Conformal correlation functions in the Brownian loop soup

Science.gov (United States)

Camia, Federico; Gandolfi, Alberto; Kleban, Matthew

2016-01-01

We define and study a set of operators that compute statistical properties of the Brownian loop soup, a conformally invariant gas of random Brownian loops (Brownian paths constrained to begin and end at the same point) in two dimensions. We prove that the correlation functions of these operators have many of the properties of conformal primaries in a conformal field theory, and compute their conformal dimension. The dimensions are real and positive, but have the novel feature that they vary continuously as a periodic function of a real parameter. We comment on the relation of the Brownian loop soup to the free field, and use this relation to establish that the central charge of the loop soup is twice its intensity.

Conformal correlation functions in the Brownian loop soup

Energy Technology Data Exchange (ETDEWEB)

Camia, Federico, E-mail: federico.camia@nyu.edu [New York University Abu Dhabi (United Arab Emirates); VU University, Amsterdam (Netherlands); Gandolfi, Alberto, E-mail: albertogandolfi@nyu.edu [New York University Abu Dhabi (United Arab Emirates); Università di Firenze (Italy); Kleban, Matthew, E-mail: kleban@nyu.edu [New York University Abu Dhabi (United Arab Emirates); Center for Cosmology and Particle Physics, Department of Physics, New York University (United States)

2016-01-15

We define and study a set of operators that compute statistical properties of the Brownian loop soup, a conformally invariant gas of random Brownian loops (Brownian paths constrained to begin and end at the same point) in two dimensions. We prove that the correlation functions of these operators have many of the properties of conformal primaries in a conformal field theory, and compute their conformal dimension. The dimensions are real and positive, but have the novel feature that they vary continuously as a periodic function of a real parameter. We comment on the relation of the Brownian loop soup to the free field, and use this relation to establish that the central charge of the loop soup is twice its intensity.

Conformal correlation functions in the Brownian loop soup

Directory of Open Access Journals (Sweden)

Federico Camia

2016-01-01

Full Text Available We define and study a set of operators that compute statistical properties of the Brownian loop soup, a conformally invariant gas of random Brownian loops (Brownian paths constrained to begin and end at the same point in two dimensions. We prove that the correlation functions of these operators have many of the properties of conformal primaries in a conformal field theory, and compute their conformal dimension. The dimensions are real and positive, but have the novel feature that they vary continuously as a periodic function of a real parameter. We comment on the relation of the Brownian loop soup to the free field, and use this relation to establish that the central charge of the loop soup is twice its intensity.

Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

Science.gov (United States)

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

2011-01-01

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

A test of conformal invariance: Correlation functions on a disk

International Nuclear Information System (INIS)

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

1985-06-01

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

Diagnosing Chaos Using Four-Point Functions in Two-Dimensional Conformal Field Theory.

Science.gov (United States)

Roberts, Daniel A; Stanford, Douglas

2015-09-25

We study chaotic dynamics in two-dimensional conformal field theory through out-of-time-order thermal correlators of the form ⟨W(t)VW(t)V⟩. We reproduce holographic calculations similar to those of Shenker and Stanford, by studying the large c Virasoro identity conformal block. The contribution of this block to the above correlation function begins to decrease exponentially after a delay of ~t_{*}-(β/2π)logβ^{2}E_{w}E_{v}, where t_{*} is the fast scrambling time (β/2π)logc and E_{w},E_{v} are the energy scales of the W,V operators.

Particles and energy fluxes from a conformal field theory perspective

International Nuclear Information System (INIS)

Fabbri, A.; Navarro-Salas, J.; Olmo, G.J.

2004-01-01

We analyze the creation of particles in two dimensions under the action of conformal transformations. We focus our attention on Mobius transformations and compare the usual approach, based on the Bogoliubov coefficients, with an alternative but equivalent viewpoint based on correlation functions. In the latter approach the absence of particle production under full Mobius transformations is manifest. Moreover, we give examples, using the moving-mirror analogy, to illustrate the close relation between the production of quanta and energy

Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis

Directory of Open Access Journals (Sweden)

Bhattacharyya Moitrayee

2010-08-01

Full Text Available Abstract Background One of the major challenges in understanding enzyme catalysis is to identify the different conformations and their populations at detailed molecular level in response to ligand binding/environment. A detail description of the ligand induced conformational changes provides meaningful insights into the mechanism of action of enzymes and thus its function. Results In this study, we have explored the ligand induced conformational changes in H.pylori LuxS and the associated mechanistic features. LuxS, a dimeric protein, produces the precursor (4,5-dihydroxy-2,3-pentanedione for autoinducer-2 production which is a signalling molecule for bacterial quorum sensing. We have performed molecular dynamics simulations on H.pylori LuxS in its various ligand bound forms and analyzed the simulation trajectories using various techniques including the structure network analysis, free energy evaluation and water dynamics at the active site. The results bring out the mechanistic details such as co-operativity and asymmetry between the two subunits, subtle changes in the conformation as a response to the binding of active and inactive forms of ligands and the population distribution of different conformations in equilibrium. These investigations have enabled us to probe the free energy landscape and identify the corresponding conformations in terms of network parameters. In addition, we have also elucidated the variations in the dynamics of water co-ordination to the Zn2+ ion in LuxS and its relation to the rigidity at the active sites. Conclusions In this article, we provide details of a novel method for the identification of conformational changes in the different ligand bound states of the protein, evaluation of ligand-induced free energy changes and the biological relevance of our results in the context of LuxS structure-function. The methodology outlined here is highly generalized to illuminate the linkage between structure and function in

Relationships between functional herd life and conformation traits in ...

African Journals Online (AJOL)

The genetic relationship between conformation traits and functional herd life of the South African Jersey population was investigated. Data on conformation traits (n = 46 238) and functional herd life (n = 90 530) on registered South African Jersey cows calving between 1989 and 2008 were obtained from the Integrated ...

Theoretical study of γ-aminobutyric acid conformers: Intramolecular interactions and ionization energies

Science.gov (United States)

Wang, Ke-Dong; Wang, Mei-Ting; Meng, Ju

2014-10-01

Allowing for all combinations of internal single-bond rotamers, 1,296 unique trial structures of γ-Aminobutyric acid (GABA) are obtained. All of these structures are optimized at the M06-2X level of theory and a total of 68 local minimal conformers are found. The nine low-lying conformers are used for further studies. According to the calculated relative Gibbs free energies at M06-2X level of theory, we find that the dispersion is important for the relative energy of GABA. The intramolecular hydrogen bonds and hyperconjugative interaction and their effects on the conformational stability are studied. The results show that both of them have great influence on the conformers. The vertical ionization energies (VIE) are calculated and match the experimental data well. The results show that the neutral GABA in the gas phase is a multi-conformer system and at least four conformations exist.

Wormhole supported by dark energy admitting conformal motion

Energy Technology Data Exchange (ETDEWEB)

Bhar, Piyali [Government General Degree College, Singur, Department of Mathematics, Hooghly, West Bengal (India); Rahaman, Farook; Banerjee, Ayan [Jadavpur University, Department of Mathematics, Kolkata, West Bengal (India); Manna, Tuhina [St. Xavier' s College, Department of Mathematics and Statistics (Commerce Evening), Kolkata, West Bengal (India)

2016-12-15

In this article, we study the possibility of sustaining static and spherically symmetric traversable wormhole geometries admitting conformal motion in Einstein gravity, which presents a more systematic approach to search a relation between matter and geometry. In wormhole physics, the presence of exotic matter is a fundamental ingredient and we show that this exotic source can be dark energy type which support the existence of wormhole spacetimes. In this work we model a wormhole supported by dark energy which admits conformal motion. We also discuss the possibility of the detection of wormholes in the outer regions of galactic halos by means of gravitational lensing. Studies of the total gravitational energy for the exotic matter inside a static wormhole configuration are also performed. (orig.)

Energy of knots and conformal geometry

CERN Document Server

O'Hara, Jun

2003-01-01

Energy of knots is a theory that was introduced to create a "canonical configuration" of a knot - a beautiful knot which represents its knot type. This book introduces several kinds of energies, and studies the problem of whether or not there is a "canonical configuration" of a knot in each knot type. It also considers this problems in the context of conformal geometry. The energies presented in the book are defined geometrically. They measure the complexity of embeddings and have applications to physical knotting and unknotting through numerical experiments. Contents: In Search of the "Optima

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

Science.gov (United States)

Sullivan, David C; Lim, Carmay

2006-08-24

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

Conformational regulation of urokinase receptor function

DEFF Research Database (Denmark)

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

2011-01-01

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

Narrowband NIR-Induced In Situ Generation of the High-Energy Trans Conformer of Trichloroacetic Acid Isolated in Solid Nitrogen and its Spontaneous Decay by Tunneling to the Low-Energy Cis Conformer

Directory of Open Access Journals (Sweden)

R. F. G. Apóstolo

2015-12-01

Full Text Available The monomeric form of trichloroacetic acid (CCl3COOH; TCA was isolated in a cryogenic nitrogen matrix (15 K and the higher energy trans conformer (O=C–O–H dihedral: 180° was generated in situ by narrowband near-infrared selective excitation the 1st OH stretching overtone of the low-energy cis conformer (O=C–O–H dihedral: 0°. The spontaneous decay, by tunneling, of the generated high-energy conformer into the cis form was then evaluated and compared with those observed previously for the trans conformers of acetic and formic acids in identical experimental conditions. The much faster decay of the high-energy conformer of TCA compared to both formic and acetic acids (by ~35 and ca. 25 times, respectively was found to correlate well with the lower energy barrier for the trans→cis isomerization in the studied compound. The experimental studies received support from quantum chemistry calculations undertaken at the DFT(B3LYP/cc-pVDZ level of approximation, which allowed a detailed characterization of the potential energy surface of the molecule and the detailed assignment of the infrared spectra of the two conformers.

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

Science.gov (United States)

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

2004-12-01

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

The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery.

Directory of Open Access Journals (Sweden)

Lili X Peng

2014-02-01

Full Text Available αβ-tubulin dimers need to convert between a 'bent' conformation observed for free dimers in solution and a 'straight' conformation required for incorporation into the microtubule lattice. Here, we investigate the free energy landscape of αβ-tubulin using molecular dynamics simulations, emphasizing implications for models of assembly, and modulation of the conformational landscape by colchicine, a tubulin-binding drug that inhibits microtubule polymerization. Specifically, we performed molecular dynamics, potential-of-mean force simulations to obtain the free energy profile for unpolymerized GDP-bound tubulin as a function of the ∼12° intradimer rotation differentiating the straight and bent conformers. Our results predict that the unassembled GDP-tubulin heterodimer exists in a continuum of conformations ranging between straight and bent, but, in agreement with existing structural data, suggests that an intermediate bent state has a lower free energy (by ∼1 kcal/mol and thus dominates in solution. In agreement with predictions of the lattice model of microtubule assembly, lateral binding of two αβ-tubulins strongly shifts the conformational equilibrium towards the straight state, which is then ∼1 kcal/mol lower in free energy than the bent state. Finally, calculations of colchicine binding to a single αβ-tubulin dimer strongly shifts the equilibrium toward the bent states, and disfavors the straight state to the extent that it is no longer thermodynamically populated.

Dimensional oscillation. A fast variation of energy embedding gives good results with the AMBER potential energy function.

Science.gov (United States)

Snow, M E; Crippen, G M

1991-08-01

The structure of the AMBER potential energy surface of the cyclic tetrapeptide cyclotetrasarcosyl is analyzed as a function of the dimensionality of coordinate space. It is found that the number of local energy minima decreases as the dimensionality of the space increases until some limit at which point equipotential subspaces appear. The applicability of energy embedding methods to finding global energy minima in this type of energy-conformation space is explored. Dimensional oscillation, a computationally fast variant of energy embedding is introduced and found to sample conformation space widely and to do a good job of finding global and near-global energy minima.

The effect of tensile stress on the conformational free energy landscape of disulfide bonds.

Directory of Open Access Journals (Sweden)

Padmesh Anjukandi

Full Text Available Disulfide bridges are no longer considered to merely stabilize protein structure, but are increasingly recognized to play a functional role in many regulatory biomolecular processes. Recent studies have uncovered that the redox activity of native disulfides depends on their C-C-S-S dihedrals, χ2 and χ'2. Moreover, the interplay of chemical reactivity and mechanical stress of disulfide switches has been recently elucidated using force-clamp spectroscopy and computer simulation. The χ2 and χ'2 angles have been found to change from conformations that are open to nucleophilic attack to sterically hindered, so-called closed states upon exerting tensile stress. In view of the growing evidence of the importance of C-C-S-S dihedrals in tuning the reactivity of disulfides, here we present a systematic study of the conformational diversity of disulfides as a function of tensile stress. With the help of force-clamp metadynamics simulations, we show that tensile stress brings about a large stabilization of the closed conformers, thereby giving rise to drastic changes in the conformational free energy landscape of disulfides. Statistical analysis shows that native TDi, DO and interchain Ig protein disulfides prefer open conformations, whereas the intrachain disulfide bridges in Ig proteins favor closed conformations. Correlating mechanical stress with the distance between the two a-carbons of the disulfide moiety reveals that the strain of intrachain Ig protein disulfides corresponds to a mechanical activation of about 100 pN. Such mechanical activation leads to a severalfold increase of the rate of the elementary redox S(N2 reaction step. All these findings constitute a step forward towards achieving a full understanding of functional disulfides.

On gravitational energy in conformal teleparallel gravity

Science.gov (United States)

da Silva, J. G.; Ulhoa, S. C.

2017-07-01

The paper deals with the definition of gravitational energy in conformal teleparallel gravity. The total energy is defined by means of the field equations which allow a local conservation law. Then such an expression is analyzed for a homogeneous and isotropic Universe. This model is implemented by the Friedmann-Robertson-Walker (FRW) line element. The energy of the Universe in the absence of matter is identified with the dark energy, however it can be expanded for curved models defining such an energy as the difference between the total energy and the energy of the perfect fluid which is the matter field in the FRW model.

Experimental parameterization of an energy function for the simulation of unfolded proteins

DEFF Research Database (Denmark)

Norgaard, A.B.; Ferkinghoff-Borg, Jesper; Lindorff-Larsen, K.

2008-01-01

The determination of conformational preferences in unfolded and disordered proteins is an important challenge in structural biology. We here describe an algorithm to optimize energy functions for the simulation of unfolded proteins. The procedure is based on the maximum likelihood principle and e...... and can be applied to a range of experimental data and energy functions including the force fields used in molecular dynamics simulations.......The determination of conformational preferences in unfolded and disordered proteins is an important challenge in structural biology. We here describe an algorithm to optimize energy functions for the simulation of unfolded proteins. The procedure is based on the maximum likelihood principle...

Conformal scalar field on the hyperelliptic curve and critical Ashkin-Teller multipoint correlation functions

International Nuclear Information System (INIS)

Zamolodchikov, A.B.

1987-01-01

A multipoint conformal block of Ramond states of the two-dimensional free scalar field is calculated. This function is related to the free energy of the scalar field on the hyperelliptic Riemann surface under a particular choice of boundary conditions. Being compactified on the circle this field leads to the crossing symmetric correlation functions with a discrete spectrum of scale dimensions. These functions are supposed to describe multipoint spin correlations of the critical Ashkin-Teller model. (orig.)

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

Science.gov (United States)

Otero, Toribio F

2017-01-18

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

Conformable Fractional Bessel Equation and Bessel Functions

OpenAIRE

Gökdoğan, Ahmet; Ünal, Emrah; Çelik, Ercan

2015-01-01

In this work, we study the fractional power series solutions around regular singular point x=0 of conformable fractional Bessel differential equation and fractional Bessel functions. Then, we compare fractional solutions with ordinary solutions. In addition, we present certain property of fractional Bessel functions.

Searching for dark matter-dark energy interactions: Going beyond the conformal case

Science.gov (United States)

van de Bruck, Carsten; Mifsud, Jurgen

2018-01-01

We consider several cosmological models which allow for nongravitational direct couplings between dark matter and dark energy. The distinguishing cosmological features of these couplings can be probed by current cosmological observations, thus enabling us to place constraints on these specific interactions which are composed of the conformal and disformal coupling functions. We perform a global analysis in order to independently constrain the conformal, disformal, and mixed interactions between dark matter and dark energy by combining current data from: Planck observations of the cosmic microwave background radiation anisotropies, a combination of measurements of baryon acoustic oscillations, a supernova type Ia sample, a compilation of Hubble parameter measurements estimated from the cosmic chronometers approach, direct measurements of the expansion rate of the Universe today, and a compilation of growth of structure measurements. We find that in these coupled dark-energy models, the influence of the local value of the Hubble constant does not significantly alter the inferred constraints when we consider joint analyses that include all cosmological probes. Moreover, the parameter constraints are remarkably improved with the inclusion of the growth of structure data set measurements. We find no compelling evidence for an interaction within the dark sector of the Universe.

Conformal invariance and pion wave functions of nonleading twist

International Nuclear Information System (INIS)

Braun, V.M.; Filyanov, I.E.

1989-01-01

The restrictions are studied for the general structure of pion wave functions of twist 3 and twist 4 imposed by the conformal symmetry and the equations of motion. A systematic expansion of wave functions in the conformal spin is built and the first order corrections to asymptotic formulae are calculated by the QCD sum rule method. In particular, we have found a multiplicatively renormalizable contribution into the two-particle wave function of twist 4 which cannot be expanded in a finite set of Gegenbauer polynomials. 19 refs.; 5 figs

Conformal and Nearly Conformal Theories at Large N

Science.gov (United States)

Tarnoplskiy, Grigory M.

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

Infinite-component conformal fields. Spectral representation of the two-point function

International Nuclear Information System (INIS)

Zaikov, R.P.; Tcholakov, V.

1975-01-01

The infinite-component conformal fields (with respect to the stability subgroup) are considered. The spectral representation of the conformally invariant two-point function is obtained. This function is nonvanishing as/lso for one ''fundamental'' and one infinite-component field

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

Science.gov (United States)

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

1997-08-01

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

Conformal four point functions and the operator product expansion

International Nuclear Information System (INIS)

Dolan, F.A.; Osborn, H.

2001-01-01

Various aspects of the four point function for scalar fields in conformally invariant theories are analysed. This depends on an arbitrary function of two conformal invariants u,v. A recurrence relation for the function corresponding to the contribution of an arbitrary spin field in the operator product expansion to the four point function is derived. This is solved explicitly in two and four dimensions in terms of ordinary hypergeometric functions of variables z,x which are simply related to u,v. The operator product expansion analysis is applied to the explicit expressions for the four point function found for free scalar, fermion and vector field theories in four dimensions. The results for four point functions obtained by using the AdS/CFT correspondence are also analysed in terms of functions related to those appearing in the operator product discussion

Hawking–Hayward quasi-local energy under conformal transformations

International Nuclear Information System (INIS)

Prain, Angus; Faraoni, Valerio; Lapierre-Léonard, Marianne; Vitagliano, Vincenzo

2016-01-01

We derive a formula describing the transformation of the Hawking–Hayward quasi-local energy under a conformal rescaling of the spacetime metric. A known formula for the transformation of the Misner–Sharp–Hernandez mass is recovered as a special case. (paper)

Efficient free energy calculations for compounds with multiple stable conformations separated by high energy barriers

NARCIS (Netherlands)

Hritz, J.; Oostenbrink, C.

2009-01-01

Compounds with high intramolecular energy barriers represent challenging targets for free energy calculations because of the difficulty to obtain sufficient conformational sampling. Existing approaches are therefore computationally very demanding, thus preventing practical applications for such

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

KAUST Repository

Wang, Wei

2017-10-06

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

Couplings between hierarchical conformational dynamics from multi-time correlation functions and two-dimensional lifetime spectra: Application to adenylate kinase

Energy Technology Data Exchange (ETDEWEB)

Ono, Junichi [Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585 (Japan); Takada, Shoji [Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585 (Japan); Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan); Saito, Shinji, E-mail: shinji@ims.ac.jp [Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585 (Japan); The Graduate University for Advanced Studies, Okazaki 444-8585 (Japan)

2015-06-07

An analytical method based on a three-time correlation function and the corresponding two-dimensional (2D) lifetime spectrum is developed to elucidate the time-dependent couplings between the multi-timescale (i.e., hierarchical) conformational dynamics in heterogeneous systems such as proteins. In analogy with 2D NMR, IR, electronic, and fluorescence spectroscopies, the waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra can provide a quantitative description of the dynamical correlations between the conformational motions with different lifetimes. The present method is applied to intrinsic conformational changes of substrate-free adenylate kinase (AKE) using long-time coarse-grained molecular dynamics simulations. It is found that the hierarchical conformational dynamics arise from the intra-domain structural transitions among conformational substates of AKE by analyzing the one-time correlation functions and one-dimensional lifetime spectra for the donor-acceptor distances corresponding to single-molecule Förster resonance energy transfer experiments with the use of the principal component analysis. In addition, the complicated waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra for the donor-acceptor distances is attributed to the fact that the time evolution of the couplings between the conformational dynamics depends upon both the spatial and temporal characters of the system. The present method is expected to shed light on the biological relationship among the structure, dynamics, and function.

Measurement of conformability and adhesion energy of polymeric ultrathin film to skin model

Science.gov (United States)

Sugano, Junki; Fujie, Toshinori; Iwata, Hiroyasu; Iwase, Eiji

2018-06-01

We measured the conformability and adhesion energy of a polymeric ultrathin film “nanosheet” with hundreds of nanometer thickness to a skin model with epidermal depressions. To compare the confirmability of the nanosheets with different thicknesses and/or under different attaching conditions, we proposed a measurement method using skin models with the same surface profile and defined the surface strain εS as the quantified value of the conformability. Then, we measured the adhesion energy of the nanosheet at each conformability through a vertical tensile test. Experimental results indicate that the adhesion energy does not depend on the liquid used in wetting the nanosheet before attaching to the skin model and increases monotonously as the surface strain εS increases.

Energy conditions of non-singular black hole spacetimes in conformal gravity

International Nuclear Information System (INIS)

Toshmatov, Bobir; Bambi, Cosimo; Ahmedov, Bobomurat; Abdujabbarov, Ahmadjon; Stuchlik, Zdenek

2017-01-01

Conformal gravity can elegantly solve the problem of spacetime singularities present in Einstein's gravity. For every physical spacetime, there is an infinite family of conformally equivalent singularity-free metrics. In the unbroken phase, every non-singular metric is equivalent and can be used to infer the physical properties of the spacetime. In the broken phase, a Higgs-like mechanism should select a certain vacuum, which thus becomes the physical one. However, in the absence of the complete theoretical framework we do not know how to select the right vacuum. In this paper, we study the energy conditions of non-singular black hole spacetimes obtained in conformal gravity assuming they are solutions of Einstein's gravity with an effective energy-momentum tensor. We check whether such conditions can be helpful to select the vacuum of the broken phase. (orig.)

Energy conditions of non-singular black hole spacetimes in conformal gravity

Energy Technology Data Exchange (ETDEWEB)

Toshmatov, Bobir [Silesian University in Opava, Faculty of Philosophy and Science, Institute of Physics, Opava (Czech Republic); Ulugh Beg Astronomical Institute, Tashkent (Uzbekistan); Bambi, Cosimo [Fudan University, Department of Physics, Center for Field Theory and Particle Physics, Shanghai (China); Eberhard-Karls Universitaet Tuebingen, Theoretical Astrophysics, Tuebingen (Germany); Ahmedov, Bobomurat [Ulugh Beg Astronomical Institute, Tashkent (Uzbekistan); National University of Uzbekistan, Tashkent (Uzbekistan); Abdujabbarov, Ahmadjon [Ulugh Beg Astronomical Institute, Tashkent (Uzbekistan); National University of Uzbekistan, Tashkent (Uzbekistan); Tashkent University of Information Technologies, Tashkent (Uzbekistan); Stuchlik, Zdenek [Silesian University in Opava, Faculty of Philosophy and Science, Institute of Physics, Opava (Czech Republic)

2017-08-15

Conformal gravity can elegantly solve the problem of spacetime singularities present in Einstein's gravity. For every physical spacetime, there is an infinite family of conformally equivalent singularity-free metrics. In the unbroken phase, every non-singular metric is equivalent and can be used to infer the physical properties of the spacetime. In the broken phase, a Higgs-like mechanism should select a certain vacuum, which thus becomes the physical one. However, in the absence of the complete theoretical framework we do not know how to select the right vacuum. In this paper, we study the energy conditions of non-singular black hole spacetimes obtained in conformal gravity assuming they are solutions of Einstein's gravity with an effective energy-momentum tensor. We check whether such conditions can be helpful to select the vacuum of the broken phase. (orig.)

CONFORMATIONAL SEARCH BY POTENTIAL-ENERGY ANNEALING - ALGORITHM AND APPLICATION TO CYCLOSPORINE-A

NARCIS (Netherlands)

VANSCHAIK, RC; VANGUNSTEREN, WF; BERENDSEN, HJC

A major problem in modelling (biological) macromolecules is the search for low-energy conformations. The complexity of a conformational search problem increases exponentially with the number of degrees of freedom which means that a systematic search can only be performed for very small structures.

The RNA Exosome Channeling and Direct Access Conformations Have Distinct In Vivo Functions

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Jaeil Han

2016-09-01

Full Text Available The RNA exosome is a 3′–5′ ribonuclease complex that is composed of nine core subunits and an essential catalytic subunit, Rrp44. Two distinct conformations of Rrp44 were revealed in previous structural studies, suggesting that Rrp44 may change its conformation to exert its function. In the channeling conformation, (Rrp44ch, RNA accesses the active site after traversing the central channel of the RNA exosome, whereas in the other conformation, (Rrp44da, RNA gains direct access to the active site. Here, we show that the Rrp44da exosome is important for nuclear function of the RNA exosome. Defects caused by disrupting the direct access conformation are distinct from those caused by channel-occluding mutations, indicating specific functions for each conformation. Our genetic analyses provide in vivo evidence that the RNA exosome employs a direct-access route to recruit specific substrates, indicating that the RNA exosome uses alternative conformations to act on different RNA substrates.

Combined experimental powder X-ray diffraction and DFT data to obtain the lowest energy molecular conformation of friedelin

International Nuclear Information System (INIS)

Oliveira, Djalma Menezes de; Mussel, Wagner da Nova; Duarte, Lucienir Pains; Silva, Gracia Divina de Fatima; Duarte, Helio Anderson; Gomes, Elionai Cassiana de Lima; Guimaraes, Luciana; Vieira Filho, Sidney A.

2012-01-01

Friedelin molecular conformers were obtained by Density Functional Theory (DFT) and by ab initio structure determination from powder X-ray diffraction. Their conformers with the five rings in chair-chair-chair-boat-boat, and with all rings in chair, are energy degenerated in gas-phase according to DFT results. The powder diffraction data reveals that rings A, B and C of friedelin are in chair, and rings D and E in boat-boat, conformation. The high correlation values among powder diffraction data, DFT and reported single crystal data indicate that the use of conventional X-ray diffractometer can be applied in routine laboratory analysis in the absence of a single-crystal diffractometer. (author)

Combined experimental powder X-ray diffraction and DFT data to obtain the lowest energy molecular conformation of friedelin

Energy Technology Data Exchange (ETDEWEB)

Oliveira, Djalma Menezes de; Mussel, Wagner da Nova; Duarte, Lucienir Pains; Silva, Gracia Divina de Fatima; Duarte, Helio Anderson; Gomes, Elionai Cassiana de Lima [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Quimica; Guimaraes, Luciana [Universidade Federal de Sao Joao Del-Rei (UFSJ), MG (Brazil). Dept. de Ciencias Naturais; Vieira Filho, Sidney A., E-mail: bibo@ef.ufop.br [Universidade Federal de Ouro Preto (UFOP), MG (Brazil). Dept. de Farmacia

2012-07-01

Friedelin molecular conformers were obtained by Density Functional Theory (DFT) and by ab initio structure determination from powder X-ray diffraction. Their conformers with the five rings in chair-chair-chair-boat-boat, and with all rings in chair, are energy degenerated in gas-phase according to DFT results. The powder diffraction data reveals that rings A, B and C of friedelin are in chair, and rings D and E in boat-boat, conformation. The high correlation values among powder diffraction data, DFT and reported single crystal data indicate that the use of conventional X-ray diffractometer can be applied in routine laboratory analysis in the absence of a single-crystal diffractometer. (author)

Exploring the conformational energy landscape of proteins

Energy Technology Data Exchange (ETDEWEB)

Nienhaus, G.U. [Univ. of Illinois, Urbana, IL (United States)]|[Universitaet Ulm (Germany); Mueller, J.D.; McMahon, B.H. [Univ. of Illinois, Urbana, IL (United States)] [and others

1997-04-01

Proteins possess a complex energy landscape with a large number of local minima called conformational substates that are arranged in a hierarchical fashion. Here we discuss experiments aimed at the elucidation of the energy landscape in carbonmonoxy myoglobin (MbCO). In the highest tier of the hierarchy, a few taxonomic substates exist. Because of their small number, these substates are accessible to detailed structural investigations. Spectroscopic experiments are discussed that elucidate the role of protonations of amino acid side chains in creating the substates. The lower tiers of the hierarchy contain a large number of statistical substates. Substate interconversions are observed in the entire temperature range from below 1 K up to the denaturation temperature, indicating a wide spectrum of energy barriers that separate the substates.

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

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Stella Fabio

2011-05-01

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

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

Science.gov (United States)

2011-01-01

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

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

Science.gov (United States)

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

2014-07-01

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

Preservation of parotid function with uncomplicated conformal radiotherapy

International Nuclear Information System (INIS)

Maes, Annelies; Weltens, Caroline; Flamen, Patrick; Lambin, Philippe; Bogaerts, Ria; Liu, Xuan; Baetens, Jan; Hermans, Robert; Van den Bogaert, Walter

2002-01-01

Background and purpose: To evaluate (1) parotid function, (2) subjective xerostomia and (3) pattern of relapses after conformal parotid-sparing radiotherapy (RT) for head and neck cancer. (4) To study dose-response curves of parotid glands. Material and methods: From September 1999 to November 2000, 39 head and neck cancer patients requiring bilateral neck RT were treated with a fairly simple conformal RT technique (three-field set-up+anterior lower neck field; two opposed oblique boost fields). The contralateral parotid was spared. Parotid function was assessed by salivary gland scintigraphies performed before, early (median 4 weeks) and late (median 28 weeks) after RT. Xerostomia was monitored by visual analogue scales (VAS) and LENT SOMA scores. Location of locoregional recurrences was studied in relation to the radiation fields. A dose-response curve of parotids was created using logistic regression. Results: (1) Early after RT, on salivary gland scintigraphy, the mean loss of secretion function in the spared parotid was 67% and total in the non-spared. Late after RT, the mean loss remained 19% in the spared and total in the non-spared parotid. Normal excretion function was regained in 75% of the spared parotids. (2) Late after RT, 78% of patients had no, minimal or acceptable subjective xerostomia. (3) No recurrence was seen near the spared parotid (11/39 locoregional recurrences). (4) The dose-response curve of parotids showed that the mean parotid dose should preferentially be ≤20 Gy, to obtain a good chance (≥70%) for preservation of its function on scintigraphy. Conclusions: An easy conformal parotid-sparing RT technique prevents moderate or severe subjective xerostomia in 78% of patients. In the spared parotids, nearly complete to complete recovery is obtained after 6-12 months

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

Science.gov (United States)

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

2011-01-01

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

Binary cluster collision dynamics and minimum energy conformations

Energy Technology Data Exchange (ETDEWEB)

Muñoz, Francisco [Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle (Germany); Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago (Chile); Centro para el Desarrollo de la Nanociencia y Nanotecnología, CEDENNA, Avenida Ecuador 3493, Santiago (Chile); Rogan, José; Valdivia, J.A. [Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago (Chile); Centro para el Desarrollo de la Nanociencia y Nanotecnología, CEDENNA, Avenida Ecuador 3493, Santiago (Chile); Varas, A. [Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago (Chile); Nano-Bio Spectroscopy Group, ETSF Scientific Development Centre, Departamento de Física de Materiales, Universidad del País Vasco UPV/EHU, Av. Tolosa 72, E-20018 San Sebastián (Spain); Kiwi, Miguel, E-mail: m.kiwi.t@gmail.com [Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago (Chile); Centro para el Desarrollo de la Nanociencia y Nanotecnología, CEDENNA, Avenida Ecuador 3493, Santiago (Chile)

2013-10-15

The collision dynamics of one Ag or Cu atom impinging on a Au{sub 12} cluster is investigated by means of DFT molecular dynamics. Our results show that the experimentally confirmed 2D to 3D transition of Au{sub 12}→Au{sub 13} is mostly preserved by the resulting planar Au{sub 12}Ag and Au{sub 12}Cu minimum energy clusters, which is quite remarkable in view of the excess energy, well larger than the 2D–3D potential barrier height. The process is accompanied by a large s−d hybridization and charge transfer from Au to Ag or Cu. The dynamics of the collision process mainly yields fusion of projectile and target, however scattering and cluster fragmentation also occur for large energies and large impact parameters. While Ag projectiles favor fragmentation, Cu favors scattering due to its smaller mass. The projectile size does not play a major role in favoring the fragmentation or scattering channels. By comparing our collision results with those obtained by an unbiased minimum energy search of 4483 Au{sub 12}Ag and 4483 Au{sub 12}Cu configurations obtained phenomenologically, we find that there is an extra bonus: without increase of computer time collisions yield the planar lower energy structures that are not feasible to obtain using semi-classical potentials. In fact, we conclude that phenomenological potentials do not even provide adequate seeds for the search of global energy minima for planar structures. Since the fabrication of nanoclusters is mainly achieved by synthesis or laser ablation, the set of local minima configurations we provide here, and their distribution as a function of energy, are more relevant than the global minimum to analyze experimental results obtained at finite temperatures, and is consistent with the dynamical coexistence of 2D and 3D liquid Au clusters conformations obtained previously.

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

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Qiang Wang

2017-02-01

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

QM/MM Geometry Optimization on Extensive Free-Energy Surfaces for Examination of Enzymatic Reactions and Design of Novel Functional Properties of Proteins.

Science.gov (United States)

Hayashi, Shigehiko; Uchida, Yoshihiro; Hasegawa, Taisuke; Higashi, Masahiro; Kosugi, Takahiro; Kamiya, Motoshi

2017-05-05

Many remarkable molecular functions of proteins use their characteristic global and slow conformational dynamics through coupling of local chemical states in reaction centers with global conformational changes of proteins. To theoretically examine the functional processes of proteins in atomic detail, a methodology of quantum mechanical/molecular mechanical (QM/MM) free-energy geometry optimization is introduced. In the methodology, a geometry optimization of a local reaction center is performed with a quantum mechanical calculation on a free-energy surface constructed with conformational samples of the surrounding protein environment obtained by a molecular dynamics simulation with a molecular mechanics force field. Geometry optimizations on extensive free-energy surfaces by a QM/MM reweighting free-energy self-consistent field method designed to be variationally consistent and computationally efficient have enabled examinations of the multiscale molecular coupling of local chemical states with global protein conformational changes in functional processes and analysis and design of protein mutants with novel functional properties.

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

Directory of Open Access Journals (Sweden)

Karim M. ElSawy

2016-01-01

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

Nilpotent weights in conformal field theory

Directory of Open Access Journals (Sweden)

S. Rouhani

2001-12-01

Full Text Available   Logarithmic conformal field theory can be obtained using nilpotent weights. Using such scale transformations various properties of the theory were derived. The derivation of four point function needs a knowledge of singular vectors which is derived by including nilpotent variables into the Kac determinant. This leads to inhomogeneous hypergeometric functions. Finally we consider the theory near a boundary and also introduce the concept of superfields where a multiplet of conformal fields are dealt with together. This leads to the OPE of superfields and a logarithmic partner for the energy momentum tensor.

Conformal field theories near a boundary in general dimensions

International Nuclear Information System (INIS)

McAvity, D.M.

1995-01-01

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

Conformational Control of Energy Transfer: A Mechanism for Biocompatible Nanocrystal-Based Sensors

OpenAIRE

Kay, Euan R.; Lee, Jungmin; Nocera, Daniel; Bawendi, Moungi G.

2012-01-01

Fold-up fluorophore: A new paradigm for designing self-referencing fluorescent nanosensors is demonstrated by interfacing a pH-triggered molecular conformational switch with quantum dots. Analytedependent, large-amplitude conformational motion controls the distance between the nanocrystal energy donor and an organic FRET acceptor. The result is a fluorescence signal capable of reporting pH values from individual endosomes in living cells.

Millimeter and Submillimeter Wave Spectroscopy of Higher Energy Conformers of 1,2-PROPANEDIOL

Science.gov (United States)

Zakharenko, Olena; Bossa, Jean-Baptiste; Lewen, Frank; Schlemmer, Stephan; Müller, Holger S. P.

2017-06-01

We have performed a study of the millimeter/submillimeter wave spectrum of four higher energy conformers of 1,2-propanediol (continuation of the previous study on the three lowest energy conformers. The present analysis of rotational transitions carried out in the frequency range 38 - 400 GHz represents a significant extension of previous microwave work. The new data were combined with previously-measured microwave transitions and fitted using a Watson's S-reduced Hamiltonian. The final fits were within experimental accuracy, and included spectroscopic parameters up to sixth order of angular momentum, for the ground states of the four higher energy conformers following previously studied ones: g'Ga, gG'g', aGg' and g'Gg. The present analysis provides reliable frequency predictions for astrophysical detection of 1,2-propanediol by radio telescope arrays at millimeter wavelengths. J.-B. Bossa, M.H. Ordu, H.S.P. Müller, F. Lewen, S. Schlemmer, A&A 570 (2014) A12)

Bootstrapping conformal field theories with the extremal functional method.

Science.gov (United States)

El-Showk, Sheer; Paulos, Miguel F

2013-12-13

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

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

International Nuclear Information System (INIS)

Hinterbichler, Kurt; Joyce, Austin; Khoury, Justin

2012-01-01

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

Implications of conformal invariance for quantum field theories in d>2

International Nuclear Information System (INIS)

Osborn, H.

1994-01-01

Recently obtained results for two and three point functions for quasi-primary operators in conformally invariant theories in arbitrary dimensions d are described. As a consequence the three point function for the energy momentum tensor has three linearly independent forms for general d compatible with conformal invariance. The corresponding coefficients may be regarded as possible generalisations of the Virasoro central charge to d larger than 2. Ward identities which link two linear combinations of the coefficients to terms appearing in the energy momentum tensor trace anomaly on curved space are discussed. The requirement of positivity for expectation values of the energy density is also shown to lead to positivity conditions which are simple for a particular choice of the three coefficients. Renormalisation group like equations which express the constraints of broken conformal invariance for quantum field theories away from critical points are postulated and applied to two point functions. (orig.)

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

Directory of Open Access Journals (Sweden)

Fabio Stella

2013-09-01

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

Quantum-chemical study on the bioactive conformation of epothilones.

Science.gov (United States)

Jiménez, Verónica A

2010-12-27

Herein, I report a DFT study on the bioactive conformation of epothilone A based on the analysis of 92 stable conformations of free and bound epothilone to a reduced model of tubulin receptor. The equilibrium structures and relative energies were studied using B3LYP and X3LYP functionals and the 6-31G(d) standard basis set, which was considered appropriate for the size of the systems under study. Calculated relative energies of free and bound epothilones led me to propose a new model for the bioactive conformation of epothilone A, which accounts for several structure-activity data.

On the Conformable Fractional Quantum Mechanics

Science.gov (United States)

Mozaffari, F. S.; Hassanabadi, H.; Sobhani, H.; Chung, W. S.

2018-05-01

In this paper, a conformable fractional quantum mechanic has been introduced using three postulates. Then in such a formalism, Schr¨odinger equation, probability density, probability flux and continuity equation have been derived. As an application of considered formalism, a fractional-radial harmonic oscillator has been considered. After obtaining its wave function and energy spectrum, effects of the conformable fractional parameter on some quantities have been investigated and plotted for different excited states.

Spontaneous Broken Local Conformal Symmetry and Dark Energy Candidate

International Nuclear Information System (INIS)

Liu, Lu-Xin

2013-01-01

The local conformal symmetry is spontaneously broken down to the Local Lorentz invariance symmetry through the approach of nonlinear realization. The resulting effective Lagrangian, in the unitary gauge, describes a cosmological vector field non-minimally coupling to the gravitational field. As a result of the Higgs mechanism, the vector field absorbs the dilaton and becomes massive, but with an independent energy scale. The Proca type vector field can be modelled as dark energy candidate. The possibility that it further triggers Lorentz symmetry violation is also pointed out

Examining Conformity to Masculinity Norms as a Function of RIASEC Vocational Interests

Science.gov (United States)

Mahalik, James R.; Perry, Justin C.; Coonerty-Femiano, Aimee; Catraio, Christine; Land, Lee N.

2006-01-01

The authors examined how college men's conformity to an array of masculinity norms varied as a function of their vocational interests to better understand the gendered context of men's vocational development. Three hundred ten mostly Caucasian and heterosexual college men completed the Conformity to Masculine Norms Inventory, and their answer to…

The dependence of the electronic coupling on energy gap and bridge conformation - Towards prediction of the distance dependence of electron transfer reactions

International Nuclear Information System (INIS)

Eng, Mattias P.; Albinsson, Bo

2009-01-01

The attenuation factor, β, for the distance dependence of electron exchange reactions is a sensitive function of the donor-bridge energy gap and bridge conformation. In this work the electronic coupling for electron and triplet excitation energy transfer has been investigated for five commonly used repeating bridge structures. The investigated bridge structures are OF (oligo fluorene), OP (oligo phenylene), OPE (oligo p-phenyleneethynylene), OPV (oligo phenylenevinylene), and OTP (oligo thiophene). Firstly, the impact of the donor-bridge energy gap was investigated by performing calculations with a variety of donors appended onto bridges that were kept in a planar conformation. This resulted in, to our knowledge, the first presented sets of bridge specific parameters to be inserted into the commonly used McConnell model. Secondly, since at experimental conditions large conformational flexibility is expected, a previously developed model that takes conformational disorder of the bridge into account has been applied to the investigated systems [M.P. Eng, T. Ljungdahl, J. Martensson, B. Albinsson, J. Phys. Chem. B 110 (2006) 6483]. This model is based on Boltzmann averaging and has been shown to describe the temperature dependence of the attenuation factor through OPE-bridges. Together, the parameters describing the donor-bridge energy gap dependence, for planar bridge structures, and the Boltzmann averaging procedure, describing the impact of rotational disorder, have the potential to a priori predict attenuation factors for electron and excitation energy transfer reactions through bridged donor-acceptor systems

Conformally symmetric traversable wormholes

International Nuclear Information System (INIS)

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

2007-01-01

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

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

Science.gov (United States)

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

2015-04-15

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

Irreversibility and higher-spin conformal field theory

CERN Document Server

Anselmi, D

2000-01-01

I discuss the idea that quantum irreversibility is a general principle of nature and a related "conformal hypothesis", stating that all fundamental quantum field theories should be renormalization-group (RG) interpolations between ultraviolet and infrared conformal fixed points. In particular, the Newton constant should be viewed as a low-energy effect of the RG scale. This approach leads naturally to consider higher-spin conformal field theories, which are here classified, as candidate high-energy theories. Bosonic conformal tensors have a positive-definite action, equal to the square of a field strength, and a higher-derivative gauge invariance. The central charges c and a are well defined and positive. I calculate their values and study the operator-product structure. Fermionic theories have no gauge invariance and can be coupled to Abelian and non-Abelian gauge fields in a renormalizable way. At the quantum level, they contribute to the one-loop beta function with the same sign as ordinary matter, admit a...

Energetics of cyclohexane isomers: a density-functional study

International Nuclear Information System (INIS)

Lee, Chang Yol

1999-01-01

The binding energies and the geometric structures of conformational isomers of cyclohexane (C 6 H 12 ) are determined from the density-functional theory combined with ultrasoft pseudopotentials and gradient-corrected nonlocal exchange-correlation functionals. The ground-state chair conformation is found to have a binding energy of 99.457 eV, and the metastable twist-boat conformation has 99.161 eV. The chair conformation converts to another conformation via a half-chair conformation with an energy barrier of 0.507 eV whereas the twist-boat conformation converts to another twist-boat conformation via a boat conformation with a much smaller energy barrier of 0.015 eV

Does human presynaptic striatal dopamine function predict social conformity?

Science.gov (United States)

Stokes, Paul R A; Benecke, Aaf; Puraite, Julita; Bloomfield, Michael A P; Shotbolt, Paul; Reeves, Suzanne J; Lingford-Hughes, Anne R; Howes, Oliver; Egerton, Alice

2014-03-01

Socially desirable responding (SDR) is a personality trait which reflects either a tendency to present oneself in an overly positive manner to others, consistent with social conformity (impression management (IM)), or the tendency to view one's own behaviour in an overly positive light (self-deceptive enhancement (SDE)). Neurochemical imaging studies report an inverse relationship between SDR and dorsal striatal dopamine D₂/₃ receptor availability. This may reflect an association between SDR and D₂/₃ receptor expression, synaptic dopamine levels or a combination of the two. In this study, we used a [¹⁸F]-DOPA positron emission tomography (PET) image database to investigate whether SDR is associated with presynaptic dopamine function. Striatal [¹⁸F]-DOPA uptake, (k(i)(cer), min⁻¹), was determined in two independent healthy participant cohorts (n=27 and 19), by Patlak analysis using a cerebellar reference region. SDR was assessed using the revised Eysenck Personality Questionnaire (EPQ-R) Lie scale, and IM and SDE were measured using the Paulhus Deception Scales. No significant associations were detected between Lie, SDE or IM scores and striatal [¹⁸F]-DOPA k(i)(cer). These results indicate that presynaptic striatal dopamine function is not associated with social conformity and suggests that social conformity may be associated with striatal D₂/₃ receptor expression rather than with synaptic dopamine levels.

Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives

Science.gov (United States)

Marianski, Mateusz; Asensio, Amparo; Dannenberg, J. J.

2012-07-01

We compare the energetic and structural properties of fully optimized α-helical and antiparallel β-sheet polyalanines and the energetic differences between axial and equatorial conformations of three cyclohexane derivatives (methyl, fluoro, and chloro) as calculated using several functionals designed to treat dispersion (B97-D, ωB97x-D, M06, M06L, and M06-2X) with other traditional functionals not specifically parametrized to treat dispersion (B3LYP, X3LYP, and PBE1PBE) and with experimental results. Those functionals developed to treat dispersion significantly overestimate interaction enthalpies of folding for the α-helix and predict unreasonable structures that contain Ramachandran ϕ and ψ and C = O…N H-bonding angles that are out of the bounds of databases compiled the β-sheets. These structures are consistent with overestimation of the interaction energies. For the cyclohexanes, these functionals overestimate the stabilities of the axial conformation, especially when used with smaller basis sets. Their performance improves when the basis set is improved from D95** to aug-cc-pVTZ (which would not be possible with systems as large as the peptides).

Conformational effects in photoelectron circular dichroism

Science.gov (United States)

Turchini, S.

2017-12-01

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

Higher genus partition functions of meromorphic conformal field theories

International Nuclear Information System (INIS)

Gaberdiel, Matthias R.; Volpato, Roberto

2009-01-01

It is shown that the higher genus vacuum amplitudes of a meromorphic conformal field theory determine the affine symmetry of the theory uniquely, and we give arguments that suggest that also the representation content with respect to this affine symmetry is specified, up to automorphisms of the finite Lie algebra. We illustrate our findings with the self-dual theories at c = 16 and c = 24; in particular, we give an elementary argument that shows that the vacuum amplitudes of the E 8 x E 8 theory and the Spin(32)/Z 2 theory differ at genus g = 5. The fact that the discrepancy only arises at rather high genus is a consequence of the modular properties of higher genus amplitudes at small central charges. In fact, we show that for c ≤ 24 the genus one partition function specifies already the partition functions up to g ≤ 4 uniquely. Finally we explain how our results generalise to non-meromorphic conformal field theories.

Conformational explosion: Understanding the complexity of short chain para-dialkylbenzene potential energy surfaces

Science.gov (United States)

Mishra, Piyush; Hewett, Daniel M.; Zwier, Timothy S.

2018-05-01

The single-conformation ultraviolet and infrared spectroscopy of three short-chain para-dialkylbenzenes (para-diethylbenzene, para-dipropylbenzene, and para-dibutylbenzene) is reported for the jet-cooled, isolated molecules. The present study builds off previous work on single-chain n-alkylbenzenes, where an anharmonic local mode Hamiltonian method was developed to account for stretch-bend Fermi resonance in the alkyl CH stretch region [D. P. Tabor et al., J. Chem. Phys. 144, 224310 (2016)]. The jet-cooled molecules are interrogated using laser-induced fluorescence (LIF) excitation, fluorescence dip infrared spectroscopy, and dispersed fluorescence. The LIF spectra in the S1 ← S0 origin region show a dramatic increase in the number of resolved transitions with increasing length of the alkyl chains, reflecting an explosion in the number of unique low-energy conformations formed when two independent alkyl chains are present. Since the barriers to isomerization of the alkyl chain are similar in size, this results in an "egg carton" shaped potential energy surface. A combination of electronic frequency shift and alkyl CH stretch infrared spectra is used to generate a consistent set of conformational assignments. Using these experimental techniques in conjunction with computational methods, subsets of origin transitions in the LIF excitation spectrum can be classified into different conformational families. Two conformations are resolved in para-diethylbenzene, seven in para-dipropylbenzene, and about nineteen in para-dibutylbenzene. These chains are largely independent of each other as there are no new single-chain conformations induced by the presence of a second chain. A cursory LIF excitation scan of para-dioctylbenzene shows a broad congested spectrum at frequencies consistent with interactions of alkyl chains with the phenyl π cloud.

Understanding modern magnets through conformal mapping

International Nuclear Information System (INIS)

Halbach, K.

1989-10-01

I want to show with the help of a number of examples that conformal mapping is a unique and enormously powerful tool for thinking about, and solving, problems. Usually one has to write down only a few equations, and sometimes none at all exclamation point When I started getting involved in work for which conformal mapping seemed to be a powerful tool, I did not think that I would ever be able to use that technique successfully because it seemed to require a nearly encyclopedic memory, an impression that was strengthened when I saw K. Kober's Dictionary of Conformal Representations. This attitude changed when I started to realize that beyond the basics of the theory of a function of a complex variable, I needed to know only about a handful of conformal maps and procedures. Consequently, my second goal for this talk is to show that in most cases conformal mapping functions can be obtained by formulating the underlying physics appropriately. This means particularly that encyclopedic knowledge of conformal maps is not necessary for successful use of conformal mapping techniques. To demonstrate these facts I have chosen examples from an area of physics/engineering in which I am active, namely accelerator physics. In order to do that successfully I start with a brief introduction into high energy charged particle storage ring technology, even though not all examples used in this paper to elucidate my points come directly from this particular field of accelerator technology

Conformational Explosion: Understanding the Complexity of the Para-Dialkylbenzene Potential Energy Surfaces

Science.gov (United States)

Mishra, Piyush; Hewett, Daniel M.; Zwier, Timothy S.

2017-06-01

This talk focuses on the single-conformation spectroscopy of small-chain para-dialkylbenzenes. This work builds on previous studies from our group on long-chain n-alkylbenzenes that identified the first folded structure in octylbenzene. The dialkylbenzenes are representative of a class of molecules that are common components of coal and aviation fuel and are known to be present in vehicle exhaust. We bring the molecules para-diethylbenzene, para-dipropylbenzene and para-dibutylbenzene into the gas phase and cool the molecules in a supersonic expansion. The jet-cooled molecules are then interrogated using laser-induced fluorescence excitation, fluorescence dip IR spectroscopy (FDIRS) and dispersed fluorescence. The LIF spectra in the S_{0}-S_{1} origin region show dramatic increases in the number of resolved transitions with increasing length of alkyl chains, reflecting an explosion in the number of unique low-energy conformations formed when two independent alkyl chains are present. Since the barriers to isomerization of the alkyl chain are similar in size, this results in an 'egg carton' shape to the potential energy surface. We use a combination of electronic frequency shift and alkyl CH stretch infrared spectra to generate a consistent set of conformational assignments.

A probabilistic model of RNA conformational space

DEFF Research Database (Denmark)

Frellsen, Jes; Moltke, Ida; Thiim, Martin

2009-01-01

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

A probabilistic model of RNA conformational space

DEFF Research Database (Denmark)

Frellsen, Jes; Moltke, Ida; Thiim, Martin

2009-01-01

efficient sampling of RNA conformations in continuous space, and with associated probabilities. We show that the model captures several key features of RNA structure, such as its rotameric nature and the distribution of the helix lengths. Furthermore, the model readily generates native-like 3-D......, the discrete nature of the fragments necessitates the use of carefully tuned, unphysical energy functions, and their non-probabilistic nature impairs unbiased sampling. We offer a solution to the sampling problem that removes these important limitations: a probabilistic model of RNA structure that allows......The increasing importance of non-coding RNA in biology and medicine has led to a growing interest in the problem of RNA 3-D structure prediction. As is the case for proteins, RNA 3-D structure prediction methods require two key ingredients: an accurate energy function and a conformational sampling...

Conformal field theory and functions of hypergeometric type

International Nuclear Information System (INIS)

Isachenkov, Mikhail

2016-03-01

Conformal field theory provides a universal description of various phenomena in natural sciences. Its development, swift and successful, belongs to the major highlights of theoretical physics of the late XX century. In contrast, advances of the theory of hypergeometric functions always assumed a slower pace throughout the centuries of its existence. Functional identities studied by this mathematical discipline are fascinating both in their complexity and beauty. This thesis investigates the interrelation of two subjects through a direct analysis of three CFT problems: two-point functions of the 2d strange metal CFT, three-point functions of primaries of the non-rational Toda CFT and kinematical parts of Mellin amplitudes for scalar four-point functions in general dimensions. We flash out various generalizations of hypergeometric functions as a natural mathematical language for two of these problems. Several new methods inspired by extensions of classical results on hypergeometric functions, are presented.

Conformal field theory and functions of hypergeometric type

Energy Technology Data Exchange (ETDEWEB)

Isachenkov, Mikhail

2016-03-15

Conformal field theory provides a universal description of various phenomena in natural sciences. Its development, swift and successful, belongs to the major highlights of theoretical physics of the late XX century. In contrast, advances of the theory of hypergeometric functions always assumed a slower pace throughout the centuries of its existence. Functional identities studied by this mathematical discipline are fascinating both in their complexity and beauty. This thesis investigates the interrelation of two subjects through a direct analysis of three CFT problems: two-point functions of the 2d strange metal CFT, three-point functions of primaries of the non-rational Toda CFT and kinematical parts of Mellin amplitudes for scalar four-point functions in general dimensions. We flash out various generalizations of hypergeometric functions as a natural mathematical language for two of these problems. Several new methods inspired by extensions of classical results on hypergeometric functions, are presented.

A conformal gauge invariant functional for Weyl structures and the first variation formula

OpenAIRE

Ichiyama, Toshiyuki; Furuhata, Hitoshi; Urakawa, Hajime

1999-01-01

We consider a new conformal gauge invariant functional which is a natural curvature functional on the space of Weyl structures. We derive the first variation formula of its functional and characterize its critical points.

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

Science.gov (United States)

2015-01-01

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

Measuring the mechanical properties of molecular conformers

Science.gov (United States)

Jarvis, S. P.; Taylor, S.; Baran, J. D.; Champness, N. R.; Larsson, J. A.; Moriarty, P.

2015-09-01

Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules.

Investigation of the Dirac Equation by Using the Conformable Fractional Derivative

Science.gov (United States)

Mozaffari, F. S.; Hassanabadi, H.; Sobhani, H.; Chung, W. S.

2018-05-01

In this paper,the Dirac equation is constructed using the conformable fractional derivative so that in its limit for the fractional parameter, the normal version is recovered. Then, the Cornell potential is considered as the interaction of the system. In this case, the wave function and the energy eigenvalue equation are derived with the aim of the bi-confluent Heun functions. use of the conformable fractional derivative is proven to lead to a branching treatment for the energy of the system. Such a treatment is obvious for small values of the fractional parameter, and a united value as the fractional parameter approaches unity.

Conformational stability and self-association equilibrium in biologics.

Science.gov (United States)

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

2016-02-01

Biologics exist in equilibrium between native, partially denatured, and denatured conformational states. The population of any of these states is dictated by their Gibbs energy and can be altered by changes in physical and solution conditions. Some conformations have a tendency to self-associate and aggregate, an undesirable phenomenon in protein therapeutics. Conformational equilibrium and self-association are linked thermodynamic functions. Given that any associative reaction is concentration dependent, conformational stability studies performed at different protein concentrations can provide early clues to future aggregation problems. This analysis can be applied to the selection of protein variants or the identification of better formulation solutions. In this review, we discuss three different aggregation situations and their manifestation in the observed conformational equilibrium of a protein. Copyright © 2015 Elsevier Ltd. All rights reserved.

Globally conformal invariant gauge field theory with rational correlation functions

CERN Document Server

Nikolov, N M; Todorov, I T; CERN. Geneva; Todorov, Ivan T.

2003-01-01

Operator product expansions (OPE) for the product of a scalar field with its conjugate are presented as infinite sums of bilocal fields $V_{\\kappa} (x_1, x_2)$ of dimension $(\\kappa, \\kappa)$. For a {\\it globally conformal invariant} (GCI) theory we write down the OPE of $V_{\\kappa}$ into a series of {\\it twist} (dimension minus rank) $2\\kappa$ symmetric traceless tensor fields with coefficients computed from the (rational) 4-point function of the scalar field. We argue that the theory of a GCI hermitian scalar field ${\\cal L} (x)$ of dimension 4 in $D = 4$ Minkowski space such that the 3-point functions of a pair of ${\\cal L}$'s and a scalar field of dimension 2 or 4 vanish can be interpreted as the theory of local observables of a conformally invariant fixed point in a gauge theory with Lagrangian density ${\\cal L} (x)$.

Two-point functions and logarithmic boundary operators in boundary logarithmic conformal field theories

International Nuclear Information System (INIS)

Ishimoto, Yukitaka

2004-01-01

Amongst conformal field theories, there exist logarithmic conformal field theories such as c p,1 models. We have investigated c p,q models with a boundary in search of logarithmic theories and have found logarithmic solutions of two-point functions in the context of the Coulomb gas picture. We have also found the relations between coefficients in the two-point functions and correlation functions of logarithmic boundary operators, and have confirmed the solutions in [hep-th/0003184]. Other two-point functions and boundary operators have also been studied in the free boson construction of boundary CFT with SU(2) k symmetry in regard to logarithmic theories. This paper is based on a part of D. Phil. Thesis [hep-th/0312160]. (author)

Hydrogen abstraction from n-butanol by the methyl radical: high level ab initio study of abstraction pathways and the importance of low energy rotational conformers.

Science.gov (United States)

Katsikadakos, D; Hardalupas, Y; Taylor, A M K P; Hunt, P A

2012-07-21

Hydrogen abstraction reactions by the methyl radical from n-butanol have been investigated at the ROCBS-QB3 level of theory. Reaction energies and product geometries for the most stable conformer of n-butanol (ROH) have been computed, the reaction energies order α channel more stable than the β-channel? Why do the two C(γ)-H H-abstraction TS differ in energy? The method and basis set dependence of the TS barriers is investigated. The Boltzmann probability distribution for the n-butanol conformers suggests that low energy conformers are present in approximately equal proportions to the most stable conformer at combustion temperatures where ĊH(3) radicals are present. Thus, the relative significance of the various H-abstraction channels has been assessed for a selection of higher energy conformers (ROH'). Key results include finding that higher energy n-butanol conformers (E(ROH') > E(ROH)) can generate lower energy product radicals, E(ROH') < E(ROH). Moreover, higher energy conformers can also have a globally competitive TS energy for H-abstraction.

Conformation of antifreeze glycoproteins as determined from conformational energy calculations and fully assigned proton NMR spectra

International Nuclear Information System (INIS)

Bush, C.A.; Rao, B.N.N.

1986-01-01

The 1 H NMR spectra of AFGP's ranging in molecular weight from 2600 to 30,000 Daltons isolated from several different species of polar fish have been measured. The spectrum of AFGP 1-4 from Pagothenia borchgrevinki with an average of 30 repeating subunits has a single resonance for each proton of the glycotripeptide repeating unit, (ala-[gal-(β-1→3) galNAc-(α--O-]thr-ala)/sub n/. Its 1 H NMR spectrum including resonances of the amide protons has been completely assigned. Coupling constants and nuclear Overhauser enhancements (n.O.e.) between protons on distant residues imply conformational order. The 2600 dalton molecular weight glycopeptides (AFGP-8) have pro in place of ala at certain specific points in the sequence and AFGP-8R of Eleginus gracilis has arg in place of one thr. The resonances of pro and arg were assigned by decoupling. The resonances of the carboxy and amino terminals have distinct chemical shifts and were assigned in AFGP-8 of Boreogadus saida by titration. n.O.e. between α--protons and amide protons of the adjacent residue (sequential n.O.e.) were used in assignments of additional resonances and to assign the distinctive resonances of thr followed by pro. Conformational energy calculations on the repeating glycotripeptide subunit of AFGP show that the α--glucosidic linkage has a fixed conformation while the β--linkage is less rigid. A conformational model for AFGP 1-4, which is based on the calculations has the peptide in an extended left-handed helix with three residues per turn similar to polyproline II. The model is consistent with CD data, amide proton coupling constants, temperature dependence of amide proton chemical shifts

Density functional study of gamma-aminopropyltriethoxysilane

International Nuclear Information System (INIS)

Bistricic, L; Volovsek, V; Daani, V; Leskovac, M

2006-01-01

Density functional theory calculations using Becke's three-parameter exchange functional in combination with the Lee-Young-Parr correlation functional (B3-LYP) and standard 6-311 + G(d,p) basis set were carried out to study the conformational stability and vibrational spectra of gamma-aminopropyltriethoxysilane. Calculations reveal the existence of two stable conformers trans and gauche. The calculated energy for the gauche conformation was found to be 608 cm -1 above the minimum energy of the trans conformation. Temperature dependence of Raman spectra of liquid APTES and DFT calculation enabled us to identify the vibrational bands characteristic for both conformers. It has been shown that there is an increase in the population of gauche conformer with increasing temperature

Conformational analysis by intersection: CONAN.

Science.gov (United States)

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

2003-01-15

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

Complete conformal field theory solution of a chiral six-point correlation function

International Nuclear Information System (INIS)

Simmons, Jacob J H; Kleban, Peter

2011-01-01

Using conformal field theory, we perform a complete analysis of the chiral six-point correlation function C(z)= 1,2 φ 1,2 Φ 1/2,0 (z, z-bar )φ 1,2 φ 1,2 >, with the four φ 1,2 operators at the corners of an arbitrary rectangle, and the point z = x + iy in the interior. We calculate this for arbitrary central charge (equivalently, SLE parameter κ > 0). C is of physical interest because for percolation (κ = 6) and many other two-dimensional critical points, it specifies the density at z of critical clusters conditioned to touch either or both vertical ends of the rectangle, with these ends 'wired', i.e. constrained to be in a single cluster, and the horizontal ends free. The correlation function may be written as the product of an algebraic prefactor f and a conformal block G, where f = f(x, y, m), with m a cross-ratio specified by the corners (m determines the aspect ratio of the rectangle). By appropriate choice of f and using coordinates that respect the symmetry of the problem, the conformal block G is found to be independent of either y or x, and given by an Appell function.

Conformal Collineations of the Ricci and Energy-Momentum Tensors in Static Plane Symmetric Space-Times

Science.gov (United States)

Akhtar, S. S.; Hussain, T.; Bokhari, A. H.; Khan, F.

2018-04-01

We provide a complete classification of static plane symmetric space-times according to conformal Ricci collineations (CRCs) and conformal matter collineations (CMCs) in both the degenerate and nondegenerate cases. In the case of a nondegenerate Ricci tensor, we find a general form of the vector field generating CRCs in terms of unknown functions of t and x subject to some integrability conditions. We then solve the integrability conditions in different cases depending upon the nature of the Ricci tensor and conclude that the static plane symmetric space-times have a 7-, 10- or 15-dimensional Lie algebra of CRCs. Moreover, we find that these space-times admit an infinite number of CRCs if the Ricci tensor is degenerate. We use a similar procedure to study CMCs in the case of a degenerate or nondegenerate matter tensor. We obtain the exact form of some static plane symmetric space-time metrics that admit nontrivial CRCs and CMCs. Finally, we present some physical applications of our obtained results by considering a perfect fluid as a source of the energy-momentum tensor.

Vanillin and isovanillin: Comparative vibrational spectroscopic studies, conformational stability and NLO properties by density functional theory calculations

Science.gov (United States)

Balachandran, V.; Parimala, K.

This study is a comparative analysis of FT-IR and FT-Raman spectra of vanillin (3-methoxy-4-hydroxybenzaldehyde) and isovanillin (3-hydroxy-4-methoxybenzaldehyde). The molecular structure, vibrational wavenumbers, infrared intensities, Raman scattering activities were calculated for both molecules using the B3LYP density functional theory (DFT) with the standard 6-311++G∗∗ basis set. The computed values of frequencies are scaled using multiple scaling factors to yield good coherence with the observed values. The calculated harmonic vibrational frequencies are compared with experimental FT-IR and FT-Raman spectra. The geometrical parameters and total energies of vanillin and isovanillin were obtained for all the eight conformers (a-h) from DFT/B3LYP method with 6-311++G∗∗ basis set. The computational results identified the most stable conformer of vanillin and isovanillin as in the "a" form. Non-linear properties such as electric dipole moment (μ), polarizability (α), and hyperpolarizability (β) values of the investigated molecules have been computed using B3LYP quantum chemical calculation. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecules.

Deep Inelastic Scattering in Conformal QCD

CERN Document Server

Cornalba, Lorenzo; Penedones, Joao

2010-01-01

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

One loop partition function of six dimensional conformal gravity using heat kernel on AdS

Energy Technology Data Exchange (ETDEWEB)

Lovreković, Iva [Institute for Theoretical Physics, Technische Universität Wien,Wiedner Hauptstrasse 8-10/136, A-1040 Vienna (Austria)

2016-10-13

We compute the heat kernel for the Laplacians of symmetric transverse traceless fields of arbitrary spin on the AdS background in even number of dimensions using the group theoretic approach introduced in http://dx.doi.org/10.1007/JHEP11(2011)010 and apply it on the partition function of six dimensional conformal gravity. The obtained partition function consists of the Einstein gravity, conformal ghost and two modes that contain mass.

Genus two partition functions of extremal conformal field theories

International Nuclear Information System (INIS)

Gaiotto, Davide; Yin Xi

2007-01-01

Recently Witten conjectured the existence of a family of 'extremal' conformal field theories (ECFTs) of central charge c = 24k, which are supposed to be dual to three-dimensional pure quantum gravity in AdS 3 . Assuming their existence, we determine explicitly the genus two partition functions of k = 2 and k = 3 ECFTs, using modular invariance and the behavior of the partition function in degenerating limits of the Riemann surface. The result passes highly nontrivial tests and in particular provides a piece of evidence for the existence of the k = 3 ECFT. We also argue that the genus two partition function of ECFTs with k ≤ 10 are uniquely fixed (if they exist)

Implications of conformal invariance in momentum space

Science.gov (United States)

Bzowski, Adam; McFadden, Paul; Skenderis, Kostas

2014-03-01

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

The logarithmic conformal field theories

International Nuclear Information System (INIS)

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

1997-01-01

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

Improvements to robotics-inspired conformational sampling in rosetta.

Directory of Open Access Journals (Sweden)

Amelie Stein

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

Solitons, τ-functions and hamiltonian reduction for non-Abelian conformal affine Toda theories

Science.gov (United States)

Ferreira, L. A.; Miramontes, J. Luis; Guillén, Joaquín Sánchez

1995-02-01

We consider the Hamiltonian reduction of the "two-loop" Wess-Zumino-Novikov-Witten model (WZNW) based on an untwisted affine Kac-Moody algebra G. The resulting reduced models, called Generalized Non-Abelian Conformal Affine Toda (G-CAT), are conformally invariant and a wide class of them possesses soliton solutions; these models constitute non-Abelian generalizations of the conformal affine Toda models. Their general solution is constructed by the Leznov-Saveliev method. Moreover, the dressing transformations leading to the solutions in the orbit of the vacuum are considered in detail, as well as the τ-functions, which are defined for any integrable highest weight representation of G, irrespectively of its particular realization. When the conformal symmetry is spontaneously broken, the G-CAT model becomes a generalized affine Toda model, whose soliton solutions are constructed. Their masses are obtained exploring the spontaneous breakdown of the conformal symmetry, and their relation to the fundamental particle masses is discussed. We also introduce what we call the two-loop Virasoro algebra, describing extended symmetries of the two-loop WZNW models.

Big bounce, slow-roll inflation, and dark energy from conformal gravity

Science.gov (United States)

Gegenberg, Jack; Rahmati, Shohreh; Seahra, Sanjeev S.

2017-02-01

We examine the cosmological sector of a gauge theory of gravity based on the SO(4,2) conformal group of Minkowski space. We allow for conventional matter coupled to the spacetime metric as well as matter coupled to the field that gauges special conformal transformations. An effective vacuum energy appears as an integration constant, and this allows us to recover the late time acceleration of the Universe. Furthermore, gravitational fields sourced by ordinary cosmological matter (i.e. dust and radiation) are significantly weakened in the very early Universe, which has the effect of replacing the big bang with a big bounce. Finally, we find that this bounce is followed by a period of nearly exponential slow roll inflation that can last long enough to explain the large scale homogeneity of the cosmic microwave background.

Study on fusion energy conformity with global environmental issues

International Nuclear Information System (INIS)

Kurihara, Kenichi

1998-01-01

Global environmental conformity has been one of the most important issues discussed recently as being required for all human activities. From this point of view, this report investigates whether nuclear fusion can be a benign energy source for the global environment. First of all, we chose the following global environmental problems: (1) Global warming, (2) Acid rain, (3) Ozonosphere destruction, (4) Air pollution, (5) Environmental hormones, (6) Radiation and radioactive materials, (7) Electromagnetic waves, and (8) Heat drainage from an energy source. Secondly, these problems were fully surveyed in terms of their relationships with proposed nuclear fusion power plant. Finally, as a result of this discussion, it was confirmed that a fusion power plant would not produce any new problems, but would partially contribute to solving some of the environmental problems. (author)

Fermion-scalar conformal blocks

Energy Technology Data Exchange (ETDEWEB)

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

2016-04-13

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

Correlation Functions of the Energy Momentum Tensor on Spaces of Constant Curvature

CERN Document Server

Osborn, H

2000-01-01

An analysis of one and two point functions of the energy momentum tensor on homogeneous spaces of constant curvature is undertaken. The possibility of proving a c-theorem in this framework is discussed, in particular in relation to the coefficients c,a, which appear in the energy momentum tensor trace on general curved backgrounds in four dimensions. Ward identities relating the correlation functions are derived and explicit expressions are obtained for free scalar, spinor field theories in general dimensions and also free vector fields in dimension four. A natural geometric formalism which is independent of any choice of coordinates is used and the role of conformal symmetries on such constant curvature spaces is analysed. The results are shown to be constrained by the operator product expansion. For negative curvature the spectral representation, involving unitary positive energy representations of $O(d-1,2)$, for two point functions of vector currents is derived in detail and extended to the energy momentu...

Conformal boundaries of warped products

DEFF Research Database (Denmark)

Kokkendorff, Simon Lyngby

2006-01-01

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

Holography beyond conformal invariance and AdS isometry?

CERN Document Server

Barvinsky, A.O.

2015-01-01

We suggest that the principle of holographic duality can be extended beyond conformal invariance and AdS isometry. Such an extension is based on a special relation between functional determinants of the operators acting in the bulk and on its boundary, provided that the boundary operator represents the inverse propagators of the theory induced on the boundary by the Dirichlet boundary value problem from the bulk spacetime. This relation holds for operators of general spin-tensor structure on generic manifolds with boundaries irrespective of their background geometry and conformal invariance, and it apparently underlies numerous $O(N^0)$ tests of AdS/CFT correspondence, based on direct calculation of the bulk and boundary partition functions, Casimir energies and conformal anomalies. The generalized holographic duality is discussed within the concept of the "double-trace" deformation of the boundary theory, which is responsible in the case of large $N$ CFT coupled to the tower of higher spin gauge fields for t...

Energy level alignment and molecular conformation at rubrene/Ag interfaces: Impact of contact contaminations on the interfaces

Energy Technology Data Exchange (ETDEWEB)

Sinha, Sumona, E-mail: sumona.net.09@gmail.com [Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064 (India); Wang, C.-H. [National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan (China); Mukherjee, M. [Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064 (India)

2017-07-01

Highlights: • Impact of contact contaminations on the energy level alignment and molecular conformation at rubrene/Ag interfaces. • Adventitious contamination layer was acted as a spacer layer between Ag substrate surface and rubrene molecular layer. • Hole injection barrier height and interface dipole at rubrene/Ag interfaces depend on the cleanliness of Ag substrate. • Molecular conformation as well as orientation controlled by the cleanliness of Ag surface. • Resulted different surface morphology of rubrene thin films on unclean and clean Ag substrate. - Abstract: This paper addresses the impact of electrode contaminations on the interfacial energy level alignment, the molecular conformation, orientation and surface morphology deposited organic film at organic semiconductor/noble metal interfaces by varying of film thickness from sub-monolayer to multilayer, which currently draws significant attention with regard to its application in organic electronics. The UHV clean Ag and unclean Ag were employed as substrate whereas rubrene was used as an organic semiconducting material. The photoelectron spectroscopy (XPS and UPS) was engaged to investigate the evolution of interfacial energetics; polarization dependent near edge x-ray absorption fine structure spectroscopy (NEXAFS) was employed to understand the molecular conformation as well as orientation whereas atomic force microscopy (AFM) was used to investigate the surface morphologies of the films. The adventitious contamination layer was acted as a spacer layer between clean Ag substrate surface and rubrene molecular layer. As a consequence, hole injection barrier height, interface dipole as well as molecular-conformation, molecular-orientation and surface morphology of rubrene thin films were found to depend on the cleanliness of Ag substrate. The results have important inferences about the understanding of the impact of substrate contamination on the energy level alignment, the molecular conformation

Conformational cooling and conformation selective aggregation in dimethyl sulfite isolated in solid rare gases

OpenAIRE

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

2006-01-01

Dimethyl sulfite has three conformers of low energy, GG, GT and GG0, which have significant populations in the gas phase at room temperature. According to theoretical predictions, the GT and GG0 conformers are higher in energy than the GG conformer by 0.83 and 1.18 kJ molK1, respectively, while the barriers associated with the GG0/GT and GT/GG isomerizations are 1.90 and 9.64 kJ molK1, respectively. Experimental data obtained for the compound isolated in solid argon, krypton and xenon demonst...

BCS wave function, matrix product states, and the Ising conformal field theory

Science.gov (United States)

Montes, Sebastián; Rodríguez-Laguna, Javier; Sierra, Germán

2017-11-01

We present a characterization of the many-body lattice wave functions obtained from the conformal blocks (CBs) of the Ising conformal field theory (CFT). The formalism is interpreted as a matrix product state using continuous ancillary degrees of freedom. We provide analytic and numerical evidence that the resulting states can be written as BCS states. We give a complete proof that the translationally invariant 1D configurations have a BCS form and we find suitable parent Hamiltonians. In particular, we prove that the ground state of the finite-size critical Ising transverse field (ITF) Hamiltonian can be obtained with this construction. Finally, we study 2D configurations using an operator product expansion (OPE) approximation. We associate these states to the weak pairing phase of the p +i p superconductor via the scaling of the pairing function and the entanglement spectrum.

Conformational Analysis of Contrast Media for X-Ray Diagnostic Radiology

International Nuclear Information System (INIS)

Solieman, A.H.M.

2010-01-01

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

Bioactive focus in conformational ensembles: a pluralistic approach

Science.gov (United States)

Habgood, Matthew

2017-12-01

Computational generation of conformational ensembles is key to contemporary drug design. Selecting the members of the ensemble that will approximate the conformation most likely to bind to a desired target (the bioactive conformation) is difficult, given that the potential energy usually used to generate and rank the ensemble is a notoriously poor discriminator between bioactive and non-bioactive conformations. In this study an approach to generating a focused ensemble is proposed in which each conformation is assigned multiple rankings based not just on potential energy but also on solvation energy, hydrophobic or hydrophilic interaction energy, radius of gyration, and on a statistical potential derived from Cambridge Structural Database data. The best ranked structures derived from each system are then assembled into a new ensemble that is shown to be better focused on bioactive conformations. This pluralistic approach is tested on ensembles generated by the Molecular Operating Environment's Low Mode Molecular Dynamics module, and by the Cambridge Crystallographic Data Centre's conformation generator software.

Astrophysical Tests of Kinematical Conformal Cosmology in Fourth-Order Conformal Weyl Gravity

Directory of Open Access Journals (Sweden)

Gabriele U. Varieschi

2014-12-01

Full Text Available In this work we analyze kinematical conformal cosmology (KCC, an alternative cosmological model based on conformal Weyl gravity (CG, and test it against current type Ia supernova (SNIa luminosity data and other astrophysical observations. Expanding upon previous work on the subject, we revise the analysis of SNIa data, confirming that KCC can explain the evidence for an accelerating expansion of the Universe without using dark energy or other exotic components. We obtain an independent evaluation of the Hubble constant, H0 = 67:53 kms-1 Mpc-1, very close to the current best estimates. The main KCC and CG parameters are re-evaluated and their revised values are found to be close to previous estimates. We also show that available data for the Hubble parameter as a function of redshift can be fitted using KCC and that this model does not suffer from any apparent age problem. Overall,

Vibrational spectrum, ab initio calculations, conformational stabilities and assignment of fundamentals of 1,2-dibromopropane

Science.gov (United States)

LaPlante, Arthur J.; Stidham, Howard D.

2009-10-01

The mid and far infrared and the Raman spectrum of 1,2-dibromopropane is reported in solid, liquid and gas. Several bands reported by earlier workers are not present in the spectrum of the purified material. Ab initio calculations of optimized geometry, energy, dipole moment, molar volume, vibrational spectrum and normal coordinate calculation were performed using the density functional B3LYP/6-311++g(3df,2pd), and the results used to assist a complete assignment of the 81 fundamental modes of vibrations of the three conformers of 1,2-dibromopropane. Relative energies found conformer A the lowest with G and G' at 815.6 and 871.4 cm -1 higher. The temperature dependence of the Raman spectrum of the liquid was investigated in the CCC bending region and the relative energies determined. It was found that the G' and G conformers lie 236 ± 11 and 327 ±11 cm -1, respectively above the A conformer, leading to the room temperature composition of the liquid as A, 65 ± 1; G', 21 ± 1; G, 14 ± 1%. It is apparent that the calculated highest energy conformer G' is stabilized more than the G conformer in the liquid. The G' conformer has the lowest molar volume effectively changing the interaction distance between conformers in the liquid, and enhancing the effect of its dipole moment.

Conformational locking by design: relating strain energy with luminescence and stability in rigid metal-organic frameworks.

Science.gov (United States)

Shustova, Natalia B; Cozzolino, Anthony F; Dincă, Mircea

2012-12-05

Minimization of the torsional barrier for phenyl ring flipping in a metal-organic framework (MOF) based on the new ethynyl-extended octacarboxylate ligand H(8)TDPEPE leads to a fluorescent material with a near-dark state. Immobilization of the ligand in the rigid structure also unexpectedly causes significant strain. We used DFT calculations to estimate the ligand strain energies in our and all other topologically related materials and correlated these with empirical structural descriptors to derive general rules for trapping molecules in high-energy conformations within MOFs. These studies portend possible applications of MOFs for studying fundamental concepts related to conformational locking and its effects on molecular reactivity and chromophore photophysics.

Conformational aspects of dibenzo-tetroxecin: A structural, Raman spectroscopic and computational study

Science.gov (United States)

Gordon, Keith C.; McAdam, C. John; Moratti, Stephen C.; Shillito, Georgina E.; Simpson, Jim

2017-10-01

Crystalline dibenzo-tetroxecin (I) has been prepared from a reaction between catechol and dichloromethane and its molecular and crystal structure, together with the Raman spectrum of the material in the solid state and in solution, is reported. The molecular structure shows the molecule adopts an anti or stepped conformation. Density functional theory (DFT) optimisation and frequency calculations using the B3LYP functional with the 6-31G(d) basis set showed the presence of syn- and anti-conformers of (I), with the anti-conformer predicted to be the lower in energy by 13.6 kJ mol-1. The vibrational frequencies and relative Raman intensities of the anti-conformer are well modelled by the DFT calculations. The bond lengths and angles obtained for the anti-conformer are also in good agreement with the crystal structure. The crystal structure of (I) is stabilised by intermolecular Csbnd H⋯O hydrogen bonds that generate a three dimensional network.

De novo protein structure prediction by dynamic fragment assembly and conformational space annealing.

Science.gov (United States)

Lee, Juyong; Lee, Jinhyuk; Sasaki, Takeshi N; Sasai, Masaki; Seok, Chaok; Lee, Jooyoung

2011-08-01

Ab initio protein structure prediction is a challenging problem that requires both an accurate energetic representation of a protein structure and an efficient conformational sampling method for successful protein modeling. In this article, we present an ab initio structure prediction method which combines a recently suggested novel way of fragment assembly, dynamic fragment assembly (DFA) and conformational space annealing (CSA) algorithm. In DFA, model structures are scored by continuous functions constructed based on short- and long-range structural restraint information from a fragment library. Here, DFA is represented by the full-atom model by CHARMM with the addition of the empirical potential of DFIRE. The relative contributions between various energy terms are optimized using linear programming. The conformational sampling was carried out with CSA algorithm, which can find low energy conformations more efficiently than simulated annealing used in the existing DFA study. The newly introduced DFA energy function and CSA sampling algorithm are implemented into CHARMM. Test results on 30 small single-domain proteins and 13 template-free modeling targets of the 8th Critical Assessment of protein Structure Prediction show that the current method provides comparable and complementary prediction results to existing top methods. Copyright © 2011 Wiley-Liss, Inc.

Virtual and solution conformations of oligosaccharides

International Nuclear Information System (INIS)

Cumming, D.A.; Carver, J.P.

1987-01-01

The possibility that observed nuclear Overhauser enhancements and bulk longitudinal relaxation times, parameters measured by 1 H NMR and often employed in determining the preferred solution conformation of biologically important molecules, are the result of averaging over many conformational states is quantitatively evaluated. Of particular interest was to ascertain whether certain 1 H NMR determined conformations are virtual in nature; i.e., the fraction of the population of molecules actually found at any time within the subset of conformational space defined as the solution conformation is vanishingly small. A statistical mechanics approach was utilized to calculate an ensemble average relaxation matrix from which (NOE)'s and (T 1 )'s are calculated. Model glycosidic linkages in four oligosaccharides were studied. The nature of the resultant population distributions is such that 50% of the molecular population is found within 1% of available microstates, while 99% of the molecular population occupies about 10% of the ensemble microstates, a number roughly equal to that sterically allowed. From this analysis the authors conclude that in many cases quantitative interpretation of NMR relaxation data, which attempts to define a single set of allowable torsion angle values consistent with the observed data, will lead to solution conformations that are either virtual or reflect torsion angle values possessed by a minority of the molecular population. Observed values of NMR relaxation data are the result of the complex interdependence of the population distribution and NOE (or T 1 ) surfaces in conformational space. In conformational analyses, NMR data can therefore be used to test different population distributions calculated from empirical potential energy functions

The influence of conformational fluctuations on enzymatic activity: modelling the functional motion of β-secretase

International Nuclear Information System (INIS)

Neri, M; Cascella, M; Micheletti, C

2005-01-01

Considerable insight into the functional activity of proteins and enzymes can be obtained by studying the low energy conformational distortions that the biopolymer can sustain. We carry out the characterization of these large scale structural changes for a protein of considerable pharmaceutical interest, the human β-secretase. Starting from the crystallographic structure of the protein, we use the recently introduced β-Gaussian model to identify, with negligible computational expenditure, the most significant distortions occurring in thermal equilibrium and the associated timescales. The application of this strategy helps us to gain considerable insight into the putative functional movements and, furthermore, allows us to identify a handful of key regions in the protein which have an important mechanical influence on the enzymatic activity despite being spatially distant from the active site. The results obtained within the Gaussian model are validated through an extensive comparison against an all-atom molecular dynamics simulation

From flexibility to function: Molecular dynamics simulations of conformational changes in chaperones and photoreceptors

NARCIS (Netherlands)

Singhal, K.

2016-01-01

Proteins are uniquely-shaped macromolecules that function as biological machines, and regulate a living cell’s behavior. Crucial to protein function is the folding of the polypeptide chain into a unique well-defined three-dimensional conformation. In complex cell environments, the spontaneous

An extension of the counterion condensation theory to conformational changes of flexible polymers

International Nuclear Information System (INIS)

Benegas, J.C.; Cesaro, A.

1988-01-01

A full report on a statistical model is presented in which an ionic polymer is taken as an aggregate of linear flexible segments (similar to the spring-bead model). This model is thought to represent fairly well some flexible ionic polymers in solution. The model assumes two factorizable energy contributions, one purely conformational the other electrostatic. The first contribution is calculated from distribution function of the end-to-end distances and can be obtained from numerical Monte Carlo calculations of chain conformations. The second contribution is the excess thermodynamic property and is calculated, by using Manning's theory of linear polyelectrolytes, as a function of the degree of ionization and of a number of physical variables. Procedures to evaluate changes in the chain conformation of polysaccharides and polypeptides bearing ionizable charged groups are presented. The results show excellent quantitative agreement of averaged functions and experimental data. They also show that statistical average over the conformational states is not equivalent to the thermodynamic property of the averaged conformation. (author). 37 refs, 17 figs

Conformational Stability, Structural Parameters And Vibrational Assignments of Allantoin

International Nuclear Information System (INIS)

Haman, S.

2008-01-01

Allantoin 2,5-Dioxo-4-imidazolinyl) urea , the diureide of glyoxylic acid, is a crystallisable oxidation product of uric acid found in allantoic and amniotic fluids, in fetal urine and in many plants. It is a healing, moisturizing, soothing and anti-irritating, keratolytic and non-toxic agent useful in dermatological, cosmetic and veterinary preparation. The optimized geometries and energies of the low-energy conformers of allantoin have been calculated using density functional theory (Daft) method. The calculations were performed with Beck's nonlocal three-parameter hybrid functional in combination with the Lee, Yang, and Parr correlation functional (By-play) using the 6-311++G(d,p) basis set. We calculated the infrared frequencies and intensities of the most stable conformers in order to assist in the assignment of the vibrational bands in the experimental spectrum. The B3LYP/6-311+G(d,p) harmonic force constants were scaled by applying the scaled quantum mechanical force field (SQM) technique. The calculated vibrational spectra were interpreted and band assignments were reported

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

KAUST Repository

Wang, Wei; Cao, Siqin; Zhu, Lizhe; Huang, Xuhui

2017-01-01

bioengineering applications and rational drug design. Constructing Markov State Models (MSMs) based on large-scale molecular dynamics simulations has emerged as a powerful approach to model functional conformational changes of the biomolecular system

Bi-conformal symmetry and static Green functions in the Schwarzschild-Tangherlini spacetimes

International Nuclear Information System (INIS)

Frolov, Valeri P.; Zelnikov, Andrei

2015-01-01

We study a static massless minimally coupled scalar field created by a source in a static D-dimensional spacetime. We demonstrate that the corresponding equation for this field is invariant under a special transformation of the background metric. This transformation consists of the static conformal transformation of the spatial part of the metric accompanied by a properly chosen transformation of the red-shift factor. Both transformations are determined by one function Ω of the spatial coordinates. We show that in a case of higher dimensional spherically symmetric black holes one can find such a bi-conformal transformation that the symmetry of the D-dimensional metric is enhanced after its application. Namely, the metric becomes a direct sum of the metric on a unit sphere and the metric of 2D anti-de Sitter space. The method of the heat kernels is used to find the Green function in this new space, which allows one, after dimensional reduction, to obtain a static Green function in the original space of the static black hole. The general useful representation of static Green functions is obtained in the Schwarzschild-Tangherlini spacetimes of arbitrary dimension. The exact explicit expressions for the static Green functions are obtained in such metrics for D<6. It is shown that in the four dimensional case the corresponding Green function coincides with the Copson solution.

Conformal symmetry breaking and the energy-momentum tensor in four dimensions

International Nuclear Information System (INIS)

Kraus, E.; Sibold, K.

1993-01-01

We derive the conformal transformation properties of the energy-momentum tensor for the massless φ 4 -theory in four dimensions. For this purpose the consistency conditions arising from Weyl-transformations are essential. The breaking of Weyl-invariance can be completely absorbed by making the coupling of the elementary theory local and by introducing an external field which couples to the composite operators φ 2 . Only then can one stay in a completely local framework. (orig.)

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

Science.gov (United States)

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

2011-11-07

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

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

Science.gov (United States)

Hao, Xiaohu; Zhang, Guijun; Zhou, Xiaogen

2018-04-01

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

Anion induced conformational preference of Cα NN motif residues in functional proteins.

Science.gov (United States)

Patra, Piya; Ghosh, Mahua; Banerjee, Raja; Chakrabarti, Jaydeb

2017-12-01

Among different ligand binding motifs, anion binding C α NN motif consisting of peptide backbone atoms of three consecutive residues are observed to be important for recognition of free anions, like sulphate or biphosphate and participate in different key functions. Here we study the interaction of sulphate and biphosphate with C α NN motif present in different proteins. Instead of total protein, a peptide fragment has been studied keeping C α NN motif flanked in between other residues. We use classical force field based molecular dynamics simulations to understand the stability of this motif. Our data indicate fluctuations in conformational preferences of the motif residues in absence of the anion. The anion gives stability to one of these conformations. However, the anion induced conformational preferences are highly sequence dependent and specific to the type of anion. In particular, the polar residues are more favourable compared to the other residues for recognising the anion. © 2017 Wiley Periodicals, Inc.

Causality Constraints in Conformal Field Theory

CERN Multimedia

CERN. Geneva

2015-01-01

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

Causality constraints in conformal field theory

Energy Technology Data Exchange (ETDEWEB)

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

2016-05-17

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

Adler function and Bjorken polarized sum rule: Perturbation expansions in powers of the S U (Nc) conformal anomaly and studies of the conformal symmetry limit

Science.gov (United States)

Cvetič, Gorazd; Kataev, A. L.

2016-07-01

We consider a new form of analytical perturbation theory expansion in the massless S U (Nc) theory, for the nonsinglet part of the e+e--annihilation to hadrons Adler function Dn s and of the Bjorken sum rule of the polarized lepton-hadron deep-inelastic scattering Cns B j p, and demonstrate its validity at the O (αs4)-level at least. It is a two-fold series in powers of the conformal anomaly and of S U (Nc) coupling αs. Explicit expressions are obtained for the {β }-expanded perturbation coefficients at O (αs4) level in MS ¯ scheme, for both considered physical quantities. Comparisons of the terms in the {β }-expanded coefficients are made with the corresponding terms obtained by using extra gluino degrees of freedom, or skeleton-motivated expansion, or Rδ-scheme motivated expansion in the Principle of Maximal Conformality. Relations between terms of the {β }-expansion for the Dn s- and Cns B j p-functions, which follow from the conformal symmetry limit and its violation, are presented. The relevance to the possible new analyses of the experimental data for the Adler function and Bjorken sum rule is discussed.

Molecular conformation changes in alkylthiol ligands as a function of size in gold nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Ramallo-Lopez, J.M.; Giovanetti, L.J.; Requejo, F.G. [Universidad Nacional de La Plata, Buenos Aires (Argentina); Isaacs, S.R.; Shon, Y.S. [Western Kentucky University, KY (United States); Salmeron, M. [Lawrence Berkeley National Laboratory, Berkeley, CA (United States)

2006-07-01

The binding of thiol molecules to gold, and in particular to gold nanoparticles (NP), is important in sensors, self-assembled monolayers and many other nanotechnological applications. For example, organic-thiolate s are extensively used as capping agents to prevent metal particle sintering and as ligands that can be functionalized to provide desirable chemical properties. An interesting feature of alkyl hydrocarbon chains is their flexibility, which allows them to change conformation to maximize space filling. This is driven by the inter-chain van der Waals nervy, which is considerably higher for longer chains and can be comparable to the stronger covalent bond of the S head with the Au. On the other hand, chain flexibility is facilitated by the easy formation of gauche distortions which require activation energies of only 0.16 eV. (author)

Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation.

Science.gov (United States)

Iida, Shinji; Nakamura, Haruki; Higo, Junichi

2016-06-15

We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein-protein or protein-ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks. © 2016 The Author(s).

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

Science.gov (United States)

Lu, H Peter

2011-04-21

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

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

International Nuclear Information System (INIS)

Zamolodchikov, A.B.

1988-01-01

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

Sampling Realistic Protein Conformations Using Local Structural Bias

DEFF Research Database (Denmark)

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

2006-01-01

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

Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.

Science.gov (United States)

Deng, Nanjie; Zhang, Bin W; Levy, Ronald M

2015-06-09

The ability to accurately model solvent effects on free energy surfaces is important for understanding many biophysical processes including protein folding and misfolding, allosteric transitions, and protein–ligand binding. Although all-atom simulations in explicit solvent can provide an accurate model for biomolecules in solution, explicit solvent simulations are hampered by the slow equilibration on rugged landscapes containing multiple basins separated by barriers. In many cases, implicit solvent models can be used to significantly speed up the conformational sampling; however, implicit solvent simulations do not fully capture the effects of a molecular solvent, and this can lead to loss of accuracy in the estimated free energies. Here we introduce a new approach to compute free energy changes in which the molecular details of explicit solvent simulations are retained while also taking advantage of the speed of the implicit solvent simulations. In this approach, the slow equilibration in explicit solvent, due to the long waiting times before barrier crossing, is avoided by using a thermodynamic cycle which connects the free energy basins in implicit solvent and explicit solvent using a localized decoupling scheme. We test this method by computing conformational free energy differences and solvation free energies of the model system alanine dipeptide in water. The free energy changes between basins in explicit solvent calculated using fully explicit solvent paths agree with the corresponding free energy differences obtained using the implicit/explicit thermodynamic cycle to within 0.3 kcal/mol out of ∼3 kcal/mol at only ∼8% of the computational cost. We note that WHAM methods can be used to further improve the efficiency and accuracy of the implicit/explicit thermodynamic cycle.

Maxwell equations in conformal invariant electrodynamics

International Nuclear Information System (INIS)

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

1983-01-01

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

Recursion Relations for Conformal Blocks

CERN Document Server

Penedones, João; Yamazaki, Masahito

2016-09-12

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

Conformational cooling and conformation selective aggregation in dimethyl sulfite isolated in solid rare gases

Science.gov (United States)

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

2006-08-01

Dimethyl sulfite has three conformers of low energy, GG, GT and GG', which have significant populations in the gas phase at room temperature. According to theoretical predictions, the GT and GG' conformers are higher in energy than the GG conformer by 0.83 and 1.18 kJ mol -1, respectively, while the barriers associated with the GG'→GT and GT→GG isomerizations are 1.90 and 9.64 kJ mol -1, respectively. Experimental data obtained for the compound isolated in solid argon, krypton and xenon demonstrated that the GG'→GT energy barrier is low enough to allow an extensive conversion of the GG' form into the GT conformer during deposition of the matrices, the extent of the conversion increasing along the series Arconformers could be trapped in both argon and krypton matrices, but, at a given temperature, the amount of GG' form trapped in krypton is considerably smaller than in argon, while the amount of GT form increases in relation to the most stable GG form. In addition, when xenon is used, no bands due to GG' are observed in the as-deposited spectra ( Tsubstrate≥10 K, the minimum substrate temperature accessible to our experimental set up), indicating that when the best relaxant gas is used the GG'→GT conversion during deposition of the matrix is complete even at 10 K. Annealing of the argon and krypton matrices shows that the increase of the temperature of the matrix first promotes the GG'→GT isomerization, and only at higher temperatures the GT→GG conversion starts to occur, in consonance with the relative energy barriers associated with these two processes. The results also indicate that dimethyl sulfite exhibits conformation selective aggregation, with the most stable form, which has the highest dipole moment, aggregating more easily than the remaining experimentally relevant conformers (GT and GG').

Protein Loop Structure Prediction Using Conformational Space Annealing.

Science.gov (United States)

Heo, Seungryong; Lee, Juyong; Joo, Keehyoung; Shin, Hang-Cheol; Lee, Jooyoung

2017-05-22

We have developed a protein loop structure prediction method by combining a new energy function, which we call E PLM (energy for protein loop modeling), with the conformational space annealing (CSA) global optimization algorithm. The energy function includes stereochemistry, dynamic fragment assembly, distance-scaled finite ideal gas reference (DFIRE), and generalized orientation- and distance-dependent terms. For the conformational search of loop structures, we used the CSA algorithm, which has been quite successful in dealing with various hard global optimization problems. We assessed the performance of E PLM with two widely used loop-decoy sets, Jacobson and RAPPER, and compared the results against the DFIRE potential. The accuracy of model selection from a pool of loop decoys as well as de novo loop modeling starting from randomly generated structures was examined separately. For the selection of a nativelike structure from a decoy set, E PLM was more accurate than DFIRE in the case of the Jacobson set and had similar accuracy in the case of the RAPPER set. In terms of sampling more nativelike loop structures, E PLM outperformed E DFIRE for both decoy sets. This new approach equipped with E PLM and CSA can serve as the state-of-the-art de novo loop modeling method.

Noether symmetries, energy-momentum tensors, and conformal invariance in classical field theory

International Nuclear Information System (INIS)

Pons, Josep M.

2011-01-01

In the framework of classical field theory, we first review the Noether theory of symmetries, with simple rederivations of its essential results, with special emphasis given to the Noether identities for gauge theories. With this baggage on board, we next discuss in detail, for Poincare invariant theories in flat spacetime, the differences between the Belinfante energy-momentum tensor and a family of Hilbert energy-momentum tensors. All these tensors coincide on shell but they split their duties in the following sense: Belinfante's tensor is the one to use in order to obtain the generators of Poincare symmetries and it is a basic ingredient of the generators of other eventual spacetime symmetries which may happen to exist. Instead, Hilbert tensors are the means to test whether a theory contains other spacetime symmetries beyond Poincare. We discuss at length the case of scale and conformal symmetry, of which we give some examples. We show, for Poincare invariant Lagrangians, that the realization of scale invariance selects a unique Hilbert tensor which allows for an easy test as to whether conformal invariance is also realized. Finally we make some basic remarks on metric generally covariant theories and classical field theory in a fixed curved background.

Conformational changes in glycine tri- and hexapeptide

DEFF Research Database (Denmark)

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

2006-01-01

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

On an application of conformal maps to inequalities for rational functions

International Nuclear Information System (INIS)

Dubinin, V N

2002-01-01

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

Asymptotic conformal invariance in a non-Abelian Chern-Simons-matter model

Energy Technology Data Exchange (ETDEWEB)

Acebal, J.L. [Centro Brasileiro de Pesquisas Fisicas (CBPF), Rio de Janeiro, RJ (Brazil). Coordenacao de Campos e Particulas]. E-mail: acebal@cbpf.br

2002-08-01

One shows here the existence of solutions to the Callan-Symanzik equation for the non-Abelian SU(2) Chern-Simons-matter model which exhibits asymptotic conformal invariance to every order in perturbative theory. The conformal symmetry in the classical domain is shown to hold by means of a local criteria based on the trace of the energy-momentum tensor. By using recently exhibited regimes for the dependence between the several couplings in which the set of {beta}-functions vanish, the asymptotic conformal invariance of the model appears to be valid in the quantum domain. By considering the SU (n) case the possible non validity of the proof for a particular {eta} would be merely accidental. (author)

Biologically important conformational features of DNA as interpreted by quantum mechanics and molecular mechanics computations of its simple fragments.

Science.gov (United States)

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

2018-02-01

Deciphering the mechanism of functioning of DNA as the carrier of genetic information requires identifying inherent factors determining its structure and function. Following this path, our previous DFT studies attributed the origin of unique conformational characteristics of right-handed Watson-Crick duplexes (WCDs) to the conformational profile of deoxydinucleoside monophosphates (dDMPs) serving as the minimal repeating units of DNA strand. According to those findings, the directionality of the sugar-phosphate chain and the characteristic ranges of dihedral angles of energy minima combined with the geometric differences between purines and pyrimidines determine the dependence on base sequence of the three-dimensional (3D) structure of WCDs. This work extends our computational study to complementary deoxydinucleotide-monophosphates (cdDMPs) of non-standard conformation, including those of Z-family, Hoogsteen duplexes, parallel-stranded structures, and duplexes with mispaired bases. For most of these systems, except Z-conformation, computations closely reproduce experimental data within the tolerance of characteristic limits of dihedral parameters for each conformation family. Computation of cdDMPs with Z-conformation reveals that their experimental structures do not correspond to the internal energy minimum. This finding establishes the leading role of external factors in formation of the Z-conformation. Energy minima of cdDMPs of non-Watson-Crick duplexes demonstrate different sequence-dependence features than those known for WCDs. The obtained results provide evidence that the biologically important regularities of 3D structure distinguish WCDs from duplexes having non-Watson-Crick nucleotide pairing.

Conformal transformations in superspace

International Nuclear Information System (INIS)

Dao Vong Duc

1977-01-01

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

Long, partial-short, and special conformal fields

Energy Technology Data Exchange (ETDEWEB)

Metsaev, R.R. [Department of Theoretical Physics, P.N. Lebedev Physical Institute,Leninsky prospect 53, Moscow 119991 (Russian Federation)

2016-05-17

In the framework of metric-like approach, totally symmetric arbitrary spin bosonic conformal fields propagating in flat space-time are studied. Depending on the values of conformal dimension, spin, and dimension of space-time, we classify all conformal field as long, partial-short, short, and special conformal fields. An ordinary-derivative (second-derivative) Lagrangian formulation for such conformal fields is obtained. The ordinary-derivative Lagrangian formulation is realized by using double-traceless gauge fields, Stueckelberg fields, and auxiliary fields. Gauge-fixed Lagrangian invariant under global BRST transformations is obtained. The gauge-fixed BRST Lagrangian is used for the computation of partition functions for all conformal fields. Using the result for the partition functions, numbers of propagating D.o.F for the conformal fields are also found.

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

Science.gov (United States)

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

2016-01-01

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

A computational study of vicinal fluorination in 2,3-difluorobutane: implications for conformational control in alkane chains.

Science.gov (United States)

Fox, Stephen J; Gourdain, Stephanie; Coulthurst, Anton; Fox, Clare; Kuprov, Ilya; Essex, Jonathan W; Skylaris, Chris-Kriton; Linclau, Bruno

2015-01-19

A comprehensive conformational analysis of both 2,3-difluorobutane diastereomers is presented based on density functional theory calculations in vacuum and in solution, as well as NMR experiments in solution. While for 1,2-difluoroethane the fluorine gauche effect is clearly the dominant effect determining its conformation, it was found that for 2,3-difluorobutane there is a complex interplay of several effects, which are of similar magnitude but often of opposite sign. As a result, unexpected deviations in dihedral angles, relative conformational energies and populations are observed which cannot be rationalised only by chemical intuition. Furthermore, it was found that it is important to consider the free energies of the various conformers, as these lead to qualitatively different results both in vacuum and in solvent, when compared to calculations based only on the electronic energies. In contrast to expectations, it was found that vicinal syn-difluoride introduction in the butane and by extension, longer hydrocarbon chains, is not expected to lead to an effective stabilisation of the linear conformation. Our findings have implications for the use of the vicinal difluoride motif for conformational control. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Conformal use of retarded Green's functions for the Maxwell field in de Sitter space

International Nuclear Information System (INIS)

Faci, S.; Huguet, E.; Renaud, J.

2011-01-01

We propose a new propagation formula for the Maxwell field in de Sitter space which exploits the conformal invariance of this field together with a conformal gauge condition. This formula allows to determine the classical electromagnetic field in the de Sitter space from given currents and initial data. It only uses the Green's function of the massless Minkowskian scalar field. This leads to drastic simplifications in practical calculations. We apply this formula to the classical problem of the two charges of opposite signs at rest at the North and South Poles of the de Sitter space.

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

Directory of Open Access Journals (Sweden)

Qi Wang

2007-09-01

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

Gluon amplitudes as 2 d conformal correlators

Science.gov (United States)

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

2017-10-01

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

Induced quantum conformal gravity

International Nuclear Information System (INIS)

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

1988-11-01

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

Correlation functions of the energy-momentum tensor on spaces of constant curvature

International Nuclear Information System (INIS)

Osborn, H.; Shore, G.M.

2000-01-01

An analysis of one- and two-point functions of the energy-momentum tensor on homogeneous spaces of constant curvature is undertaken. The possibility of proving a c-theorem in this framework is discussed, in particular in relation to the coefficients c,a, which appear in the energy-momentum tensor trace on general curved backgrounds in four dimensions. Ward identities relating the correlation functions are derived and explicit expressions are obtained for free scalar, spinor field theories in general dimensions and also free vector fields in dimension four. A natural geometric formalism which is independent of any choice of coordinates is used and the role of conformal symmetries on such constant curvature spaces is analysed. The results are shown to be constrained by the operator product expansion. For negative curvature the spectral representation, involving unitary positive energy representations of O(d-1,2), for two-point functions of vector currents is derived in detail and extended to the energy-momentum tensor by analogy. It is demonstrated that, at non-coincident points, the two-point functions are not related to a in any direct fashion and there is no straightforward demonstration obtainable in this framework of irreversibility under renormalisation group flow of any function of the couplings for four-dimensional field theories which reduces to a at fixed points

Superintegrability of d-dimensional conformal blocks

International Nuclear Information System (INIS)

Isachenkov, Mikhail

2016-02-01

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

Superintegrability of d-dimensional conformal blocks

Energy Technology Data Exchange (ETDEWEB)

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

2016-02-15

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

Einstein gravity 3-point functions from conformal field theory

Science.gov (United States)

Afkhami-Jeddi, Nima; Hartman, Thomas; Kundu, Sandipan; Tajdini, Amirhossein

2017-12-01

We study stress tensor correlation functions in four-dimensional conformal field theories with large N and a sparse spectrum. Theories in this class are expected to have local holographic duals, so effective field theory in anti-de Sitter suggests that the stress tensor sector should exhibit universal, gravity-like behavior. At the linearized level, the hallmark of locality in the emergent geometry is that stress tensor three-point functions 〈 T T T 〉, normally specified by three constants, should approach a universal structure controlled by a single parameter as the gap to higher spin operators is increased. We demonstrate this phenomenon by a direct CFT calculation. Stress tensor exchange, by itself, violates causality and unitarity unless the three-point functions are carefully tuned, and the unique consistent choice exactly matches the prediction of Einstein gravity. Under some assumptions about the other potential contributions, we conclude that this structure is universal, and in particular, that the anomaly coefficients satisfy a ≈ c as conjectured by Camanho et al. The argument is based on causality of a four-point function, with kinematics designed to probe bulk locality, and invokes the chaos bound of Maldacena, Shenker, and Stanford.

Conformal partition functions of critical percolation from D 3 thermodynamic Bethe Ansatz equations

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Morin-Duchesne, Alexi; Klümper, Andreas; Pearce, Paul A.

2017-08-01

Using the planar Temperley-Lieb algebra, critical bond percolation on the square lattice can be reformulated as a loop model. In this form, it is incorporated as {{ L}}{{ M}}(2, 3) in the Yang-Baxter integrable family of logarithmic minimal models {{ L}}{{ M}}( p, p\\prime) . We consider this model of percolation in the presence of boundaries and with periodic boundary conditions. Inspired by Kuniba, Sakai and Suzuki, we rewrite the recently obtained infinite Y-system of functional equations. In this way, we obtain nonlinear integral equations in the form of a closed finite set of TBA equations described by a D 3 Dynkin diagram. Following the methods of Klümper and Pearce, we solve the TBA equations for the conformal finite-size corrections. For the ground states of the standard modules on the strip, these agree with the known central charge c  =  0 and conformal weights Δ1, s for \\renewcommand≥≥slant} s\\in {{ Z}≥slant 1} with Δr, s=\\big((3r-2s){\\hspace{0pt}}^2-1\\big)/24 . For the periodic case, the finite-size corrections agree with the conformal weights Δ0, s , Δ1, s with \\renewcommand{≥{≥slant} s\\in\\frac{1}{2}{{ Z}≥slant 0} . These are obtained analytically using Rogers dilogarithm identities. We incorporate all finite excitations by formulating empirical selection rules for the patterns of zeros of all the eigenvalues of the standard modules. We thus obtain the conformal partition functions on the cylinder and the modular invariant partition function (MIPF) on the torus. By applying q-binomial and q-Narayana identities, it is shown that our refined finitized characters on the strip agree with those of Pearce, Rasmussen and Zuber. For percolation on the torus, the MIPF is a non-diagonal sesquilinear form in affine u(1) characters given by the u(1) partition function Z2, 3(q)=Z2, 3{Circ}(q) . The u(1) operator content is {{ N}}Δ, \\barΔ=1 for Δ=\\barΔ=-\\frac{1}{24}, \\frac{35}{24} and {{ N}}Δ, \\barΔ=2 for �

Inverse bootstrapping conformal field theories

Science.gov (United States)

Li, Wenliang

2018-01-01

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

The conformally invariant Laplace-Beltrami operator and factor ordering

International Nuclear Information System (INIS)

Ryan, Michael P.; Turbiner, Alexander V.

2004-01-01

In quantum mechanics the kinetic energy term for a single particle is usually written in the form of the Laplace-Beltrami operator. This operator is a factor ordering of the classical kinetic energy. We investigate other relatively simple factor orderings and show that the only other solution for a conformally flat metric is the conformally invariant Laplace-Beltrami operator. For non-conformally-flat metrics this type of factor ordering fails, by just one term, to give the conformally invariant Laplace-Beltrami operator

General solution of an exact correlation function factorization in conformal field theory

International Nuclear Information System (INIS)

Simmons, Jacob J H; Kleban, Peter

2009-01-01

The correlation function factorization with K a boundary operator product expansion coefficient, is known to hold for certain scaling operators at the two-dimensional percolation point and in a few other cases. Here the correlation functions are evaluated in the upper half-plane (or any conformally equivalent region) with x 1 and x 2 arbitrary points on the real axis, and z an arbitrary point in the interior. This type of result is of interest because it is both exact and universal, relates higher-order correlation functions to lower-order ones and has a simple interpretation in terms of cluster or loop probabilities in several statistical models. This motivated us to use the techniques of conformal field theory to determine the general conditions for its validity. Here, we discover that either (see display) factorizes in this way for any central charge c, generalizing previous results. In particular, the factorization holds for either FK (Fortuin–Kasteleyn) or spin clusters in the Q-state Potts models; it also applies to either the dense or dilute phases of the O(n) loop models. Further, only one other non-trivial set of highest-weight operators (in an irreducible Verma module) factorizes in this way. In this case the operators have negative dimension (for c<1) and do not seem to have a physical realization

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

Science.gov (United States)

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

2014-10-01

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

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

International Nuclear Information System (INIS)

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

2014-01-01

The conformational space of α-phenylglycine (PG) have been investigated theoretically at both the DFT/B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) levels of approximation. Seventeen different minima were found on the investigated potential energy surfaces, which are characterized by different dominant intramolecular interactions: type I conformers are stabilized by hydrogen bonds of the type N–H···O=C, type II by a strong O–H···N hydrogen bond, type III by weak N–H···O–H hydrogen bonds, and type IV by a C=O···H–C contact. The calculations indicate also that entropic effects are relevant in determining the equilibrium populations of the conformers of PG in the gas phase, in particular in the case of conformers of type II, where the strong intramolecular O–H···N hydrogen bond considerably diminishes entropy by reducing the conformational mobility of the molecule. In consonance with the relative energies of the conformers and barriers for conformational interconversion, only 3 conformers of PG were observed for the compound isolated in cryogenic Ar, Xe, and N 2 matrices: the conformational ground state (ICa), and forms ICc and IITa. All other significantly populated conformers existing in the gas phase prior to deposition convert either to conformer ICa or to conformer ICc during matrix deposition. The experimental observation of ICc had never been achieved hitherto. Narrowband near-IR irradiation of the first overtone of νOH vibrational mode of ICa and ICc in nitrogen matrices (at 6910 and 6930 cm −1 , respectively) led to selective generation of two additional conformers of high-energy, ITc and ITa, respectively, which were also observed experimentally for the first time. In addition, these experiments also provided the key information for the detailed vibrational characterization of the 3 conformers initially present in the matrices. On the other hand, UV irradiation (λ = 255 nm) of PG isolated in a xenon matrix revealed that PG

A microscopic insight from conformational thermodynamics to functional ligand binding in proteins.

Science.gov (United States)

Sikdar, Samapan; Chakrabarti, J; Ghosh, Mahua

2014-12-01

We show that the thermodynamics of metal ion-induced conformational changes aid to understand the functions of protein complexes. This is illustrated in the case of a metalloprotein, alpha-lactalbumin (aLA), a divalent metal ion binding protein. We use the histograms of dihedral angles of the protein, generated from all-atom molecular dynamics simulations, to calculate conformational thermodynamics. The thermodynamically destabilized and disordered residues in different conformational states of a protein are proposed to serve as binding sites for ligands. This is tested for β-1,4-galactosyltransferase (β4GalT) binding to the Ca(2+)-aLA complex, in which the binding residues are known. Among the binding residues, the C-terminal residues like aspartate (D) 116, glutamine (Q) 117, tryptophan (W) 118 and leucine (L) 119 are destabilized and disordered and can dock β4GalT onto Ca(2+)-aLA. No such thermodynamically favourable binding residues can be identified in the case of the Mg(2+)-aLA complex. We apply similar analysis to oleic acid binding and predict that the Ca(2+)-aLA complex can bind to oleic acid through the basic histidine (H) 32 of the A2 helix and the hydrophobic residues, namely, isoleucine (I) 59, W60 and I95, of the interfacial cleft. However, the number of destabilized and disordered residues in Mg(2+)-aLA are few, and hence, the oleic acid binding to Mg(2+)-bound aLA is less stable than that to the Ca(2+)-aLA complex. Our analysis can be generalized to understand the functionality of other ligand bound proteins.

Assessment of conformity and suitability for use of the energy subsystem of interoperable high-speed lines; Konformitaetsbewertung und EG-Pruefverfahren fuer das Teilsystem Energie

Energy Technology Data Exchange (ETDEWEB)

Behrends, D. [Steglitzer Damm, Deutschen Bahn, Berlin (Germany); Brodkorb, A.; Matthes, R. [Siemens AG, Erlangen (Germany)

2003-05-01

The directive 96/48/EG governs the conformity assessment of conformity of interoperability constituents and of suitability for use of subsystems of the trans-European high-speed rail system. The assessment of the overhead contact line type SICAT H 1.0 and the energy subsystem of the new high-speed line Belgian boundary-Rotterdam-Hoofddop (HSL Zuid) in the Netherlands establish examples for the application of the technical specification for the energy subsystem. (orig.) [German] Die Richtlinie 96/48/EG regelt die Bewertung der Konformitaet von Komponenten und das EG-Pruefverfahren von Teilsystemen des interoperablen transeuropaeischen Hochgeschwindigkeitsbahnsystems. Beispiele fuer diese beiden Vorgaenge sind die Bewertung der Oberleitungsbauart SICAT H 1.0 und die Pruefung der Energieversorgung der Hochgeschwindigkeitsstrecke belgische Grenze-Rotterdam-Hoofddop (HSL Zuid) in den Niederlanden. (orig.)

High energy asymptotics of multi-colour QCD and two-dimensional conformal field theories

International Nuclear Information System (INIS)

Lipatov, L.N.; Deutsches Elektronen-Synchrotron

1993-04-01

In the multi-colour limit of perturbative QCD the holomorphic factorization of wave functions of compound states of n reggeized gluons in the impact parameter space is shown. The conformally invariant Hamiltonian for each holomorphic factor has a nontrivial integral of motion. The odderon in QCD is the simplest example of the composite system with these properties. (orig.)

Spatial and null infinity via advanced and retarded conformal factors

International Nuclear Information System (INIS)

Hayward, Sean A.

2003-01-01

A new approach to space-time asymptotics is presented, refining Penrose's idea of conformal transformations with infinity represented by the conformal boundary of space-time. It is proposed that the Penrose conformal factor be a product of advanced and retarded conformal factors, which asymptotically relate physical and conformal null coordinates and vanish at future and past null infinity respectively. A refined definition of asymptotic flatness at both spatial and null infinity is given, including that the conformal boundary is locally a light cone, with spatial infinity as the vertex. It is shown how to choose the conformal factors so that this asymptotic light cone is locally a metric light cone. The theory is implemented in the spin-coefficient (or null-tetrad) formalism by a joint transformation of the spin-metric and spin-basis (or metric and tetrad). Asymptotic regularity conditions are proposed, based on the conformal boundary locally being a smoothly embedded metric light cone. These conditions ensure that the Bondi-Sachs energy-flux integrals of ingoing and outgoing gravitational radiation decay at spatial infinity such that the total radiated energy is finite, and that the Bondi-Sachs energy-momentum has a unique limit at spatial infinity, coinciding with the uniquely rendered ADM energy-momentum

Conformal consistency relations for single-field inflation

International Nuclear Information System (INIS)

Creminelli, Paolo; Noreña, Jorge; Simonović, Marko

2012-01-01

We generalize the single-field consistency relations to capture not only the leading term in the squeezed limit — going as 1/q 3 , where q is the small wavevector — but also the subleading one, going as 1/q 2 . This term, for an (n+1)-point function, is fixed in terms of the variation of the n-point function under a special conformal transformation; this parallels the fact that the 1/q 3 term is related with the scale dependence of the n-point function. For the squeezed limit of the 3-point function, this conformal consistency relation implies that there are no terms going as 1/q 2 . We verify that the squeezed limit of the 4-point function is related to the conformal variation of the 3-point function both in the case of canonical slow-roll inflation and in models with reduced speed of sound. In the second case the conformal consistency conditions capture, at the level of observables, the relation among operators induced by the non-linear realization of Lorentz invariance in the Lagrangian. These results mean that, in any single-field model, primordial correlation functions of ζ are endowed with an SO(4,1) symmetry, with dilations and special conformal transformations non-linearly realized by ζ. We also verify the conformal consistency relations for any n-point function in models with a modulation of the inflaton potential, where the scale dependence is not negligible. Finally, we generalize (some of) the consistency relations involving tensors and soft internal momenta

Hypotrochoids in conformal restriction systems and Virasoro descendants

International Nuclear Information System (INIS)

Doyon, Benjamin

2013-01-01

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

Exploring perturbative conformal field theory in Mellin space

Energy Technology Data Exchange (ETDEWEB)

Nizami, Amin A. [International Centre for Theoretical Sciences, TIFR,Hesaraghatta, Hubli, Bengaluru-560089 (India); Rudra, Arnab [Center for Quantum Mathematics and Physics (QMAP), Department of Physics,University of California, Davis, 1 Shields Ave, Davis, CA 95616 (United States); Sarkar, Sourav [Institut für Mathematik und Institut für Physik, Humboldt-Universität zu Berlin, IRIS-Adlershof,Zum Großen Windkanal 6, 12489 Berlin (Germany); Max-Planck-Institut für Gravitationsphysik, Albert-Einstein-Institut,Am Mühlenberg 1, 14476 Potsdam (Germany); Verma, Mritunjay [International Centre for Theoretical Sciences, TIFR,Hesaraghatta, Hubli, Bengaluru-560089 (India); Harish-Chandra Research Institute,Chhatnag Road, Jhunsi, Allahabad-211019 (India)

2017-01-24

We explore the Mellin representation of correlation functions in conformal field theories in the weak coupling regime. We provide a complete proof for a set of Feynman rules to write the Mellin amplitude for a general tree level Feynman diagram involving only scalar operators. We find a factorised form involving beta functions associated to the propagators, similar to tree level Feynman rules in momentum space for ordinary QFTs. We also briefly consider the case where a generic scalar perturbation of the free CFT breaks conformal invariance. Mellin space still has some utility and one can consider non-conformal Mellin representations. In this context, we find that the beta function corresponding to conformal propagator uplifts to a hypergeometric function.

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

DEFF Research Database (Denmark)

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

2002-01-01

S-Adenosylmethionine (AdoMet) and other sulfonium ions play central roles in the metabolism of all organisms. The conformational preferences of AdoMet and two other biologically important sulfonium ions, S-methylmethionine and dimethylsulfonioproprionic acid, have been investigated by NMR...... and computational studies. Molecular mechanics parameters for the sulfonium center have been developed for the AMBER force field to permit analysis of NMR results and to enable comparison of the relative energies of the different conformations of AdoMet that have been found in crystal structures of complexes...... with proteins. S-Methylmethionine and S-dimethylsulfonioproprionate adopt a variety of conformations in aqueous solution; a conformation with an electrostatic interaction between the sulfonium sulfur and the carboxylate group is not noticeably favored, in contrast to the preferred conformation found by in vacuo...

Substrate-specific reorganization of the conformational ensemble of CSK implicates novel modes of kinase function.

Directory of Open Access Journals (Sweden)

Michael A Jamros

Full Text Available Protein kinases use ATP as a phosphoryl donor for the posttranslational modification of signaling targets. It is generally thought that the binding of this nucleotide induces conformational changes leading to closed, more compact forms of the kinase domain that ideally orient active-site residues for efficient catalysis. The kinase domain is oftentimes flanked by additional ligand binding domains that up- or down-regulate catalytic function. C-terminal Src kinase (Csk is a multidomain tyrosine kinase that is up-regulated by N-terminal SH2 and SH3 domains. Although the X-ray structure of Csk suggests the enzyme is compact, X-ray scattering studies indicate that the enzyme possesses both compact and open conformational forms in solution. Here, we investigated whether interactions with the ATP analog AMP-PNP and ADP can shift the conformational ensemble of Csk in solution using a combination of small angle x-ray scattering and molecular dynamics simulations. We find that binding of AMP-PNP shifts the ensemble towards more extended rather than more compact conformations. Binding of ADP further shifts the ensemble towards extended conformations, including highly extended conformations not adopted by the apo protein, nor by the AMP-PNP bound protein. These ensembles indicate that any compaction of the kinase domain induced by nucleotide binding does not extend to the overall multi-domain architecture. Instead, assembly of an ATP-bound kinase domain generates further extended forms of Csk that may have relevance for kinase scaffolding and Src regulation in the cell.

Regulation of β2-adrenergic receptor function by conformationally selective single-domain intrabodies

DEFF Research Database (Denmark)

Staus, Dean P; Wingler, Laura M; Strachan, Ryan T

2014-01-01

. However, a monomeric single-domain antibody (nanobody) from the Camelid family was recently found to allosterically bind and stabilize an active conformation of the β2-adrenergic receptor (β2AR). Here, we set out to study the functional interaction of 18 related nanobodies with the β2AR to investigate...... their roles as novel tools for studying GPCR biology. Our studies revealed several sequence-related nanobody families with preferences for active (agonist-occupied) or inactive (antagonist-occupied) receptors. Flow cytometry analysis indicates that all nanobodies bind to epitopes displayed...... on the intracellular receptor surface; therefore, we transiently expressed them intracellularly as "intrabodies" to test their effects on β2AR-dependent signaling. Conformational specificity was preserved after intrabody conversion as demonstrated by the ability for the intracellularly expressed nanobodies...

Impact of graphene-based nanomaterials (GBNMs) on the structural and functional conformations of hepcidin peptide

Science.gov (United States)

Singh, Krishna P.; Baweja, Lokesh; Wolkenhauer, Olaf; Rahman, Qamar; Gupta, Shailendra K.

2018-03-01

Graphene-based nanomaterials (GBNMs) are widely used in various industrial and biomedical applications. GBNMs of different compositions, size and shapes are being introduced without thorough toxicity evaluation due to the unavailability of regulatory guidelines. Computational toxicity prediction methods are used by regulatory bodies to quickly assess health hazards caused by newer materials. Due to increasing demand of GBNMs in various size and functional groups in industrial and consumer based applications, rapid and reliable computational toxicity assessment methods are urgently needed. In the present work, we investigate the impact of graphene and graphene oxide nanomaterials on the structural conformations of small hepcidin peptide and compare the materials for their structural and conformational changes. Our molecular dynamics simulation studies revealed conformational changes in hepcidin due to its interaction with GBMNs, which results in a loss of its functional properties. Our results indicate that hepcidin peptide undergo severe structural deformations when superimposed on the graphene sheet in comparison to graphene oxide sheet. These observations suggest that graphene is more toxic than a graphene oxide nanosheet of similar area. Overall, this study indicates that computational methods based on structural deformation, using molecular dynamics (MD) simulations, can be used for the early evaluation of toxicity potential of novel nanomaterials.

The decomposition of global conformal invariants

CERN Document Server

Alexakis, Spyros

2012-01-01

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

Conformal changes of metrics and the initial-value problem of general relativity

International Nuclear Information System (INIS)

Mielke, E.W.

1977-01-01

Conformal techniques are reviewed with respect to applications to the initial-value problem of general relativity. Invariant transverse traceless decompositions of tensors, one of its main tools, are related to representations of the group of 'conformeomorphisms' acting on the space of all Riemannian metrics on M. Conformal vector fields, a kernel in the decomposition, are analyzed on compact manifolds with constant scalar curvature. The realization of arbitrary functions as scalar curvature of conformally equivalent metrics, a generalization of Yamabe's (Osaka Math. J.; 12:12 (1960)) conjecture, is applied to the Hamiltonian constraint and to the issue of positive energy of gravitational fields. Various approaches to the solution of the initial-value equations produced by altering the scaling behaviour of the second fundamental form are compared. (author)

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

Directory of Open Access Journals (Sweden)

Barry J Grant

2009-03-01

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

Particle dynamics around time conformal regular black holes via Noether symmetries

Science.gov (United States)

Jawad, Abdul; Umair Shahzad, M.

The time conformal regular black hole (RBH) solutions which are admitting the time conformal factor e𝜖g(t), where g(t) is an arbitrary function of time and 𝜖 is the perturbation parameter are being considered. The approximate Noether symmetries technique is being used for finding the function g(t) which leads to t α. The dynamics of particles around RBHs are also being discussed through symmetry generators which provide approximate energy as well as angular momentum of the particles. In addition, we analyze the motion of neutral and charged particles around two well known RBHs such as charged RBH using Fermi-Dirac distribution and Kehagias-Sftesos asymptotically flat RBH. We obtain the innermost stable circular orbit and corresponding approximate energy and angular momentum. The behavior of effective potential, effective force and escape velocity of the particles in the presence/absence of magnetic field for different values of angular momentum near horizons are also being analyzed. The stable and unstable regions of particle near horizons due to the effect of angular momentum and magnetic field are also explained.

Conformal Nets II: Conformal Blocks

Science.gov (United States)

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

2017-08-01

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

Selective stimulation of conformational conversions in free molecules

International Nuclear Information System (INIS)

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

2014-01-01

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

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

Directory of Open Access Journals (Sweden)

Cuiling Xu

2009-10-01

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

Sampling Molecular Conformers in Solution with Quantum Mechanical Accuracy at a Nearly Molecular-Mechanics Cost.

Science.gov (United States)

Rosa, Marta; Micciarelli, Marco; Laio, Alessandro; Baroni, Stefano

2016-09-13

We introduce a method to evaluate the relative populations of different conformers of molecular species in solution, aiming at quantum mechanical accuracy, while keeping the computational cost at a nearly molecular-mechanics level. This goal is achieved by combining long classical molecular-dynamics simulations to sample the free-energy landscape of the system, advanced clustering techniques to identify the most relevant conformers, and thermodynamic perturbation theory to correct the resulting populations, using quantum-mechanical energies from density functional theory. A quantitative criterion for assessing the accuracy thus achieved is proposed. The resulting methodology is demonstrated in the specific case of cyanin (cyanidin-3-glucoside) in water solution.

Eikonal Approximation in AdS/CFT: Conformal Partial Waves and Finite N Four-Point Functions

CERN Document Server

Cornalba, L; Penedones, J; Schiappa, R; Cornalba, Lorenzo; Costa, Miguel S.; Penedones, Joao; Schiappa, Ricardo

2007-01-01

We introduce the impact-parameter representation for conformal field theory correlators of the form A ~ . This representation is appropriate in the eikonal kinematical regime, and approximates the conformal partial-wave decomposition in the limit of large spin and dimension of the exchanged primary. Using recent results on the two-point function _{shock} in the presence of a shock wave in Anti-de Sitter, and its relation to the discontinuity of the four-point amplitude A across a kinematical branch-cut, we find the high spin and dimension conformal partial- wave decomposition of all tree-level Anti-de Sitter Witten diagrams. We show that, as in flat space, the eikonal kinematical regime is dominated by the T-channel exchange of the massless particle with highest spin (graviton dominance). We also compute the anomalous dimensions of the high-spin O_1 O_2 composites. Finally, we conjecture a formula re-summing crossed-ladder Witten diagrams to all orders in the gravitational coupling.

Defects in conformal field theory

International Nuclear Information System (INIS)

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

2016-01-01

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

Defects in conformal field theory

Energy Technology Data Exchange (ETDEWEB)

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

2016-04-15

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

On the linear conformal gravitation

International Nuclear Information System (INIS)

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

1984-01-01

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

Z/NZ conformal field theories

International Nuclear Information System (INIS)

Degiovanni, P.

1990-01-01

We compute the modular properties of the possible genus-one characters of some Rational Conformal Field Theories starting from their fusion rules. We show that the possible choices of S matrices are indexed by some automorphisms of the fusion algebra. We also classify the modular invariant partition functions of these theories. This gives the complete list of modular invariant partition functions of Rational Conformal Field Theories with respect to the A N (1) level one algebra. (orig.)

Conformational analysis of 9β,19-cyclopropyl sterols: Detection of the pseudoplanar conformer by nuclear Overhauser effects and its functional implications

International Nuclear Information System (INIS)

Nes, W.D.; Benson, M.; Lundin, R.E.; Le, P.H.

1988-01-01

Nuclear Overhauser difference spectroscopy and variable temperature studies of the 9β,19-cyclopropyl sterols 24,25-dehydropollinastanol (4,4-desmethyl-5α-cycloart-24-en-3β-ol) and cyclolaudenol [(24S)-24-methyl-5α-cycloart-25(27)-en-3β-ol] have shown the solution conformation of the B/C rings to be twist-chair/twist-boat rather than boat/chair as suggested in the literature. This is very similar to the known crystal structure conformation of 9β,19-cyclopropyl sterols. The effect of these conformations on the molecular shape is highly significant; the first conformation orients into a pseudoplanar or flat shape analogous to lanosterol, whereas the latter conformation exhibits a bent shape. The results are interpreted to imply that, for conformational reasons, cyclopropyl sterols can be expected to maintain the pseudoplanar shape in membrane bilayers

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

Science.gov (United States)

Chashmniam, Saeed; Tafazzoli, Mohsen

2017-11-01

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

Prediction of conformationally dependent atomic multipole moments in carbohydrates.

Science.gov (United States)

Cardamone, Salvatore; Popelier, Paul L A

2015-12-15

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

Hartree-Fock and density functional theory study of alpha-cyclodextrin conformers.

Science.gov (United States)

Jiménez, Verónica; Alderete, Joel B

2008-01-31

Herein, we report the geometry optimization of four conformers of alpha-cyclodextrin (alpha-CD) by means of PM3, HF/STO-3G, HF/3-21G, HF/6-31G(d), B3LYP/6-31G(d), and X3LYP/6-31G(d) calculations. The analysis of several geometrical parameters indicates that all conformers possess bond lengths, angles, and dihedrals that agree fairly well with the crystalline structure of alpha-CD. However, only three of them (1-3) resemble the polar character of CDs and show intramolecular hydrogen-bonding patterns that agree with experimental NMR data. Among them, conformer 3 appears to be the most stable species both in the gas phase and in solution; therefore, it is expected to be the most suitable representative structure for alpha-CD conformation. The purpose of selecting such a species is to identify an appropriate structure to be employed as a starting point for reliable computational studies on complexation phenomena. Our results indicate that the choice of a particular alpha-CD conformer should affect the results of ab initio computational studies on the inclusion complexation with this cyclodextrin since both the direction and the magnitude of the dipole moment depend strongly on the conformation of alpha-CD.

Using 1H and 13C NMR chemical shifts to determine cyclic peptide conformations: a combined molecular dynamics and quantum mechanics approach.

Science.gov (United States)

Nguyen, Q Nhu N; Schwochert, Joshua; Tantillo, Dean J; Lokey, R Scott

2018-05-10

Solving conformations of cyclic peptides can provide insight into structure-activity and structure-property relationships, which can help in the design of compounds with improved bioactivity and/or ADME characteristics. The most common approaches for determining the structures of cyclic peptides are based on NMR-derived distance restraints obtained from NOESY or ROESY cross-peak intensities, and 3J-based dihedral restraints using the Karplus relationship. Unfortunately, these observables are often too weak, sparse, or degenerate to provide unequivocal, high-confidence solution structures, prompting us to investigate an alternative approach that relies only on 1H and 13C chemical shifts as experimental observables. This method, which we call conformational analysis from NMR and density-functional prediction of low-energy ensembles (CANDLE), uses molecular dynamics (MD) simulations to generate conformer families and density functional theory (DFT) calculations to predict their 1H and 13C chemical shifts. Iterative conformer searches and DFT energy calculations on a cyclic peptide-peptoid hybrid yielded Boltzmann ensembles whose predicted chemical shifts matched the experimental values better than any single conformer. For these compounds, CANDLE outperformed the classic NOE- and 3J-coupling-based approach by disambiguating similar β-turn types and also enabled the structural elucidation of the minor conformer. Through the use of chemical shifts, in conjunction with DFT and MD calculations, CANDLE can help illuminate conformational ensembles of cyclic peptides in solution.

Two dimensional infinite conformal symmetry

International Nuclear Information System (INIS)

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

1993-01-01

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

Conformational changes in hemoglobin triggered by changing the iron charge

International Nuclear Information System (INIS)

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

2008-01-01

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

Eikonal approximation in AdS/CFT: Conformal partial waves and finite N four-point functions

International Nuclear Information System (INIS)

Cornalba, Lorenzo; Costa, Miguel S.; Penedones, Joao; Schiappa, Ricardo

2007-01-01

We introduce the impact parameter representation for conformal field theory correlators of the form A∼ 1 O 2 O 1 O 2 >. This representation is appropriate in the eikonal kinematical regime, and approximates the conformal partial wave decomposition in the limit of large spin and dimension of the exchanged primary. Using recent results on the two-point function 1 O 1 > shock in the presence of a shock wave in anti-de Sitter, and its relation to the discontinuity of the four-point amplitude A across a kinematical branch cut, we find the high spin and dimension conformal partial wave decomposition of all tree-level anti-de Sitter Witten diagrams. We show that, as in flat space, the eikonal kinematical regime is dominated by the T-channel exchange of the massless particle with highest spin (graviton dominance). We also compute the anomalous dimensions of the high spin O 1 O 2 composites. Finally, we conjecture a formula re-summing crossed-ladder Witten diagrams to all orders in the gravitational coupling

Real-time observation of the conformational dynamics of mitochondrial Hsp70 by spFRET.

Science.gov (United States)

Sikor, Martin; Mapa, Koyeli; von Voithenberg, Lena Voith; Mokranjac, Dejana; Lamb, Don C

2013-05-29

The numerous functions of the important class of molecular chaperones, heat shock proteins 70 (Hsp70), rely on cycles of intricate conformational changes driven by ATP-hydrolysis and regulated by cochaperones and substrates. Here, we used Förster resonance energy transfer to study the conformational dynamics of individual molecules of Ssc1, a mitochondrial Hsp70, in real time. The intrinsic dynamics of the substrate-binding domain of Ssc1 was observed to be uncoupled from the dynamic interactions between substrate- and nucleotide-binding domains. Analysis of the fluctuations in the interdomain separation revealed frequent transitions to a nucleotide-free state. The nucleotide-exchange factor Mge1 did not induce ADP release, as expected, but rather facilitated binding of ATP. These results indicate that the conformational cycle of Ssc1 is more elaborate than previously thought and provide insight into how the Hsp70s can perform a wide variety of functions.

18 CFR 153.21 - Conformity with requirements.

Science.gov (United States)

2010-04-01

... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Conformity with requirements. 153.21 Section 153.21 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY... Requirements § 153.21 Conformity with requirements. (a) General Rule. Applications under subparts B and C of...

Lipid Regulated Intramolecular Conformational Dynamics of SNARE-Protein Ykt6

Science.gov (United States)

Dai, Yawei; Seeger, Markus; Weng, Jingwei; Song, Song; Wang, Wenning; Tan, Yan-Wen

2016-08-01

Cellular informational and metabolic processes are propagated with specific membrane fusions governed by soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNARE). SNARE protein Ykt6 is highly expressed in brain neurons and plays a critical role in the membrane-trafficking process. Studies suggested that Ykt6 undergoes a conformational change at the interface between its longin domain and the SNARE core. In this work, we study the conformational state distributions and dynamics of rat Ykt6 by means of single-molecule Förster Resonance Energy Transfer (smFRET) and Fluorescence Cross-Correlation Spectroscopy (FCCS). We observed that intramolecular conformational dynamics between longin domain and SNARE core occurred at the timescale ~200 μs. Furthermore, this dynamics can be regulated and even eliminated by the presence of lipid dodecylphoshpocholine (DPC). Our molecular dynamic (MD) simulations have shown that, the SNARE core exhibits a flexible structure while the longin domain retains relatively stable in apo state. Combining single molecule experiments and theoretical MD simulations, we are the first to provide a quantitative dynamics of Ykt6 and explain the functional conformational change from a qualitative point of view.

Role of Detergents in Conformational Exchange of a G Protein-coupled Receptor*

Science.gov (United States)

Chung, Ka Young; Kim, Tae Hun; Manglik, Aashish; Alvares, Rohan; Kobilka, Brian K.; Prosser, R. Scott

2012-01-01

The G protein-coupled β2-adrenoreceptor (β2AR) signals through the heterotrimeric G proteins Gs and Gi and β-arrestin. As such, the energy landscape of β2AR-excited state conformers is expected to be complex. Upon tagging Cys-265 of β2AR with a trifluoromethyl probe, 19F NMR was used to assess conformations and possible equilibria between states. Here, we report key differences in β2AR conformational dynamics associated with the detergents used to stabilize the receptor. In dodecyl maltoside (DDM) micelles, the spectra are well represented by a single Lorentzian line that shifts progressively downfield with activation by appropriate ligand. The results are consistent with interconversion between two or more states on a time scale faster than the greatest difference in ligand-dependent chemical shift (i.e. >100 Hz). Given that high detergent off-rates of DDM monomers may facilitate conformational exchange between functional states of β2AR, we utilized the recently developed maltose-neopentyl glycol (MNG-3) diacyl detergent. In MNG-3 micelles, spectra indicated at least three distinct states, the relative populations of which depended on ligand, whereas no ligand-dependent shifts were observed, consistent with the slow exchange limit. Thus, detergent has a profound effect on the equilibrium kinetics between functional states. MNG-3, which has a critical micelle concentration in the nanomolar regime, exhibits an off-rate that is 4 orders of magnitude lower than that of DDM. High detergent off-rates are more likely to facilitate conformational exchange between distinct functional states associated with the G protein-coupled receptor. PMID:22893704

Role of detergents in conformational exchange of a G protein-coupled receptor.

Science.gov (United States)

Chung, Ka Young; Kim, Tae Hun; Manglik, Aashish; Alvares, Rohan; Kobilka, Brian K; Prosser, R Scott

2012-10-19

The G protein-coupled β(2)-adrenoreceptor (β(2)AR) signals through the heterotrimeric G proteins G(s) and G(i) and β-arrestin. As such, the energy landscape of β(2)AR-excited state conformers is expected to be complex. Upon tagging Cys-265 of β(2)AR with a trifluoromethyl probe, (19)F NMR was used to assess conformations and possible equilibria between states. Here, we report key differences in β(2)AR conformational dynamics associated with the detergents used to stabilize the receptor. In dodecyl maltoside (DDM) micelles, the spectra are well represented by a single Lorentzian line that shifts progressively downfield with activation by appropriate ligand. The results are consistent with interconversion between two or more states on a time scale faster than the greatest difference in ligand-dependent chemical shift (i.e. >100 Hz). Given that high detergent off-rates of DDM monomers may facilitate conformational exchange between functional states of β(2)AR, we utilized the recently developed maltose-neopentyl glycol (MNG-3) diacyl detergent. In MNG-3 micelles, spectra indicated at least three distinct states, the relative populations of which depended on ligand, whereas no ligand-dependent shifts were observed, consistent with the slow exchange limit. Thus, detergent has a profound effect on the equilibrium kinetics between functional states. MNG-3, which has a critical micelle concentration in the nanomolar regime, exhibits an off-rate that is 4 orders of magnitude lower than that of DDM. High detergent off-rates are more likely to facilitate conformational exchange between distinct functional states associated with the G protein-coupled receptor.

Extended conformal algebras

International Nuclear Information System (INIS)

Goddard, Peter

1990-01-01

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

Conformational elasticity can facilitate TALE-DNA recognition.

Science.gov (United States)

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

2014-01-01

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

All unitary ray representations of the conformal group SU(2,2) with positive energy

International Nuclear Information System (INIS)

Mack, G.

1975-12-01

We find all those unitary irreducible representations of the infinitely - sheeted covering group G tilde of the conformal group SU(2,2)/Z 4 which have positive energy P 0 >= O. They are all finite component field representations and are labelled by dimension d and a finite dimensional irreducible representation (j 1 , j 2 ) of the Lorentz group SL(2C). They all decompose into a finite number of unitary irreducible representations of the Poincare subgroup with dilations. (orig.) [de

Harmony of spinning conformal blocks

Energy Technology Data Exchange (ETDEWEB)

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

2016-12-07

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

Harmony of spinning conformal blocks

Energy Technology Data Exchange (ETDEWEB)

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

2017-03-15

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

Homothetic and conformal symmetries of solutions to Einstein's equations

International Nuclear Information System (INIS)

Eardley, D.; Isenberg, J.; Marsden, J.; Moncrief, V.; Yale Univ., New Haven, CT

1986-01-01

We present several results about the nonexistence of solutions of Einstein's equations with homoethetic or conformal symmetry. We show that the only spatially compact, globally hyperbolic spacetimes admitting a hypersurface of constant mean extrinsic curvature, and also admitting an infinitesimal proper homothetic symmetry, are everywhere locally flat; this assumes that the matter fields either obey certain energy conditions, or are the Yang-Mills or massless Klein-Gordon fields. We find that the only vacuum solutions admitting an infinitesimal proper conformal symmetry are everywhere locally flat spacetimes and certain plane wave solutions. We show that if the dominant energy condition is assumed, then Minkowski spacetime is the only asymptotically flat solution which has an infinitesimal conformal symmetry that is asymptotic to a dilation. In other words, with the exceptions cited, homothetic or conformal Killing fields are in fact Killing in spatially compact or asymptotically flat spacetimes. In the conformal procedure for solving the initial value problem, we show that data with infinitesimal conformal symmetry evolves to a spacetime with full isometry. (orig.)

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

International Nuclear Information System (INIS)

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

1987-01-01

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

Theoretical conformational analysis of the bovine adrenal medulla 12 residue peptide molecule

Science.gov (United States)

Akhmedov, N. A.; Tagiyev, Z. H.; Hasanov, E. M.; Akverdieva, G. A.

2003-02-01

The spatial structure and conformational properties of the bovine adrenal medulla 12 residue peptide Tyr1-Gly2-Gly3-Phe4-Met5-Arg6-Arg7-Val8-Gly9-Arg10-Pro11-Glu12 (BAM-12P) molecule were studied by theoretical conformational analysis. It is revealed that this molecule can exist in several stable states. The energy and geometrical parameters for the low-energy conformations are obtained. The conformationally rigid and labile segments of this molecule were revealed.

Frustration-guided motion planning reveals conformational transitions in proteins.

Science.gov (United States)

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

2017-10-01

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

Lattice models and conformal field theories

International Nuclear Information System (INIS)

Saleur, H.

1988-01-01

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

Conformational kinetics of aliphatic tails

Science.gov (United States)

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

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

Conformal symmetry in two dimensions: An explicit recurrence formula for the conformal partial wave amplitude

International Nuclear Information System (INIS)

Zamolodchikov, A.B.

1984-01-01

An explicit recurrence relation for the conformal block functions is presented. This relation permits one to evaluate the X-expansion of these functions order-by-order and appropriate for numerical calculations. (orig.)

Conformal techniques for OPE in asymptotically free quantum field theory

International Nuclear Information System (INIS)

Craigie, N.S.; Dobrev, V.K.

1982-06-01

We discuss the relationship between the short-distance behaviour of vertex functions and conformal invariance in asymptotically free theories. We show how conformal group techniques can be used to derive spectral representations of wave functions and vertex functions in QCD. (author)

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

DEFF Research Database (Denmark)

Christensen, I T; Jørgensen, Flemming Steen

1997-01-01

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

Investigating ion channel conformational changes using voltage clamp fluorometry.

Science.gov (United States)

Talwar, Sahil; Lynch, Joseph W

2015-11-01

Ion channels are membrane proteins whose functions are governed by conformational changes. The widespread distribution of ion channels, coupled with their involvement in most physiological and pathological processes and their importance as therapeutic targets, renders the elucidation of these conformational mechanisms highly compelling from a drug discovery perspective. Thanks to recent advances in structural biology techniques, we now have high-resolution static molecular structures for members of the major ion channel families. However, major questions remain to be resolved about the conformational states that ion channels adopt during activation, drug modulation and desensitization. Patch-clamp electrophysiology has long been used to define ion channel conformational states based on functional criteria. It achieves this by monitoring conformational changes at the channel gate and cannot detect conformational changes occurring in regions distant from the gate. Voltage clamp fluorometry involves labelling cysteines introduced into domains of interest with environmentally sensitive fluorophores and inferring structural rearrangements from voltage or ligand-induced fluorescence changes. Ion channel currents are monitored simultaneously to verify the conformational status. By defining real time conformational changes in domains distant from the gate, this technique provides unexpected new insights into ion channel structure and function. This review aims to summarise the methodology and highlight recent innovative applications of this powerful technique. This article is part of the Special Issue entitled 'Fluorescent Tools in Neuropharmacology'. Copyright © 2015 Elsevier Ltd. All rights reserved.

Analytic aspects of rational conformal field theories

International Nuclear Information System (INIS)

Kiritsis, E.B.; Lawrence Berkeley Lab., CA

1990-01-01

The problem of deriving linear differential equations for correlation functions of Rational Conformal Field Theories is considered. Techniques from the theory of fuchsian differential equations are used to show that knowledge of the central charge, dimensions of primary fields and fusion rules are enough to fix the differential equations for one- and two-point functions on the tours. Any other correlation function can be calculated along similar lines. The results settle the issue of 'exact solution' of rational conformal field theories. (orig.)

Emotional and Behavioral Functioning After Conformal Radiation Therapy for Pediatric Ependymoma

International Nuclear Information System (INIS)

Willard, Victoria W.; Conklin, Heather M.; Boop, Frederick A.; Wu, Shengjie; Merchant, Thomas E.

2014-01-01

Purpose: The standard of care for pediatric patients with ependymoma involves postoperative radiation therapy. Prior research suggests that conformal radiation therapy (CRT) is associated with relative sparing of cognitive and academic functioning, but little is known about the effect of CRT on emotional and behavioral functioning. Methods and Materials: A total of 113 patients with pediatric ependymoma underwent CRT using photons as part of their enrollment on an institutional trial. Patients completed annual evaluations of neurocognitive functioning during the first 5 years after CRT. Emotional and behavioral functioning was assessed via the Child Behavior Checklist. Results: Before CRT, emotional and behavioral functioning were commensurate with those of the normative population and within normal limits. After 5 years, means remained within normal limits but were significantly below the normative mean. Linear mixed models revealed a significant increase in attention problems over time. These problems were associated with age at diagnosis/CRT, tumor location, and extent of resection. A higher-than-expected incidence of school problems was present at all assessment points after baseline. Conclusions: The use of photon CRT for ependymoma is associated with relatively stable emotional and behavioral functioning during the first 5 years after treatment. The exception is an increase in attention problems. Results suggest that intervening earlier in the survivorship period—during the first year posttreatment—may be beneficial

Emotional and Behavioral Functioning After Conformal Radiation Therapy for Pediatric Ependymoma

Energy Technology Data Exchange (ETDEWEB)

Willard, Victoria W.; Conklin, Heather M. [Department of Psychology, St. Jude Children' s Research Hospital, Memphis, Tennessee (United States); Boop, Frederick A. [Department of Surgery, St. Jude Children' s Research Hospital, Memphis, Tennessee (United States); Department of Neurosurgery, Semmes-Murphey Neurologic and Spine Institute, Memphis, Tennessee (United States); Wu, Shengjie [Department of Biostatistics, St. Jude Children' s Research Hospital, Memphis, Tennessee (United States); Merchant, Thomas E., E-mail: thomas.merchant@stjude.org [Division of Radiation Oncology, St. Jude Children' s Research Hospital, Memphis, Tennessee (United States)

2014-03-15

Purpose: The standard of care for pediatric patients with ependymoma involves postoperative radiation therapy. Prior research suggests that conformal radiation therapy (CRT) is associated with relative sparing of cognitive and academic functioning, but little is known about the effect of CRT on emotional and behavioral functioning. Methods and Materials: A total of 113 patients with pediatric ependymoma underwent CRT using photons as part of their enrollment on an institutional trial. Patients completed annual evaluations of neurocognitive functioning during the first 5 years after CRT. Emotional and behavioral functioning was assessed via the Child Behavior Checklist. Results: Before CRT, emotional and behavioral functioning were commensurate with those of the normative population and within normal limits. After 5 years, means remained within normal limits but were significantly below the normative mean. Linear mixed models revealed a significant increase in attention problems over time. These problems were associated with age at diagnosis/CRT, tumor location, and extent of resection. A higher-than-expected incidence of school problems was present at all assessment points after baseline. Conclusions: The use of photon CRT for ependymoma is associated with relatively stable emotional and behavioral functioning during the first 5 years after treatment. The exception is an increase in attention problems. Results suggest that intervening earlier in the survivorship period—during the first year posttreatment—may be beneficial.

Perspectives on electrostatics and conformational motions in enzyme catalysis.

Science.gov (United States)

Hanoian, Philip; Liu, C Tony; Hammes-Schiffer, Sharon; Benkovic, Stephen

2015-02-17

CONSPECTUS: Enzymes are essential for all living organisms, and their effectiveness as chemical catalysts has driven more than a half century of research seeking to understand the enormous rate enhancements they provide. Nevertheless, a complete understanding of the factors that govern the rate enhancements and selectivities of enzymes remains elusive, due to the extraordinary complexity and cooperativity that are the hallmarks of these biomolecules. We have used a combination of site-directed mutagenesis, pre-steady-state kinetics, X-ray crystallography, nuclear magnetic resonance (NMR), vibrational and fluorescence spectroscopies, resonance energy transfer, and computer simulations to study the implications of conformational motions and electrostatic interactions on enzyme catalysis in the enzyme dihydrofolate reductase (DHFR). We have demonstrated that modest equilibrium conformational changes are functionally related to the hydride transfer reaction. Results obtained for mutant DHFRs illustrated that reductions in hydride transfer rates are correlated with altered conformational motions, and analysis of the evolutionary history of DHFR indicated that mutations appear to have occurred to preserve both the hydride transfer rate and the associated conformational changes. More recent results suggested that differences in local electrostatic environments contribute to finely tuning the substrate pKa in the initial protonation step. Using a combination of primary and solvent kinetic isotope effects, we demonstrated that the reaction mechanism is consistent across a broad pH range, and computer simulations suggested that deprotonation of the active site Tyr100 may play a crucial role in substrate protonation at high pH. Site-specific incorporation of vibrational thiocyanate probes into the ecDHFR active site provided an experimental tool for interrogating these microenvironments and for investigating changes in electrostatics along the DHFR catalytic cycle

Hot Conformal Gauge Theories

DEFF Research Database (Denmark)

Mojaza, Matin; Pica, Claudio; Sannino, Francesco

2010-01-01

of flavors. Surprisingly this number, if computed to the order g^2, agrees with previous predictions for the lower boundary of the conformal window for nonsupersymmetric gauge theories. The higher order results tend to predict a higher number of critical flavors. These are universal properties, i......We compute the nonzero temperature free energy up to the order g^6 \\ln(1/g) in the coupling constant for vector like SU(N) gauge theories featuring matter transforming according to different representations of the underlying gauge group. The number of matter fields, i.e. flavors, is arranged...... in such a way that the theory develops a perturbative stable infrared fixed point at zero temperature. Due to large distance conformality we trade the coupling constant with its fixed point value and define a reduced free energy which depends only on the number of flavors, colors and matter representation. We...

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

Directory of Open Access Journals (Sweden)

Jiang Hualiang

2010-11-01

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

Characterizing highly dynamic conformational states: The transcription bubble in RNAP-promoter open complex as an example

Science.gov (United States)

Lerner, Eitan; Ingargiola, Antonino; Weiss, Shimon

2018-03-01

Bio-macromolecules carry out complicated functions through structural changes. To understand their mechanism of action, the structure of each step has to be characterized. While classical structural biology techniques allow the characterization of a few "structural snapshots" along the enzymatic cycle (usually of stable conformations), they do not cover all (and often fast interconverting) structures in the ensemble, where each may play an important functional role. Recently, several groups have demonstrated that structures of different conformations in solution could be solved by measuring multiple distances between different pairs of residues using single-molecule Förster resonance energy transfer (smFRET) and using them as constrains for hybrid/integrative structural modeling. However, this approach is limited in cases where the conformational dynamics is faster than the technique's temporal resolution. In this study, we combine existing tools that elucidate sub-millisecond conformational dynamics together with hybrid/integrative structural modeling to study the conformational states of the transcription bubble in the bacterial RNA polymerase-promoter open complex (RPo). We measured microsecond alternating laser excitation-smFRET of differently labeled lacCONS promoter dsDNA constructs. We used a combination of burst variance analysis, photon-by-photon hidden Markov modeling, and the FRET-restrained positioning and screening approach to identify two conformational states for RPo. The experimentally derived distances of one conformational state match the known crystal structure of bacterial RPo. The experimentally derived distances of the other conformational state have characteristics of a scrunched RPo. These findings support the hypothesis that sub-millisecond dynamics in the transcription bubble are responsible for transcription start site selection.

On C{sub J} and C{sub T} in conformal QED

Energy Technology Data Exchange (ETDEWEB)

Giombi, Simone; Tarnopolsky, Grigory [Princeton University, Department of Physics,Jadwin Hall, Washington Road, Princeton NJ 08544 (United States); Klebanov, Igor R. [Princeton University, Department of Physics,Jadwin Hall, Washington Road, Princeton NJ 08544 (United States); Princeton Center for Theoretical Science, Princeton University,Jadwin Hall, Washington Road, Princeton NJ 08544 (United States)

2016-08-26

QED with a large number N of massless fermionic degrees of freedom has a conformal phase in a range of space-time dimensions. We use a large N diagrammatic approach to calculate the leading corrections to C{sub T}, the coefficient of the two-point function of the stress-energy tensor, and C{sub J}, the coefficient of the two-point function of the global symmetry current. We present explicit formulae as a function of d and check them versus the expectations in 2 and 4−ϵ dimensions. Using our results in higher even dimensions we find a concise formula for C{sub T} of the conformal Maxwell theory with higher derivative action F{sub μν}(−∇{sup 2}){sup (d/2)−2}F{sup μν}. In d=3, QED has a topological symmetry current, and we calculate the correction to its two-point function coefficient, C{sub J}{sup top}. We also show that some RG flows involving QED in d=3 obey C{sub T}{sup UV}>C{sub T}{sup IR} and discuss possible implications of this inequality for the symmetry breaking at small values of N.

From Extraction of Local Structures of Protein Energy Landscapes to Improved Decoy Selection in Template-Free Protein Structure Prediction.

Science.gov (United States)

Akhter, Nasrin; Shehu, Amarda

2018-01-19

Due to the essential role that the three-dimensional conformation of a protein plays in regulating interactions with molecular partners, wet and dry laboratories seek biologically-active conformations of a protein to decode its function. Computational approaches are gaining prominence due to the labor and cost demands of wet laboratory investigations. Template-free methods can now compute thousands of conformations known as decoys, but selecting native conformations from the generated decoys remains challenging. Repeatedly, research has shown that the protein energy functions whose minima are sought in the generation of decoys are unreliable indicators of nativeness. The prevalent approach ignores energy altogether and clusters decoys by conformational similarity. Complementary recent efforts design protein-specific scoring functions or train machine learning models on labeled decoys. In this paper, we show that an informative consideration of energy can be carried out under the energy landscape view. Specifically, we leverage local structures known as basins in the energy landscape probed by a template-free method. We propose and compare various strategies of basin-based decoy selection that we demonstrate are superior to clustering-based strategies. The presented results point to further directions of research for improving decoy selection, including the ability to properly consider the multiplicity of native conformations of proteins.

From Extraction of Local Structures of Protein Energy Landscapes to Improved Decoy Selection in Template-Free Protein Structure Prediction

Directory of Open Access Journals (Sweden)

Nasrin Akhter

2018-01-01

Full Text Available Due to the essential role that the three-dimensional conformation of a protein plays in regulating interactions with molecular partners, wet and dry laboratories seek biologically-active conformations of a protein to decode its function. Computational approaches are gaining prominence due to the labor and cost demands of wet laboratory investigations. Template-free methods can now compute thousands of conformations known as decoys, but selecting native conformations from the generated decoys remains challenging. Repeatedly, research has shown that the protein energy functions whose minima are sought in the generation of decoys are unreliable indicators of nativeness. The prevalent approach ignores energy altogether and clusters decoys by conformational similarity. Complementary recent efforts design protein-specific scoring functions or train machine learning models on labeled decoys. In this paper, we show that an informative consideration of energy can be carried out under the energy landscape view. Specifically, we leverage local structures known as basins in the energy landscape probed by a template-free method. We propose and compare various strategies of basin-based decoy selection that we demonstrate are superior to clustering-based strategies. The presented results point to further directions of research for improving decoy selection, including the ability to properly consider the multiplicity of native conformations of proteins.

Conformational sampling in template-free protein loop structure modeling: an overview.

Science.gov (United States)

Li, Yaohang

2013-01-01

Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a "mini protein folding problem" under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the approaches of sampling loop conformation space, which is a critical step to obtain high resolution models in template-free methods. We review the potential energy functions for loop modeling, loop buildup mechanisms to satisfy geometric constraints, and loop conformation sampling algorithms. The recent loop modeling results are also summarized.

CONFORMATIONAL SAMPLING IN TEMPLATE-FREE PROTEIN LOOP STRUCTURE MODELING: AN OVERVIEW

Directory of Open Access Journals (Sweden)

Yaohang Li

2013-02-01

Full Text Available Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a “mini protein folding problem” under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the approaches of sampling loop conformation space, which is a critical step to obtain high resolution models in template-free methods. We review the potential energy functions for loop modeling, loop buildup mechanisms to satisfy geometric constraints, and loop conformation sampling algorithms. The recent loop modeling results are also summarized.

Seed conformal blocks in 4D CFT

Energy Technology Data Exchange (ETDEWEB)

Echeverri, Alejandro Castedo; Elkhidir, Emtinan; Karateev, Denis [SISSA and INFN,Via Bonomea 265, I-34136 Trieste (Italy); Serone, Marco [SISSA and INFN,Via Bonomea 265, I-34136 Trieste (Italy); ICTP,Strada Costiera 11, I-34151 Trieste (Italy)

2016-02-29

We compute in closed analytical form the minimal set of “seed' conformal blocks associated to the exchange of generic mixed symmetry spinor/tensor operators in an arbitrary representation (ℓ,ℓ̄) of the Lorentz group in four dimensional conformal field theories. These blocks arise from 4-point functions involving two scalars, one (0,|ℓ−ℓ̄|) and one (|ℓ−ℓ̄|,0) spinors or tensors. We directly solve the set of Casimir equations, that can elegantly be written in a compact form for any (ℓ,ℓ̄), by using an educated ansatz and reducing the problem to an algebraic linear system. Various details on the form of the ansatz have been deduced by using the so called shadow formalism. The complexity of the conformal blocks depends on the value of p=|ℓ−ℓ̄| and grows with p, in analogy to what happens to scalar conformal blocks in d even space-time dimensions as d increases. These results open the way to bootstrap 4-point functions involving arbitrary spinor/tensor operators in four dimensional conformal field theories.

The structure and binding energy of K+endash ether complexes: A comparison of MP2, RI-MP2, and density functional methods

International Nuclear Information System (INIS)

Feller, D.; Apra, E.; Nichols, J.A.; Bernholdt, D.E.

1996-01-01

The structures and binding energies of several cation:ether complexes (K + :dimethyl ether, K + :dimethoxyethane, K + :12-crown-4 and K + :18-crown-6) were determined with second and fourth order perturbation theory using correlation consistent basis sets. Several of these are the largest correlated calculations yet attempted on crown ethers. The observed systematic convergence to the complete basis set limit provides a standard by which the accuracy of previous studies can be measured and facilitates the calibration of density functional methods. Recent Fouier transform ion cyclotron resonance experiments predicted K + :18-crown-6 binding energies which were significantly smaller than ab initio calculations. None of the potential sources of error examined in the present study were large enough to explain this difference. Although the 6-31+G* basis set used in an earlier theoretical study was smaller than the smallest of the correlation consistent basis sets, with suitable correction for basis set superposition error, it appears capable of yielding binding energies within several kcal/mol of the basis set limit. Perturbation theory calculations exploiting the open-quote open-quote resolution of the identity close-quote close-quote approximation were found to faithfully reproduce binding energies and conformational differences. Although the cation endash ether interaction is dominated by classical electrostatics, the accuracy of density functional techniques was found to be quite sensitive to the choice of functionals. The local density SVWN procedure performed well for binding energies and conformational differences, while underestimating K + O distances by up to 0.08 A. The gradient-corrected Becke endash Lee endash Yang endash Parr functional underestimated the K + :12c4 binding energy by 4 endash 7 kcal/mol or 15%. copyright 1996 American Institute of Physics

Conformal field theory in conformal space

International Nuclear Information System (INIS)

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

1999-01-01

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

A non-renormalization theorem for conformal anomalies

International Nuclear Information System (INIS)

Petkou, Anastasios; Skenderis, Kostas

1999-01-01

We provide a non-renormalization theorem for the coefficients of the conformal anomaly associated with operators with vanishing anomalous dimensions. Such operators include conserved currents and chiral operators in superconformal field theories. We illustrate the theorem by computing the conformal anomaly of 2-point functions both by a computation in the conformal field theory and via the AdS/CFT correspondence. Our results imply that 2- and 3-point functions of chiral primary operators in N=4 SU(N) SYM will not renormalize provided that a 'generalized Adler-Bardeen theorem' holds. We further show that recent arguments connecting the non-renormalizability of the above-mentioned correlation functions to a bonus U(1) Y symmetry are incomplete due to possible U(1) Y violating contact terms. The tree level contribution to the contact terms may be set to zero by considering appropriately normalized operators. Non-renormalizability of the above-mentioned correlation functions, however, will follow only if these contact terms saturate by free fields

Conformal dimension theory and application

CERN Document Server

Mackay, John M

2010-01-01

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

Nonlinear conformally invariant generalization of the Poisson equation to D>2 dimensions

International Nuclear Information System (INIS)

Milgrom, M.

1997-01-01

I propound a nonlinear generalization of the scalar-field Poisson equation [(var-phi , i var-phi ,i ) D/2-1 var-phi ; k ] ;k ∝ρ, in curved D-dimensional space. It is derivable from the Lagrangian density L D =L f D -Aρ var-phi, with L f D ∝-(var-phi , i var-phi ,i ) D/2 , and ρ the distribution of sources. Specializing to Euclidean spaces, where the field equation is ∇·(|∇ var-phi | D-2 ∇ var-phi)∝ρ, I find that L f D is the only conformally invariant (CI) Lagrangian in D dimensions, containing only first derivatives of var-phi, beside the free Lagrangian (∇ var-phi) 2 , which underlies the Laplace equation. When var-phi is coupled to the sources in the above manner, L D is left as the only CI Lagrangian. The symmetry is one's only recourse in solving this nonlinear theory for some nontrivial configurations. Systems comprising N point charges are special and afford further application of the symmetry. In spite of the CI, the energy function for such a system is not invariant under conformal transformations of the charges' positions. The anomalous transformation properties of the energy stem from effects of the self-energies of the charges. It follows from these that the forces F i on the charges q i at positions r i must satisfy certain constraints beside the vanishing of the net force and net moment: e.g., summation i r i ·F i must equal some given function of the charges. The constraints total (D+1)(D+2)/2, which tallies with the dimension of the conformal group in D dimensions. Among other things I use all these to derive exact expressions for the following quantities: (1) The general two-point-charge force. (Abstract Truncated)

On the effects of basis set truncation and electron correlation in conformers of 2-hydroxy-acetamide

Science.gov (United States)

Szarecka, A.; Day, G.; Grout, P. J.; Wilson, S.

Ab initio quantum chemical calculations have been used to study the differences in energy between two gas phase conformers of the 2-hydroxy-acetamide molecule that possess intramolecular hydrogen bonding. In particular, rotation around the central C-C bond has been considered as a factor determining the structure of the hydrogen bond and stabilization of the conformer. Energy calculations include full geometiy optimization using both the restricted matrix Hartree-Fock model and second-order many-body perturbation theory with a number of commonly used basis sets. The basis sets employed ranged from the minimal STO-3G set to [`]split-valence' sets up to 6-31 G. The effects of polarization functions were also studied. The results display a strong basis set dependence.

Open conformal systems and perturbations of transfer operators

CERN Document Server

Pollicott, Mark

2017-01-01

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

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

International Nuclear Information System (INIS)

Joerss, M.

1996-07-01

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

Wormholes admitting conformal Killing vectors and supported by generalized Chaplygin gas

Energy Technology Data Exchange (ETDEWEB)

Kuhfittig, Peter K.F. [Milwaukee School of Engineering, Department of Mathematics, Milwaukee, WI (United States)

2015-08-15

When Morris and Thorne first proposed that traversable wormholes may be actual physical objects, they concentrated on the geometry by specifying the shape and redshift functions. This mathematical approach necessarily raises questions regarding the determination of the required stress-energy tensor. This paper discusses a natural way to obtain a complete wormhole solution by assuming that the wormhole (1) is supported by generalized Chaplygin gas and (2) admits conformal Killing vectors. (orig.)

Quantum chemical studies on molecular structural conformations and hydrated forms of salicylamide and O-hydroxybenzoyl cyanide

Science.gov (United States)

Anandan, K.; Kolandaivel, P.; Kumaresan, R.

Ab initio and density functional theory (DFT) methods have been employed to study the molecular structural conformations and hydrated forms of both salicylamide (SAM) and O-hydroxybenzoyl cyanide (OHBC). Molecular geometries and energetics have been obtained in the gaseous phase by employing the Møller-Plesset type 2 MP2/6-311G(2d,2p) and B3LYP/6-311G(2d,2p) levels of theory. The presence of an electron-releasing group (SAM) leads to an increase in the energy of the molecular system, while the presence of an electron-withdrawing group (OHBC) drastically decreases the energy. Chemical reactivity parameters (η and μ) have been calculated using the energy values of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) obtained at the Hartree-Fock (HF)/6-311G(2d,2p) level of theory for all the conformers and the principle of maximum hardness (MHP) has been tested. The condensed Fukui functions have been calculated using the atomic charges obtained through the natural bond orbital (NBO) analysis scheme for all the optimized structures at the B3LYP/6-311G(2d,2p) level of theory, and the most reactive sites of the molecules have been identified. Nuclear magnetic resonance (NMR) studies have been carried out at the B3LYP/6-311G(2d,2p) level of theory for all the conformers in the gaseous phase on the basis of the method of Cheeseman and coworkers. The calculated chemical shift values have been used to discuss the delocalization activity of the electron clouds. The dimeric structures of the most stable conformers of both SAM and OHBC in the gaseous phase have been optimized at the B3LYP/6-311G(2d,2p) level of theory, and the interaction energies have been calculated. The most stable conformers of both compounds bear an intramolecular hydrogen bond, which gives rise to the formation of a pseudo-aromatic ring. These conformers have been allowed to interact with the water molecule. Special emphasis has been given to analysis of the

Conformal field theory construction for non-Abelian hierarchy wave functions

Science.gov (United States)

Tournois, Yoran; Hermanns, Maria

2017-12-01

The fractional quantum Hall effect is the paradigmatic example of topologically ordered phases. One of its most fascinating aspects is the large variety of different topological orders that may be realized, in particular non-Abelian ones. Here we analyze a class of non-Abelian fractional quantum Hall model states which are generalizations of the Abelian Haldane-Halperin hierarchy. We derive their topological properties and show that the quasiparticles obey non-Abelian fusion rules of type su (q)k . For a subset of these states we are able to derive the conformal field theory description that makes the topological properties—in particular braiding—of the state manifest. The model states we study provide explicit wave functions for a large variety of interesting topological orders, which may be relevant for certain fractional quantum Hall states observed in the first excited Landau level.

Longitudinal Investigation of Adaptive Functioning following Conformal Irradiation for Pediatric Craniopharyngioma and Low-Grade Glioma

Science.gov (United States)

Netson, Kelli L.; Conklin, Heather M.; Wu, Shengjie; Xiong, Xiaoping; Merchant, Thomas E.

2013-01-01

Purpose Children treated for brain tumors with conformal radiation therapy experience preserved cognitive outcomes. Early evidence suggests that adaptive functions or independent living skills may be spared. This longitudinal investigation prospectively examined intellectual and adaptive functioning during the first 5 years following irradiation for childhood craniopharyngioma and low-grade glioma (LGG). The effect of visual impairment on adaptive outcomes was investigated. Methods and Materials Children with craniopharyngioma (n=62) and LGG (n=77) were treated using conformal or intensity-modulated radiation therapy. The median age was 8.05 years (3.21 years –17.64 years) and 8.09 years (2.20 years–19.27 years), respectively. Serial cognitive evaluations including measures of intelligence quotient (IQ) and the Vineland Adaptive Behavior Scales (VABS) were conducted at pre-irradiation baseline, 6 months after treatment, and annually through 5 years. A total of 588 evaluations were completed during the follow-up period. Results Baseline assessment revealed no deficits in IQ and VABS indices for children with craniopharyngioma, with significant (p craniopharyngioma. Children with LGG performed below population norms (p < .05) at baseline on VABS Communication, Daily Living Indices, and the Adaptive Behavior Composite, with significant (p < .05) longitudinal decline limited to VABS Communication. Older age at irradiation was a protective factor against longitudinal decline. Severe visual impairment did not independently correlate with poorer adaptive outcomes for either tumor group. Conclusions There was relative sparing of post-irradiation functional outcomes over time in this sample. Baseline differences in functional abilities prior to the initiation of irradiation suggested that other factors influence functional outcomes above and beyond the effects of irradiation. PMID:23245284

Towards conformal loop quantum gravity

International Nuclear Information System (INIS)

Wang, Charles H-T

2006-01-01

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

On non-conformal limit of the AGT relations

International Nuclear Information System (INIS)

Marshakov, A.; Mironov, A.; Morozov, A.

2009-01-01

The Seiberg-Witten prepotentials for N=2 SUSY gauge theories with N f c fundamental multiplets are obtained from conformal N f =2N c theory by decoupling 2N c -N f multiplets of heavy matter. This procedure can be lifted to the level of Nekrasov functions with arbitrary background parameters ε 1 and ε 2 . The AGT relations imply that similar limit exists for conformal blocks (or, for generic N c >2, for the blocks in conformal theories with W N c chiral algebra). We consider the limit of the four-point function explicitly in the Virasoro case of N c =2, by bringing the dimensions of external states to infinity. The calculation is performed entirely in terms of representation theory for the Virasoro algebra and reproduces the answers conjectured in [D. Gaiotto, (arXiv:0908.0307)] with the help of the brane-compactification analysis and computer simulations. In this limit, the conformal block involving four external primaries, corresponding to the theory with vanishing beta-function, turns either into a 2-point or 3-point function, with certain coherent rather than primary external states.

Conformational composition of neutral leucine. Matrix isolation infrared and ab initio study

International Nuclear Information System (INIS)

Stepanian, Stepan G.; Ivanov, Alexander Yu.; Adamowicz, Ludwik

2013-01-01

Highlights: • FTIR spectra of leucine isolated in argon, neon and xenon matrices are obtained. • UV irradiation is used to separate bands of the leucine conformers. • Populations of the leucine conformers is determined. - Abstract: Low-temperature matrix-isolation FTIR spectroscopy and ab initio calculations are employed to determine conformational composition of neutral leucine. The presence of three leucine conformers in the matrices is revealed. This is in agreement with the results of a detailed study of the potential energy surface of leucine which demonstrates that only five out of 105 possible conformers should have populations in the matrices larger than 2% and only three conformers, which are the ones detected in the experiment, should have populations larger than 10%. UV irradiation of the matrix samples are used to separate bands of the different conformers. We also show that the populations of the leucine conformers in the gas phase at 440 K are significantly different from the ones in matrices. The population of the lowest energy conformer in the gas phase being approximately 23% in the gas phase increases to over 64% in matrices

Conformal anomaly and elimination of infrared divergences in curved spacetime

International Nuclear Information System (INIS)

Grib, A.A.; Nesteruk, A.V.; Pritomanov, S.A.

1984-01-01

The relation between the problem of eliminating the infrared divergences and the conformal anomaly of the regularized energy-momentum tensor is studied in homogeneous isotropic and anisotropic spacetime. It is shown that elimination of the infrared divergence by means of a cutoff or the introduction of a conformally invariant mass of the field leads to the absence of the conformal anomaly

Determinants of conformal wave operators in four dimensions

International Nuclear Information System (INIS)

Blau, S.K.; Visser, M.; Wipf, A.

1988-01-01

We consider conformally coupled wave operators in four dimensions. Such operators are associated with conformally coupled massless scalars, massless spin 1/2 particles, and abelian gauge bosons. We explicitly calculate the change in the determinant of these wave operators as a function of conformal deformations of the background metric. This variation is given in terms of a geometrical object, the second Seeley-de Witt coefficient. (orig.)

Phosphorylation-induced conformational changes in short peptides probed by fluorescence resonance energy transfer in the 10A domain.

Science.gov (United States)

Sahoo, Harekrushna; Nau, Werner M

2007-03-26

Phosphorylation-induced conformational changes in short polypeptides were probed by a fluorescence resonance energy transfer (FRET) method by employing a short-distance FRET pair (R(0) approximately 10 A) based on tryptophan as natural donor and a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine (Dbo) as synthetic acceptor. Two substrates for kinases, LeuArgArgTrpSerLeuGly-Dbo (peptide I) and TrpLysArgThrLeuArgArg-Dbo (peptide II), were investigated, with serine and threonine, respectively, as phosphorylation sites. Steady-state and time-resolved fluorescence experiments in H(2)O revealed a decrease in FRET efficiency for peptide I and an increase for peptide II; this suggested that the effective distances between donor and acceptor increased and decreased, respectively. The same trends and similar absolute variations in effective donor-acceptor distances were observed in propylene glycol, a less polar and highly viscous solvent; this suggested that the variations are due to intrinsic structural preferences. Fitting of the time-resolved decay traces according to a distribution function model (Gaussian distribution) provided the mean donor-acceptor distances, which showed an increase upon phosphorylation for peptide I (from 9.7 to 10.5 A) and a decrease for peptide II (from 10.9 to 9.3 A) in H(2)O. The broadness (half-width) of the distributions, which provides a measure of the rigidity of the peptides, remained similar upon phosphorylation of peptide I (3.0 versus 3.1 A), but decreased for peptide II (from 3.1 to 0.73 A in H(2)O); this suggests a more compact, structured conformation upon phosphorylation of the latter peptide. The elongation of the peptide backbone (by ca. 0.7 A) for peptide I is attributed to an increase in steric demand upon phosphorylation, which favors an extended conformation. The contraction (by ca. 1.4 A) and structural rigidification of peptide II is attributed to attractive Coulombic interactions and hydrogen bonding between the

ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations.

Science.gov (United States)

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

2018-05-08

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

Conformal operator product expansion in the Yukawa model

International Nuclear Information System (INIS)

Prati, M.C.

1983-01-01

Conformal techniques are applied to the Yukawa model, as an example of a theory with spinor fields. It is written the partial-wave analysis of the 4-point function of two scalars and two spinors in the channel phi psi → phi psi in terms of spinor tensor representations of the conformal group. Using this conformal expansion, it is diagonalized the Bethe-Salpeter equation, which is reduced to algebraic relations among the partial waves. It is shown that in the γ 5 -invariant model, but not in the general case, it is possible to derive dynamically from the expansions of the 4-point function the vacuum operator product phi psi>

Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

Energy Technology Data Exchange (ETDEWEB)

Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States); Assadi, Amir [University of Wisconsin-Madison, Mathematics Department (United States); Markley, John L. [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States)], E-mail: eghbalni@nmrfam.wisc.edu

2005-05-15

We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states.

Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

International Nuclear Information System (INIS)

Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash; Assadi, Amir; Markley, John L.

2005-01-01

We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states

Peer influence: neural mechanisms underlying in-group conformity.

Science.gov (United States)

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

2013-01-01

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

Conformal atomic layer deposition of alumina on millimeter tall, vertically-aligned carbon nanotube arrays.

Science.gov (United States)

Stano, Kelly L; Carroll, Murphy; Padbury, Richard; McCord, Marian; Jur, Jesse S; Bradford, Philip D

2014-11-12

Atomic layer deposition (ALD) can be used to coat high aspect ratio and high surface area substrates with conformal and precisely controlled thin films. Vertically aligned arrays of multiwalled carbon nanotubes (MWCNTs) with lengths up to 1.5 mm were conformally coated with alumina from base to tip. The nucleation and growth behaviors of Al2O3 ALD precursors on the MWCNTs were studied as a function of CNT surface chemistry. CNT surfaces were modified through a series of post-treatments including pyrolytic carbon deposition, high temperature thermal annealing, and oxygen plasma functionalization. Conformal coatings were achieved where post-treatments resulted in increased defect density as well as the extent of functionalization, as characterized by X-ray photoelectron spectroscopy and Raman spectroscopy. Using thermogravimetric analysis, it was determined that MWCNTs treated with pyrolytic carbon and plasma functionalization prior to ALD coating were more stable to thermal oxidation than pristine ALD coated samples. Functionalized and ALD coated arrays had a compressive modulus more than two times higher than a pristine array coated for the same number of cycles. Cross-sectional energy dispersive X-ray spectroscopy confirmed that Al2O3 could be uniformly deposited through the entire thickness of the vertically aligned MWCNT array by manipulating sample orientation and mounting techniques. Following the ALD coating, the MWCNT arrays demonstrated hydrophilic wetting behavior and also exhibited foam-like recovery following compressive strain.

Interconversion of two GDP-bound conformations and their selection in an Arf-family small G protein.

Science.gov (United States)

Okamura, Hideyasu; Nishikiori, Masaki; Xiang, Hongyu; Ishikawa, Masayuki; Katoh, Etsuko

2011-07-13

ADP-ribosylation factor (Arf) and other Arf-family small G proteins participate in many cellular functions via their characteristic GTP/GDP conformational cycles, during which a nucleotide(∗)Mg(2+)-binding site communicates with a remote N-terminal helix. However, the conformational interplay between the nucleotides, the helix, the protein core, and Mg(2+) has not been fully delineated. Herein, we report a study of the dynamics of an Arf-family protein, Arl8, under various conditions by means of NMR relaxation spectroscopy. The data indicated that, when GDP is bound, the protein core, which does not include the N-terminal helix, reversibly transition between an Arf-family GDP form and another conformation that resembles the Arf-family GTP form. Additionally, we found that the N-terminal helix and Mg(2+), respectively, stabilize the aforementioned former and latter conformations in a population-shift manner. Given the dynamics of the conformational changes, we can describe the Arl8 GTP/GDP cycle in terms of an energy diagram. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

NARCIS (Netherlands)

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

2011-01-01

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

Extraction of conformal data in critical quantum spin chains using the Koo-Saleur formula

Science.gov (United States)

Milsted, Ashley; Vidal, Guifre

2017-12-01

We study the emergence of two-dimensional conformal symmetry in critical quantum spin chains on the finite circle. Our goal is to characterize the conformal field theory (CFT) describing the universality class of the corresponding quantum phase transition. As a means to this end, we propose and demonstrate automated procedures which, using only the lattice Hamiltonian H =∑jhj as an input, systematically identify the low-energy eigenstates corresponding to Virasoro primary and quasiprimary operators, and assign the remaining low-energy eigenstates to conformal towers. The energies and momenta of the primary operator states are needed to determine the primary operator scaling dimensions and conformal spins, an essential part of the conformal data that specifies the CFT. Our techniques use the action, on the low-energy eigenstates of H , of the Fourier modes Hn of the Hamiltonian density hj. The Hn were introduced as lattice representations of the Virasoro generators by Koo and Saleur [Nucl. Phys. B 426, 459 (1994), 10.1016/0550-3213(94)90018-3]. In this paper, we demonstrate that these operators can be used to extract conformal data in a nonintegrable quantum spin chain.

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

Science.gov (United States)

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

2016-01-01

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

Longitudinal Investigation of Adaptive Functioning Following Conformal Irradiation for Pediatric Craniopharyngioma and Low-Grade Glioma

Energy Technology Data Exchange (ETDEWEB)

Netson, Kelli L. [Department of Psychiatry and Behavioral Sciences, Kansas University School of Medicine—Wichita, Kansas (United States); Conklin, Heather M. [Department of Psychology, St Jude Children' s Research Hospital, Memphis, Tennessee (United States); Wu, Shengjie; Xiong, Xiaoping [Department of Biostatistics, St Jude Children' s Research Hospital, Memphis, Tennessee (United States); Merchant, Thomas E., E-mail: thomas.merchant@stjude.org [Division of Radiation Oncology, St Jude Children' s Research Hospital, Memphis, Tennessee (United States)

2013-04-01

Purpose: Children treated for brain tumors with conformal radiation therapy experience preserved cognitive outcomes. Early evidence suggests that adaptive functions or independent-living skills may be spared. This longitudinal investigation prospectively examined intellectual and adaptive functioning during the first 5 years following irradiation for childhood craniopharyngioma and low-grade glioma (LGG). The effect of visual impairment on adaptive outcomes was investigated. Methods and Materials: Children with craniopharyngioma (n=62) and LGG (n=77) were treated using conformal or intensity modulated radiation therapy. The median age was 8.05 years (3.21-17.64 years) and 8.09 years (2.20-19.27 years), respectively. Serial cognitive evaluations including measures of intelligence quotient (IQ) and the Vineland Adaptive Behavior Scales (VABS) were conducted at preirradiation baseline, 6 months after treatment, and annually through 5 years. Five hundred eighty-eight evaluations were completed during the follow-up period. Results: Baseline assessment revealed no deficits in IQ and VABS indices for children with craniopharyngioma, with significant (P<.05) longitudinal decline in VABS Communication and Socialization indices. Clinical factors associated with more rapid decline included females and preirradiation chemotherapy (interferon). The only change in VABS Daily Living Skills correlated with IQ change (r=0.34; P=.01) in children with craniopharyngioma. Children with LGG performed below population norms (P<.05) at baseline on VABS Communication, Daily Living Indices, and the Adaptive Behavior Composite, with significant (P<.05) longitudinal decline limited to VABS Communication. Older age at irradiation was a protective factor against longitudinal decline. Severe visual impairment did not independently correlate with poorer adaptive outcomes for either tumor group. Conclusions: There was relative sparing of postirradiation functional outcomes over time in this sample

Longitudinal Investigation of Adaptive Functioning Following Conformal Irradiation for Pediatric Craniopharyngioma and Low-Grade Glioma

International Nuclear Information System (INIS)

Netson, Kelli L.; Conklin, Heather M.; Wu, Shengjie; Xiong, Xiaoping; Merchant, Thomas E.

2013-01-01

Purpose: Children treated for brain tumors with conformal radiation therapy experience preserved cognitive outcomes. Early evidence suggests that adaptive functions or independent-living skills may be spared. This longitudinal investigation prospectively examined intellectual and adaptive functioning during the first 5 years following irradiation for childhood craniopharyngioma and low-grade glioma (LGG). The effect of visual impairment on adaptive outcomes was investigated. Methods and Materials: Children with craniopharyngioma (n=62) and LGG (n=77) were treated using conformal or intensity modulated radiation therapy. The median age was 8.05 years (3.21-17.64 years) and 8.09 years (2.20-19.27 years), respectively. Serial cognitive evaluations including measures of intelligence quotient (IQ) and the Vineland Adaptive Behavior Scales (VABS) were conducted at preirradiation baseline, 6 months after treatment, and annually through 5 years. Five hundred eighty-eight evaluations were completed during the follow-up period. Results: Baseline assessment revealed no deficits in IQ and VABS indices for children with craniopharyngioma, with significant (P<.05) longitudinal decline in VABS Communication and Socialization indices. Clinical factors associated with more rapid decline included females and preirradiation chemotherapy (interferon). The only change in VABS Daily Living Skills correlated with IQ change (r=0.34; P=.01) in children with craniopharyngioma. Children with LGG performed below population norms (P<.05) at baseline on VABS Communication, Daily Living Indices, and the Adaptive Behavior Composite, with significant (P<.05) longitudinal decline limited to VABS Communication. Older age at irradiation was a protective factor against longitudinal decline. Severe visual impairment did not independently correlate with poorer adaptive outcomes for either tumor group. Conclusions: There was relative sparing of postirradiation functional outcomes over time in this sample

Molecular conformation, receptor binding, and hormone action of natural and synthetic estrogens and antiestrogens.

Science.gov (United States)

Duax, W L; Griffin, J F; Weeks, C M; Korach, K S

1985-01-01

The X-ray crystallographic structural determinations of synthetic estrogens and antiestrogens provide reliable information on the global minimum energy conformation of these molecules or a local minimum energy conformation that is within 1 or 2 kcal/mole of the global minimum. In favorable cases, state-of-the-art molecular mechanics calculations provide quantitative agreement with X-ray results and information on the relative energy of other local minimum energy conformations not observed crystallographically. Because the conformation of diethylstilbestrol (DES) observed in solvated crystals has an overall conformation and dipole moment more similar to estradiol it is the form more likely to bind to the receptor and produce hormone activity. Either phenol ring of DES can successfully mimic the estradiol A-ring in binding to the receptor. Indenestrol A (INDA) and indenestrol B (INDB) have nearly identical fully extended planar conformations. Either the alpha or gamma rings of these compounds may mimic the A ring of estradiol and compete for the estrogen receptor. Although there are eight distinct ways in which molecules of a racemic mixture of INDA or INDB can bind to the receptor, not all of them may be able to elicit a hormonal response. This may account for the reduced biological activity of the compounds despite their successful competition for receptor binding. The minimum energy conformations of Z-pseudodiethylstilbestrol (ZPD) and E-pseudodiethylstilbestrol (EPD) are bent in a fashion similar to that of indanestrol (INDC). These molecules have good binding affinity suggesting that the receptor does not require a flat molecule. Therefore these conformations would appear to be compatible with receptor binding, but only the Z isomer has an energetically allowed extended conformation that accounts for its observed biological activity relative to DES. PMID:3905370

Sewing constraints for conformal field theories on surfaces with boundaries

International Nuclear Information System (INIS)

Lewellen, D.C.

1992-01-01

In a conformal field theory, correlation functions on any Riemann surface are in principle unambiguously defined by sewing together three-point functions on the sphere, provided that the four-point functions on the sphere are crossing symmetric, and the one-point functions on the torus are modular covariant. In this work we extend Sonoda's proof of this result to conformal field theories defined on surfaces with boundaries. Four additional sewing constraints arise; three on the half-plane and one on the cylinder. These relate the various OPE coefficients in the theory (bulk, boundary, and bulk-boundary) to one another. In rational theories these relations can be expressed in terms of data arising solely within the bulk theory: The matrix S which implements modular transformations on the characters, and the matrices implementing duality transformations on the four-point conformal-block functions. As an example we solve these relations for the boundary and bulk-boundary structure constants in the Ising model with all possible conformally invariant boundary conditions. The role of the basic sewing constraints in the construction of open string theories is discussed. (orig.)

Asymptotic mass degeneracies in conformal field theories

International Nuclear Information System (INIS)

Kani, I.; Vafa, C.

1990-01-01

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

Irregular conformal block, spectral curve and flow equations

International Nuclear Information System (INIS)

Choi, Sang Kwan; Rim, Chaiho; Zhang, Hong

2016-01-01

Irregular conformal block is motivated by the Argyres-Douglas type of N=2 super conformal gauge theory. We investigate the classical/NS limit of irregular conformal block using the spectral curve on a Riemann surface with irregular punctures, which is equivalent to the loop equation of irregular matrix model. The spectral curve is reduced to the second order (Virasoro symmetry, SU(2) for the gauge theory) and third order (W_3 symmetry, SU(3)) differential equations of a polynomial with finite degree. The conformal and W symmetry generate the flow equations in the spectral curve and determine the irregular conformal block, hence the partition function of the Argyres-Douglas theory ala AGT conjecture.

Functional fluorescent protein insertions in herpes simplex virus gB report on gB conformation before and after execution of membrane fusion.

Directory of Open Access Journals (Sweden)

John R Gallagher

2014-09-01

Full Text Available Entry of herpes simplex virus (HSV into a target cell requires complex interactions and conformational changes by viral glycoproteins gD, gH/gL, and gB. During viral entry, gB transitions from a prefusion to a postfusion conformation, driving fusion of the viral envelope with the host cell membrane. While the structure of postfusion gB is known, the prefusion conformation of gB remains elusive. As the prefusion conformation of gB is a critical target for neutralizing antibodies, we set out to describe its structure by making genetic insertions of fluorescent proteins (FP throughout the gB ectodomain. We created gB constructs with FP insertions in each of the three globular domains of gB. Among 21 FP insertion constructs, we found 8 that allowed gB to remain membrane fusion competent. Due to the size of an FP, regions in gB that tolerate FP insertion must be solvent exposed. Two FP insertion mutants were cell-surface expressed but non-functional, while FP insertions located in the crown were not surface expressed. This is the first report of placing a fluorescent protein insertion within a structural domain of a functional viral fusion protein, and our results are consistent with a model of prefusion HSV gB constructed from the prefusion VSV G crystal structure. Additionally, we found that functional FP insertions from two different structural domains could be combined to create a functional form of gB labeled with both CFP and YFP. FRET was measured with this construct, and we found that when co-expressed with gH/gL, the FRET signal from gB was significantly different from the construct containing CFP alone, as well as gB found in syncytia, indicating that this construct and others of similar design are likely to be powerful tools to monitor the conformation of gB in any model system accessible to light microscopy.

Nonlocal kinetic energy functionals by functional integration

Science.gov (United States)

Mi, Wenhui; Genova, Alessandro; Pavanello, Michele

2018-05-01

Since the seminal studies of Thomas and Fermi, researchers in the Density-Functional Theory (DFT) community are searching for accurate electron density functionals. Arguably, the toughest functional to approximate is the noninteracting kinetic energy, Ts[ρ], the subject of this work. The typical paradigm is to first approximate the energy functional and then take its functional derivative, δ/Ts[ρ ] δ ρ (r ) , yielding a potential that can be used in orbital-free DFT or subsystem DFT simulations. Here, this paradigm is challenged by constructing the potential from the second-functional derivative via functional integration. A new nonlocal functional for Ts[ρ] is prescribed [which we dub Mi-Genova-Pavanello (MGP)] having a density independent kernel. MGP is constructed to satisfy three exact conditions: (1) a nonzero "Kinetic electron" arising from a nonzero exchange hole; (2) the second functional derivative must reduce to the inverse Lindhard function in the limit of homogenous densities; (3) the potential is derived from functional integration of the second functional derivative. Pilot calculations show that MGP is capable of reproducing accurate equilibrium volumes, bulk moduli, total energy, and electron densities for metallic (body-centered cubic, face-centered cubic) and semiconducting (crystal diamond) phases of silicon as well as of III-V semiconductors. The MGP functional is found to be numerically stable typically reaching self-consistency within 12 iterations of a truncated Newton minimization algorithm. MGP's computational cost and memory requirements are low and comparable to the Wang-Teter nonlocal functional or any generalized gradient approximation functional.

From spinning conformal blocks to matrix Calogero-Sutherland models

Science.gov (United States)

Schomerus, Volker; Sobko, Evgeny

2018-04-01

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

Geometrical formulation of the conformal Ward identity

International Nuclear Information System (INIS)

Kachkachi, M.

2002-08-01

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

SURFACE SYMMETRY ENERGY OF NUCLEAR ENERGY DENSITY FUNCTIONALS

Energy Technology Data Exchange (ETDEWEB)

Nikolov, N; Schunck, N; Nazarewicz, W; Bender, M; Pei, J

2010-12-20

We study the bulk deformation properties of the Skyrme nuclear energy density functionals. Following simple arguments based on the leptodermous expansion and liquid drop model, we apply the nuclear density functional theory to assess the role of the surface symmetry energy in nuclei. To this end, we validate the commonly used functional parametrizations against the data on excitation energies of superdeformed band-heads in Hg and Pb isotopes, and fission isomers in actinide nuclei. After subtracting shell effects, the results of our self-consistent calculations are consistent with macroscopic arguments and indicate that experimental data on strongly deformed configurations in neutron-rich nuclei are essential for optimizing future nuclear energy density functionals. The resulting survey provides a useful benchmark for further theoretical improvements. Unlike in nuclei close to the stability valley, whose macroscopic deformability hangs on the balance of surface and Coulomb terms, the deformability of neutron-rich nuclei strongly depends on the surface-symmetry energy; hence, its proper determination is crucial for the stability of deformed phases of the neutron-rich matter and description of fission rates for r-process nucleosynthesis.

Theoretical searches and spectral computations of preferred conformations of various absolute configurations for a cyclodipeptide, cordycedipeptide A from the culture liquid of Cordyceps sinensis

Science.gov (United States)

Mang, Chao-Yong; Liu, Cai-Ping; Liu, Guang-Ming; Jiang, Bei; Lan, Hai; Wu, Ke-Chen; Yan, Ya; Li, Hai-Fei; Yang, Ming-Hui; Zhao, Yu

2015-02-01

A cyclic dipeptide often has the multiple configurations and the abundant conformations. The density functional theory (DFT) method is used to search the preferred conformation of the most probable configuration for cordycedipeptide A isolated from the culture liquid of Cordyceps sinensis. The time-dependent DFT approach is exploited to describe the profile of electronic circular dichroism (CD). The calculated results show that the most probable configuration is 3S6R7S, whose preferred conformation has a negative optical rotation and a positive lowest energy electronic CD band.

Rapid roll inflation with conformal coupling

International Nuclear Information System (INIS)

Kofman, Lev; Mukohyama, Shinji

2008-01-01

Usual inflation is realized with a slow rolling scalar field minimally coupled to gravity. In contrast, we consider dynamics of a scalar with a flat effective potential, conformally coupled to gravity. Surprisingly, it contains an attractor inflationary solution with the rapidly rolling inflaton field. We discuss models with the conformal inflaton with a flat potential (including hybrid inflation). There is no generation of cosmological fluctuations from the conformally coupled inflaton. We consider realizations of modulated (inhomogeneous reheating) or curvaton cosmological fluctuations in these models. We also implement these unusual features for the popular string-theoretic warped inflationary scenario, based on the interacting D3-D3 branes. The original warped brane inflation suffers a large inflaton mass due to conformal coupling to 4-dimensional gravity. Instead of considering this as a problem and trying to cure it with extra engineering, we show that warped inflation with the conformally coupled, rapidly rolling inflaton is yet possible with N=37 efoldings, which requires low-energy scales 1-100 TeV of inflation. Coincidentally, the same warping numerology can be responsible for the hierarchy. It is shown that the scalars associated with angular isometries of the warped geometry of compact manifold (e.g. S 3 of Klebanov-Strassler (KS) geometry) have solutions identical to conformally coupled modes and also cannot be responsible for cosmological fluctuations. We discuss other possibilities

Rapid roll inflation with conformal coupling

Science.gov (United States)

Kofman, Lev; Mukohyama, Shinji

2008-02-01

Usual inflation is realized with a slow rolling scalar field minimally coupled to gravity. In contrast, we consider dynamics of a scalar with a flat effective potential, conformally coupled to gravity. Surprisingly, it contains an attractor inflationary solution with the rapidly rolling inflaton field. We discuss models with the conformal inflaton with a flat potential (including hybrid inflation). There is no generation of cosmological fluctuations from the conformally coupled inflaton. We consider realizations of modulated (inhomogeneous reheating) or curvaton cosmological fluctuations in these models. We also implement these unusual features for the popular string-theoretic warped inflationary scenario, based on the interacting D3-D¯3 branes. The original warped brane inflation suffers a large inflaton mass due to conformal coupling to 4-dimensional gravity. Instead of considering this as a problem and trying to cure it with extra engineering, we show that warped inflation with the conformally coupled, rapidly rolling inflaton is yet possible with N=37 efoldings, which requires low-energy scales 1 100 TeV of inflation. Coincidentally, the same warping numerology can be responsible for the hierarchy. It is shown that the scalars associated with angular isometries of the warped geometry of compact manifold (e.g. S3 of Klebanov-Strassler (KS) geometry) have solutions identical to conformally coupled modes and also cannot be responsible for cosmological fluctuations. We discuss other possibilities.

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

Directory of Open Access Journals (Sweden)

Tomáš Valenta

2017-01-01

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

Conformal invariance in quantum field theory

International Nuclear Information System (INIS)

Grensing, G.

1978-01-01

We study the transformation law of interacting fields under the universal covering group of the conformal group. It is defined with respect to the representations of the discrete series. These representations are field representations in the sense that they act on finite component fields defined over Minkowski space. The conflict with Einstein causality is avoided as in the case of free fields with canonical dimension. Furthermore, we determine the conformal invariant two-point function of arbitrary spin. Our result coincides with that obtained by Ruehl. In particular, we investigate the two-point function of symmetric and traceless tensor fields and give the explicit form of the trace terms

Conformational Profiling of the AT1 Angiotensin II Receptor Reflects Biased Agonism, G Protein Coupling, and Cellular Context.

Science.gov (United States)

Devost, Dominic; Sleno, Rory; Pétrin, Darlaine; Zhang, Alice; Shinjo, Yuji; Okde, Rakan; Aoki, Junken; Inoue, Asuka; Hébert, Terence E

2017-03-31

Here, we report the design and use of G protein-coupled receptor-based biosensors to monitor ligand-mediated conformational changes in receptors in intact cells. These biosensors use bioluminescence resonance energy transfer with Renilla luciferase (RlucII) as an energy donor, placed at the distal end of the receptor C-tail, and the small fluorescent molecule FlAsH as an energy acceptor, its binding site inserted at different positions throughout the intracellular loops and C-terminal tail of the angiotensin II type I receptor. We verified that the modifications did not compromise receptor localization or function before proceeding further. Our biosensors were able to capture effects of both canonical and biased ligands, even to the extent of discriminating between different biased ligands. Using a combination of G protein inhibitors and HEK 293 cell lines that were CRISPR/Cas9-engineered to delete Gα q , Gα 11 , Gα 12 , and Gα 13 or β-arrestins, we showed that Gα q and Gα 11 are required for functional responses in conformational sensors in ICL3 but not ICL2. Loss of β-arrestin did not alter biased ligand effects on ICL2P2. We also demonstrate that such biosensors are portable between different cell types and yield context-dependent readouts of G protein-coupled receptor conformation. Our study provides mechanistic insights into signaling events that depend on either G proteins or β-arrestin. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Energy-momentum tensor in quantum field theory

International Nuclear Information System (INIS)

Fujikawa, K.

1981-01-01

The definition of the energy-momentum tensor as a source current coupled to the background gravitational field receives an important modification in quantum theory. In the path-integral approach, the manifest covariance of the integral measure under general coordinate transformations dictates that field variables with weight 1/2 should be used as independent integration variables. An improved energy-momentum tensor is then generated by the variational derivative, and it gives rise to well-defined gravitational conformal (Weyl) anomalies. In the flat--space-time limit, all the Ward-Takahashi identities associated with space-time transformations including the global dilatation become free from anomalies in terms of this energy-momentum tensor, reflecting the general covariance of the integral measure; the trace of this tensor is thus finite at zero momentum transfer for renormalizable theories. The Jacobian for the local conformal transformation, however, becomes nontrivial, and it gives rise to an anomaly for the conformal identity. All the familiar anomalies are thus reduced to either chiral or conformal anomalies. The consistency of the dilatation and conformal identities at vanishing momentum transfer determines the trace anomaly of this energy-momentum tensor in terms of the renormalization-group b function and other parameters. In contrast, the trace of the conventional energy-momentum tensor generally diverges even at vanishing momentum transfer depending on the regularization scheme, and it is subtractively renormalized. We also explain how the apparently different renormalization properties of the chiral and trace anomalies arise

Energy-momentum tensor in quantum field theory

International Nuclear Information System (INIS)

Fujikawa, Kazuo.

1980-12-01

The definition of the energy-momentum tensor as a source current coupled to the background gravitational field receives an important modification in quantum theory. In the path integral approach, the manifest covariance of the integral measure under general coordinate transformations dictates that field variables with weight 1/2 should be used as independent integration variables. An improved energy-momentum tensor is then generated by the variational derivative, and it gives rise to well-defined gravitational conformal (Weyl) anomalies. In the flat space-time limit, all the Ward-Takahashi identities associate with space-time transformations including the global dilatation become free from anomalies, reflecting the general covariance of the integral measure; the trace of this energy-momentum tensor is thus finite at the zero momentum transfer. The Jacobian for the local conformal transformation however becomes non-trivial, and it gives rise to an anomaly for the conformal identity. All the familiar anomalies are thus reduced to either chiral or conformal anomalies. The consistency of the dilatation and conformal identities at the vanishing momentum transfer determines the trace anomaly of this energy-momentum tensor in terms of the renormalization group β-function and other parameters. In contrast, the trace of the conventional energy-momentum tensor generally diverges even at the vanishing momentum transfer depending on the regularization scheme, and it is subtractively renormalized. We also explain how the apparently different renormalization properties of the chiral and trace anomalies arise. (author)

Cost Function Network-based Design of Protein-Protein Interactions: predicting changes in binding affinity.

Science.gov (United States)

Viricel, Clément; de Givry, Simon; Schiex, Thomas; Barbe, Sophie

2018-02-20

Accurate and economic methods to predict change in protein binding free energy upon mutation are imperative to accelerate the design of proteins for a wide range of applications. Free energy is defined by enthalpic and entropic contributions. Following the recent progresses of Artificial Intelligence-based algorithms for guaranteed NP-hard energy optimization and partition function computation, it becomes possible to quickly compute minimum energy conformations and to reliably estimate the entropic contribution of side-chains in the change of free energy of large protein interfaces. Using guaranteed Cost Function Network algorithms, Rosetta energy functions and Dunbrack's rotamer library, we developed and assessed EasyE and JayZ, two methods for binding affinity estimation that ignore or include conformational entropic contributions on a large benchmark of binding affinity experimental measures. If both approaches outperform most established tools, we observe that side-chain conformational entropy brings little or no improvement on most systems but becomes crucial in some rare cases. as open-source Python/C ++ code at sourcesup.renater.fr/projects/easy-jayz. thomas.schiex@inra.fr and sophie.barbe@insa-toulouse.fr. Supplementary data are available at Bioinformatics online.

Workers’ Conformism

Directory of Open Access Journals (Sweden)

Nikolay Ivantchev

2013-10-01

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

Conformational energy calculations on polypeptides and proteins: use of a statistical mechanical procedure for evaluating structure and properties.

Science.gov (United States)

Scheraga, H A; Paine, G H

1986-01-01

We are using a variety of theoretical and computational techniques to study protein structure, protein folding, and higher-order structures. Our earlier work involved treatments of liquid water and aqueous solutions of nonpolar and polar solutes, computations of the stabilities of the fundamental structures of proteins and their packing arrangements, conformations of small cyclic and open-chain peptides, structures of fibrous proteins (collagen), structures of homologous globular proteins, introduction of special procedures as constraints during energy minimization of globular proteins, and structures of enzyme-substrate complexes. Recently, we presented a new methodology for predicting polypeptide structure (described here); the method is based on the calculation of the probable and average conformation of a polypeptide chain by the application of equilibrium statistical mechanics in conjunction with an adaptive, importance sampling Monte Carlo algorithm. As a test, it was applied to Met-enkephalin.

A 5-Year Investigation of Children's Adaptive Functioning Following Conformal Radiation Therapy for Localized Ependymoma

International Nuclear Information System (INIS)

Netson, Kelli L.; Conklin, Heather M.; Wu Shengjie; Xiong Xiaoping; Merchant, Thomas E.

2012-01-01

Purpose: Conformal and intensity modulated radiation therapies have the potential to preserve cognitive outcomes in children with ependymoma; however, functional behavior remains uninvestigated. This longitudinal investigation prospectively examined intelligence quotient (IQ) and adaptive functioning during the first 5 years after irradiation in children diagnosed with ependymoma. Methods and Materials: The study cohort consisted of 123 children with intracranial ependymoma. Mean age at irradiation was 4.60 years (95% confidence interval [CI], 3.85-5.35). Serial neurocognitive evaluations, including an age-appropriate IQ measure and the Vineland Adaptive Behavior Scales (VABS), were completed before irradiation, 6 months after treatment, and annually for 5 years. A total of 579 neurocognitive evaluations were included in these analyses. Results: Baseline IQ and VABS were below normative means (P<.05), although within the average range. Linear mixed models revealed stable IQ and VABS across the follow-up period, except for the VABS Communication Index, which declined significantly (P=.015). Annual change in IQ (−.04 points) did not correlate with annual change in VABS (−.90 to +.44 points). Clinical factors associated with poorer baseline performance (P<.05) included preirradiation chemotherapy, cerebrospinal fluid shunt placement, number and extent of surgical resections, and younger age at treatment. No clinical factors significantly affected the rate of change in scores. Conclusions: Conformal and intensity modulated radiation therapies provided relative sparing of functional outcomes including IQ and adaptive behaviors, even in very young children. Communication skills remained vulnerable and should be the target of preventive and rehabilitative interventions.

Arbitrary spin conformal fields in (A)dS

International Nuclear Information System (INIS)

Metsaev, R.R.

2014-01-01

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

Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives

OpenAIRE

Marianski, Mateusz; Asensio, Amparo; Dannenberg, J. J.

2012-01-01

We compare the energetic and structural properties of fully optimized α-helical and antiparallel β-sheet polyalanines and the energetic differences between axial and equatorial conformations of three cyclohexane derivatives (methyl, fluoro, and chloro) as calculated using several functionals designed to treat dispersion (B97-D, ωB97x-D, M06, M06L, and M06-2X) with other traditional functionals not specifically parametrized to treat dispersion (B3LYP, X3LYP, and PBE1PBE) and with experimental ...

Molecular Orbital and Density Functional Study of the Formation, Charge Transfer, Bonding and the Conformational Isomerism of the Boron Trifluoride (BF3 and Ammonia (NH3 Donor-Acceptor Complex

Directory of Open Access Journals (Sweden)

Dulal C. Ghosh

2004-09-01

Full Text Available The formation of the F3B–NH3 supermolecule by chemical interaction of its fragment parts, BF3 and NH3, and the dynamics of internal rotation about the ‘B–N’ bond have been studied in terms of parameters provided by the molecular orbital and density functional theories. It is found that the pairs of frontier orbitals of the interacting fragments have matching symmetry and are involved in the charge transfer interaction. The donation process stems from the HOMO of the donor into the LUMO of the acceptor and simultaneously, back donation stems from the HOMO of acceptor into the LUMO of the donor. The density functional computation of chemical activation in the donor and acceptor fragments, associated with the physical process of structural reorganization just prior to the event of chemical reaction, indicates that BF3 becomes more acidic and NH3 becomes more basic, compared to their separate equilibrium states. Theoretically it is observed that the chemical reaction event of the formation of the supermolecule from its fragment parts is in accordance with the chemical potential equalization principle of the density functional theory and the electronegativity equalization principle of Sanderson. The energetics of the chemical reaction, the magnitude of the net charge transfer and the energy of the newly formed bond are quite consistent, both internally and with the principle of maximum hardness, PMH. The dynamics of the internal rotation of one part with respect to the other part of the supermolecule about the ‘B–N’ bond mimics the pattern of the conformational isomerism of the isostructural ethane molecule. It is also observed that the dynamics and evolution of molecular conformations as a function of dihedral angles is also in accordance with the principle of maximum hardness, PMH. Quite consistent with spectroscopic predictions, the height of the molecule

Investigation of light-induced conformation changes in spiropyran-modified succinylated poly(L-lysine).

Science.gov (United States)

Cooper, T M; Stone, M O; Natarajan, L V; Crane, R L

1995-08-01

To determine the maximum range of coupling between side-chain photochromism and polypeptide conformation change, we modified the carboxylate side chains of succinylated poly(L-lysine) with a spiropyran to form polypeptide I. The extent of modification was determined to be 35.5%. The spacer group length between the polypeptide alpha-carbon and the dye was 12 atoms, providing minimum polypeptide-dye interaction. Conformation changes were monitored by circular dichroism as a function of light adaptation and solvent composition (hexafluoroisopropanol [HFIP] vs trifluoroethanol [TFE]). Under all solvent compositions, the dark-adapted dye was in the merocyanine form. Light adaptation by visible light converted the dye to the spiropyran form. When dissolved in TFE, I adopted a helical conformation insensitive to light adaptation. With increasing percentage HFIP, a solvent-induced helix-to-coil transition was observed around 80% (vol/vol) HFIP. At 100% HFIP, both light- and dark-adapted forms of I were in the coil state. Near the midpoint of the solvent-induced helix-to-coil transition, light adaptation caused conformation changes. Applying helix-to-coil transition theory, we measured a statistically significant difference in coil segment-HFIP binding constant for light- vs dark-adapted solutions (6.38 +/- 0.03 M-1 vs 6.56 +/- 0.03 M-1), but not for the nucleation parameter sigma (1.2 +/- 0.4 10(-3) vs 1.3 +/- 0.3 x 10(-3). The small binding constant difference translated to a light-induced binding energy difference of 17 cal/mol/monomer. Near the midpoint of the helix-to-coil transition, collective interactions between monomer units made possible the translation of a small energy difference (less than RT) into large macromolecular conformation changes.(ABSTRACT TRUNCATED AT 250 WORDS)

Conformation radiotherapy and conformal radiotherapy

International Nuclear Information System (INIS)

Morita, Kozo

1999-01-01

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

Killing tensors and conformal Killing tensors from conformal Killing vectors

International Nuclear Information System (INIS)

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

2003-01-01

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

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

DEFF Research Database (Denmark)

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

2005-01-01

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

Conformal intensity-modulated radiotherapy (IMRT) delivered by robotic linac-conformality versus efficiency of dose delivery

International Nuclear Information System (INIS)

Webb, Steve

2000-01-01

Intensity-modulated radiotherapy (IMRT) may be delivered with a high-energy-photon linac mounted on a robotic gantry and executing a complex trajectory. In a previous paper an inverse-planning technique was developed for such an application. Here the work is extended to demonstrate the dependence of conformality on the size of the elemental pencil beam, on the complexity of the trajectory and on the sampling of azimuth and elevation of the collimated source. The improved conformality of complex trajectories is demonstrated and benchmarked relative to simpler trajectories, more representative of existing non-robotic IMRT techniques. Specifically, by choosing a very fine pencil beam, exquisitely conformal dose distributions have been obtained. Important sampling considerations have been determined. Expressions have been derived for the dosimetry and monitor-unit efficiency of robotic IMRT. Equivalent trajectories were computed for executing the complex robotic trajectories instead by using a conventional linac. The work benchmarks an ideal in IMRT against which more practical and more common techniques may be measured. (author)

Conformation sensitive charge transport in conjugated polymers

International Nuclear Information System (INIS)

Mattias Andersson, L.; Hedström, Svante; Persson, Petter

2013-01-01

Temperature dependent charge carrier mobility measurements using field effect transistors and density functional theory calculations are combined to show how the conformation dependent frontier orbital delocalization influences the hole- and electron mobilities in a donor-acceptor based polymer. A conformationally sensitive lowest unoccupied molecular orbital results in an electron mobility that decreases with increasing temperature above room temperature, while a conformationally stable highest occupied molecular orbital is consistent with a conventional hole mobility behavior and also proposed to be one of the reasons for why the material works well as a hole transporter in amorphous bulk heterojunction solar cells

Conformal invariance in the long-range Ising model

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Miguel F. Paulos

2016-01-01

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

Conformal Invariance in the Long-Range Ising Model

CERN Document Server

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

2016-01-01

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

Conformal invariance in the long-range Ising model

Energy Technology Data Exchange (ETDEWEB)

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

2016-01-15

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

Structural and Conformational Chemistry from Electrochemical Molecular Machines. Replicating Biological Functions. A Review.

Science.gov (United States)

Otero, Toribio F

2017-12-14

Each constitutive chain of a conducting polymer electrode acts as a reversible multi-step electrochemical molecular motor: reversible reactions drive reversible conformational movements of the chain. The reaction-driven cooperative actuation of those molecular machines generates, or destroys, inside the film the free volume required to lodge/expel balancing counterions and solvent: reactions drive reversible film volume variations, which basic structural components are here identified and quantified from electrochemical responses. The content of the reactive dense gel (chemical molecular machines, ions and water) mimics that of the intracellular matrix in living functional cells. Reaction-driven properties (composition-dependent properties) and devices replicate biological functions and organs. An emerging technological world of soft, wet, reaction-driven, multifunctional and biomimetic devices and the concomitant zoomorphic or anthropomorphic robots is presented. © 2017 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Conformations of Trimethyl Phosphite: a Matrix Isolation Infrared and AB Initio Study

Science.gov (United States)

Ramanathan, N.; Sundararajan, K.; Kar, Bishnu Prasad; Viswanathan, K. S.

2011-06-01

Hyperconjugative interactions have received considerable attention because of its importance in determining structure and reactivity in organic compounds. In all these molecules, our studies, as many others in the literature, indicated that the O-P-O and O-C-O segments played a crucial role in conformational preferences. In the case of the organic phosphates, in addition to the O-P-O segments, the P=O group was also found to influence the structures. To address this issue further, it was thought interesting to study the conformations of trimethylphosphite (TMPhite), which lacks a P=O group. A comparison of the conformations of trimethylphosphate (TMP) and TMPhite was expected to highlight the role of the P=O group in the conformational preference of organic phosphates, which is the motivation for the present work. The conformations of TMPhite were studied using matrix isolation infrared spectroscopy. TMPhite was trapped in a nitrogen matrix using an effusive source maintained at 298 K and 410 K and also a supersonic source. These experiments were designed to enable us to assign the infrared features of the higher energy conformer(s). As a result of these experiments, infrared spectra of the conformations of TMPhite were obtained. The experimental studies were supported by ab initio computations performed at the B3LYP/6-31++G** level. Computations indicated four minima corresponding to conformers with the following symmetries: C_1, C_s, C1a and C_3, given in order of increasing energy. This conformational picture was clearly different from that of TMP, in which the C_3 was the lowest energy structure, thereby clearly indicating the role of the P=O group in structural preferences in these systems. We also performed a photochemical insertion of oxygen in TMPhite to produce TMP in the matrix, in an effort to correlate the conformers of the two molecules. These experiments also gave rise to interesting side reactions, where in addition to TMP, we also observed the

Vertex operator algebras and conformal field theory

International Nuclear Information System (INIS)

Huang, Y.Z.

1992-01-01

This paper discusses conformal field theory, an important physical theory, describing both two-dimensional critical phenomena in condensed matter physics and classical motions of strings in string theory. The study of conformal field theory will deepen the understanding of these theories and will help to understand string theory conceptually. Besides its importance in physics, the beautiful and rich mathematical structure of conformal field theory has interested many mathematicians. New relations between different branches of mathematics, such as representations of infinite-dimensional Lie algebras and Lie groups, Riemann surfaces and algebraic curves, the Monster sporadic group, modular functions and modular forms, elliptic genera and elliptic cohomology, Calabi-Yau manifolds, tensor categories, and knot theory, are revealed in the study of conformal field theory. It is therefore believed that the study of the mathematics involved in conformal field theory will ultimately lead to new mathematical structures which would be important to both mathematics and physics

Elementary introduction to conformal invariance

International Nuclear Information System (INIS)

Grandati, Y.

1992-01-01

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

Ferrocene Orientation Determined Intramolecular Interactions Using Energy Decomposition Analysis

Directory of Open Access Journals (Sweden)

Feng Wang

2015-11-01

Full Text Available Two very different quantum mechanically based energy decomposition analyses (EDA schemes are employed to study the dominant energy differences between the eclipsed and staggered ferrocene conformers. One is the extended transition state (ETS based on the Amsterdam Density Functional (ADF package and the other is natural EDA (NEDA based in the General Atomic and Molecular Electronic Structure System (GAMESS package. It reveals that in addition to the model (theory and basis set, the fragmentation channels more significantly affect the interaction energy terms (ΔE between the conformers. It is discovered that such an interaction energy can be absorbed into the pre-partitioned fragment channels so that to affect the interaction energies in a particular conformer of Fc. To avoid this, the present study employs a complete fragment channel—the fragments of ferrocene are individual neutral atoms. It therefore discovers that the major difference between the ferrocene conformers is due to the quantum mechanical Pauli repulsive energy and orbital attractive energy, leading to the eclipsed ferrocene the energy preferred structure. The NEDA scheme further indicates that the sum of attractive (negative polarization (POL and charge transfer (CL energies prefers the eclipsed ferrocene. The repulsive (positive deformation (DEF energy, which is dominated by the cyclopentadienyle (Cp rings, prefers the staggered ferrocene. Again, the cancellation results in a small energy residue in favour of the eclipsed ferrocene, in agreement with the ETS scheme. Further Natural Bond Orbital (NBO analysis indicates that all NBO energies, total Lewis (no Fe and lone pair (LP deletion all prefer the eclipsed Fc conformer. The most significant energy preferring the eclipsed ferrocene without cancellation is the interactions between the donor lone pairs (LP of the Fe atom and the acceptor antibond (BD* NBOs of all C–C and C–H bonds in the ligand, LP(Fe-BD*(C–C & C�

94: Treatment plan optimization for conformal therapy

International Nuclear Information System (INIS)

Rosen, I.I.; Lane, R.G.

1987-01-01

Computer-controlled conformal radiation therapy techniques can deliver complex treatments utilizing large numbers of beams, gantry angles and beam shapes. Linear programming is well-suited for planning conformal treatments. Given a list of available treatment beams, linear programming calculates the relative weights of the beams such that the objective function is optimized and doses to constraint points are within the prescribed limits. 5 refs.; 3 figs

New open conformation of SMYD3 implicates conformational selection and allostery

Directory of Open Access Journals (Sweden)

Nicholas Spellmon

2016-12-01

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

On conformal invariance in gauge theories. Quantum electrodynamics

International Nuclear Information System (INIS)

Zaikov, R.P.

1983-01-01

In the present paper another nontrivial model of the conformal quantum electrodynamics is proposed. The main hypothesis is that the electromagnetic potential together with an additional zero scale, dimensional scalar field is transformed by a nonbasic and, consequently, nondecomposable representation of the conformal group. There are found nontrivial conformal covariant two-point functions and an invariant action from which equations of motion are derived. There is considered the covariant procedure of quantization and it is shown that the norm of one-particle physical states is positive definite

Replacement between conformity and counter-conformity in consumption decisions.

Science.gov (United States)

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

2013-02-01

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

Notes on the Verlinde formula in nonrational conformal field theories

International Nuclear Information System (INIS)

Jego, Charles; Troost, Jan

2006-01-01

We review and extend evidence for the validity of a generalized Verlinde formula, in particular, nonrational conformal field theories. We identify a subset of representations of the chiral algebra in nonrational conformal field theories that give rise to an analogue of the relation between modular S-matrices and fusion coefficients in rational conformal field theories. To that end we review and extend the Cardy-type brane calculations in bosonic and supersymmetric Liouville theory (and its duals) as well as in H 3 + . We analyze the three-point functions of Liouville theory and of H 3 + in detail to directly identify the fusion coefficients from the operator product expansion. Moreover, we check the validity of a proposed generic formula for localized brane one-point functions in nonrational conformal field theories

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

Science.gov (United States)

Richman, Daniel Eric

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

Investigation of the molecular conformations of ethanol using electron momentum spectroscopy

International Nuclear Information System (INIS)

Ning, C G; Luo, Z H; Huang, Y R; Liu, K; Zhang, S F; Deng, J K; Hajgato, B; Morini, F; Deleuze, M S

2008-01-01

The valence electronic structure and momentum-space electron density distributions of ethanol have been investigated with our newly constructed high-resolution electron momentum spectrometer. The measurements are compared to thermally averaged simulations based on Kohn-Sham (B3LYP) orbital densities as well as one-particle Green's function calculations of ionization spectra and Dyson orbital densities, assuming Boltzmann's statistical distribution of the molecular structure over the two energy minima defining the anti and gauche conformers. One-electron ionization energies and momentum distributions in the outer-valence region were found to be highly dependent upon the molecular conformation. Calculated momentum distributions indeed very sensitively reflect the distortions and topological changes that molecular orbitals undergo due to the internal rotation of the hydroxyl group, and thereby exhibit variations which can be traced experimentally. The B3LYP model Kohn-Sham orbital densities are overall in good agreement with the experimental distributions, and closely resemble benchmark ADC(3) Dyson orbital densities. Both approaches fail to quantitatively reproduce the experimental momentum distributions characterizing the highest occupied molecular orbital. Since electron momentum spectroscopy measurements at various electron impact energies indicate that the plane wave impulse approximation is valid, this discrepancy between theory and experiment is tentatively ascribed to thermal disorder, i.e. large-amplitude and thermally induced dynamical distortions of the molecular structure in the gas phase

Double-trace deformations of conformal correlations

Science.gov (United States)

Giombi, Simone; Kirilin, Vladimir; Perlmutter, Eric

2018-02-01

Large N conformal field theories often admit unitary renormalization group flows triggered by double-trace deformations. We compute the change in scalar four-point functions under double-trace flow, to leading order in 1/ N. This has a simple dual in AdS, where the flow is implemented by a change of boundary conditions, and provides a physical interpretation of single-valued conformal partial waves. We extract the change in the conformal dimensions and three-point coefficients of infinite families of double-trace composite operators. Some of these quantities are found to be sign-definite under double-trace flow. As an application, we derive anomalous dimensions of spinning double-trace operators comprised of non-singlet constituents in the O( N) vector model.

Conformal amplitude hierarchy and the Poincaré disk

Science.gov (United States)

Shimada, Hirohiko

2018-02-01

The amplitude for the singlet channels in the 4-point function of the fundamental field in the conformal field theory of the 2d O(n) model is studied as a function of n. For a generic value of n, the 4-point function has infinitely many amplitudes, whose landscape can be very spiky as the higher amplitude changes its sign many times at the simple poles, which generalize the unique pole of the energy operator amplitude at n = 0. In the stadard parameterization of n by angle in unit of π, we find that the zeros and poles happen at the rational angles, forming a hierarchical tree structure inherent in the Poincaré disk. Some relation between the amplitude and the Farey path, a piecewise geodesic that visits these zeros and poles, is suggested. In this hierarchy, the symmetry of the congruence subgroup Γ(2) of SL(2, ℤ) naturally arises from the two clearly distinct even/odd classes of the rational angles, in which one respectively gets the truncated operator algebras and the logarithmic 4-point functions.

First-principle study of nanostructures of functionalized graphene

Indian Academy of Sciences (India)

We present first-principle calculations of 2D nanostructures of graphene functionalized with hydrogen and fluorine, respectively, in chair conformation. The partial density of states, band structure, binding energy and transverse displacement of C atoms due to functionalization (buckling) have been calculated within the ...

Supergravitational conformal Galileons

Science.gov (United States)

Deen, Rehan; Ovrut, Burt

2017-08-01

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

Isomers and conformational barriers of gas phase nicotine, nornicotine and their protonated forms

Energy Technology Data Exchange (ETDEWEB)

Yoshida, Tomoki; Farone, William A.; Xantheas, Sotiris S.

2014-07-17

We report extensive conformational searches of the neutral nicotine, nornicotine and their protonated analogs that are based on ab-initio second order Møller-Plesset perturbation (MP2) electronic structure calculations. Initial searches were performed with the 6-31G(d,p) and the energetics of the most important structures were further refined from geometry optimizations with the aug-cc-pVTZ basis set. Based on the calculated free energies at T=298 K for the gas phase molecules, neutral nicotine has two dominant trans conformers, whereas neutral nornicotine is a mixture of several conformers. For nicotine, the protonation on both the pyridine and the pyrrolidine sites is energetically competitive, whereas nornicotine prefers protonation on the pyridine nitrogen. The protonated form of nicotine is mainly a mixture of two pyridine-protonated trans conformers and two pyrrolidine-protonated trans conformers, whereas the protonated form of nornicotine is a mixture of four pyridine-protonated trans conformers. Nornicotine is conformationally more flexible than nicotine, however it is less protonated at the biologically important pyrrolidine nitrogen site. The lowest energy isomers for each case were found to interconvert via low (< 6 kcal/mol) rotational barriers around the pyridine-pyrrolidine bond.

Diagonal Limit for Conformal Blocks in d Dimensions

CERN Document Server

Hogervorst, Matthijs; Rychkov, Slava

2013-01-01

Conformal blocks in any number of dimensions depend on two variables z, zbar. Here we study their restrictions to the special "diagonal" kinematics z = zbar, previously found useful as a starting point for the conformal bootstrap analysis. We show that conformal blocks on the diagonal satisfy ordinary differential equations, third-order for spin zero and fourth-order for the general case. These ODEs determine the blocks uniquely and lead to an efficient numerical evaluation algorithm. For equal external operator dimensions, we find closed-form solutions in terms of finite sums of 3F2 functions.

Ab initio Hartree-Fock and density functional theory investigations on the conformational stability, molecular structure and vibrational spectra of 5-chloro-3-(2-(4-methylpiperazin-1-yl)-2-oxoethyl)benzo[d]thiazol-2(3H)-one drug molecule.

Science.gov (United States)

Taşal, Erol; Kumalar, Mustafa

2012-09-01

In this work, the experimental and theoretical spectra of 5-chloro-3-(2-(4-methylpiperazin-1-yl)-2-oxoethyl)benzo[d]thiazol-2(3H)-one molecule (abbreviated as 5CMOT) are studied. The molecular geometry and vibrational frequencies are calculated in the ground state of molecule using ab initio Hartree-Fock (HF) and Density Function Theory (DFT) methods with 6-311++G(d,p), 6-31G++(d,p), 6-31G(d,p), 6-31G(d) and 6-31G basis sets. Three staggered stable conformers were observed on the torsional potential energy surfaces. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes calculated. The comparison of the theoretical and experimental geometries of the title compound indicated that the X-ray parameters fairly well agree with the theoretically obtained values for the most stable conformer. The theoretical results showed an excellent agreement with the experimental values. The calculated HOMO and LUMO energies show that the charge transfer occurs within the molecule. Copyright © 2012 Elsevier B.V. All rights reserved.

Anomalies, conformal manifolds, and spheres

Energy Technology Data Exchange (ETDEWEB)

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

2016-03-04

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

Dilaton vs Higgs: Nearly Conformal Physics

Science.gov (United States)

Kozlov, G. A.

2016-04-01

We consider the model in which the conformal symmetry can be broken spontaneously, and a light scalar dilaton could emerge in the low-energy spectrum. The contribution of the dark photon production relevant to two photons decays of a Higgs boson/dilaton is discussed.

Synthesis and conformational characterization of functional di-block copolymer brushes for microarray technology

Energy Technology Data Exchange (ETDEWEB)

Di Carlo, Gabriele; Damin, Francesco [Institute of Chemistry of Molecular Recognition, National Research Council of Italy, Via M. Bianco 9, 20131 Milano (Italy); Armelao, Lidia [ISTM-CNR and INSTM, Department of Chemistry, University of Padova, Via F. Marzolo 1, 35131 Padova (Italy); Maccato, Chiara [Department of Chemistry and INSTM, University of Padova, Via F. Marzolo 1, 35131 Padova (Italy); Unlu, Selim [Department of Electrical and Computer Engineering, Boston University, St. Mary Street 8, Boston, MA 02215 (United States); Department of Biomedical Engineering, Boston University, St. Mary Street 8, Boston, MA 02215 (United States); Spuhler, Philipp S. [Department of Biomedical Engineering, Boston University, St. Mary Street 8, Boston, MA 02215 (United States); Chiari, Marcella, E-mail: marcella.chiari@icrm.cnr.it [Institute of Chemistry of Molecular Recognition, National Research Council of Italy, Via M. Bianco 9, 20131 Milano (Italy)

2012-02-01

Surface initiated polymerization (SIP) coupled with reversible addition-fragmentation chain transfer polymerization (RAFT) was used to functionalize microarray glass slides with block polymer brushes. N,N-dimethylacrylamide (DMA) and N-acryloyloxysuccinimide (NAS) (graft-poly[DMA-b-(DMA-co-NAS)]) brushes, with di-block architecture, were prepared from a novel RAFT chain transfer agent bearing a silanating moiety (RAFT silane) directly anchored onto the glass surfaces. Conformational characterization of the coatings was performed by Self Spectral Interference Fluorescence Microscopy (SSFM), an innovative technique that describes the location of a fluorescent DNA molecule relative to a surface with sub-nanometer accuracy. X-ray Photoelectron Spectroscopy (XPS) and Scanning Electron Microscopy (SEM) were used to characterize the coatings composition and morphology.

Synthesis and conformational characterization of functional di-block copolymer brushes for microarray technology

International Nuclear Information System (INIS)

Di Carlo, Gabriele; Damin, Francesco; Armelao, Lidia; Maccato, Chiara; Unlu, Selim; Spuhler, Philipp S.; Chiari, Marcella

2012-01-01

Surface initiated polymerization (SIP) coupled with reversible addition-fragmentation chain transfer polymerization (RAFT) was used to functionalize microarray glass slides with block polymer brushes. N,N-dimethylacrylamide (DMA) and N-acryloyloxysuccinimide (NAS) (graft-poly[DMA-b-(DMA-co-NAS)]) brushes, with di-block architecture, were prepared from a novel RAFT chain transfer agent bearing a silanating moiety (RAFT silane) directly anchored onto the glass surfaces. Conformational characterization of the coatings was performed by Self Spectral Interference Fluorescence Microscopy (SSFM), an innovative technique that describes the location of a fluorescent DNA molecule relative to a surface with sub-nanometer accuracy. X-ray Photoelectron Spectroscopy (XPS) and Scanning Electron Microscopy (SEM) were used to characterize the coatings composition and morphology.

Energetics and Structural Characterization of the large-scale Functional Motion of Adenylate Kinase

Science.gov (United States)

Formoso, Elena; Limongelli, Vittorio; Parrinello, Michele

2015-02-01

Adenylate Kinase (AK) is a signal transducing protein that regulates cellular energy homeostasis balancing between different conformations. An alteration of its activity can lead to severe pathologies such as heart failure, cancer and neurodegenerative diseases. A comprehensive elucidation of the large-scale conformational motions that rule the functional mechanism of this enzyme is of great value to guide rationally the development of new medications. Here using a metadynamics-based computational protocol we elucidate the thermodynamics and structural properties underlying the AK functional transitions. The free energy estimation of the conformational motions of the enzyme allows characterizing the sequence of events that regulate its action. We reveal the atomistic details of the most relevant enzyme states, identifying residues such as Arg119 and Lys13, which play a key role during the conformational transitions and represent druggable spots to design enzyme inhibitors. Our study offers tools that open new areas of investigation on large-scale motion in proteins.

Conformal symmetry and non-relativistic second-order fluid dynamics

International Nuclear Information System (INIS)

Chao Jingyi; Schäfer, Thomas

2012-01-01

We study the constraints imposed by conformal symmetry on the equations of fluid dynamics at second order in the gradients of the hydrodynamic variables. At zeroth order, conformal symmetry implies a constraint on the equation of state, E 0 =2/3 P, where E 0 is the energy density and P is the pressure. At first order, conformal symmetry implies that the bulk viscosity must vanish. We show that at second order, conformal invariance requires that two-derivative terms in the stress tensor must be traceless, and that it determines the relaxation of dissipative stresses to the Navier–Stokes form. We verify these results by solving the Boltzmann equation at second order in the gradient expansion. We find that only a subset of the terms allowed by conformal symmetry appear. - Highlights: ► We derive conformal constraints for the stress tensor of a scale invariant fluid. ► We determine the relaxation time in kinetic theory. ► We compute the rate of entropy production in second-order fluid dynamics.

Conformational landscape of an amyloid intra-cellular domain and Landau-Ginzburg-Wilson paradigm in protein dynamics

Energy Technology Data Exchange (ETDEWEB)

Dai, Jin; He, Jianfeng, E-mail: Antti.Niemi@physics.uu.se, E-mail: hjf@bit.edu.cn [School of Physics, Beijing Institute of Technology, Beijing 100081 (China); Niemi, Antti J., E-mail: Antti.Niemi@physics.uu.se, E-mail: hjf@bit.edu.cn [School of Physics, Beijing Institute of Technology, Beijing 100081 (China); Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108 Uppsala (Sweden); Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200 Tours (France)

2016-07-28

The Landau-Ginzburg-Wilson paradigm is proposed as a framework, to investigate the conformational landscape of intrinsically unstructured proteins. A universal Cα-trace Landau free energy is deduced from general symmetry considerations, with the ensuing all-atom structure modeled using publicly available reconstruction programs Pulchra and Scwrl. As an example, the conformational stability of an amyloid precursor protein intra-cellular domain (AICD) is inspected; the reference conformation is the crystallographic structure with code 3DXC in Protein Data Bank (PDB) that describes a heterodimer of AICD and a nuclear multi-domain adaptor protein Fe65. Those conformations of AICD that correspond to local or near-local minima of the Landau free energy are identified. For this, the response of the original 3DXC conformation to variations in the ambient temperature is investigated, using the Glauber algorithm. The conclusion is that in isolation the AICD conformation in 3DXC must be unstable. A family of degenerate conformations that minimise the Landau free energy is identified, and it is proposed that the native state of an isolated AICD is a superposition of these conformations. The results are fully in line with the presumed intrinsically unstructured character of isolated AICD and should provide a basis for a systematic analysis of AICD structure in future NMR experiments.

Conformational landscape of an amyloid intra-cellular domain and Landau-Ginzburg-Wilson paradigm in protein dynamics

International Nuclear Information System (INIS)

Dai, Jin; He, Jianfeng; Niemi, Antti J.

2016-01-01

The Landau-Ginzburg-Wilson paradigm is proposed as a framework, to investigate the conformational landscape of intrinsically unstructured proteins. A universal Cα-trace Landau free energy is deduced from general symmetry considerations, with the ensuing all-atom structure modeled using publicly available reconstruction programs Pulchra and Scwrl. As an example, the conformational stability of an amyloid precursor protein intra-cellular domain (AICD) is inspected; the reference conformation is the crystallographic structure with code 3DXC in Protein Data Bank (PDB) that describes a heterodimer of AICD and a nuclear multi-domain adaptor protein Fe65. Those conformations of AICD that correspond to local or near-local minima of the Landau free energy are identified. For this, the response of the original 3DXC conformation to variations in the ambient temperature is investigated, using the Glauber algorithm. The conclusion is that in isolation the AICD conformation in 3DXC must be unstable. A family of degenerate conformations that minimise the Landau free energy is identified, and it is proposed that the native state of an isolated AICD is a superposition of these conformations. The results are fully in line with the presumed intrinsically unstructured character of isolated AICD and should provide a basis for a systematic analysis of AICD structure in future NMR experiments.

Conformal house

DEFF Research Database (Denmark)

Ryttov, Thomas Aaby; Sannino, Francesco

2010-01-01

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

Green close-quote s function method with energy-independent vertex functions

International Nuclear Information System (INIS)

Tsay Tzeng, S.Y.; Kuo, T.T.; Tzeng, Y.; Geyer, H.B.; Navratil, P.

1996-01-01

In conventional Green close-quote s function methods the vertex function Γ is generally energy dependent. However, a model-space Green close-quote s function method where the vertex function is manifestly energy independent can be formulated using energy-independent effective interaction theories based on folded diagrams and/or similarity transformations. This is discussed in general and then illustrated for a 1p1h model-space Green close-quote s function applied to a solvable Lipkin many-fermion model. The poles of the conventional Green close-quote s function are obtained by solving a self-consistent Dyson equation and model space calculations may lead to unphysical poles. For the energy-independent model-space Green close-quote s function only the physical poles of the model problem are reproduced and are in satisfactory agreement with the exact excitation energies. copyright 1996 The American Physical Society

Parental Power and Behaviors as Antecedents of Adolescent Conformity.

Science.gov (United States)

Henry, Carolyn S.; And Others

Several authorities have observed that a moderate degree of conformity by the young may be necessary for a society to function effectively. In order to examine the relationship between adolescents' perceptions of parental power and behavior and adolescent conformity, adolescents (N=368) in 184 families completed questionnaires concerning aspects…

Enhanced conformational sampling using enveloping distribution sampling.

Science.gov (United States)

Lin, Zhixiong; van Gunsteren, Wilfred F

2013-10-14

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

Analysis of Conformational B-Cell Epitopes in the Antibody-Antigen Complex Using the Depth Function and the Convex Hull.

Directory of Open Access Journals (Sweden)

Wei Zheng

Full Text Available The prediction of conformational b-cell epitopes plays an important role in immunoinformatics. Several computational methods are proposed on the basis of discrimination determined by the solvent-accessible surface between epitopes and non-epitopes, but the performance of existing methods is far from satisfying. In this paper, depth functions and the k-th surface convex hull are used to analyze epitopes and exposed non-epitopes. On each layer of the protein, we compute relative solvent accessibility and four different types of depth functions, i.e., Chakravarty depth, DPX, half-sphere exposure and half space depth, to analyze the location of epitopes on different layers of the proteins. We found that conformational b-cell epitopes are rich in charged residues Asp, Glu, Lys, Arg, His; aliphatic residues Gly, Pro; non-charged residues Asn, Gln; and aromatic residue Tyr. Conformational b-cell epitopes are rich in coils. Conservation of epitopes is not significantly lower than that of exposed non-epitopes. The average depths (obtained by four methods for epitopes are significantly lower than that of non-epitopes on the surface using the Wilcoxon rank sum test. Epitopes are more likely to be located in the outer layer of the convex hull of a protein. On the benchmark dataset, the cumulate 10th convex hull covers 84.6% of exposed residues on the protein surface area, and nearly 95% of epitope sites. These findings may be helpful in building a predictor for epitopes.

The Functional Quality of Soluble Recombinant Polypeptides Produced in Escherichia coli Is Defined by a Wide Conformational Spectrum▿

Science.gov (United States)

Martínez-Alonso, Mónica; González-Montalbán, Nuria; García-Fruitós, Elena; Villaverde, Antonio

2008-01-01

We have observed that a soluble recombinant green fluorescent protein produced in Escherichia coli occurs in a wide conformational spectrum. This results in differently fluorescent protein fractions in which morphologically diverse soluble aggregates abound. Therefore, the functional quality of soluble versions of aggregation-prone recombinant proteins is defined statistically rather than by the prevalence of a canonical native structure. PMID:18836021

An Efficient Null Model for Conformational Fluctuations in Proteins

DEFF Research Database (Denmark)

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

2012-01-01

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

Contribution to the study of conformal theories and integrable models

International Nuclear Information System (INIS)

Sochen, N.

1992-05-01

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

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

Science.gov (United States)

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

2014-08-14

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

An introduction to conformal field theory

International Nuclear Information System (INIS)

Gaberdiel, Matthias R.; Fitzwilliam College, Cambridge

2000-01-01

A comprehensive introduction to two-dimensional conformal field theory is given. The structure of the meromorphic subtheory is described in detail, and a number of examples are presented explicitly. Standard constructions such as the coset and the orbifold construction are explained. The concept of a representation of the meromorphic theory is introduced, and the role of Zhu's algebra in classifying highest weight representations is elucidated. The fusion product of two representations and the corresponding fusion rules are defined, and Verlinde's formula is explained. Finally, higher correlation functions are considered, and the polynomial relations of Moore and Seiberg and the quantum group structure of chiral conformal field theory are discussed. The treatment is relatively general and also allows for a description of less well known classes of theories such as logarithmic conformal field theories. (author)

Functional and conformational properties of phaseolin (Phaseolus vulgris L.) and kidney bean protein isolate: a comparative study.

Science.gov (United States)

Yin, Shou-Wei; Tang, Chuan-He; Wen, Qi-Biao; Yang, Xiao-Quan

2010-03-15

Kidney bean (Phaseolus vulgris L.) seed is an underutilised plant protein source with good potential to be applied in the food industry. Phaseolin (also named G1 globulin) represents about 50 g kg(-1) of total storage protein in the seed. The aim of the present study was to characterise physicochemical, functional and conformational properties of phaseolin, and to compare these properties with those of kidney bean protein isolate (KPI). Compared with kidney bean protein isolate (KPI), the acid-extracted phaseolin-rich protein product (PRP) had much lower protein recovery of 320 g kg(-1) (dry weight basis) but higher phaseolin purity (over 950 g kg(-1)). PRP contained much lower sulfhydryl (SH) and disulfide bond contents than KPI. Differential scanning calorimetry analyses showed that the phaseolin in PRP was less denatured than in KPI. Thermal analyses in the presence or absence of dithiothreitol, in combination with SH and SS content analyses showed the contributions of SS to the thermal stability of KPI. The analyses of near-UV circular dichroism and intrinsic fluorescence spectra indicated more compacted tertiary conformation of the proteins in PRP than in KPI. PRP exhibited much better protein solubility, emulsifying activity index, and gel-forming ability than KPI. The relatively poor functional properties of KPI may be associated with protein denaturation/unfolding, with subsequent protein aggregation. The results presented here suggest the potential for acid-extracted PRP to be applied in food formulations, in view of its functional properties.

Complex analysis conformal inequalities and the Bieberbach conjecture

CERN Document Server

Kythe, Prem K

2015-01-01

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

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

Science.gov (United States)

2015-01-01

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

Theoretical study on the adsorption and relative stability of conformers of L-ascorbic acid on γ - alumina (100) surface

Science.gov (United States)

Mozaffari Majd, M.; Dabbagh, H. A.; Farrokhpour, H.; Najafi Chermahini, A.

2017-11-01

The adsorption energies (Eads) and relative stabilities of selected conformers of the most stable tautomer of L-ascorbic acid (vitamin C) on the dehydroxylated γ-alumina (100) surface were calculated in both gas phase and solvent (water) using the density functional theory (DFT) method. The selected conformers were related to the different rotational angles of OH groups of L-ascorbic acid. The conformational analysis of bare tautomer in both gas and water showed that the conformer No.20 (conf. 20) and 13 (conf. 13) with the dihedral angles of H15sbnd O10sbnd C11sbnd C9 (-73°) and H20sbnd O19sbnd C9sbnd C11 (-135°) were the most stable and unstable conformers, respectively. The performed calculations in the presence of surface showed that the interaction of the conformers with the surface changes their relative stabilities and structures in both gas phase and water. The Ead of each conformer was calculated and it was determined that conf. 8 and conf. 16 have the highest value of Ead in the gas phase (-62.56 kcal/mol) and water (-54.44 kcal/mol), respectively. The optimized structure of each conformer on the surface and the number of hydrogen bonds between it and surface along with their bond lengths were determined.

Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria.

Directory of Open Access Journals (Sweden)

M Olivia Kim

2015-10-01

Full Text Available BACE-1 is the β-secretase responsible for the initial amyloidogenesis in Alzheimer's disease, catalyzing hydrolytic cleavage of substrate in a pH-sensitive manner. The catalytic mechanism of BACE-1 requires water-mediated proton transfer from aspartyl dyad to the substrate, as well as structural flexibility in the flap region. Thus, the coupling of protonation and conformational equilibria is essential to a full in silico characterization of BACE-1. In this work, we perform constant pH replica exchange molecular dynamics simulations on both apo BACE-1 and five BACE-1-inhibitor complexes to examine the effect of pH on dynamics and inhibitor binding properties of BACE-1. In our simulations, we find that solution pH controls the conformational flexibility of apo BACE-1, whereas bound inhibitors largely limit the motions of the holo enzyme at all levels of pH. The microscopic pKa values of titratable residues in BACE-1 including its aspartyl dyad are computed and compared between apo and inhibitor-bound states. Changes in protonation between the apo and holo forms suggest a thermodynamic linkage between binding of inhibitors and protons localized at the dyad. Utilizing our recently developed computational protocol applying the binding polynomial formalism to the constant pH molecular dynamics (CpHMD framework, we are able to obtain the pH-dependent binding free energy profiles for various BACE-1-inhibitor complexes. Our results highlight the importance of correctly addressing the binding-induced protonation changes in protein-ligand systems where binding accompanies a net proton transfer. This work comprises the first application of our CpHMD-based free energy computational method to protein-ligand complexes and illustrates the value of CpHMD as an all-purpose tool for obtaining pH-dependent dynamics and binding free energies of biological systems.

Daily conformity drinking motivations are associated with increased odds of consuming alcohol mixed with energy drinks.

Science.gov (United States)

Linden-Carmichael, Ashley N; Lau-Barraco, Cathy

2018-04-01

Recent research indicates that individuals drank more heavily and experienced more harms on days they consumed alcohol mixed with energy drinks (AmEDs). Limited research, thus far, has examined predictors of AmED use on a daily level. Drinking motives, or reasons for drinking, are shown to discern AmED users from non-users, but the extent to which daily drinking motives covary with AmED use has not been tested. The current study used a daily diary design to determine how motives differ between AmED and other drinking occasions. Participants included 122 college students (73.8% women) with a mean age of 20.39years. Participants completed up to 14 daily surveys, resulting in 389 drinking days (40days involved AmED use). Participants reported on their drinking motives at baseline as well as on each drinking day. Multilevel models revealed that, after controlling for other motives, AmED use was more likely on days where conformity motives were higher than usual and was less likely when enhancement motives were higher. Daily social and coping motives as well as all motives measured at baseline were unassociated with AmED use. Our findings suggest that conformity motives, or drinking to fit in with others, are the most salient drinking motive predicting AmED use on a drinking day. Given that conformity motives are often less associated with alcohol use outcomes in general, these findings highlight AmEDs as a unique alcoholic beverage. Clinicians and interventionists working with frequent AmED users should consider the unique conditions under which AmEDs are consumed. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

Science.gov (United States)

Kishimoto, Naoki; Waizumi, Hiroki

2017-10-01

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

Hidden symmetries of integrable conformal mechanical systems

International Nuclear Information System (INIS)

Hakobyan, Tigran; Krivonos, Sergey; Lechtenfeld, Olaf; Nersessian, Armen

2010-01-01

We split the generic conformal mechanical system into a 'radial' and an 'angular' part, where the latter is defined as the Hamiltonian system on the orbit of the conformal group, with the Casimir function in the role of the Hamiltonian. We reduce the analysis of the constants of motion of the full system to the study of certain differential equations on this orbit. For integrable mechanical systems, the conformal invariance renders them superintegrable, yielding an additional series of conserved quantities originally found by Wojciechowski in the rational Calogero model. Finally, we show that, starting from any N=4 supersymmetric 'angular' Hamiltonian system one may construct a new system with full N=4 superconformal D(1,2;α) symmetry.

Conformal geometry and quasiregular mappings

CERN Document Server

Vuorinen, Matti

1988-01-01

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

Renyi entropy and conformal defects

Energy Technology Data Exchange (ETDEWEB)

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

2016-04-18

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

Renyi entropy and conformal defects

International Nuclear Information System (INIS)

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

2016-01-01

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

Nonlocal kinetic-energy-density functionals

International Nuclear Information System (INIS)

Garcia-Gonzalez, P.; Alvarellos, J.E.; Chacon, E.

1996-01-01

In this paper we present nonlocal kinetic-energy functionals T[n] within the average density approximation (ADA) framework, which do not require any extra input when applied to any electron system and recover the exact kinetic energy and the linear response function of a homogeneous system. In contrast with previous ADA functionals, these present good behavior of the long-range tail of the exact weight function. The averaging procedure for the kinetic functional (averaging the Fermi momentum of the electron gas, instead of averaging the electron density) leads to a functional without numerical difficulties in the calculation of extended systems, and it gives excellent results when applied to atoms and jellium surfaces. copyright 1996 The American Physical Society

Ground state hydrogen conformations and vibrational analysis of 1,2-dihdroxyanthraquinone (alizarin) molecule by AB initio Hartree-Fock and density functional theory calculations

International Nuclear Information System (INIS)

Delta, E.; Ucun, F.; Saglam, A.

2010-01-01

The ground state hydrogen conformations of 1,2-dihydroxyanthraquinone (alizarin) molecule have been investigated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-31G(d,p) basis set. The calculations indicate that the compound in the ground state exist with the doubly bonded O atom linked intra molecularly by the two hydrogen bonds. The vibrational analyses of the ground state conformation of the compound were also made and its optimized geometry parameters were given.

Effect of Side Chains on Molecular Conformation of Anthracene-Ethynylene-Phenylene-Vinylene Oligomers: A Comparative Density Functional Study With and Without Dispersion Interaction.

Science.gov (United States)

Dong, Chuanding; Hoppe, Harald; Beenken, Wichard J D

2016-06-02

Using density functional calculations with and without dispersion interaction, we studied the effects of linear octyl and branched 2-ethylhexyl side chains on the oligomer conformation of the conjugated copolymer poly(p-anthracene-ethynylene)-alt-poly(p-phenylene-vinylene). With dispersion included, the branched side chains can cause significant bending of the oligomer backbone, while without dispersion they induce mainly torsional disorder. The oligomers with mainly linear side chains keep good planarity when optimized with and without dispersion. Despite their dramatically different conformations, the calculated absorption spectra of the oligomers with various side chain combinations are very similar, indicating that the conformation of the copolymer is not the main reason for the experimentally observed different spectra of ordered and disordered phases.

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

Science.gov (United States)

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

2018-01-01

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

Recursive representation of the torus 1-point conformal block

Science.gov (United States)

Hadasz, Leszek; Jaskólski, Zbigniew; Suchanek, Paulina

2010-01-01

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

Radial expansion for spinning conformal blocks

CERN Document Server

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

2016-07-12

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

Quantum critical phenomena and conformal invariance

International Nuclear Information System (INIS)

Zhe Chang.

1995-05-01

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

THz time domain spectroscopy of biomolecular conformational modes

International Nuclear Information System (INIS)

Markelz, Andrea; Whitmire, Scott; Hillebrecht, Jay; Birge, Robert

2002-01-01

We discuss the use of terahertz time domain spectroscopy for studies of conformational flexibility and conformational change in biomolecules. Protein structural dynamics are vital to biological function with protein flexibility affecting enzymatic reaction rates and sensory transduction cycling times. Conformational mode dynamics occur on the picosecond timescale and with the collective vibrational modes associated with these large scale structural motions in the 1-100 cm -1 range. We have performed THz time domain spectroscopy (TTDS) of several biomolecular systems to explore the sensitivity of TTDS to distinguish different molecular species, different mutations within a single species and different conformations of a given biomolecule. We compare the measured absorbances to normal mode calculations and find that the TTDS absorbance reflects the density of normal modes determined by molecular mechanics calculations, and is sensitive to both conformation and mutation. These early studies demonstrate some of the advantages and limitations of using TTDS for the study of biomolecules

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

Science.gov (United States)

Jaiyong, Panichakorn; Bryce, Richard A

2017-06-14

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

Quantum effects and elimination of the conformal anomaly in anisotropic space-time

International Nuclear Information System (INIS)

Grib, A.A.; Nesteruk, A.V.

1988-01-01

In homogeneous anisotropic space-time the connection between the problem of the elimination of infrared divergences and the conformal anomaly of the regularized energy-momentum tensor is studied. It is shown that removal of the infrared divergence by means of a cutoff leads to the absence of a conformal anomaly. A physical interpretation of the infrared cutoff as a shift in the particle-energy spectrum by an amount equal to the effective temperature of the gravitational field is proposed

Irreversibility and higher-spin conformal field theory

Science.gov (United States)

Anselmi, Damiano

2000-08-01

I discuss the properties of the central charges c and a for higher-derivative and higher-spin theories (spin 2 included). Ordinary gravity does not admit a straightforward identification of c and a in the trace anomaly, because it is not conformal. On the other hand, higher-derivative theories can be conformal, but have negative c and a. A third possibility is to consider higher-spin conformal field theories. They are not unitary, but have a variety of interesting properties. Bosonic conformal tensors have a positive-definite action, equal to the square of a field strength, and a higher-derivative gauge invariance. There exists a conserved spin-2 current (not the canonical stress tensor) defining positive central charges c and a. I calculate the values of c and a and study the operator-product structure. Higher-spin conformal spinors have no gauge invariance, admit a standard definition of c and a and can be coupled to Abelian and non-Abelian gauge fields in a renormalizable way. At the quantum level, they contribute to the one-loop beta function with the same sign as ordinary matter, admit a conformal window and non-trivial interacting fixed points. There are composite operators of high spin and low dimension, which violate the Ferrara-Gatto-Grillo theorem. Finally, other theories, such as conformal antisymmetric tensors, exhibit more severe internal problems. This research is motivated by the idea that fundamental quantum field theories should be renormalization-group (RG) interpolations between ultraviolet and infrared conformal fixed points, and quantum irreversibility should be a general principle of nature.

High energy physics signatures from inflation and conformal symmetry of de Sitter

International Nuclear Information System (INIS)

Kehagias, A.; Riotto, A.

2015-01-01

During inflation, the geometry of spacetime is described by a (quasi-)de Sitter phase. Inflationary observables are determined by the underlying (softly broken) de Sitter isometry group SO(1, 4) which acts like a conformal group on R 3 : when the fluctuations are on super-Hubble scales, the correlators of the scalar fields are constrained by conformal invariance. Heavy fields with mass m larger than the Hubble rate H correspond to operators with imaginary dimensions in the dual Euclidean three-dimensional conformal field theory. By making use of the dS/CFT correspondence we show that, besides the Boltzmann suppression expected from the thermal properties of de Sitter space, the generic effect of heavy fields in the inflationary correlators of the light fields is to introduce power-law suppressed corrections of the form O(H 2 / m 2 ). This can be seen, for instance, at the level of the four-point correlator for which we provide the correction due to a massive scalar field exchange. (copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Nonrelativistic Conformed Symmetry in 2 + 1 Dimensional Field Theory.

Science.gov (United States)

Bergman, Oren

This thesis is devoted to the study of conformal invariance and its breaking in non-relativistic field theories. It is a well known feature of relativistic field theory that theories which are conformally invariant at the classical level can acquire a conformal anomaly upon quantization and renormalization. The anomaly appears through the introduction of an arbitrary, but dimensionful, renormalization scale. One does not usually associate the concepts of renormalization and anomaly with nonrelativistic quantum mechanics, but there are a few examples where these concepts are useful. The most well known case is the two-dimensional delta -function potential. In two dimensions the delta-function scales like the kinetic term of the Hamiltonian, and therefore the problem is classically conformally invariant. Another example of classical conformal invariance is the famous Aharonov-Bohm (AB) problem. In that case each partial wave sees a 1/r^2 potential. We use the second quantized formulation of these problems, namely the nonrelativistic field theories, to compute Green's functions and derive the conformal anomaly. In the case of the AB problem we also solve an old puzzle, namely how to reproduce the result of Aharonov and Bohm in perturbation theory. The thesis is organized in the following manner. Chapter 1 is an introduction to nonrelativistic field theory, nonrelativistic conformal invariance, contact interactions and the AB problem. In Chapter 2 we discuss nonrelativistic scalar field theory, and how its quantization produces the anomaly. Chapter 3 is devoted to the AB problem, and the resolution of the perturbation puzzle. In Chapter 4 we generalize the discussion of Chapter 3 to particles carrying nonabelian charges. The structure of the nonabelian theory is much richer, and deserves a separate discussion. We also comment on the issues of forward scattering and single -valuedness of wavefunctions, which are important for Chapter 3 as well. (Copies available

Field theories on conformally related space-times: Some global considerations

International Nuclear Information System (INIS)

Candelas, P.; Dowker, J.S.

1979-01-01

The nature of the vacua appearing in the relation between the vacuum expectation value of stress tensors in conformally flat spaces is clarified. The simple but essential point is that the relevant spaces should have conformally related global Cauchy surfaces. Some commonly occurring conformally flat space-times are divided into two families according to whether they are conformally equivalent to Minkowski space or to the Rindler wedge. Expressions, some new, are obtained for the vacuum expectation value of the stress tensor for a number of illustrative cases. It is noted that thermalization relates the Green's functions of these two families

On holography for (pseudo-)conformal cosmology

CERN Document Server

Libanov, M.; Sibiryakov, S.

2015-01-01

We propose a holographic dual for (pseudo-)conformal cosmological scenario, with a scalar field that forms a moving domain wall in adS_5. The domain wall separates two vacua with unequal energy densities. Unlike in the existing construction, the 5d solution is regular in the relevant space-time domain.

Microscopically Based Nuclear Energy Functionals

International Nuclear Information System (INIS)

Bogner, S. K.

2009-01-01

A major goal of the SciDAC project 'Building a Universal Nuclear Energy Density Functional' is to develop next-generation nuclear energy density functionals that give controlled extrapolations away from stability with improved performance across the mass table. One strategy is to identify missing physics in phenomenological Skyrme functionals based on our understanding of the underlying internucleon interactions and microscopic many-body theory. In this contribution, I describe ongoing efforts to use the density matrix expansion of Negele and Vautherin to incorporate missing finite-range effects from the underlying two- and three-nucleon interactions into phenomenological Skyrme functionals.

Gratitude facilitates private conformity: A test of the social alignment hypothesis.

Science.gov (United States)

Ng, Jomel W X; Tong, Eddie M W; Sim, Dael L Y; Teo, Samantha W Y; Loy, Xingqi; Giesbrecht, Timo

2017-03-01

Past research has established clear support for the prosocial function of gratitude in improving the well-being of others. The present research provides evidence for another hypothesized function of gratitude: the social alignment function, which enhances the tendency of grateful individuals to follow social norms. We tested the social alignment hypothesis of gratitude in 2 studies with large samples. Using 2 different conformity paradigms, participants were subjected to a color judgment task (Experiment 1) and a material consumption task (Experiment 2). They were provided with information showing choices allegedly made by others, but were allowed to state their responses in private. Supporting the social alignment hypothesis, the results showed that induced gratitude increased private conformity. Specifically, participants induced to feel gratitude were more likely to conform to the purportedly popular choice, even if the option was factually incorrect (Experiment 1). This effect appears to be specific to gratitude; induction of joy produced significantly less conformity than gratitude (Experiment 2). We discuss whether the social alignment function provides a behavioral pathway in the role of gratitude in building social relationships. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Anomalous Dimensions of Conformal Baryons

DEFF Research Database (Denmark)

Pica, Claudio; Sannino, Francesco

2016-01-01

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

Universality of sparse d>2 conformal field theory at large N

Energy Technology Data Exchange (ETDEWEB)

Belin, Alexandre; Boer, Jan de; Kruthoff, Jorrit [Institute for Theoretical Physics Amsterdam and Delta Institute for Theoretical Physics,University of Amsterdam, Science Park 904, Amsterdam, 1098 XH The (Netherlands); Michel, Ben; Shaghoulian, Edgar; Shyani, Milind [Department of Physics, University of California,Santa Barbara, CA, 93106 (United States)

2017-03-13

We derive necessary and sufficient conditions for large N conformal field theories to have a universal free energy and an extended range of validity of the higher-dimensional Cardy formula. These constraints are much tighter than in two dimensions and must be satisfied by any conformal field theory dual to Einstein gravity. We construct and analyze symmetric product orbifold theories on T{sup d} and show that they only realize the necessary phase structure and extended range of validity if the seed theory is assumed to have a universal vacuum energy.

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

Directory of Open Access Journals (Sweden)

Qing Wang

2016-05-01

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

3D Printers Can Provide an Added Dimension for Teaching Structure-Energy Relationships

Science.gov (United States)

Blauch, David N.; Carroll, Felix A.

2014-01-01

A 3D printer is used to prepare a variety of models representing potential energy as a function of two geometric coordinates. These models facilitate the teaching of structure-energy relationships in molecular conformations and in chemical reactions.

Watching Conformations of Biomolecules: a Microwave Spectroscopy Approach

Science.gov (United States)

Lopez, J. C.

2011-06-01

The combination of laser ablation with Fourier transform microwave spectroscopy in supersonic jets (LA-MB-FTMW) has made possible the gas-phase study of solid biomolecules with high melting points. In the experiment, solids are efficiently vaporized by a high-energy laser pulse, supersonically expanded into a evacuated Fabry-Perot cavity and characterised by their rotational spectra. Recent improvements such as the use of picosecond pulse lasers, new ablation nozzles and the extension of the range of the spectrometers to low frequecy have notably increased the sensitivity of our experimental setup. To date different α-, β- and γ-amino acids have been studied using this technique, making possible the characterization of their preferred conformations and gaining insight in the role of intramolecular interactions. Even in conformationally challenging systems the different rotamers of such biomolecules can be identified by rotational spectroscopy as can be illustrated by the assignment of six low-energy conformers in cysteine and aspartic acid, seven in serine and threonine,^a and nine in γ-amino butyric acid (GABA). In all cases the low-energy conformers have been conclusive identified from their experimental rotational and 14N quadrupole coupling constants. The spectra of neurotransmitters and of the nucleic acid bases uracil, thymine, cytosine and guanine have also been studied and their preferred conformers or tautomeric forms determined. The complexes between amino acids and nucleic acid bases with water have also been investigated to obtain information on the possible changes induced in the conformational or tautomeric preferences by the addition of solvent molecules. J. L. Alonso, C. Pérez, M. E. Sanz, J. C. López, S. Blanco, Phys. Chem. Chem. Phys. 11, 617-627 (2009) and references therein M. E. Sanz, J. C. López, J. L. Alonso, Phys. Chem. Chem. Phys., 12, 3573-3578 (2010) S. Blanco, J. C. López, S. Mata and J. L. Alonso, Angew. Chem. Int. Ed. 49, 9187

Graded associative conformal algebras of finite type

OpenAIRE

Kolesnikov, Pavel

2011-01-01

In this paper, we consider graded associative conformal algebras. The class of these objects includes pseudo-algebras over non-cocommutative Hopf algebras of regular functions on some linear algebraic groups. In particular, an associative conformal algebra which is graded by a finite group $\\Gamma $ is a pseudo-algebra over the coordinate Hopf algebra of a linear algebraic group $G$ such that the identity component $G^0$ is the affine line and $G/G^0\\simeq \\Gamma $. A classification of simple...

On holography for (pseudo-)conformal cosmology

Energy Technology Data Exchange (ETDEWEB)

Libanov, M. [Institute for Nuclear Research of the Russian Academy of Sciences, 60th October Anniversary Prospect, 7a, 117312, Moscow (Russian Federation); Moscow Institute of Physics and Technology, Institutskii per., 9, 141700, Dolgoprudny, Moscow Region (Russian Federation); Rubakov, V. [Institute for Nuclear Research of the Russian Academy of Sciences, 60th October Anniversary Prospect, 7a, 117312, Moscow (Russian Federation); Department of Particle Physics and Cosmology, Physics Faculty, Moscow State University, Vorobjevy Gory, 119991, Moscow (Russian Federation); Sibiryakov, S., E-mail: sibir@ms2.inr.ac.ru [Institute for Nuclear Research of the Russian Academy of Sciences, 60th October Anniversary Prospect, 7a, 117312, Moscow (Russian Federation); Theory Group, Physics Department, CERN, CH-1211 Geneva 23 (Switzerland); FSB/ITP/LPPC, Ecole Polytechnique Federale de Lausanne, CH-1015 Lausanne (Switzerland)

2015-02-04

We propose a holographic dual for (pseudo-)conformal cosmological scenario, with a scalar field that forms a moving domain wall in adS{sub 5}. The domain wall separates two vacua with unequal energy densities. Unlike in the existing construction, the 5d solution is regular in the relevant space–time domain.

Quantum Conformal Algebras and Closed Conformal Field Theory

CERN Document Server

Anselmi, D

1999-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2017-02-15

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

FT-IR, FT-Raman spectra, density functional computations of the vibrational spectra and molecular conformational analysis of 2,5-di-tert-butyl-hydroquinone

Science.gov (United States)

Subramanian, N.; Sundaraganesan, N.; Dereli, Ö.; Türkkan, E.

2011-12-01

The purpose of finding conformer among six different possible conformers of 2,5-di-tert-butyl-hydroquinone (DTBHQ), its equilibrium geometry and harmonic wavenumbers were calculated by the B3LYP/6-31G(d,p) method. The infrared and Raman spectra of DTBHQ were recorded in the region 400-4000 cm -1 and 50-3500 cm -1, respectively. In addition, the IR spectra in CCl 4 at various concentrations of DTBHQ are also recorded. The computed vibrational wavenumbers were compared with the IR and Raman experimental data. Computational calculations at B3LYP level with two different basis sets 6-31G(d,p) and 6-311++G(d,p) are also employed in the study of the possible conformer of DTBHQ. The complete assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes, calculated using VEDA 4 program. The general agreement between the observed and calculated frequencies was established.

A 5-Year Investigation of Children's Adaptive Functioning Following Conformal Radiation Therapy for Localized Ependymoma

Energy Technology Data Exchange (ETDEWEB)

Netson, Kelli L.; Conklin, Heather M. [Department of Psychology, St. Jude Children' s Research Hospital, Memphis, Tennessee (United States); Wu Shengjie; Xiong Xiaoping [Department of Biostatistics, St. Jude Children' s Research Hospital, Memphis, Tennessee (United States); Merchant, Thomas E., E-mail: thomas.merchant@stjude.org [Division of Radiation Oncology, St. Jude Children' s Research Hospital, Memphis, Tennessee (United States)

2012-09-01

Purpose: Conformal and intensity modulated radiation therapies have the potential to preserve cognitive outcomes in children with ependymoma; however, functional behavior remains uninvestigated. This longitudinal investigation prospectively examined intelligence quotient (IQ) and adaptive functioning during the first 5 years after irradiation in children diagnosed with ependymoma. Methods and Materials: The study cohort consisted of 123 children with intracranial ependymoma. Mean age at irradiation was 4.60 years (95% confidence interval [CI], 3.85-5.35). Serial neurocognitive evaluations, including an age-appropriate IQ measure and the Vineland Adaptive Behavior Scales (VABS), were completed before irradiation, 6 months after treatment, and annually for 5 years. A total of 579 neurocognitive evaluations were included in these analyses. Results: Baseline IQ and VABS were below normative means (P<.05), although within the average range. Linear mixed models revealed stable IQ and VABS across the follow-up period, except for the VABS Communication Index, which declined significantly (P=.015). Annual change in IQ (-.04 points) did not correlate with annual change in VABS (-.90 to +.44 points). Clinical factors associated with poorer baseline performance (P<.05) included preirradiation chemotherapy, cerebrospinal fluid shunt placement, number and extent of surgical resections, and younger age at treatment. No clinical factors significantly affected the rate of change in scores. Conclusions: Conformal and intensity modulated radiation therapies provided relative sparing of functional outcomes including IQ and adaptive behaviors, even in very young children. Communication skills remained vulnerable and should be the target of preventive and rehabilitative interventions.

Dissecting Protein Configurational Entropy into Conformational and Vibrational Contributions.

Science.gov (United States)

Chong, Song-Ho; Ham, Sihyun

2015-10-01

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

Decipher the mechanisms of protein conformational changes induced by nucleotide binding through free-energy landscape analysis: ATP binding to Hsp70.

Directory of Open Access Journals (Sweden)

Adrien Nicolaï

Full Text Available ATP regulates the function of many proteins in the cell by transducing its binding and hydrolysis energies into protein conformational changes by mechanisms which are challenging to identify at the atomic scale. Based on molecular dynamics (MD simulations, a method is proposed to analyze the structural changes induced by ATP binding to a protein by computing the effective free-energy landscape (FEL of a subset of its coordinates along its amino-acid sequence. The method is applied to characterize the mechanism by which the binding of ATP to the nucleotide-binding domain (NBD of Hsp70 propagates a signal to its substrate-binding domain (SBD. Unbiased MD simulations were performed for Hsp70-DnaK chaperone in nucleotide-free, ADP-bound and ATP-bound states. The simulations revealed that the SBD does not interact with the NBD for DnaK in its nucleotide-free and ADP-bound states whereas the docking of the SBD was found in the ATP-bound state. The docked state induced by ATP binding found in MD is an intermediate state between the initial nucleotide-free and final ATP-bound states of Hsp70. The analysis of the FEL projected along the amino-acid sequence permitted to identify a subset of 27 protein internal coordinates corresponding to a network of 91 key residues involved in the conformational change induced by ATP binding. Among the 91 residues, 26 are identified for the first time, whereas the others were shown relevant for the allosteric communication of Hsp70 s in several experiments and bioinformatics analysis. The FEL analysis revealed also the origin of the ATP-induced structural modifications of the SBD recently measured by Electron Paramagnetic Resonance. The pathway between the nucleotide-free and the intermediate state of DnaK was extracted by applying principal component analysis to the subset of internal coordinates describing the transition. The methodology proposed is general and could be applied to analyze allosteric communication in

Supergravity, Non-Conformal Field Theories and Brane-Worlds

CERN Document Server

Gherghetta, Tony; Gherghetta, Tony; Oz, Yaron

2002-01-01

We consider the supergravity dual descriptions of non-conformal super Yang-Mills theories realized on the world-volume of Dp-branes. We use the dual description to compute stress-energy tensor and current correlators. We apply the results to the study of dilatonic brane-worlds described by non-conformal field theories coupled to gravity. We find that brane-worlds based on D4 and D5 branes exhibit a localization of gauge and gravitational fields. We calculate the corrections to the Newton and Coulomb laws in these theories.

Study of conformally flat polytropes with tilted congruence

Science.gov (United States)

Sharif, M.; Sadiq, Sobia

This paper is aimed to study the modeling of spherically symmetric spacetime in the presence of anisotropic dissipative fluid configuration. This is accomplished for an observer moving relative to matter content using two cases of polytropic equation-of-state under conformally flat condition. We formulate the corresponding generalized Tolman-Oppenheimer-Volkoff equation, mass equation, as well as energy conditions for both cases. The conformally flat condition is imposed to find an expression for anisotropy which helps to study spherically symmetric polytropes. Finally, Tolman mass is used to analyze stability of the resulting models.

Conformal Tachyons

CERN Document Server

Tomaschitz, R

2000-01-01

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

Conformal Symmetry as a Template for QCD

Energy Technology Data Exchange (ETDEWEB)

Brodsky, S

2004-08-04

Conformal symmetry is broken in physical QCD; nevertheless, one can use conformal symmetry as a template, systematically correcting for its nonzero {beta} function as well as higher-twist effects. For example, commensurate scale relations which relate QCD observables to each other, such as the generalized Crewther relation, have no renormalization scale or scheme ambiguity and retain a convergent perturbative structure which reflects the underlying conformal symmetry of the classical theory. The ''conformal correspondence principle'' also dictates the form of the expansion basis for hadronic distribution amplitudes. The AdS/CFT correspondence connecting superstring theory to superconformal gauge theory has important implications for hadron phenomenology in the conformal limit, including an all-orders demonstration of counting rules for hard exclusive processes as well as determining essential aspects of hadronic light-front wavefunctions. Theoretical and phenomenological evidence is now accumulating that QCD couplings based on physical observables such as {tau} decay become constant at small virtuality; i.e., effective charges develop an infrared fixed point in contradiction to the usual assumption of singular growth in the infrared. The near-constant behavior of effective couplings also suggests that QCD can be approximated as a conformal theory even at relatively small momentum transfer. The importance of using an analytic effective charge such as the pinch scheme for unifying the electroweak and strong couplings and forces is also emphasized.

Conformal Symmetry as a Template for QCD

International Nuclear Information System (INIS)

Brodsky, S

2004-01-01

Conformal symmetry is broken in physical QCD; nevertheless, one can use conformal symmetry as a template, systematically correcting for its nonzero β function as well as higher-twist effects. For example, commensurate scale relations which relate QCD observables to each other, such as the generalized Crewther relation, have no renormalization scale or scheme ambiguity and retain a convergent perturbative structure which reflects the underlying conformal symmetry of the classical theory. The ''conformal correspondence principle'' also dictates the form of the expansion basis for hadronic distribution amplitudes. The AdS/CFT correspondence connecting superstring theory to superconformal gauge theory has important implications for hadron phenomenology in the conformal limit, including an all-orders demonstration of counting rules for hard exclusive processes as well as determining essential aspects of hadronic light-front wavefunctions. Theoretical and phenomenological evidence is now accumulating that QCD couplings based on physical observables such as τ decay become constant at small virtuality; i.e., effective charges develop an infrared fixed point in contradiction to the usual assumption of singular growth in the infrared. The near-constant behavior of effective couplings also suggests that QCD can be approximated as a conformal theory even at relatively small momentum transfer. The importance of using an analytic effective charge such as the pinch scheme for unifying the electroweak and strong couplings and forces is also emphasized

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

Directory of Open Access Journals (Sweden)

Ksenija Kogej

2016-04-01

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

Microscopic insights into the NMR relaxation based protein conformational entropy meter

Science.gov (United States)

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

2013-01-01

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

Conformal fields. From Riemann surfaces to integrable hierarchies

International Nuclear Information System (INIS)

Semikhatov, A.M.

1991-01-01

I discuss the idea of translating ingredients of conformal field theory into the language of hierarchies of integrable differential equations. Primary conformal fields are mapped into (differential or matrix) operators living on the phase space of the hierarchy, whereas operator insertions of, e.g., a current or the energy-momentum tensor, become certain vector fields on the phase space and thus acquire a meaning independent of a given Riemann surface. A number of similarities are observed between the structures arising on the hierarchy and those of the theory on the world-sheet. In particular, there is an analogue of the operator product algebra with the Cauchy kernel replaced by its 'off-shell' hierarchy version. Also, hierarchy analogues of certain operator insertions admit two (equivalent, but distinct) forms, resembling the 'bosonized' and 'fermionized' versions respectively. As an application, I obtain a useful reformulation of the Virasoro constraints of the type that arise in matrix models, as a system of equations on dressing (or Lax) operators (rather than correlation functions, i.e., residues or traces). This also suggests an interpretation in terms of a 2D topological field theory, which might be extended to a correspondence between Virasoro-constrained hierarchies and topological theories. (orig.)

Non-conformable, partial and conformable transposition

DEFF Research Database (Denmark)

König, Thomas; Mäder, Lars Kai

2013-01-01

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

Conformation of poly(γ-glutamic acid) in aqueous solution.

Science.gov (United States)

Muroga, Yoshio; Nakaya, Asami; Inoue, Atsuki; Itoh, Daiki; Abiru, Masaya; Wada, Kaori; Takada, Masako; Ikake, Hiroki; Shimizu, Shigeru

2016-04-01

Local conformation and overall conformation of poly(γ-DL-glutamic acid) (PγDLGA) and poly(γ-L-glutamic acid) (PγLGA) in aqueous solution was studied as a function of degree of ionization ε by (1) H-NMR, circular dichroism, and potentiometric titration. It was clarified that their local conformation is represented by random coil over an entire ε range and their overall conformation is represented by expanded random-coil in a range of ε > ε(*) , where ε(*) is about 0.3, 0.35, 0.45, and 0.5 for added-salt concentration of 0.02M, 0.05M, 0.1M, and 0.2M, respectively. In a range of ε acidic media. © 2015 Wiley Periodicals, Inc.

Prion protein β2–α2 loop conformational landscape

Science.gov (United States)

Caldarulo, Enrico; Wüthrich, Kurt; Parrinello, Michele

2017-01-01

In transmissible spongiform encephalopathies (TSEs), which are lethal neurodegenerative diseases that affect humans and a wide range of other mammalian species, the normal “cellular” prion protein (PrPC) is transformed into amyloid aggregates representing the “scrapie form” of the protein (PrPSc). Continued research on this system is of keen interest, since new information on the physiological function of PrPC in healthy organisms is emerging, as well as new data on the mechanism of the transformation of PrPC to PrPSc. In this paper we used two different approaches: a combination of the well-tempered ensemble (WTE) and parallel tempering (PT) schemes and metadynamics (MetaD) to characterize the conformational free-energy surface of PrPC. The focus of the data analysis was on an 11-residue polypeptide segment in mouse PrPC(121–231) that includes the β2–α2 loop of residues 167–170, for which a correlation between structure and susceptibility to prion disease has previously been described. This study includes wild-type mouse PrPC and a variant with the single-residue replacement Y169A. The resulting detailed conformational landscapes complement in an integrative manner the available experimental data on PrPC, providing quantitative insights into the nature of the structural transition-related function of the β2–α2 loop. PMID:28827331

Conformal Einstein spaces

International Nuclear Information System (INIS)

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

1985-01-01

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

Conformal Gravity

International Nuclear Information System (INIS)

Hooft, G.

2012-01-01

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

Conformal boundary state for the rectangular geometry

Energy Technology Data Exchange (ETDEWEB)

Bondesan, R., E-mail: roberto.bondesan@cea.fr [Institute de Physique Theorique, CEA Saclay, F-91191 Gif-sur-Yvette (France); LPTENS, Ecole Normale Superieure, 24 rue Lhomond, 75231 Paris (France); Institut Henri Poincare, 11 rue Pierre et Marie Curie, 75231 Paris (France); Dubail, J. [Department of Physics, Yale University, P.O. Box 208120, New Haven, CT 06520-8120 (United States); Jacobsen, J.L. [LPTENS, Ecole Normale Superieure, 24 rue Lhomond, 75231 Paris (France); Institut Henri Poincare, 11 rue Pierre et Marie Curie, 75231 Paris (France); Universite Pierre et Marie Curie, 4 place Jussieu, 75252 Paris (France); Saleur, H. [Institute de Physique Theorique, CEA Saclay, F-91191 Gif-sur-Yvette (France); Institut Henri Poincare, 11 rue Pierre et Marie Curie, 75231 Paris (France); Physics Department, USC, Los Angeles, CA 90089-0484 (United States)

2012-09-11

We discuss conformal field theories (CFTs) in rectangular geometries, and develop a formalism that involves a conformal boundary state for the 1+1d open system. We focus on the case of homogeneous boundary conditions (no insertion of a boundary condition changing operator), for which we derive an explicit expression of the associated boundary state, valid for any arbitrary CFT. We check the validity of our solution, comparing it with known results for partition functions, numerical simulations of lattice discretizations, and coherent state expressions for free theories.

Dimension of non-conformal repellers: a survey

International Nuclear Information System (INIS)

Chen, Jianyu; Pesin, Yakov

2010-01-01

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

Prion protein β2-α2 loop conformational landscape.

Science.gov (United States)

Caldarulo, Enrico; Barducci, Alessandro; Wüthrich, Kurt; Parrinello, Michele

2017-09-05

In transmissible spongiform encephalopathies (TSEs), which are lethal neurodegenerative diseases that affect humans and a wide range of other mammalian species, the normal "cellular" prion protein ([Formula: see text]) is transformed into amyloid aggregates representing the "scrapie form" of the protein ([Formula: see text]). Continued research on this system is of keen interest, since new information on the physiological function of [Formula: see text] in healthy organisms is emerging, as well as new data on the mechanism of the transformation of [Formula: see text] to [Formula: see text] In this paper we used two different approaches: a combination of the well-tempered ensemble (WTE) and parallel tempering (PT) schemes and metadynamics (MetaD) to characterize the conformational free-energy surface of [Formula: see text] The focus of the data analysis was on an 11-residue polypeptide segment in mouse [Formula: see text](121-231) that includes the [Formula: see text]2-[Formula: see text]2 loop of residues 167-170, for which a correlation between structure and susceptibility to prion disease has previously been described. This study includes wild-type mouse [Formula: see text] and a variant with the single-residue replacement Y169A. The resulting detailed conformational landscapes complement in an integrative manner the available experimental data on [Formula: see text], providing quantitative insights into the nature of the structural transition-related function of the [Formula: see text]2-[Formula: see text]2 loop.

Rotational Spectroscopy and Conformational Studies of 4-PENTYNENITRILE, 4-PENTENENITRILE, and Glutaronitrile

Science.gov (United States)

Hays, Brian M.; Mehta-Hurt, Deepali; Jawad, Khadija M.; Hernandez-Castillo, Alicia O.; Abeysekera, Chamara; Zhang, Di; Zwier, Timothy S.

2017-06-01

The pure rotational spectra of 4-pentynenitrile, 4-pentenenitrile, and glutaronitrile were acquired using chirped pulse Fouirer transform microwave spectroscopy. 4-pentynenitrile and 4-pentenenitrile are the recombination products of two resonance stabilized radicals, propargyl + cyanomethyl or allyl + cyanomethyl, respectively, and are thus anticipated to be significant among the more complex nitriles in Titan's atmosphere. Indeed, these partially unsaturated alkyl cyanides have been found in laboratory analogs of tholins and are also expected to have interesting photochemistry. The optimized structures of all conformers below predicted energies of 500 \\wn were calculated for each molecule. Both of the conformers, trans and gauche, for 4-pentynenitrile have been identified and assigned. Five conformers were assigned in 4-pentenenitrile. The eclipsed conformers, with respect to the vinyl group, dominate the spectrum but some population was found in the syn conformers including the syn-gauche conformer, calculated to be 324 \\wn above the global minimum. The glutaronitrile spectrum contained only the two conformers below 500 \\wn, with reduced amount of the gauche trans conformer. The assigned spectra and structural assignments will be presented.

The Conformational Landscape of L-Threonine Matrix Isolation Infrared and {AB-INITIO Studies

Science.gov (United States)

Dubey, Pankaj; Mukhopadhyay, Anamika; Viswanathan, K. S.

2017-06-01

Amino acids, containing hydroxy side chains such as L-threonine and tyrosine play an important role in molecular recognition, such as in the docking of propofol, which is a commonly used anaesthetic. A rich conformational landscape of these amino acids makes them interesting candidates in the study of intra and intermolecular interactions. In this work, the conformational landscape of L-threonine was studied, as it can be expected to serve as a basis for understanding structure and functions of polypeptides and other biomolecules. The matrix isolation technique (MI) coupled with a high temperature effusive molecular beam (EMB) nozzle was used to trap conformers of amino acid, which were then characterized using FTIR spectroscopy. The usefulness of MI-EMB-FTIR spectroscopy is that it can trap structures corresponding to the local minima along with the global minimum and hence allows for a better exploration of the potential energy surface. A major challenge in conformational analysis of amino acids using matrix isolation FTIR arises from its non-volatile nature. A home built heating system which was mounted close to the cryotip, was used to evaporate the non-volatile amino acids. Our infrared spectra show that three conformations were trapped in the matrix. Experimental results were supported by {ab-initio calculations performed using the CCSD(T), MP2 and M06-2X methods together with 6-311++G(d,p) and aug/cc-pVDZ basis sets. The side chains of the amino acids appeared to have an influence on the preferential stabilisation of a particular backbone structure of amino acids. Factors such as entropy, anomeric effect and intramolecular H-bonding were also found to play an important role in determining conformal preferences, which will be discussed.

Holographic multiverse and conformal invariance

Energy Technology Data Exchange (ETDEWEB)

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

2009-11-01

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

Holographic multiverse and conformal invariance

International Nuclear Information System (INIS)

Garriga, Jaume; Vilenkin, Alexander

2009-01-01

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

Conformal constraint in canonical quantum gravity

NARCIS (Netherlands)

t Hooft, G.

2010-01-01

Perturbative canonical quantum gravity is considered, when coupled to a renormalizable model for matter fields. It is proposed that the functional integral over the dilaton field should be disentangled from the other integrations over the metric fields. This should generate a conformally invariant

Conformational analysis of glutamic acid: a density functional approach using implicit continuum solvent model.

Science.gov (United States)

Turan, Başak; Selçuki, Cenk

2014-09-01

Amino acids are constituents of proteins and enzymes which take part almost in all metabolic reactions. Glutamic acid, with an ability to form a negatively charged side chain, plays a major role in intra and intermolecular interactions of proteins, peptides, and enzymes. An exhaustive conformational analysis has been performed for all eight possible forms at B3LYP/cc-pVTZ level. All possible neutral, zwitterionic, protonated, and deprotonated forms of glutamic acid structures have been investigated in solution by using polarizable continuum model mimicking water as the solvent. Nine families based on the dihedral angles have been classified for eight glutamic acid forms. The electrostatic effects included in the solvent model usually stabilize the charged forms more. However, the stability of the zwitterionic form has been underestimated due to the lack of hydrogen bonding between the solute and solvent; therefore, it is observed that compact neutral glutamic acid structures are more stable in solution than they are in vacuum. Our calculations have shown that among all eight possible forms, some are not stable in solution and are immediately converted to other more stable forms. Comparison of isoelectronic glutamic acid forms indicated that one of the structures among possible zwitterionic and anionic forms may dominate over the other possible forms. Additional investigations using explicit solvent models are necessary to determine the stability of charged forms of glutamic acid in solution as our results clearly indicate that hydrogen bonding and its type have a major role in the structure and energy of conformers.

Comments on conformal Killing vector fields and quantum field theory

International Nuclear Information System (INIS)

Brown, M.R.; Ottewill, A.C.; Siklos, S.T.C.

1982-01-01

We give a comprehensive analysis of those vacuums for flat and conformally flat space-times which can be defined by timelike, hypersurface-orthogonal, conformal Killing vector fields. We obtain formulas for the difference in stress-energy density between any two such states and display the correspondence with the renormalized stress tensors. A brief discussion is given of the relevance of these results to quantum-mechanical measurements made by noninertial observers moving through flat space

Regular and conformal regular cores for static and rotating solutions

Energy Technology Data Exchange (ETDEWEB)

Azreg-Aïnou, Mustapha

2014-03-07

Using a new metric for generating rotating solutions, we derive in a general fashion the solution of an imperfect fluid and that of its conformal homolog. We discuss the conditions that the stress–energy tensors and invariant scalars be regular. On classical physical grounds, it is stressed that conformal fluids used as cores for static or rotating solutions are exempt from any malicious behavior in that they are finite and defined everywhere.

Regular and conformal regular cores for static and rotating solutions

International Nuclear Information System (INIS)

Azreg-Aïnou, Mustapha

2014-01-01

Using a new metric for generating rotating solutions, we derive in a general fashion the solution of an imperfect fluid and that of its conformal homolog. We discuss the conditions that the stress–energy tensors and invariant scalars be regular. On classical physical grounds, it is stressed that conformal fluids used as cores for static or rotating solutions are exempt from any malicious behavior in that they are finite and defined everywhere.

Conformal symmetry and string theories

International Nuclear Information System (INIS)

Kumar, A.

1987-01-01

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

Conformational analysis of the chemical shifts for molecules containing diastereotopic methylene protons

Science.gov (United States)

Borowski, Piotr

2012-01-01

Quantum chemistry SCF/GIAO calculations were carried out on a set of compounds containing diastereotopic protons. Five molecules, including recently synthesized 1,3-di(2,3-epoxypropoxy)benzene, containing the chiral or pro-chiral center and the neighboring methylene group, were chosen. The rotational averages (i.e. normalized averages with respect to the rotation about the torsional angle τ with the exponential energy weight at temperature T) calculated individually for each of the methylene protons in 1,3-di(2,3-epoxypropoxy)benzene differ by ca. 0.6 ppm, which is significantly less than the value calculated for the lowest energy conformer. This value turned out to be low enough to guarantee the proper ordering of theoretical chemical shifts, supporting the interpretation of the 1H NMR spectrum of this important compound. The rotational averages of chemical shifts for methylene protons for a given type of conformer are shown to be essentially equal to the Boltzmann averages (here, the population-weighted averages for the individual conformers representing minima on the E( τ) cross-section). The calculated Boltzmann averages in the representative conformational space may exhibit completely different ordering as compared to the chemical shifts calculated for the lowest-energy conformer. This is especially true in the case of molecules, for which no significant steric effects are present. In this case, only Boltzmann averages account for the experimental pattern of proton signals. In addition, better overall agreement with experiment (lower value of the root-mean-square deviation between calculated and measured chemical shifts) is typically obtained when Boltzmann averages are used.

Rényi entropy and conformal defects

International Nuclear Information System (INIS)

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

2016-01-01

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