ell$ the conformal partial waves depend on two parameters $a,b$ related to the dimensions of the operators in the four point function. Expressions for the Mellin transform of conformal partial waves are obtained in terms of polynomials of the Mellin transform variables given in terms of finite sums. Differential operators which change $a,b$ by $\\pm 1$, shift the dimension $d$ by $\\pm 2$ and also change $\\Delta,\\ell$ are found. Previous results for $d=2,4,6$ are recovered. The trivial case of $d=1$ and also $d=3$ are also discussed. For $d=3$ formulae for the conformal partial waves in some restricted cases as a single variable integral representation based on the Bateman transform are found.

  18. Conformational flexibility in biochemical regulation

    SciTech Connect

    Trewhella, J.

    1993-09-01

    Small-angle X-ray and neutron scattering have proven extremely useful for studying the evolutionarily related dumbbell-shaped Ca {sup 2+} -binding proteins calmodulin and troponin C and their interactions with the target proteins whose activity they regulate. Calmodulin contracts about target enzyme binding domains with the common characteristic of having a high propensity for forming a basic, amphipathic a-helix. The contraction is achieved via flexibility in the interconnecting helix region of the molecule that links its two globular domains. This flexibility allows calmodulin to optimize its binding to different arrangements of hydrophobic and charged residues important in forming these complexes. In contrast calmodulin remains extended in its interaction with the catalytic subunit of phosphorylase kinase. There are structural and functional similarities between this interaction and that of troponin C and troponin I. Our most recent neutron scattering experiments confirm our prediction that troponin C also remains extended in this complex. The ability of the dumbbell-shaped Ca {sup 2+} -binding proteins to modulate their conformations via flexibility in the interconnecting helix region in order to accommodate different target binding domains is a remarkable example nature building functional diversity as well as specificity into a compact and unusual shape.

  19. Conformational changes of channelrhodopsin-2.

    PubMed

    Radu, Ionela; Bamann, Christian; Nack, Melanie; Nagel, Georg; Bamberg, Ernst; Heberle, Joachim

    2009-06-01

    Channelrhodopsin-2 (ChR2) is a member of the new class of light-gated ion channels which serve as phototaxis receptors in the green alga Chlamydomonas reinhardtii. The protein is employed in optogenetics where neural circuits are optically stimulated under high spatiotemporal control. Despite its rapidly growing use in physiological experiments, the reaction mechanism of ChR2 is poorly understood. Here, we applied vibrational spectroscopy to trace structural changes of ChR2 after light-excitation of the retinal chromophore. FT-IR difference spectra of the various photocycle intermediates revealed that stages of the photoreaction preceding (P(1) state) and succeeding (P(4)) the conductive state of the channel (P(3)) are associated with large conformational changes of the protein backbone as indicate by strong differences in the amide I bands. Critical hydrogen-bonding changes of protonated carboxylic amino acid side chains (D156, E90) were detected and discussed with regard to the functional mechanism. We used the C128T mutant where the lifetime of P(3) is prolonged and applied FT-IR and resonance Raman spectroscopy to study the conductive P(3) state of ChR2. Finally, a mechanistic model is proposed that links the observed structural changes of ChR2 to the changes in the channel's conductance. PMID:19422231

  20. Toward Focusing Conformational Ensembles on Bioactive Conformations: A Molecular Mechanics/Quantum Mechanics Study.

    PubMed

    Avgy-David, Hannah H; Senderowitz, Hanoch

    2015-10-26

    The identification of bound conformations, namely, conformations adopted by ligands when binding their target is critical for target-based and ligand-based drug design. Bound conformations could be obtained computationally from unbound conformational ensembles generated by conformational search tools. However, these tools also generate many nonrelevant conformations thus requiring a focusing mechanism. To identify such a mechanism, this work focuses on a comparison of energies and structural properties of bound and unbound conformations for a set of FDA approved drugs whose complexes are available in the PDB. Unbound conformational ensembles were initially obtained with three force fields. These were merged, clustered, and reminimized using the same force fields and four QM methods. Bound conformations of all ligands were represented by their crystal structures or by approximations to these structures. Energy differences were calculated between global minima of the unbound state or the Boltzmann averaged energies of the unbound ensemble and the approximated bound conformations. Ligand conformations which resemble the X-ray conformation (RMSD < 1.0 Å) were obtained in 91%-97% and 96%-98% of the cases using the ensembles generated by the individual force fields and the reminimized ensembles, respectively, yet only in 52%-56% (original ensembles) and 47%-65% (reminimized ensembles) as global energy minima. The energy window within which the different methods identified the bound conformation (approximated by its closest local energy minimum) was found to be at 4-6 kcal/mol with respect to the global minimum and marginally lower with respect to a Boltzmann averaged energy of the unbound ensemble. Better approximations to the bound conformation obtained with a constrained minimization using the crystallographic B-factors or with a newly developed Knee Point Detection (KPD) method gave lower values (2-5 kcal/mol). Overall, QM methods gave lower energy differences than force field methods. These energy thresholds could be used for focusing conformational ensembles on bound conformations. For example, when using energy cutoffs which corresponded to retaining 50% and 70% of the ensembles, QM methods and CHARMm offer 60-65% and 80-84% probability of obtaining the bound conformation, respectively. In contrast, none of the structural criteria considered in this work was able to differentiate between bound and unbound conformations. PMID:26406154

  1. Conformity, Anticonformity, andIndependence: Their Dimensionality and Generality

    ERIC Educational Resources Information Center

    Stricker, Lawrence J.; And Others

    1970-01-01

    Examines response to group pressure involving different judgments and social situations. One bipolar dimension included conformity and anticonformity, the other, conformity and independence. Tables, graphs, and bibliography. (RW)

  2. The conformal Killing equation on forms -- prolongations and applications

    E-print Network

    A. Rod Gover; Josef Silhan

    2006-01-31

    We construct a conformally invariant vector bundle connection such that its equation of parallel transport is a first order system that gives a prolongation of the conformal Killing equation on differential forms. Parallel sections of this connection are related bijectively to solutions of the conformal Killing equation. We construct other conformally invariant connections, also giving prolongations of the conformal Killing equation, that bijectively relate solutions of the conformal Killing equation on $k$-forms to a twisting of the conformal Killing equation on (k - l)-forms for various integers l. These tools are used to develop a helicity raising and lowering construction in the general setting and on conformally Einstein manifolds.

  3. Structure, Intent and Conformance Monitoring in ATC

    NASA Technical Reports Server (NTRS)

    Reynolds, Tom G.; Histon, Jonathan M.; Davison, Hayley J.; Hansman, R. John

    2004-01-01

    Infield studies of current Air Traffic Control operations it is found that controllers rely on underlying airspace structure to reduce the complexity of the planning and conformance monitoring tasks. The structure appears to influence the controller's working mental model through abstractions that reduce the apparent cognitive complexity. These structure-based abstractions are useful for the controller's key tasks of planning, implementing, monitoring, and evaluating tactical situations. In addition, the structure-based abstractions appear to be important in the maintenance of Situation Awareness. The process of conformance monitoring is analyzed in more detail and an approach to conformance monitoring which utilizes both the structure-based abstractions and intent is presented.

  4. Twisted conformal algebra related to ? -Minkowski space

    NASA Astrophysics Data System (ADS)

    Meljanac, Stjepan; Pacho?, Anna; Pikuti?, Danijel

    2015-11-01

    Twisted deformations of the conformal symmetry in the Hopf algebraic framework are constructed. The first one is obtained by a Jordanian twist built up from dilatation and momenta generators. The second is the lightlike ? -deformation of the Poincaré algebra extended to the conformal algebra, obtained by a twist corresponding to the extended Jordanian r -matrix. The ? -Minkowski spacetime is covariant quantum space under both of these deformations. The extension of the conformal algebra by the noncommutative coordinates is presented in two cases. The differential realizations for ? -Minkowski coordinates, as well as their left-right dual counterparts, are also included.

  5. Scale without Conformal Invariance: An Example

    E-print Network

    Jean-François Fortin; Benjamín Grinstein; Andreas Stergiou

    2015-09-11

    We give an explicit example of a model in D=4-epsilon space-time dimensions that is scale but not conformally invariant, is unitary, and has finite correlators. The invariance is associated with a limit cycle renormalization group (RG) trajectory. We also prove, to second order in the loop expansion, in D=4-epsilon, that scale implies conformal invariance for models of any number of real scalars. For models with one real scalar and any number of Weyl spinors we show that scale implies conformal invariance to all orders in perturbation theory.

  6. Conformal Gravity: Dark Matter and Dark Energy

    E-print Network

    Robert K. Nesbet

    2013-01-13

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

  7. Conformational and Vibrational Studies of Triclosan

    NASA Astrophysics Data System (ADS)

    Özi?ik, Haci; Bayari, S. Haman; Sa?lam, Semran

    2010-01-01

    The conformational equilibrium of triclosan (5-chloro-2-(2, 4-dichlorophenoxy) phenol) have been calculated using density functional theory (DFTe/B3LYP/6-311++G(d, p)) method. Four different geometries were found to correspond to energy minimum conformations. The IR spectrum of triclosan was measured in the 4000-400 cm-1 region. We calculated the harmonic frequencies and intensities of the most stable conformers in order to assist in the assignment of the vibrational bands in the experimental spectrum. The fundamental vibrational modes were characterized depending on their total energy distribution (TED%) using scaled quantum mechanical (SQM) force field method.

  8. Matching univalent functions and conformal welding

    E-print Network

    Grong, Erlend; Vasil'ev, Alexander

    2008-01-01

    Given a conformal mapping $f$ of the unit disk $\\mathbb D$ onto a simply connected domain $D$ in the complex plane bounded by a closed Jordan curve, we consider the problem of constructing a matching conformal mapping, i.e., the mapping of the exterior of the unit disk $\\mathbb D^*$ onto the exterior domain $D^*$ regarding to $D$. The answer is expressed in terms of a linear differential equation with a driving term given as the kernel of an operator dependent on the original mapping $f$. Examples are provided. This study is related to the problem of conformal welding and to representation of the Virasoro algebra in the space of univalent functions.

  9. Matching univalent functions and conformal welding

    E-print Network

    Erlend Grong; Pavel Gumenyuk; Alexander Vasil'ev

    2008-06-05

    Given a conformal mapping $f$ of the unit disk $\\mathbb D$ onto a simply connected domain $D$ in the complex plane bounded by a closed Jordan curve, we consider the problem of constructing a matching conformal mapping, i.e., the mapping of the exterior of the unit disk $\\mathbb D^*$ onto the exterior domain $D^*$ regarding to $D$. The answer is expressed in terms of a linear differential equation with a driving term given as the kernel of an operator dependent on the original mapping $f$. Examples are provided. This study is related to the problem of conformal welding and to representation of the Virasoro algebra in the space of univalent functions.

  10. On Conformal Conic Mappings of Spherical Domains

    PubMed Central

    Bourchtein, Ludmila

    2014-01-01

    The problem of the generation of homogeneous grids for spherical domains is considered in the class of conformal conic mappings. The equivalence between secant and tangent projections is shown and splitting the set of conformal conic mappings into equivalence classes is presented. The problem of minimization of the mapping factor variation is solved in the class of conformal conic mappings. Obtained results can be used in applied sciences, such as geophysical fluid dynamics and cartography, where the flattening of the Earth surface is required. PMID:24558337

  11. Single Molecule Conformational Memory Extraction: P5ab RNA Hairpin

    PubMed Central

    2015-01-01

    Extracting kinetic models from single molecule data is an important route to mechanistic insight in biophysics, chemistry, and biology. Data collected from force spectroscopy can probe discrete hops of a single molecule between different conformational states. Model extraction from such data is a challenging inverse problem because single molecule data are noisy and rich in structure. Standard modeling methods normally assume (i) a prespecified number of discrete states and (ii) that transitions between states are Markovian. The data set is then fit to this predetermined model to find a handful of rates describing the transitions between states. We show that it is unnecessary to assume either (i) or (ii) and focus our analysis on the zipping/unzipping transitions of an RNA hairpin. The key is in starting with a very broad class of non-Markov models in order to let the data guide us toward the best model from this very broad class. Our method suggests that there exists a folding intermediate for the P5ab RNA hairpin whose zipping/unzipping is monitored by force spectroscopy experiments. This intermediate would not have been resolved if a Markov model had been assumed from the onset. We compare the merits of our method with those of others. PMID:24898871

  12. Raman, infrared and microwave spectra, r0 structural parameters, and conformational stability of isopropylisocyanate

    NASA Astrophysics Data System (ADS)

    Durig, James R.; Deodhar, Bhushan S.; Zhou, Sarah Xiaohua; Herrebout, Wouter; Dom, Johan J. J.; van der Veken, Benjamin J.; Gounev, Todor K.

    2015-11-01

    The microwave spectrum of isopropylisocyanate, (CH3)2CHNCO, has been investigated from 11,000 to 21,000 MHz and 18 transitions for the more stable trans conformer were assigned and A = 6693.23(15), B = 2263.10(3), C = 1960.05(2) MHz were obtained. By utilizing these rotational constants along with ab initio MP2(full)/6-311 + G(d,p) predicted structural values, adjusted r0 parameters have been obtained for the trans conformer along with estimated values for the gauche conformer. Variable temperature Raman and infrared spectra of xenon solutions have been recorded and a ?H value of 115 ± 11 cm-1 (1.38 ± 0.13 kJ/mol) has been determined. The conformational stabilities have been predicted from ab initio calculations utilizing several different basis sets up to cc-PVQZ for MP2(full) and 6-311 + G(3df,3pd) for density functional theory calculations by the B3LYP method. From the MP2(full)/cc-PVQZ calculations an energy difference of 87 cm-1 (1.04 kJ/mol) is predicted between the trans and the gauche forms and 168 cm-1 (2.01 kJ/mol) for the cis form which is a transition state.

  13. Metric transition

    NASA Technical Reports Server (NTRS)

    1992-01-01

    This report describes NASA's metric transition in terms of seven major program elements. Six are technical areas involving research, technology development, and operations; they are managed by specific Program Offices at NASA Headquarters. The final program element, Institutional Management, covers both NASA-wide functional management under control of NASA Headquarters and metric capability development at the individual NASA Field Installations. This area addresses issues common to all NASA program elements, including: Federal, state, and local coordination; standards; private industry initiatives; public-awareness initiatives; and employee training. The concluding section identifies current barriers and impediments to metric transition; NASA has no specific recommendations for consideration by the Congress.

  14. Conformal Ricci and Matter Collineations for Anisotropic Fluid

    E-print Network

    M. Sharif; Naghmana Tehseen

    2007-07-20

    We study the consequences of timelike and spaccelike conformal Ricci and conformal matter collineations for anisotropic fluid in the context of General Relativity. Necessary and sufficient conditions are derived for a spacetime with anisotropic fluid to admit conformal Ricci and conformal matter collineations parallel to u^a and x^a. These conditions for timelike and spacelike conformal Ricci and conformal matter collineations for anisotropic fluid reduce to the conditions of perfect fluid when the heat flux and the traceless anisotropic stress tensor vanish. Further, for $\\alpha=0$ (the conformal factor), we recover the earlier results of Ricci collineations and matter collineations in each case of timelike and spacelike conformal Ricci collineations and conformal matter collineations for the perfect fluid. Thus our results give the generalization of the results already available in the literature. It is worth noticing that the conditions of conformal matter collineations can be derived from the conditions of conformal Ricci collineations or vice versa under certain constraints.

  15. Fat/Dachsous Signaling Promotes Drosophila Wing Growth by Regulating the Conformational State of the NDR Kinase Warts.

    PubMed

    Vrabioiu, Alina M; Struhl, Gary

    2015-12-21

    Nuclear Dbf2-related (NDR) kinases play a central role in limiting growth in most animals. Signals that promote growth do so in part by suppressing the activation of NDR kinases by STE20/Hippo kinases. Here, we identify another mechanism for downregulating NDR kinase activity. Specifically, we show that activity of the Drosophila NDR kinase Warts in the developing wing depends on its transition from an inactive, "closed" conformation to a potentially active, "open" conformation mediated by Mats, a conserved Mps1-binder (Mob) protein. Further, we show that signaling interactions between the protocadherins Fat and Dachsous, organized by the morphogens Wingless and Decapentaplegic, suppress Warts by acting via the atypical myosin Dachs to inhibit or reverse this transition. The regulation of Warts conformation by Mats, Fat/Dachsous signaling, and Dachs appears independent of Warts phosphorylation by Hippo kinase, establishing a precedent for the control of NDR kinases, and hence growth, by distinct allosteric and phosphorylation mechanisms. PMID:26702832

  16. Conformation-dependent DNA attraction

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

    Understanding how DNA molecules interact with other biomolecules is related to how they utilize their functions and is therefore critical for understanding their structure-function relationships. For a long time, the existence of Z-form DNA (a left-handed double helical version of DNA, instead of the common right-handed B-form) has puzzled the scientists, and the definitive biological significance of Z-DNA has not yet been clarified. In this study, the effects of DNA conformation in DNA-DNA interactions are explored by molecular dynamics simulations. Using umbrella sampling, we find that for both B- and Z-form DNA, surrounding Mg2+ ions always exert themselves to screen the Coulomb repulsion between DNA phosphates, resulting in very weak attractive force. On the contrary, a tight and stable bound state is discovered for Z-DNA in the presence of Mg2+ or Na+, benefiting from their hydrophobic nature. Based on the contact surface and a dewetting process analysis, a two-stage binding process of Z-DNA is outlined: two Z-DNA first attract each other through charge screening and Mg2+ bridges to phosphate groups in the same way as that of B-DNA, after which hydrophobic contacts of the deoxyribose groups are formed via a dewetting effect, resulting in stable attraction between two Z-DNA molecules. The highlighted hydrophobic nature of Z-DNA interaction from the current study may help to understand the biological functions of Z-DNA in gene transcription.Understanding how DNA molecules interact with other biomolecules is related to how they utilize their functions and is therefore critical for understanding their structure-function relationships. For a long time, the existence of Z-form DNA (a left-handed double helical version of DNA, instead of the common right-handed B-form) has puzzled the scientists, and the definitive biological significance of Z-DNA has not yet been clarified. In this study, the effects of DNA conformation in DNA-DNA interactions are explored by molecular dynamics simulations. Using umbrella sampling, we find that for both B- and Z-form DNA, surrounding Mg2+ ions always exert themselves to screen the Coulomb repulsion between DNA phosphates, resulting in very weak attractive force. On the contrary, a tight and stable bound state is discovered for Z-DNA in the presence of Mg2+ or Na+, benefiting from their hydrophobic nature. Based on the contact surface and a dewetting process analysis, a two-stage binding process of Z-DNA is outlined: two Z-DNA first attract each other through charge screening and Mg2+ bridges to phosphate groups in the same way as that of B-DNA, after which hydrophobic contacts of the deoxyribose groups are formed via a dewetting effect, resulting in stable attraction between two Z-DNA molecules. The highlighted hydrophobic nature of Z-DNA interaction from the current study may help to understand the biological functions of Z-DNA in gene transcription. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr03235c

  17. Structure, Intent & Conformance Monitoring in ATC

    E-print Network

    Reynolds, Tom G.

    In field studies of current Air Traffic Control operations it is found that controllers rely on underlying airspace structure to reduce the complexity of the planning and conformance monitoring tasks. The structure appears ...

  18. Conformal Carroll groups and BMS symmetry

    E-print Network

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

    2014-04-03

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

  19. Conformable apparatus in a drill string

    SciTech Connect

    Hall, David R.; Hall, Jr., H. Tracy; Pixton, David S.; Fox, Joe

    2007-08-28

    An apparatus in a drill string comprises an internally upset drill pipe. The drill pipe comprises a first end, a second end, and an elongate tube intermediate the first and second ends. The elongate tube and the ends comprising a continuous an inside surface with a plurality of diameters. A conformable metal tube is disposed within the drill pipe intermediate the ends thereof and terminating adjacent to the ends of the drill pipe. The conformable metal tube substantially conforms to the continuous inside surface of the metal tube. The metal tube may comprise a non-uniform section which is expanded to conform to the inside surface of the drill pipe. The non-uniform section may comprise protrusions selected from the group consisting of convolutions, corrugations, flutes, and dimples. The non-uniform section extends generally longitudinally along the length of the tube. The metal tube may be adapted to stretch as the drill pipes stretch.

  20. Aluminized fiberglass insulation conforms to curved surfaces

    NASA Technical Reports Server (NTRS)

    1966-01-01

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

  1. Supersymmetric Dualities beyond the Conformal Window

    SciTech Connect

    Spiridonov, V. P.; Vartanov, G. S.

    2010-08-06

    Using the superconformal (SC) indices techniques, we construct Seiberg type dualities for N=1 supersymmetric field theories outside the conformal windows. These theories are physically distinguished by the presence of chiral superfields with small or negative R charges.

  2. Testing Library Specifications by Verifying Conformance Tests

    E-print Network

    Zimmerman, Daniel M.

    Testing Library Specifications by Verifying Conformance Tests Joseph R. Kiniry1 , Daniel M. Formal specifications of standard libraries are necessary when statically verifying software that uses those libraries. Library specifica- tions must be both correct, accurately reflecting library behavior

  3. Isomonodromic ?-functions and W N conformal blocks

    NASA Astrophysics Data System (ADS)

    Gavrylenko, P.

    2015-09-01

    We study the solution of the Schlesinger system for the 4-point s{l}_N isomonodromy problem and conjecture an expression for the isomonodromic ?-function in terms of 2d conformal field theory beyond the known N = 2 Painlevé VI case. We show that this relation can be used as an alternative definition of conformal blocks for the W N algebra and argue that the infinite number of arbitrary constants arising in the algebraic construction of W N conformal block can be expressed in terms of only a finite set of parameters of the monodromy data of rank N Fuchsian system with three regular singular points. We check this definition explicitly for the known conformal blocks of the W 3 algebra and demonstrate its consistency with the conjectured form of the structure constants.

  4. Conformal higher-order viscoelastic fluid mechanics

    E-print Network

    Masafumi Fukuma; Yuho Sakatani

    2012-05-28

    We present a generally covariant formulation of conformal higher-order viscoelastic fluid mechanics with strain allowed to take arbitrarily large values. We give a general prescription to determine the dynamics of a relativistic viscoelastic fluid in a way consistent with the hypothesis of local thermodynamic equilibrium and the second law of thermodynamics. We then elaborately study the transient time scales at which the strain almost relaxes and becomes proportional to the gradients of velocity. We particularly show that a conformal second-order fluid with all possible parameters in the constitutive equations can be obtained without breaking the hypothesis of local thermodynamic equilibrium, if the conformal fluid is defined as the long time limit of a conformal second-order viscoelastic system. We also discuss how local thermodynamic equilibrium could be understood in the context of the fluid/gravity correspondence.

  5. Conformational electroresistance and hysteresis in nanoclusters.

    PubMed

    Li, Xiang-Guo; Zhang, X-G; Cheng, Hai-Ping

    2014-08-13

    The existence of multiple thermodynamically stable isomer states is one of the most fundamental properties of small clusters. This work shows that the conformational dependence of the Coulomb charging energy of a nanocluster leads to a giant electroresistance, where charging induced conformational distortion changes the blockade voltage. The intricate interplay between charging and conformation change is demonstrated in a nanocluster Zn3O4 by combining a first-principles calculation with a temperature-dependent transport model. The predicted hysteretic Coulomb blockade staircase in the current-voltage curve adds another dimension to the rich phenomena of tunneling electroresistance. The new mechanism provides a better controlled and repeatable platform to study conformational electroresistance. PMID:24987929

  6. Conformational electroresistance and hysteresis in nanoclusters

    NASA Astrophysics Data System (ADS)

    Li, Xiang-Guo; Zhang, Xiao-Guang; Cheng, Hai-Ping

    2015-03-01

    Abstract: Existence of multiple thermodynamically stable isomer states is one of the most fundamental properties of small clusters. We show that the conformational dependence of the Coulomb charging energy of a nanocluster leads to a giant electroresistance, where charging induced conformational distortion changes the blockade voltage. The intricate interplay between charging and conformation change is demonstrated in a nanocluster Zn3O4 by combining a first-principles calculation with a temperature-dependent transport model. The predicted hysteretic Coulomb blockade staircase in the current-voltage curve adds another dimension to the rich phenomena of tunneling electroresistance. The new mechanism provides a better controlled and repeatable platform to study conformational electroresistance. Acknowledgement: DOE/BES-DE-FG02-02ER45995; NERSC.

  7. Conformational analysis of cyclo(Phe-Ser) by UVUV and IRUV double resonance spectroscopy and ab initio calculations

    E-print Network

    de Vries, Mattanjah S.

    Conformational analysis of cyclo(Phe-Ser) by UV­UV and IR­UV double resonance spectroscopy and ab Phe-Ser. The R2PI spectrum shows five strong transitions in the region of 37 500­37 900 cmÀ1, we report such comparisons for the cyclic peptide Phe-Ser. We obtained isomer selective vibrational

  8. 75 FR 29537 - Draft Transportation Conformity Guidance for Quantitative Hot-spot Analyses in PM2.5

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-26

    ...Transportation Conformity Guidance for Quantitative Hot- spot Analyses in PM 2.5 and PM...quantitative PM 2.5 and PM 10 hot-spot analyses for project- level transportation...certain highway and transit projects. A hot-spot analysis includes an estimation...

  9. Interplay between conformational selection and induced fit in multidomain proteinligand binding probed by paramagnetic relaxation enhancement

    E-print Network

    Clore, G. Marius

    of conformational space in the vicinity of the holo state. · Partially closed-states may facilitate the transition to the holo state upon ligand binding. G R A P H I C A L A B S T R A C T a b s t r a c ta r t i c l e i n f o rearrangements upon ligand binding from an open apo state to a closed ligand-bound holo state. We show

  10. pH-Induced conformational isomerization of leghemoglobin from Arachis hypogea.

    PubMed

    Basak, P; Pattanayak, R; Nag, S; Bhattacharyya, M

    2014-11-01

    The pH dependence of proteins is related to the thermodynamic stability and electrostatic interactions in the native state of a protein. Here we report the pH-induced conformational transition of the heme protein leghemoglobin (Lb) isolated from root nodules of the leguminous plant Arachis hypogea. Unlike the other heme proteins myoglobin, hemoglobin, and cytochrome c, the structural characteristics and interactions of Lb is almost unknown, though its functional importance is already established since it binds oxygen to maintain the environment for N2 fixation. We investigated pH-induced unfolding of this protein and identified a number of conformational isomers using multiple fluorescence observables as a function of pH titration. We have characterized the acid- and base-induced conformational transitions among the structural states over the pH range 2-11. Depending on the solution conditions, Lb can exist in one of three phases: pH 2, 3, 4; pH 5, 6, 7; pH 8, 9, 10. The secondary structure as revealed by CD spectroscopy indicated the maximum percentage of ?-helix to be present at pH 7, where the structure of Lb is also most rigid according to fluorescence anisotropy experiments. The fluorescence lifetime of tryptophan was observed to be maximum at pH 10 and minimum at pH 6, suggesting unfolding transitions of Lb. Thus, alteration of the microenvironment of the globin moiety during pH transition ultimately leads to the conformational change of this monomeric protein Lb. PMID:25540011

  11. Conformality in many-flavour lattice QCD at strong coupling

    E-print Network

    Philippe de Forcrand; Seyong Kim; Wolfgang Unger

    2013-02-04

    It is widely believed that chiral symmetry is spontaneously broken at zero temperature in the strong coupling limit of staggered fermions, for any number of colors and flavors. Using Monte Carlo simulations, we show that this conventional wisdom, based on a mean-field analysis, is wrong. For sufficiently many fundamental flavors, chiral symmetry is restored via a bulk, first-order transition. This chirally symmetric phase appears to be analytically connected with the expected conformal window of many-flavor continuum QCD. We perform simulations in the chirally symmetric phase at zero quark mass for various system sizes L, and measure the torelon mass, the Dirac spectrum and the hadron spectrum. All masses go to zero with 1/L. L is hence the only infrared length scale. Thus, the strong-coupling chirally restored phase appears as a convenient laboratory to study IR-conformality. Finally, we present a conjecture for the phase diagram of lattice QCD as a function of the bare coupling and the number of quark flavors.

  12. Porphyrin-Mediated Photoinduced Conformational Changes to Albumin

    NASA Astrophysics Data System (ADS)

    Rozinek, Sarah; Brancaleon, Lorenzo

    2011-10-01

    Many biological and nonbiological uses of protoporphyrin-IX (PPIX) depend on its ability to bind large macromolecules such as human serum albumin (HSA). HSA is both biomedically and technologically relevant to PPIX (free base and metal), and its binding site for PPIX-derivatives is well established. The irradiation of PPIX noncovalently bound to BetaLactoglobulin (BLG) is known to cause protein conformational changes that are pH-dependent due to BLG's intrinsic conformational transitions. These processes have not been extensively studied in nonphysiological pH conditions for FePPIX or PPIX bound to HSA. This study implemented a combination of optical and computational methods to compare binding characteristics of hemin and PPIX to HSA as well as structural effects of lowdose irradiation of the ligand on the protein. Spectroscopic data suggests that irradiation of the Soret band of PPIX bound to HSA is capable of modifying the globular protein structure by direct charge transfer between the porphyrin and the binding site at both physiological and acidic pH confirmations. Computational docking simulations predict lower free energy of binding for PPIX than for heme.

  13. Classical Virasoro irregular conformal block II

    E-print Network

    Chaiho Rim; Hong Zhang

    2015-08-18

    We present a new systematic way to evaluate the classical limit of the Virasoro irregular conformal block for arbitrary rank n based on the irregular partition function. In addition, we prove that the classical irregular conformal block has the exponential form as suggested by A. Zamolodchikov and Al. Zamolodchikov for the regular case. We provide an explicit calculation for the rank 2 case in detail.

  14. Condensate mechanism of conformal symmetry breaking

    E-print Network

    V. Pervushin; A. Arbuzov; B. Barbashov; A. Cherny; A. Dorokhov; A. Borowiec; R. Nazmitdinov; A. Pavlov; V. Shilin; A. Zakharov

    2012-11-19

    The low energy Gell-Mann-Oakes-Renner relation, Higgs particle mass value, and the new observational cosmological data are considered as evidence of the condensate mechanism of conformal symmetry breaking at the quantum level. The condensate mechanism occurs by means of normal ordering of field operators in QCD, Minimal Standard Model of electroweak interactions without the Higgs potential, and the Dirac conformal General Relativity with long range forces.

  15. The research of conformal optical design

    NASA Astrophysics Data System (ADS)

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

    2009-07-01

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

  16. Scale-invariant breaking of conformal symmetry

    NASA Astrophysics Data System (ADS)

    Dymarsky, Anatoly; Zhiboedov, Alexander

    2015-10-01

    Known examples of unitary relativistic scale but not conformal-invariant field theories (SFTs) can be embedded into conventional conformal field theories (CFTs). We show that any SFT which is a subsector of a unitary CFT is a free theory. Our discussion applies to an arbitrary number of spacetime dimensions and explains triviality of known SFTs in four spacetime dimensions. We comment on examples of unitary SFTs which are not captured by our construction.

  17. Scale-invariant breaking of conformal symmetry

    E-print Network

    Anatoly Dymarsky; Alexander Zhiboedov

    2015-05-05

    Known examples of unitary relativistic scale but not conformal-invariant field theories (SFTs) can be embedded into conventional conformal field theories (CFTs). We show that any SFT which is a subsector of a unitary CFT is a free theory. Our discussion applies to an arbitrary number of spacetime dimensions and explains triviality of known SFTs in four spacetime dimensions. We comment on examples of unitary SFTs which are not captured by our construction.

  18. Conformally invariant spinorial equations in six dimensions

    NASA Astrophysics Data System (ADS)

    Batista, Carlos

    2016-01-01

    This work deals with the conformal transformations in six-dimensional spinorial formalism. Several conformally invariant equations are obtained and their geometrical interpretations are worked out. Finally, the integrability conditions for some of these equations are established. Moreover, in the course of the article, some useful identities involving the curvature of the spinorial connection are attained and a digression about harmonic forms and more general massless fields is made.

  19. Scale-invariant breaking of conformal symmetry

    E-print Network

    Dymarsky, Anatoly

    2015-01-01

    Known examples of unitary relativistic scale but not conformal-invariant field theories (SFTs) can be embedded into conventional conformal field theories (CFTs). We show that any SFT which is a subsector of a unitary CFT is a free theory. Our discussion applies to an arbitrary number of spacetime dimensions and explains triviality of known SFTs in four spacetime dimensions. We comment on examples of unitary SFTs which are not captured by our construction.

  20. Conformal field theory of Painlevé VI

    NASA Astrophysics Data System (ADS)

    Gamayun, O.; Iorgov, N.; Lisovyy, O.

    2012-10-01

    Generic Painlevé VI tau function ? ( t) can be interpreted as four-point correlator of primary fields of arbitrary dimensions in 2D CFT with c = 1. Using AGT combinatorial representation of conformal blocks and determining the corresponding structure constants, we obtain full and completely explicit expansion of ? ( t) near the singular points. After a check of this expansion, we discuss examples of conformal blocks arising from Riccati, Picard, Chazy and algebraic solutions of Painlevé VI.