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Sample records for noncommuting complex structures

  1. Noncommutative complex Grosse-Wulkenhaar model

    SciTech Connect

    Hounkonnou, Mahouton Norbert; Samary, Dine Ousmane

    2008-11-18

    This paper stands for an application of the noncommutative (NC) Noether theorem, given in our previous work [AIP Proc 956(2007) 55-60], for the NC complex Grosse-Wulkenhaar model. It provides with an extension of a recent work [Physics Letters B 653(2007) 343-345]. The local conservation of energy-momentum tensors (EMTs) is recovered using improvement procedures based on Moyal algebraic techniques. Broken dilatation symmetry is discussed. NC gauge currents are also explicitly computed.

  2. Noncommutative Biology: Sequential Regulation of Complex Networks

    PubMed Central

    Letsou, William; Cai, Long

    2016-01-01

    Single-cell variability in gene expression is important for generating distinct cell types, but it is unclear how cells use the same set of regulatory molecules to specifically control similarly regulated genes. While combinatorial binding of transcription factors at promoters has been proposed as a solution for cell-type specific gene expression, we found that such models resulted in substantial information bottlenecks. We sought to understand the consequences of adopting sequential logic wherein the time-ordering of factors informs the final outcome. We showed that with noncommutative control, it is possible to independently control targets that would otherwise be activated simultaneously using combinatorial logic. Consequently, sequential logic overcomes the information bottleneck inherent in complex networks. We derived scaling laws for two noncommutative models of regulation, motivated by phosphorylation/neural networks and chromosome folding, respectively, and showed that they scale super-exponentially in the number of regulators. We also showed that specificity in control is robust to the loss of a regulator. Lastly, we connected these theoretical results to real biological networks that demonstrate specificity in the context of promiscuity. These results show that achieving a desired outcome often necessitates roundabout steps. PMID:27560383

  3. Complex analysis methods in noncommutative probability

    NASA Astrophysics Data System (ADS)

    Teodor Belinschi, Serban

    2006-02-01

    In this thesis we study convolutions that arise from noncommutative probability theory. We prove several regularity results for free convolutions, and for measures in partially defined one-parameter free convolution semigroups. We discuss connections between Boolean and free convolutions and, in the last chapter, we prove that any infinitely divisible probability measure with respect to monotonic additive or multiplicative convolution belongs to a one-parameter semigroup with respect to the corresponding convolution. Earlier versions of some of the results in this thesis have already been published, while some others have been submitted for publication. We have preserved almost entirely the specific format for PhD theses required by Indiana University. This adds several unnecessary pages to the document, but we wanted to preserve the specificity of the document as a PhD thesis at Indiana University.

  4. Groenewold-Moyal product, α*-cohomology, and classification of translation-invariant non-commutative structures

    SciTech Connect

    Varshovi, Amir Abbass

    2013-07-15

    The theory of α*-cohomology is studied thoroughly and it is shown that in each cohomology class there exists a unique 2-cocycle, the harmonic form, which generates a particular Groenewold-Moyal star product. This leads to an algebraic classification of translation-invariant non-commutative structures and shows that any general translation-invariant non-commutative quantum field theory is physically equivalent to a Groenewold-Moyal non-commutative quantum field theory.

  5. Exact solutions with noncommutative symmetries in Einstein and gauge gravity

    NASA Astrophysics Data System (ADS)

    Vacaru, Sergiu I.

    2005-04-01

    We present new classes of exact solutions with noncommutative symmetries constructed in vacuum Einstein gravity (in general, with nonzero cosmological constant), five-dimensional (5D) gravity and (anti) de Sitter gauge gravity. Such solutions are generated by anholonomic frame transforms and parametrized by generic off-diagonal metrics. For certain particular cases, the new classes of metrics have explicit limits with Killing symmetries but, in general, they may be characterized by certain anholonomic noncommutative matrix geometries. We argue that different classes of noncommutative symmetries can be induced by exact solutions of the field equations in commutative gravity modeled by a corresponding moving real and complex frame geometry. We analyze two classes of black ellipsoid solutions (in the vacuum case and with cosmological constant) in four-dimensional gravity and construct the analytic extensions of metrics for certain classes of associated frames with complex valued coefficients. The third class of solutions describes 5D wormholes which can be extended to complex metrics in complex gravity models defined by noncommutative geometric structures. The anholonomic noncommutative symmetries of such objects are analyzed. We also present a descriptive account how the Einstein gravity can be related to gauge models of gravity and their noncommutative extensions and discuss such constructions in relation to the Seiberg-Witten map for the gauge gravity. Finally, we consider a formalism of vielbeins deformations subjected to noncommutative symmetries in order to generate solutions for noncommutative gravity models with Moyal (star) product.

  6. Branes as Stable Holomorphic Line Bundles On the Non-Commutative Torus

    NASA Astrophysics Data System (ADS)

    Grange, Pascal

    2004-10-01

    It was suggested by A. Kapustin that turning on a B-field, and allowing some discrepancy between the left and and right-moving complex structures, must induce an identification of B-branes with holomorphic line bundles on a non-commutative complex torus. The stability condition for the branes is written as a topological identity of non-commutative gauge theory. This identifies stable B-branes with previously proposed non-commutative instanton equations. Consistency of the non-commutative description with complex geometry is examined, using the non-linearities of the Seiberg-Witten map.

  7. Møller's Energy-Momentum Complex for a Spacetime Geometry on a Noncommutative Curved D3-Brane

    NASA Astrophysics Data System (ADS)

    Radinschi, I.; Grammenos, T.

    2008-05-01

    Møller’s energy-momentum complex is employed in order to determine the energy and momentum distributions for a spacetime described by a “generalized Schwarzschild” geometry in (3+1)-dimensions on a noncommutative curved D3-brane in an effective, open bosonic string theory. The geometry considered is obtained by an effective theory of gravity coupled with a nonlinear electromagnetic field and depends only on the generalized (effective) mass and charge which incorporate corrections of first order in the noncommutativity parameter.

  8. Resonant detectors of gravitational wave as a possible probe of the noncommutative structure of space

    NASA Astrophysics Data System (ADS)

    Saha, Anirban; Gangopadhyay, Sunandan

    2016-10-01

    We report the plausibility of using quantum mechanical transitions, induced by the combined effect of gravitational waves (GWs) and noncommutative (NC) structure of space, among the states of a 2-dimensional harmonic oscillator, to probe the spatial NC geometry. The phonon modes excited by the passing GW within the resonant bar-detector or spherical detectors are formally identical to forced harmonic oscillator and they represent a length variation of roughly the same order of magnitude as the characteristic length-scale of spatial noncommutativity estimated from the phenomenological upper bound of the NC parameter. This motivates our present work. We employ various GW wave-forms that are typically expected from possible astronomical sources. We find that the transition probablities are quite sensitive to the nature of polarization of the GW. We also elaborate on the particular type of sources of GW, radiation from which one can induce such transitions. We speculate that this can be used as an effective probe of the spatial noncommutative structure when the quantum limit of sensitivity is achieved/surpassed in resonant bar/spherical detectors of GWs in the near future.

  9. Noncommutative topological theories of gravity

    NASA Astrophysics Data System (ADS)

    García-Compeán, H.; Obregón, O.; Ramírez, C.; Sabido, M.

    2003-08-01

    The possibility of noncommutative topological gravity arising in the same manner as Yang-Mills theory is explored. We use the Seiberg-Witten map to construct such a theory based on a SL(2,C) complex connection, from which the Euler characteristic and the signature invariant are obtained. Finally, we speculate on the description of noncommutative gravitational instantons, as well as noncommutative local gravitational anomalies.

  10. Physics on noncommutative spacetimes

    NASA Astrophysics Data System (ADS)

    Padmanabhan, Pramod

    The structure of spacetime at the Planck scale remains a mystery to this date with a lot of insightful attempts to unravel this puzzle. One such attempt is the proposition of a 'pointless' structure for spacetime at this scale. This is done by studying the geometry of the spacetime through a noncommutative algebra of functions defined on it. We call such spacetimes 'noncommutative spacetimes'. This dissertation probes physics on several such spacetimes. These include compact noncommutative spaces called fuzzy spaces and noncompact spacetimes. The compact examples we look at are the fuzzy sphere and the fuzzy Higg's manifold. The noncompact spacetimes we study are the Groenewold-Moyal plane and the Bcn⃗ plane. A broad range of physical effects are studied on these exotic spacetimes. We study spin systems on the fuzzy sphere. The construction of Dirac and chirality operators for an arbitrary spin j is studied on both S2F and S2 in detail. We compute the spectrums of the spin 1 and spin 32 Dirac operators on S2F . These systems have novel thermodynamical properties which have no higher dimensional analogs, making them interesting models. The fuzzy Higg's manifold is found to exhibit topology change, an important property for any theory attempting to quantize gravity. We study how this change occurs in the classical setting and how quantizing this manifold smoothens the classical conical singularity. We also show the construction of the star product on this manifold using coherent states on the noncommutative algebra describing this noncommutative space. On the Moyal plane we develop the LSZ formulation of scalar quantum field theory. We compute scattering amplitudes and remark on renormalization of this theory. We show that the LSZ formalism is equivalent to the interaction representation formalism for computing scattering amplitudes on the Moyal plane. This result is true for on-shell Green's functions and fails to hold for off-shell Green's functions. With the

  11. Morita equivalence of noncommutative supertori

    NASA Astrophysics Data System (ADS)

    Chang-Young, Ee; Kim, Hoil; Nakajima, Hiroaki

    2010-06-01

    In this paper we study the extension of Morita equivalence of noncommutative tori to the supersymmetric case. The structure of the symmetry group yielding Morita equivalence appears to be intact but its parameter field becomes supersymmetrized having both body and soul parts. Our result is mainly in the two dimensional case in which noncommutative supertori have been constructed recently: The group SO(2,2,VZ0), where VZ0 denotes Grassmann even number whose body part belongs to Z, yields Morita equivalent noncommutative supertori in two dimensions.

  12. Morita equivalence of noncommutative supertori

    SciTech Connect

    Chang-Young, Ee; Kim, Hoil; Nakajima, Hiroaki

    2010-06-15

    In this paper we study the extension of Morita equivalence of noncommutative tori to the supersymmetric case. The structure of the symmetry group yielding Morita equivalence appears to be intact but its parameter field becomes supersymmetrized having both body and soul parts. Our result is mainly in the two dimensional case in which noncommutative supertori have been constructed recently: The group SO(2,2,V{sub Z}{sup 0}), where V{sub Z}{sup 0} denotes Grassmann even number whose body part belongs to Z, yields Morita equivalent noncommutative supertori in two dimensions.

  13. The Geometry of Noncommutative Space-Time

    NASA Astrophysics Data System (ADS)

    Mendes, R. Vilela

    2016-10-01

    Stabilization, by deformation, of the Poincaré-Heisenberg algebra requires both the introduction of a fundamental lentgh and the noncommutativity of translations which is associated to the gravitational field. The noncommutative geometry structure that follows from the deformed algebra is studied both for the non-commutative tangent space and the full space with gravity. The contact points of this approach with the work of David Finkelstein are emphasized.

  14. Noncommutativity and the Friedmann Equations

    SciTech Connect

    Sabido, M.; Socorro, J.; Guzman, W.

    2010-07-12

    In this paper we study noncommutative scalar field cosmology, we find the noncommutative Friedmann equations as well as the noncommutative Klein-Gordon equation, interestingly the noncommutative contributions are only present up to second order in the noncommutitive parameter.

  15. Mexican contributions to Noncommutative Theories

    SciTech Connect

    Vergara, J. David; Garcia-Compean, H.

    2006-09-25

    In this paper we summarize the Mexican contributions to the subject of Noncommutative theories. These contributions span several areas: Quantum Groups, Noncommutative Field Theories, Hopf algebra of renormalization, Deformation Quantization, Noncommutative Gravity, and Noncommutative Quantum Mechanics.

  16. Arik-Coon q-oscillator cat states on the noncommutative complex plane ℂq‑1 and their nonclassical properties

    NASA Astrophysics Data System (ADS)

    Fakhri, H.; Sayyah-Fard, M.

    The normalized even and odd q-cat states corresponding to Arik-Coon q-oscillator on the noncommutative complex plane ℂq‑1 are constructed as the eigenstates of the lowering operator of a q-deformed su(1, 1) algebra with the left eigenvalues. We present the appropriate noncommutative measures in order to realize the resolution of the identity condition by the even and odd q-cat states. Then, we obtain the q-Bargmann-Fock realizations of the Fock representation of the q-deformed su(1, 1) algebra as well as the inner products of standard states in the q-Bargmann representations of the even and odd subspaces. Also, the Euler’s formula of the q-factorial and the Gaussian integrals based on the noncommutative q-integration are obtained. Violation of the uncertainty relation, photon antibunching effect and sub-Poissonian photon statistics by the even and odd q-cat states are considered in the cases 0 < q < 1 and q > 1.

  17. Dirac equation on coordinate dependent noncommutative space-time

    NASA Astrophysics Data System (ADS)

    Kupriyanov, V. G.

    2014-05-01

    In this paper we discuss classical aspects of spinor field theory on the coordinate dependent noncommutative space-time. The noncommutative Dirac equation describing spinning particle in an external vector field and the corresponding action principle are proposed. The specific choice of a star product allows us to derive a conserved noncommutative probability current and to obtain the energy-momentum tensor for free noncommutative spinor field. Finally, we consider a free noncommutative Dirac fermion and show that if the Poisson structure is Lorentz-covariant, the standard energy-momentum dispersion relation remains valid.

  18. A Riemann-Roch theorem for the noncommutative two torus

    NASA Astrophysics Data System (ADS)

    Khalkhali, Masoud; Moatadelro, Ali

    2014-12-01

    We prove the analogue of the Riemann-Roch formula for the noncommutative two torus Aθ = C(Tθ2)equipped with an arbitrary translation invariant complex structure and a Weyl factor represented by a positive element k ∈C∞(Tθ2). We consider a topologically trivial line bundle equipped with a general holomorphic structure and the corresponding twisted Dolbeault Laplacians. We define a spectral triple (Aθ , H , D) that encodes the twisted Dolbeault complex of Aθ and whose index gives the left hand side of the Riemann-Roch formula. Using Connes' pseudodifferential calculus and heat equation techniques, we explicitly compute the b2 terms of the asymptotic expansion of Tr(e-tD2) . We find that the curvature term on the right hand side of the Riemann-Roch formula coincides with the scalar curvature of the noncommutative torus recently defined and computed in Connes and Moscovici (2014) and independently computed in Fathizadeh and Khalkhali (2014).

  19. Noncommutative scalar fields from symplectic deformation

    SciTech Connect

    Daoud, M.; Hamama, A.

    2008-02-15

    This paper is concerned with the quantum theory of noncommutative scalar fields in two dimensional space-time. It is shown that the noncommutativity originates from the the deformation of symplectic structures. The quantization is performed and the modes expansions of the fields, in the presence of an electromagnetic background, are derived. The Hamiltonian of the theory is given and the degeneracies lifting, induced by the deformation, is also discussed.

  20. Noncommutative Valuation of Options

    NASA Astrophysics Data System (ADS)

    Herscovich, Estanislao

    2016-12-01

    The aim of this note is to show that the classical results in finance theory for pricing of derivatives, given by making use of the replication principle, can be extended to the noncommutative world. We believe that this could be of interest in quantum probability. The main result called the First fundamental theorem of asset pricing, states that a noncommutative stock market admits no-arbitrage if and only if it admits a noncommutative equivalent martingale probability.

  1. Noncommutative geometry of Zitterbewegung

    NASA Astrophysics Data System (ADS)

    Eckstein, Michał; Franco, Nicolas; Miller, Tomasz

    2017-03-01

    Drawing from the advanced mathematics of noncommutative geometry, we model a "classical" Dirac fermion propagating in a curved spacetime. We demonstrate that the inherent causal structure of the model encodes the possibility of Zitterbewegung—the "trembling motion" of the fermion. We recover the well-known frequency of Zitterbewegung as the highest possible speed of change in the fermion's "internal space." Furthermore, we show that the bound does not change in the presence of an external electromagnetic field and derive its explicit analogue when the mass parameter is promoted to a Yukawa field. We explain the universal character of the model and discuss a table-top experiment in the domain of quantum simulation to test its predictions.

  2. Noncommutative integrable systems and quasideterminants

    SciTech Connect

    Hamanaka, Masashi

    2010-03-08

    We discuss extension of soliton theories and integrable systems into noncommutative spaces. In the framework of noncommutative integrable hierarchy, we give infinite conserved quantities and exact soliton solutions for many noncommutative integrable equations, which are represented in terms of Strachan's products and quasi-determinants, respectively. We also present a relation to an noncommutative anti-self-dual Yang-Mills equation, and make comments on how 'integrability' should be considered in noncommutative spaces.

  3. The Bell states in noncommutative algebraic geometry

    NASA Astrophysics Data System (ADS)

    Beil, Charlie

    2014-10-01

    We introduce new mathematical aspects of the Bell states using matrix factorizations, non-noetherian singularities, and noncommutative blowups. A matrix factorization of a polynomial p consists of two matrices ϕ1, ϕ2 such that ϕ1ϕ2 = ϕ2ϕ1 = p id. Using this notion, we show how the Bell states emerge from the separable product of two mixtures, by defining pure states over complex matrices rather than just the complex numbers. We then show in an idealized algebraic setting that pure states are supported on non-noetherian singularities. Moreover, we find that the collapse of a Bell state is intimately related to the representation theory of the noncommutative blowup along its singular support. This presents an exchange in geometry: the nonlocal commutative spacetime of the entangled state emerges from an underlying local noncommutative spacetime.

  4. Noncommutative black hole thermodynamics

    SciTech Connect

    Banerjee, Rabin; Majhi, Bibhas Ranjan; Samanta, Saurav

    2008-06-15

    We give a general derivation, for any static spherically symmetric metric, of the relation T{sub h}=(K/2{pi}) connecting the black hole temperature (T{sub h}) with the surface gravity (K), following the tunneling interpretation of Hawking radiation. This derivation is valid even beyond the semi-classical regime, i.e. when quantum effects are not negligible. The formalism is then applied to a spherically symmetric, stationary noncommutative Schwarzschild space-time. The effects of backreaction are also included. For such a black hole the Hawking temperature is computed in a closed form. A graphical analysis reveals interesting features regarding the variation of the Hawking temperature (including corrections due to noncommutativity and backreaction) with the small radius of the black hole. The entropy and tunneling rate valid for the leading order in the noncommutative parameter are calculated. We also show that the noncommutative Bekenstein-Hawking area law has the same functional form as the usual one.

  5. Covariant Noncommutative Field Theory

    SciTech Connect

    Estrada-Jimenez, S.; Garcia-Compean, H.; Obregon, O.; Ramirez, C.

    2008-07-02

    The covariant approach to noncommutative field and gauge theories is revisited. In the process the formalism is applied to field theories invariant under diffeomorphisms. Local differentiable forms are defined in this context. The lagrangian and hamiltonian formalism is consistently introduced.

  6. Noncommutativity in near horizon symmetries in gravity

    NASA Astrophysics Data System (ADS)

    Majhi, Bibhas Ranjan

    2017-02-01

    We have a new observation that near horizon symmetry generators, corresponding to diffeomorphisms which leave the horizon structure invariant, satisfy noncommutative Heisenberg algebra. The results are valid for any null surfaces (which have Rindler structure in the near null surface limit) and in any spacetime dimensions. Using the Sugawara construction technique the central charge is identified. It is shown that the horizon entropy is consistent with the standard form of the Cardy formula. Therefore we feel that the noncommutative algebra might lead to quantum mechanics of horizon and also can probe into the microscopic description of entropy.

  7. Noncommutative potential theory: A survey

    NASA Astrophysics Data System (ADS)

    Cipriani, Fabio

    2016-07-01

    The aim of these notes is to provide an introduction to Noncommutative Potential Theory as given at I.N.D.A.M.-C.N.R.S. ;Noncommutative Geometry and Applications; Lectures, Villa Mondragone-Frascati June 2014.

  8. Towards Noncommutative Supersymmetric Quantum Cosmology

    SciTech Connect

    Sabido, M.; Socorro, J.; Guzman, W.

    2010-12-07

    In this work a construction of supersymmetric noncommutative cosmology is presented. We start with a ''noncommutative'' deformation of the minisuperspace variables, and by using the time reparametrization invariance of the noncommutative bosonic model we proceed to construct a super field description of the model.

  9. Noncommuting spherical coordinates

    SciTech Connect

    Bander, Myron

    2004-10-15

    Restricting the states of a charged particle to the lowest Landau level introduces a noncommutativity between Cartesian coordinate operators. This idea is extended to the motion of a charged particle on a sphere in the presence of a magnetic monopole. Restricting the dynamics to the lowest energy level results in noncommutativity for angular variables and to a definition of a noncommuting spherical product. The values of the commutators of various angular variables are not arbitrary but are restricted by the discrete magnitude of the magnetic monopole charge. An algebra, isomorphic to angular momentum, appears. This algebra is used to define a spherical star product. Solutions are obtained for dynamics in the presence of additional angular dependent potentials.

  10. Noncommutative spacetime realized in Ad Sn+1 space: Nonlocal field theory out of noncommutative spacetime

    NASA Astrophysics Data System (ADS)

    Naka, S.; Toyoda, H.; Takanashi, T.; Umezawa, E.

    2014-04-01

    In kappa -Minkowski spacetime, the coordinates are Lie algebraic elements such that time and space coordinates do not commute, whereas space coordinates commute with each other. The noncommutativity is proportional to a Planck-length-scale constant kappa ^{-1}, which is a universal constant other than the velocity of light, under the kappa -Poincaré transformation. In this sense, the spacetime has a structure called "doubly special relativity." Such a noncommutative structure is known to be realized by SO(1,4) generators in 4-dimensional de Sitter space. In this paper, we try to construct a noncommutative spacetime having a commutative n-dimensional Minkowski spacetime based on AdS_{n+1} space with SO(2,n) symmetry. We also study an invariant wave equation corresponding to the first Casimir invariant of this symmetry as a nonlocal field equation expected to yield finite loop amplitudes.

  11. An Asymmetric Noncommutative Torus

    NASA Astrophysics Data System (ADS)

    Dąbrowski, Ludwik; Sitarz, Andrzej

    2015-09-01

    We introduce a family of spectral triples that describe the curved noncommutative two-torus. The relevant family of new Dirac operators is given by rescaling one of two terms in the flat Dirac operator. We compute the dressed scalar curvature and show that the Gauss-Bonnet theorem holds (which is not covered by the general result of Connes and Moscovici).

  12. Noncommutative geometry and arithmetics

    NASA Astrophysics Data System (ADS)

    Almeida, P.

    2009-09-01

    We intend to illustrate how the methods of noncommutative geometry are currently used to tackle problems in class field theory. Noncommutative geometry enables one to think geometrically in situations in which the classical notion of space formed of points is no longer adequate, and thus a “noncommutative space” is needed; a full account of this approach is given in [3] by its main contributor, Alain Connes. The class field theory, i.e., number theory within the realm of Galois theory, is undoubtedly one of the main achievements in arithmetics, leading to an important algebraic machinery; for a modern overview, see [23]. The relationship between noncommutative geometry and number theory is one of the many themes treated in [22, 7-9, 11], a small part of which we will try to put in a more down-to-earth perspective, illustrating through an example what should be called an “application of physics to mathematics,” and our only purpose is to introduce nonspecialists to this beautiful area.

  13. Noncommutative Riemannian geometry on graphs

    NASA Astrophysics Data System (ADS)

    Majid, Shahn

    2013-07-01

    We show that arising out of noncommutative geometry is a natural family of edge Laplacians on the edges of a graph. The family includes a canonical edge Laplacian associated to the graph, extending the usual graph Laplacian on vertices, and we find its spectrum. We show that for a connected graph its eigenvalues are strictly positive aside from one mandatory zero mode, and include all the vertex degrees. Our edge Laplacian is not the graph Laplacian on the line graph but rather it arises as the noncommutative Laplace-Beltrami operator on differential 1-forms, where we use the language of differential algebras to functorially interpret a graph as providing a 'finite manifold structure' on the set of vertices. We equip any graph with a canonical 'Euclidean metric' and a canonical bimodule connection, and in the case of a Cayley graph we construct a metric compatible connection for the Euclidean metric. We make use of results on bimodule connections on inner calculi on algebras, which we prove, including a general relation between zero curvature and the braid relations.

  14. Noncommutativity and scalar field cosmology

    SciTech Connect

    Guzman, W.; Sabido, M.; Socorro, J.

    2007-10-15

    In this work we extend and apply a previous proposal to study noncommutative cosmology to the Friedmann-Robertson-Walker cosmological background coupled to a scalar field. This is done in classical and quantum scenarios. In both cases noncommutativity is introduced in the gravitational field as well as in the scalar field through a deformation of minisuperspace, and we are able to find exact solutions. Finally, the effects of noncommutativity on the classical evolution are analyzed.

  15. Towards noncommutative quantum black holes

    SciTech Connect

    Lopez-Dominguez, J. C.; Obregon, O.; Sabido, M.; Ramirez, C.

    2006-10-15

    In this paper we study noncommutative black holes. We use a diffeomorphism between the Schwarzschild black hole and the Kantowski-Sachs cosmological model, which is generalized to noncommutative minisuperspace. Through the use of the Feynman-Hibbs procedure we are able to study the thermodynamics of the black hole, in particular, we calculate the Hawking's temperature and entropy for the noncommutative Schwarzschild black hole.

  16. Solving the Noncommutative Batalin-Vilkovisky Equation

    NASA Astrophysics Data System (ADS)

    Barannikov, Serguei

    2013-06-01

    Given an odd symmetry acting on an associative algebra, I show that the summation over arbitrary ribbon graphs gives the construction of the solutions to the noncommutative Batalin-Vilkovisky equation, introduced in (Barannikov in IMRN, rnm075, 2007), and to the equivariant version of this equation. This generalizes the known construction of A ∞-algebra via summation over ribbon trees. I give also the generalizations to other types of algebras and graph complexes, including the stable ribbon graph complex. These solutions to the noncommutative Batalin-Vilkovisky equation and to its equivariant counterpart, provide naturally the supersymmetric matrix action functionals, which are the gl( N)-equivariantly closed differential forms on the matrix spaces, as in (Barannikov in Comptes Rendus Mathematique vol 348, pp. 359-362.

  17. On non-commutative geodesic motion

    NASA Astrophysics Data System (ADS)

    Ulhoa, S. C.; Amorim, R. G. G.; Santos, A. F.

    2014-07-01

    In this work we study the geodesic motion on a noncommutative space-time. As a result we find a non-commutative geodesic equation and then we derive corrections of the deviation angle per revolution in terms of the non-commutative parameter when we specify the problem of Mercury's perihelion. In this way, we estimate the noncommutative parameter based in experimental data.

  18. The Gribov problem in noncommutative QED

    NASA Astrophysics Data System (ADS)

    Canfora, Fabrizio; Kurkov, Maxim A.; Rosa, Luigi; Vitale, Patrizia

    2016-01-01

    It is shown that in the noncommutative version of QED (NCQED) Gribov copies induced by the noncommutativity of space-time appear in the Landau gauge. This is a genuine effect of noncommutative geometry which disappears when the noncommutative parameter vanishes.

  19. Noncommutative Quantum Scalar Field Cosmology

    SciTech Connect

    Diaz Barron, L. R.; Lopez-Dominguez, J. C.; Sabido, M.; Yee, C.

    2010-07-12

    In this work we study noncommutative Friedmann-Robertson-Walker (FRW) cosmology coupled to a scalar field endowed with an exponential potential. The quantum scenario is analyzed in the Bohmian formalism of quantum trajectories to investigate the effects of noncommutativity in the evolution of the universe.

  20. A non-commutative framework for topological insulators

    NASA Astrophysics Data System (ADS)

    Bourne, C.; Carey, A. L.; Rennie, A.

    2016-04-01

    We study topological insulators, regarded as physical systems giving rise to topological invariants determined by symmetries both linear and anti-linear. Our perspective is that of non-commutative index theory of operator algebras. In particular, we formulate the index problems using Kasparov theory, both complex and real. We show that the periodic table of topological insulators and superconductors can be realized as a real or complex index pairing of a Kasparov module capturing internal symmetries of the Hamiltonian with a spectral triple encoding the geometry of the sample’s (possibly non-commutative) Brillouin zone.

  1. A remark on polar noncommutativity

    NASA Astrophysics Data System (ADS)

    Iskauskas, Andrew

    2015-06-01

    Noncommutative space has been found to be of use in a number of different contexts. In particular, one may use noncommutative spacetime to generate quantised gravity theories. Via an identification between the Moyal ⋆-product on function space and commutators on a Hilbert space, one may use the Seiberg-Witten map to generate corrections to such gravity theories. However, care must be taken with the derivation of commutation relations. We examine conditions for the validity of such an approach, and motivate the correct form for polar noncommutativity in R2. Such an approach lends itself readily to extension to more complicated spacetime parametrisations.

  2. Phase space quantization, noncommutativity, and the gravitational field

    NASA Astrophysics Data System (ADS)

    Chatzistavrakidis, Athanasios

    2014-07-01

    In this paper we study the structure of the phase space in noncommutative geometry in the presence of a nontrivial frame. Our basic assumptions are that the underlying space is a symplectic and parallelizable manifold. Furthermore, we assume the validity of the Leibniz rule and the Jacobi identities. We consider noncommutative spaces due to the quantization of the symplectic structure and determine the momentum operators that guarantee a set of canonical commutation relations, appropriately extended to include the nontrivial frame. We stress the important role of left vs right acting operators and of symplectic duality. This enables us to write down the form of the full phase space algebra on these noncommutative spaces, both in the noncompact and in the compact case. We test our results against the class of four-dimensional and six-dimensional symplectic nilmanifolds, thus presenting a large set of nontrivial examples that realizes the general formalism.

  3. Non-Commutative Martingale Inequalities

    NASA Astrophysics Data System (ADS)

    Pisier, Gilles; Xu, Quanhua

    We prove the analogue of the classical Burkholder-Gundy inequalites for non-commutative martingales. As applications we give a characterization for an Ito-Clifford integral to be an Lp-martingale via its integrand, and then extend the Ito-Clifford integral theory in L2, developed by Barnett, Streater and Wilde, to Lp for all 1non-commutative analogue of the classical Fefferman duality between $H1 and BMO.

  4. Principal Fibrations from Noncommutative Spheres

    NASA Astrophysics Data System (ADS)

    Landi, Giovanni; Suijlekom, Walter Van

    2005-11-01

    We construct noncommutative principal fibrations Sθ7→Sθ4 which are deformations of the classical SU(2) Hopf fibration over the four sphere. We realize the noncommutative vector bundles associated to the irreducible representations of SU(2) as modules of coequivariant maps and construct corresponding projections. The index of Dirac operators with coefficients in the associated bundles is computed with the Connes-Moscovici local index formula. "The algebra inclusion is an example of a not-trivial quantum principal bundle."

  5. Two roads to noncommutative causality

    NASA Astrophysics Data System (ADS)

    Besnard, Fabien

    2015-08-01

    We review the physical motivations and the mathematical results obtained so far in the isocone-based approach to noncommutative causality. We also give a briefer account of the alternative framework of Franco and Eckstein which is based on Lorentzian spectral triples. We compare the two theories on the simple example of the product geometry of the Minkowski plane by the finite noncommutative space with algebra M2(C).

  6. Particle phenomenology on noncommutative spacetime

    SciTech Connect

    Joseph, Anosh

    2009-05-01

    We introduce particle phenomenology on the noncommutative spacetime called the Groenewold-Moyal plane. The length scale of spacetime noncommutativity is constrained from the CPT violation measurements in the K{sup 0}-K{sup 0} system and g-2 difference of {mu}{sup +}-{mu}{sup -}. The K{sup 0}-K{sup 0} system provides an upper bound on the length scale of spacetime noncommutativity of the order of 10{sup -32} m, corresponding to a lower energy bound E of the order of E > or approx. 10{sup 16} GeV. The g-2 difference of {mu}{sup +}-{mu}{sup -} constrains the noncommutativity length scale to be of the order of 10{sup -20} m, corresponding to a lower energy bound E of the order of E > or approx. 10{sup 3} GeV. We also present the phenomenology of the electromagnetic interaction of electrons and nucleons at the tree level on the noncommutative spacetime. We show that the distributions of charge and magnetization of nucleons are affected by spacetime noncommutativity. The analytic properties of electromagnetic form factors are also changed and it may give rise to interesting experimental signals.

  7. Complex DNA structures and structures of DNA complexes

    SciTech Connect

    Chazin, W.J.; Carlstroem, G.; Shiow-Meei Chen; Miick, S.; Gomez-Paloma, L.; Smith, J.; Rydzewski, J.

    1994-12-01

    Complex DNA structures (for example, triplexes, quadruplexes, junctions) and DNA-ligand complexes are more difficult to study by NMR than standard DNA duplexes are because they have high molecular weights, show nonstandard or distorted local conformations, and exhibit large resonance linewidths and severe {sup 1}H spectral overlap. These systems also tend to have limited solubility and may require specialized solution conditions to maintain favorable spectral characteristics, which adds to the spectroscopic difficulties. Furthermore, with more atoms in the system, both assignment and structure calculation become more challenging. In this article, we focus on demonstrating the current status of NMR studies of such systems and the limitations to further progress; we also indicate in what ways isotopic enrichment can be useful.

  8. SHM in complex structural components

    NASA Astrophysics Data System (ADS)

    Croxford, Anthony J.; Wilcox, Paul D.; Courtney, Charles R. P.; Drinkwater, Bruce W.

    2009-03-01

    The use of permanently attached arrays of sensors has made it clear that guided waves can be used for the SHM of structures. The approaches developed have relied on the use of reference signal subtraction to indicate changes to the state of the structure, such as the appearance of damage. The limit of performance of any system is defined by the post subtraction noise. In order to confirm the basic principles at work the majority of this work has been carried out on simple metallic plates. While important to confirm the levels of understanding, this is not sufficient for practical use. This paper looks at the application of SHM techniques in more complex structures, more typical of those any system would be used on in practise. A rib from a BaE 146 aircraft is used to demonstrate the practical difficulties of applying guided wave SHM methods to densely featured structures. A model system comprising a plate with a single stringer is used to demonstrate a method for normalizing signals to give responses directly related to the scattering properties of the change in the system, mitigating the effect of the position of the change, and a method is proposed to generalize the approach to complex systems. Preliminary tests in the region of the stringer are used to identify the experimental challenges to realizing the calibration on complex systems.

  9. Quanta of geometry: noncommutative aspects.

    PubMed

    Chamseddine, Ali H; Connes, Alain; Mukhanov, Viatcheslav

    2015-03-06

    In the construction of spectral manifolds in noncommutative geometry, a higher degree Heisenberg commutation relation involving the Dirac operator and the Feynman slash of real scalar fields naturally appears and implies, by equality with the index formula, the quantization of the volume. We first show that this condition implies that the manifold decomposes into disconnected spheres, which will represent quanta of geometry. We then refine the condition by involving the real structure and two types of geometric quanta, and show that connected spin manifolds with large quantized volume are then obtained as solutions. The two algebras M_{2}(H) and M_{4}(C) are obtained, which are the exact constituents of the standard model. Using the two maps from M_{4} to S^{4} the four-manifold is built out of a very large number of the two kinds of spheres of Planckian volume. We give several physical applications of this scheme such as quantization of the cosmological constant, mimetic dark matter, and area quantization of black holes.

  10. Structural Complexity of DNA Sequence

    PubMed Central

    Liou, Cheng-Yuan; Cheng, Wei-Chen; Tsai, Huai-Ying

    2013-01-01

    In modern bioinformatics, finding an efficient way to allocate sequence fragments with biological functions is an important issue. This paper presents a structural approach based on context-free grammars extracted from original DNA or protein sequences. This approach is radically different from all those statistical methods. Furthermore, this approach is compared with a topological entropy-based method for consistency and difference of the complexity results. PMID:23662161

  11. Asymptotic Analysis of the Ponzano-Regge Model with Non-Commutative Metric Boundary Data

    NASA Astrophysics Data System (ADS)

    Oriti, Daniele; Raasakka, Matti

    2014-06-01

    We apply the non-commutative Fourier transform for Lie groups to formulate the non-commutative metric representation of the Ponzano-Regge spin foam model for 3d quantum gravity. The non-commutative representation allows to express the amplitudes of the model as a first order phase space path integral, whose properties we consider. In particular, we study the asymptotic behavior of the path integral in the semi-classical limit. First, we compare the stationary phase equations in the classical limit for three different non-commutative structures corresponding to the symmetric, Duflo and Freidel-Livine-Majid quantization maps. We find that in order to unambiguously recover discrete geometric constraints for non-commutative metric boundary data through the stationary phase method, the deformation structure of the phase space must be accounted for in the variational calculus. When this is understood, our results demonstrate that the non-commutative metric representation facilitates a convenient semi-classical analysis of the Ponzano-Regge model, which yields as the dominant contribution to the amplitude the cosine of the Regge action in agreement with previous studies. We also consider the asymptotics of the SU(2) 6j-symbol using the non-commutative phase space path integral for the Ponzano-Regge model, and explain the connection of our results to the previous asymptotic results in terms of coherent states.

  12. Space-time symmetries of noncommutative spaces

    SciTech Connect

    Calmet, Xavier

    2005-04-15

    We define a noncommutative Lorentz symmetry for canonical noncommutative spaces. The noncommutative vector fields and the derivatives transform under a deformed Lorentz transformation. We show that the star product is invariant under noncommutative Lorentz transformations. We then apply our idea to the case of actions obtained by expanding the star product and the fields taken in the enveloping algebra via the Seiberg-Witten maps and verify that these actions are invariant under these new noncommutative Lorentz transformations. We finally consider general coordinate transformations and show that the metric is undeformed.

  13. Quantum entanglement of fermions-antifermions pair creation modes in noncommutative Bianchi I space-time

    NASA Astrophysics Data System (ADS)

    Ghiti, M. F.; Mebarki, N.; Aissaoui, H.

    2015-08-01

    The noncommutative Bianchi I curved space-time vierbeins and spin connections are derived. Moreover, the corresponding noncommutative Dirac equation as well as its solutions are presented. As an application within the quantum field theory approach using Bogoliubov transformations, the von Neumann fermion-antifermion pair creation quantum entanglement entropy is studied. It is shown that its behavior is strongly dependent on the value of the noncommutativity θ parameter, k⊥-modes frequencies and the structure of the curved space-time. Various discussions of the obtained features are presented.

  14. Noncommutative QFT and renormalization

    NASA Astrophysics Data System (ADS)

    Grosse, H.; Wulkenhaar, R.

    2006-03-01

    It was a great pleasure for me (Harald Grosse) to be invited to talk at the meeting celebrating the 70th birthday of Prof. Julius Wess. I remember various interactions with Julius during the last years: At the time of my studies at Vienna with Walter Thirring, Julius left already Vienna, I learned from his work on effective chiral Lagrangians. Next we met at various conferences and places like CERN (were I worked with Andre Martin, an old friend of Julius), and we all learned from Julius' and Bruno's creation of supersymmetry, next we realized our common interests in noncommutative quantum field theory and did have an intensive exchange. Julius influenced our perturbative approach to gauge field theories were we used the Seiberg-Witten map after his advice. And finally I lively remember the sad days when during my invitation to Vienna Julius did have the serious heart attack. So we are very happy, that you recovered so well, and we wish you all the best for the forthcoming years. Many happy recurrences.

  15. Efficient Analysis of Complex Structures

    NASA Technical Reports Server (NTRS)

    Kapania, Rakesh K.

    2000-01-01

    Last various accomplishments achieved during this project are : (1) A Survey of Neural Network (NN) applications using MATLAB NN Toolbox on structural engineering especially on equivalent continuum models (Appendix A). (2) Application of NN and GAs to simulate and synthesize substructures: 1-D and 2-D beam problems (Appendix B). (3) Development of an equivalent plate-model analysis method (EPA) for static and vibration analysis of general trapezoidal built-up wing structures composed of skins, spars and ribs. Calculation of all sorts of test cases and comparison with measurements or FEA results. (Appendix C). (4) Basic work on using second order sensitivities on simulating wing modal response, discussion of sensitivity evaluation approaches, and some results (Appendix D). (5) Establishing a general methodology of simulating the modal responses by direct application of NN and by sensitivity techniques, in a design space composed of a number of design points. Comparison is made through examples using these two methods (Appendix E). (6) Establishing a general methodology of efficient analysis of complex wing structures by indirect application of NN: the NN-aided Equivalent Plate Analysis. Training of the Neural Networks for this purpose in several cases of design spaces, which can be applicable for actual design of complex wings (Appendix F).

  16. Noncommuting Momenta of Topological Solitons

    NASA Astrophysics Data System (ADS)

    Watanabe, Haruki; Murayama, Hitoshi

    2014-05-01

    We show that momentum operators of a topological soliton may not commute among themselves when the soliton is associated with the second cohomology H2 of the target space. The commutation relation is proportional to the winding number, taking a constant value within each topological sector. The noncommutativity makes it impossible to specify the momentum of a topological soliton, and induces a Magnus force.

  17. Noncommutativity from exact renormalization group dualities

    NASA Astrophysics Data System (ADS)

    Gangopadhyay, Sunandan; Scholtz, Frederik G.

    2014-08-01

    Here we demonstrate, first, the construction of dualities using the exact renormalization group approach and, second, that spatial noncommutativity can emerge as such a duality. This is done in a simple quantum mechanical setting that establishes an exact duality between the commutative and noncommutative quantum Hall systems with harmonic interactions. It is also demonstrated that this link can be understood as a blocking (coarse graining) transformation in time that relates commutative and noncommutative degrees of freedom.

  18. Laser intensity effects in noncommutative QED

    SciTech Connect

    Heinzl, Thomas; Ilderton, Anton; Marklund, Mattias

    2010-03-01

    We discuss a twofold extension of QED assuming the presence of strong external fields provided by an ultraintense laser and noncommutativity of spacetime. While noncommutative effects leave the electron's intensity induced mass shift unchanged, photons change significantly in character: they acquire a quasimomentum that is no longer lightlike. We study the consequences of this combined noncommutative strong-field effect for the basic lepton-photon interactions.

  19. Twisted covariant noncommutative self-dual gravity

    SciTech Connect

    Estrada-Jimenez, S.; Garcia-Compean, H.; Obregon, O.; Ramirez, C.

    2008-12-15

    A twisted covariant formulation of noncommutative self-dual gravity is presented. The formulation for constructing twisted noncommutative Yang-Mills theories is used. It is shown that the noncommutative torsion is solved at any order of the {theta} expansion in terms of the tetrad and some extra fields of the theory. In the process the first order expansion in {theta} for the Plebanski action is explicitly obtained.

  20. Late time acceleration in a non-commutative model of modified cosmology

    NASA Astrophysics Data System (ADS)

    Malekolkalami, B.; Atazadeh, K.; Vakili, B.

    2014-12-01

    We investigate the effects of non-commutativity between the position-position, position-momentum and momentum-momentum of a phase space corresponding to a modified cosmological model. We show that the existence of such non-commutativity results in a Moyal Poisson algebra between the phase space variables in which the product law between the functions is of the kind of an α-deformed product. We then transform the variables in such a way that the Poisson brackets between the dynamical variables take the form of a usual Poisson bracket but this time with a noncommutative structure. For a power law expression for the function of the Ricci scalar with which the action of the gravity model is modified, the exact solutions in the commutative and noncommutative cases are presented and compared. In terms of these solutions we address the issue of the late time acceleration in cosmic evolution.

  1. SO(2, 3) noncommutative gravity model

    NASA Astrophysics Data System (ADS)

    Dimitrijević, M.; Radovanović, V.

    2014-12-01

    In this paper the noncommutative gravity is treated as a gauge theory of the non-commutative SO(2, 3)★ group, while the noncommutativity is canonical. The Seiberg-Witten (SW) map is used to express noncommutative fields in terms of the corresponding commutative fields. The commutative limit of the model is the Einstein-Hilbert action plus the cosmological term and the topological Gauss-Bonnet term. We calculate the second order correction to this model and obtain terms that are zeroth, first, ... and fourth power of the curvature tensor. Finally, we discuss physical consequences of those correction terms in the limit of big cosmological constant.

  2. Structurally Complex Surface of Europa

    NASA Technical Reports Server (NTRS)

    1997-01-01

    This is a composite of two images of Jupiter's icy moon Europa obtained from a range of 2119 miles (3410 kilometers) by the Galileo spacecraft during its fourth orbit around Jupiter and its first close pass of Europa. The mosaic spans 11 miles by 30 miles (17 km by 49 km) and shows features as small as 230 feet (70 meters) across. This mosaic is the first very high resolution image data obtained of Europa, and has a resolution more than 50 times better than the best Voyager coverage and 500 times better than Voyager coverage in this area. The mosaic shows the surface of Europa to be structurally complex. The sun illuminates the scene from the right, revealing complex overlapping ridges and fractures in the upper and lower portions of the mosaic, and rugged, more chaotic terrain in the center. Lateral faulting is revealed where ridges show offsets along their lengths (upper left of the picture). Missing ridge segments indicate obliteration of pre-existing materials and emplacement of new terrain (center of the mosaic). Only a small number of impact craters can be seen, indicating the surface is not geologically ancient.

    The Jet Propulsion Laboratory, Pasadena, CA manages the mission for NASA's Office of Space Science, Washington, DC.

    This image and other images and data received from Galileo are posted on the Galileo mission home page on the World Wide Web at http://galileo.jpl.nasa.gov. Background information and educational context for the images can be found at URL http://www.jpl.nasa.gov/galileo/sepo

  3. Noncommutativity Parameter and Composite Fermions

    NASA Astrophysics Data System (ADS)

    Jellal, Ahmed

    We determine some particular values of the noncommutativity parameter θ and show that the Murthy Shankar approach is in fact a particular case of a more general one. Indeed, using the fractional quantum Hall effect (FQHE) experimental data, we give a measurement of θ. This measurement can be obtained by considering some values of the filling factor ν and other ingredients, magnetic field B and electron density ρ. Moreover, it is found that θ can be quantized either fractionally or integrally in terms of the magnetic length l0 and the quantization is exactly what Murthy and Shankar formulated recently for the FQHE. On the other hand, we show that the mapping of the FQHE in terms of the composite fermion basis has a noncommutative geometry nature and therefore there is a more general way than the Murthy Shankar method to do this mapping.

  4. Non-commutative Nash inequalities

    SciTech Connect

    Kastoryano, Michael; Temme, Kristan

    2016-01-15

    A set of functional inequalities—called Nash inequalities—are introduced and analyzed in the context of quantum Markov process mixing. The basic theory of Nash inequalities is extended to the setting of non-commutative L{sub p} spaces, where their relationship to Poincaré and log-Sobolev inequalities is fleshed out. We prove Nash inequalities for a number of unital reversible semigroups.

  5. Noncommutativity in the early universe

    NASA Astrophysics Data System (ADS)

    Oliveira-Neto, G.; Silva de Oliveira, M.; Monerat, G. A.; Corrêa Silva, E. V.

    In the present work, we study the noncommutative version of a quantum cosmology model. The model has a Friedmann-Robertson-Walker (FRW) geometry, the matter content is a radiative perfect fluid and the spatial sections have zero constant curvature. In this model, the scale factor takes values in a bounded domain. Therefore, its quantum mechanical version has a discrete energy spectrum. We compute the discrete energy spectrum and the corresponding eigenfunctions. The energies depend on a noncommutative parameter β. We compute the scale factor expected value () for several values of β. For all of them, oscillates between maxima and minima values and never vanishes. It gives an initial indication that those models are free from singularities, at the quantum level. We improve this result by showing that if we subtract a quantity proportional to the standard deviation of a from , this quantity is still positive. The behavior, for the present model, is a drastic modification of the behavior in the corresponding commutative version of the present model. There, grows without limits with the time variable. Therefore, if the present model may represent the early stages of the universe, the results of the present paper give an indication that may have been, initially, bounded due to noncommutativity. We also compute the Bohmian trajectories for a, which are in accordance with , and the quantum potential Q. From Q, we may understand why that model is free from singularities, at the quantum level.

  6. Design space for complex DNA structures.

    PubMed

    Wei, Bryan; Dai, Mingjie; Myhrvold, Cameron; Ke, Yonggang; Jungmann, Ralf; Yin, Peng

    2013-12-04

    Nucleic acids have emerged as effective materials for assembling complex nanoscale structures. To tailor the structures to function optimally for particular applications, a broad structural design space is desired. Despite the many discrete and extended structures demonstrated in the past few decades, the design space remains to be fully explored. In particular, the complex finite-sized structures produced to date have been typically based on a small number of structural motifs. Here, we perform a comprehensive study of the design space for complex DNA structures, using more than 30 distinct motifs derived from single-stranded tiles. These motifs self-assemble to form structures with diverse strand weaving patterns and specific geometric properties, such as curvature and twist. We performed a systematic study to control and characterize the curvature of the structures, and constructed a flat structure with a corrugated strand pattern. The work here reveals the broadness of the design space for complex DNA nanostructures.

  7. Noncommutative de Sitter and FRW spaces

    NASA Astrophysics Data System (ADS)

    Burić, Maja; Madore, John

    2015-10-01

    Several versions of fuzzy four-dimensional de Sitter space are constructed using the noncommutative frame formalism. Although all noncommutative spacetimes which are found have commutative de Sitter metric as a classical limit, the algebras and the differential calculi which define them have many differences, which we derive and discuss.

  8. Effective Potential in Noncommutative BTZ Black Hole

    NASA Astrophysics Data System (ADS)

    Sadeghi, Jafar; Shajiee, Vahid Reza

    2016-02-01

    In this paper, we investigated the noncommutative rotating BTZ black hole and showed that such a space-time is not maximally symmetric. We calculated effective potential for the massive and the massless test particle by geodesic equations, also we showed effect of non-commutativity on the minimum mass of BTZ black hole.

  9. Identification of Complex Carbon Nanotube Structures

    NASA Technical Reports Server (NTRS)

    Han, Jie; Saini, Subhash (Technical Monitor)

    1998-01-01

    A variety of complex carbon nanotube (CNT) structures have been observed experimentally. These include sharp bends, branches, tori, and helices. They are believed to be formed by using topological defects such as pentagons and heptagons to connect different CNT. The effects of type, number, and arrangement (separation and orientation) of defects on atomic structures and energetics of complex CNT are investigated using topology, quantum mechanics and molecular mechanics calculations. Energetically stable models are derived for identification of observed complex CNT structures.

  10. Noncommutative spaces and Poincaré symmetry

    NASA Astrophysics Data System (ADS)

    Meljanac, Stjepan; Meljanac, Daniel; Mercati, Flavio; Pikutić, Danijel

    2017-03-01

    We present a framework which unifies a large class of noncommutative spacetimes that can be described in terms of a deformed Heisenberg algebra. The commutation relations between spacetime coordinates are up to linear order in the coordinates, with structure constants depending on the momenta plus terms depending only on the momenta. The possible implementations of the action of Lorentz transformations on these deformed phase spaces are considered, together with the consistency requirements they introduce. It is found that Lorentz transformations in general act nontrivially on tensor products of momenta. In particular the Lorentz group element which acts on the left and on the right of a composition of two momenta is different, and depends on the momenta involved in the process. We conclude with two representative examples, which illustrate the mentioned effect.

  11. Noncommutative Skyrmions in Quantum Hall Systems

    NASA Astrophysics Data System (ADS)

    Ezawa, Z. F.; Tsitsishvili, G.

    Charged excitations in quantum Hall (QH) systems are noncommutative skyrmions. QH systems represent an ideal system equipped with noncommutative geometry. When an electron is confined within the lowest Landau level, its position is described solely by the guiding center, whose X and Y coordinates do not commute with one another. Topological excitations in such a noncommutative plane are noncommutative skyrmions flipping several spins coherently. We construct a microscopic skyrmion state by applying a certain unitary transformation to an electron or hole state. A remarkable property is that a noncommutative skyrmion carries necessarily the electron number proportional to the topological charge. More remarkable is the bilayer QH system with the layer degree of freedom acting as the pseudospin, where the quasiparticle is a topological soliton to be identified with the pseudospin skyrmion. Such a skyrmion is deformed into a bimeron (a pair of merons) by the parallel magnetic field penetrated between the two layers. Each meron carries the electric charge ±e/2.

  12. Causality in noncommutative two-sheeted space-times

    NASA Astrophysics Data System (ADS)

    Franco, Nicolas; Eckstein, Michał

    2015-10-01

    We investigate the causal structure of two-sheeted space-times using the tools of Lorentzian spectral triples. We show that the noncommutative geometry of these spaces allows for causal relations between the two sheets. The computation is given in detail when the sheet is a 2- or 4-dimensional globally hyperbolic spin manifold. The conclusions are then generalised to a point-dependent distance between the two sheets resulting from the fluctuations of the Dirac operator.

  13. Group theoretical construction of planar noncommutative phase spaces

    SciTech Connect

    Ngendakumana, Ancille Todjihoundé, Leonard; Nzotungicimpaye, Joachim

    2014-01-15

    Noncommutative phase spaces are generated and classified in the framework of centrally extended anisotropic planar kinematical Lie groups as well as in the framework of noncentrally abelian extended planar absolute time Lie groups. Through these constructions the coordinates of the phase spaces do not commute due to the presence of naturally introduced fields giving rise to minimal couplings. By symplectic realizations methods, physical interpretations of generators coming from the obtained structures are given.

  14. Batalin-Fradkin-Tyutin embedding of noncommutative chiral bosons

    SciTech Connect

    Kim, Wontae; Park, Young-Jai; Shin, Hyeonjoon; Yoon, Myung Seok

    2007-04-15

    A two dimensional model of chiral bosons in noncommutative field space is considered in the framework of the Batalin-Fradkin-Tyutin Hamiltonian embedding method converting the second-class constrained system into the first-class one. The symmetry structure associated with the first-class constraints is explored and the propagation speed of fields is equivalent to that of the second-class constraint system.

  15. Operator Algebras and Noncommutative Geometric Aspects in Conformal Field Theory

    NASA Astrophysics Data System (ADS)

    Longo, Roberto

    2010-03-01

    The Operator Algebraic approach to Conformal Field Theory has been particularly fruitful in recent years (leading for example to the classification of all local conformal nets on the circle with central charge c < 1, jointly with Y. Kawahigashi). On the other hand the Operator Algebraic viewpoint offers a natural perspective for a Noncommutative Geometric context within Conformal Field Theory. One basic point here is to uncover the relevant structures. In this talk I will explain some of the basic steps in this "Noncommutative Geometrization program" up to the recent construction of a spectral triple associated with certain Ramond representations of the Supersymmetric Virasoro net. So Alain Connes framework enters into play. This is a joint work with S. Carpi, Y. Kawahigashi, and R. Hillier.

  16. Signature change in p-adic and noncommutative FRW cosmology

    NASA Astrophysics Data System (ADS)

    Djordjevic, Goran S.; Nesic, Ljubisa; Radovancevic, Darko

    2014-10-01

    The significant matter for the construction of the so-called no-boundary proposal is the assumption of signature transition, which has been a way to deal with the problem of initial conditions of the universe. On the other hand, results of Loop Quantum Gravity indicate that the signature change is related to the discrete nature of space at the Planck scale. Motivated by possibility of non-Archimedean and/or noncommutative structure of space-time at the Planck scale, in this work we consider the classical, p-adic and (spatial) noncommutative form of a cosmological model with Friedmann-Robertson-Walker (FRW) metric coupled with a self-interacting scalar field.

  17. Predicting complex mineral structures using genetic algorithms.

    PubMed

    Mohn, Chris E; Kob, Walter

    2015-10-28

    We show that symmetry-adapted genetic algorithms are capable of finding the ground state of a range of complex crystalline phases including layered- and incommensurate super-structures. This opens the way for the atomistic prediction of complex crystal structures of functional materials and mineral phases.

  18. Active impedance matching of complex structural systems

    NASA Technical Reports Server (NTRS)

    Macmartin, Douglas G.; Miller, David W.; Hall, Steven R.

    1991-01-01

    Viewgraphs on active impedance matching of complex structural systems are presented. Topics covered include: traveling wave model; dereverberated mobility model; computation of dereverberated mobility; control problem: optimal impedance matching; H2 optimal solution; statistical energy analysis (SEA) solution; experimental transfer functions; interferometer actuator and sensor locations; active strut configurations; power dual variables; dereverberation of complex structure; dereverberated transfer function; compensators; and relative power flow.

  19. Structure of DNA-liposome complexes

    SciTech Connect

    Lasic, D.D.; Strey, H.; Podgornik, R.; Stuart, M.C.A.; Frederik, P.M.

    1997-01-29

    Despite numerous studies and commericially available liposome kits, however, the structure of DNA-cationic liposome complexes is still not yet well understood. We have investigated the structure of these complexes using high-resolution cryo electron microscopy (EM) and small angle X-ray scattering (SAXS). 14 refs., 3 figs.

  20. Lexical Structure and Parsing Complexity.

    ERIC Educational Resources Information Center

    Stevenson, Suzanne; Merlo, Paolo

    1997-01-01

    Focuses on the consequences that the structural configuration of lexical knowledge has for the timecourse of parsing. Discusses reduced relative clauses and proposes a new lexical-structural analysis for manner of motion verbs. The article examines consequences for frequency-based models and all models whose difficulty derives from the ambiguity…

  1. TASI Lectures on Complex Structures

    NASA Astrophysics Data System (ADS)

    Denef, Frederik

    2012-11-01

    These lecture notes give an introduction to a number of ideas and methods that have been useful in the study of complex systems ranging from spin glasses to D-branes on Calabi-Yau manifolds. Topics include the replica formalism, Parisi's solution of the Sherrington-Kirkpatrick model, overlap order parameters, supersymmetric quantum mechanics, D-brane landscapes and their black hole duals.

  2. Quantum mechanics on SO(3) via noncommutative dual variables

    NASA Astrophysics Data System (ADS)

    Oriti, Daniele; Raasakka, Matti

    2011-07-01

    We formulate quantum mechanics on the group SO(3) using a noncommutative dual space representation for the quantum states, inspired by recent work in quantum gravity. The new noncommutative variables have a clear connection to the corresponding classical variables, and our analysis confirms them as the natural phase space variables, both mathematically and physically. In particular, we derive the first order (Hamiltonian) path integral in terms of the noncommutative variables, as a formulation of the transition amplitudes alternative to that based on harmonic analysis. We find that the nontrivial phase space structure gives naturally rise to quantum corrections to the action for which we find a closed expression. We then study both the semiclassical approximation of the first order path integral and the example of a free particle on SO(3). On the basis of these results, we comment on the relevance of similar structures and methods for more complicated theories with group-based configuration spaces, such as loop quantum gravity and spin foam models.

  3. Computational complexity in electronic structure.

    PubMed

    Whitfield, James Daniel; Love, Peter John; Aspuru-Guzik, Alán

    2013-01-14

    In quantum chemistry, the price paid by all known efficient model chemistries is either the truncation of the Hilbert space or uncontrolled approximations. Theoretical computer science suggests that these restrictions are not mere shortcomings of the algorithm designers and programmers but could stem from the inherent difficulty of simulating quantum systems. Extensions of computer science and information processing exploiting quantum mechanics has led to new ways of understanding the ultimate limitations of computational power. Interestingly, this perspective helps us understand widely used model chemistries in a new light. In this article, the fundamentals of computational complexity will be reviewed and motivated from the vantage point of chemistry. Then recent results from the computational complexity literature regarding common model chemistries including Hartree-Fock and density functional theory are discussed.

  4. Structure-based characterization of multiprotein complexes.

    PubMed

    Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J

    2014-07-08

    Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies.

  5. Complex ceramic structures. I. Weberites.

    PubMed

    Cai, Lu; Nino, Juan C

    2009-06-01

    The weberite structure (A2B2X7) is an anion-deficient fluorite-related superstructure. Compared with fluorites, the reduction in the number of anions leads to a decrease in the coordination number of the B cations (VI coordination) with respect to the A cations (VIII coordination), thus allowing the accommodation of diverse cations. As a result, weberite compounds have a broad range of chemical and physical properties and great technological potential. This article summarizes the structural features of weberite and describes the structure in several different ways. This is the first time that the stacking vector and stacking angle are used to represent the weberite structure. This paper also discusses the crystallographic relationship between weberite, fluorite and pyrochlore (another fluorite-related structure). The cation sublattices of weberite and pyrochlore are correlated by an axial transformation. It has been shown that the different coordination environment of anions is due to the alternating layering of the AB3 and A3B close-packed cation layers. A stability field of weberite oxides is proposed in terms of the ratio of ionic radius of cations and relative bond ionicity. In addition, a selection of weberite compounds with interesting properties is discussed.

  6. Noncommutative spaces from matrix models

    NASA Astrophysics Data System (ADS)

    Lu, Lei

    Noncommutative (NC) spaces commonly arise as solutions to matrix model equations of motion. They are natural generalizations of the ordinary commutative spacetime. Such spaces may provide insights into physics close to the Planck scale, where quantum gravity becomes relevant. Although there has been much research in the literature, aspects of these NC spaces need further investigation. In this dissertation, we focus on properties of NC spaces in several different contexts. In particular, we study exact NC spaces which result from solutions to matrix model equations of motion. These spaces are associated with finite-dimensional Lie-algebras. More specifically, they are two-dimensional fuzzy spaces that arise from a three-dimensional Yang-Mills type matrix model, four-dimensional tensor-product fuzzy spaces from a tensorial matrix model, and Snyder algebra from a five-dimensional tensorial matrix model. In the first part of this dissertation, we study two-dimensional NC solutions to matrix equations of motion of extended IKKT-type matrix models in three-space-time dimensions. Perturbations around the NC solutions lead to NC field theories living on a two-dimensional space-time. The commutative limit of the solutions are smooth manifolds which can be associated with closed, open and static two-dimensional cosmologies. One particular solution is a Lorentzian fuzzy sphere, which leads to essentially a fuzzy sphere in the Minkowski space-time. In the commutative limit, this solution leads to an induced metric that does not have a fixed signature, and have a non-constant negative scalar curvature, along with singularities at two fixed latitudes. The singularities are absent in the matrix solution which provides a toy model for resolving the singularities of General relativity. We also discussed the two-dimensional fuzzy de Sitter space-time, which has irreducible representations of su(1,1) Lie-algebra in terms of principal, complementary and discrete series. Field

  7. Novel gene complex structure determination

    SciTech Connect

    Gatewood, J.M.

    1997-08-01

    This is the final report of a one-year, Laboratory-Directed Research and Development (LORD) project at the Los Alamos National Laboratory. `Operative` chromatin containing exclusively the minor hasten variants was successfully isolated. Linker hasten H1 is quantitatively missing from operative chromatin. One of the aims of this proposal was to determine the proteins responsible for stabilizing operative chromatin. This chromatin is stabilized by microtubule proteins tar and tubulin. Another goal of this project was the structural characterization of operate chromatin nucleosomes. Using solution scattering, nucleosomes containing the minor variants were shown to be structurally distinct from major variant containing nucleosomes. The unusual structure and stabilization of operative chromatin by microtubule proteins provides a possible mechanism for direct interaction of transcription machinery with specific chromatin domains.

  8. Coherent quantum squeezing due to the phase space noncommutativity

    NASA Astrophysics Data System (ADS)

    Bernardini, Alex E.; Mizrahi, Salomon S.

    2015-06-01

    The effects of general noncommutativity of operators on producing deformed coherent squeezed states is examined in phase space. A two-dimensional noncommutative (NC) quantum system supported by a deformed mathematical structure, similar to that of Hadamard billiard, is obtained and the components behaviour is monitored in time. It is assumed that the independent degrees of freedom are two free 1D harmonic oscillators (HOs), so the system Hamiltonian does not contain interaction terms. Through the NC deformation parameterized by a Seiberg-Witten transform on the original canonical variables, one gets the standard commutation relations for the new ones, such that the obtained, new, Hamiltonian represents two interacting 1D HOs. By admitting that one HO is inverted relatively to the other, we show that their effective interaction induces a squeezing dynamics for initial coherent states imaged in the phase space. A suitable pattern of logarithmic spirals is obtained and some relevant properties are discussed in terms of Wigner functions, which are essential to put in evidence the effects of the noncommutativity.

  9. Noncommutative geometry and fluid dynamics

    NASA Astrophysics Data System (ADS)

    Das, Praloy; Ghosh, Subir

    2016-11-01

    In the present paper we have developed a Non-Commutative (NC) generalization of perfect fluid model from first principles, in a Hamiltonian framework. The noncommutativity is introduced at the Lagrangian (particle) coordinate space brackets and the induced NC fluid bracket algebra for the Eulerian (fluid) field variables is derived. Together with a Hamiltonian this NC algebra generates the generalized fluid dynamics that satisfies exact local conservation laws for mass and energy, thereby maintaining mass and energy conservation. However, nontrivial NC correction terms appear in the charge and energy fluxes. Other non-relativistic spacetime symmetries of the NC fluid are also discussed in detail. This constitutes the study of kinematics and dynamics of NC fluid. In the second part we construct an extension of the Friedmann-Robertson-Walker (FRW) cosmological model based on the NC fluid dynamics presented here. We outline the way in which NC effects generate cosmological perturbations bringing about anisotropy and inhomogeneity in the model. We also derive a NC extended Friedmann equation.

  10. Noncommutative via closed star product

    NASA Astrophysics Data System (ADS)

    Kupriyanov, V. G.; Vitale, P.

    2015-08-01

    We consider linear star products on of Lie algebra type. First we derive the closed formula for the polydifferential representation of the corresponding Lie algebra generators. Using this representation we define the Weyl star product on the dual of the Lie algebra. Then we construct a gauge operator relating the Weyl star product with the one which is closed with respect to some trace functional, Tr ( f ⋆ g) = Tr ( f · g). We introduce the derivative operator on the algebra of the closed star product and show that the corresponding Leibniz rule holds true up to a total derivative. As a particular example we study the space R {/θ 3} with type noncommutativity and show that in this case the closed star product is the one obtained from the Duflo quantization map. As a result a Laplacian can be defined such that its commutative limit reproduces the ordinary commutative one. The deformed Leibniz rule is applied to scalar field theory to derive conservation laws and the corresponding noncommutative currents.

  11. Measures of Complexity to quantify Bone Structure

    NASA Astrophysics Data System (ADS)

    Saparin, Peter; Gowin, Wolfgang; Kurths, Jürgen; Felsenberg, Dieter

    1998-03-01

    We propose a technique to assess structure of the bone in its spatial distribution by describing and quantifying the structural architecture as a whole. The concept of measures of complexity based on symbolic dynamics is applied to computed tomography (CT) - images obtained from human lumbar vertebra. CT-images have been transformed into images consisting of 5 different symbols, whereby both statical and dynamical coding are included. Different aspects of the bone structure are quantified by several measures which have been introduced: index of global ensemble of elements composing the bone; complexity, homogeneity and dynamics within the bone architecture; complexity and inhomogeneity of the trabecular net. This leads to new insides to the understanding of bone's internal structure. The results give the first experimental and quantitative evidence of the theoretical prediction that complexity of bone structure declines rapidly with the increased disintegration of bone structures leading to the loss of bone mass and specify experimentally that bone structure is exponentially related to its density. Especially, osteoporotic vertebrae are less complex organized than normal ones. In addition, this method is significantly sensitive to changes in bone structure and provides improvements of diagnostic of pathological structural loss.

  12. Constraining noncommutative spacetime from GW150914

    NASA Astrophysics Data System (ADS)

    Kobakhidze, Archil; Lagger, Cyril; Manning, Adrian

    2016-09-01

    The gravitational wave signal GW150914, recently detected by LIGO and Virgo collaborations, is used to place a bound on the scale of quantum fuzziness of noncommutative space-time. We show that the leading noncommutative correction to the phase of the gravitational waves produced by a binary system appears at the second order of the post-Newtonian expansion. This correction is proportional to Λ2≡|θ0 i|2/(lPtP)2, where θμ ν is the antisymmetric tensor of noncommutativity. To comply with GW150914 data, we find that √{Λ }≲3.5 , namely at the order of the Planck scale. This is the most stringent bound on the noncommutative scale, exceeding the previous constraints from particle physics processes by ˜15 orders of magnitude.

  13. Higgs couplings in noncommutative Standard Model

    NASA Astrophysics Data System (ADS)

    Batebi, S.; Haghighat, M.; Tizchang, S.; Akafzade, H.

    2015-06-01

    We consider the Higgs and Yukawa parts of the Noncommutative Standard Model (NCSM). We explore the NC-action to give all Feynman rules for couplings of the Higgs boson to electroweak gauge fields and fermions.

  14. Entropic force, noncommutative gravity, and ungravity

    SciTech Connect

    Nicolini, Piero

    2010-08-15

    After recalling the basic concepts of gravity as an emergent phenomenon, we analyze the recent derivation of Newton's law in terms of entropic force proposed by Verlinde. By reviewing some points of the procedure, we extend it to the case of a generic quantum gravity entropic correction to get compelling deviations to the Newton's law. More specifically, we study: (1) noncommutative geometry deviations and (2) ungraviton corrections. As a special result in the noncommutative case, we find that the noncommutative character of the manifold would be equivalent to the temperature of a thermodynamic system. Therefore, in analogy to the zero temperature configuration, the description of spacetime in terms of a differential manifold could be obtained only asymptotically. Finally, we extend the Verlinde's derivation to a general case, which includes all possible effects, noncommutativity, ungravity, asymptotically safe gravity, electrostatic energy, and extra dimensions, showing that the procedure is solid versus such modifications.

  15. Variable Complexity Optimization of Composite Structures

    NASA Technical Reports Server (NTRS)

    Haftka, Raphael T.

    2002-01-01

    The use of several levels of modeling in design has been dubbed variable complexity modeling. The work under the grant focused on developing variable complexity modeling strategies with emphasis on response surface techniques. Applications included design of stiffened composite plates for improved damage tolerance, the use of response surfaces for fitting weights obtained by structural optimization, and design against uncertainty using response surface techniques.

  16. Haag's theorem in noncommutative quantum field theory

    SciTech Connect

    Antipin, K. V.; Mnatsakanova, M. N.; Vernov, Yu. S.

    2013-08-15

    Haag's theorem was extended to the general case of noncommutative quantum field theory when time does not commute with spatial variables. It was proven that if S matrix is equal to unity in one of two theories related by unitary transformation, then the corresponding one in the other theory is equal to unity as well. In fact, this result is valid in any SO(1, 1)-invariant quantum field theory, an important example of which is noncommutative quantum field theory.

  17. Noncommutative Gauge Theory with Covariant Star Product

    SciTech Connect

    Zet, G.

    2010-08-04

    We present a noncommutative gauge theory with covariant star product on a space-time with torsion. In order to obtain the covariant star product one imposes some restrictions on the connection of the space-time. Then, a noncommutative gauge theory is developed applying this product to the case of differential forms. Some comments on the advantages of using a space-time with torsion to describe the gravitational field are also given.

  18. Structure of mammalian respiratory complex I

    PubMed Central

    Hirst, Judy

    2016-01-01

    Complex I (NADH:ubiquinone oxidoreductase), one of the largest membrane-bound enzymes in the cell, powers ATP synthesis in mammalian mitochondria by using the reducing potential of NADH to drive protons across the inner membrane. Mammalian complex I1 contains 45 subunits, comprising 14 core subunits that house the catalytic machinery and are conserved from bacteria to humans, and a mammalian-specific cohort of 31 supernumerary subunits1,2. Knowledge about the structures and functions of the supernumerary subunits is fragmentary. Here, we describe a 4.2 Å resolution single-particle cryoEM structure of complex I from Bos taurus. We locate and model all 45 subunits to provide the entire structure of the mammalian complex. Furthermore, computational sorting of the particles identified different structural classes, related by subtle domain movements, which reveal conformationally-dynamic regions and match biochemical descriptions of the ‘active-to-deactive’ enzyme transition that occurs during hypoxia3,4. Thus, our structures provide a foundation for understanding complex I assembly5 and the effects of mutations that cause clinically-relevant complex I dysfunctions6, insights into the structural and functional roles of the supernumerary subunits, and new information on the mechanism and regulation of catalysis. PMID:27509854

  19. Quantum mechanics with coordinate dependent noncommutativity

    NASA Astrophysics Data System (ADS)

    Kupriyanov, V. G.

    2013-11-01

    Noncommutative quantum mechanics can be considered as a first step in the construction of quantum field theory on noncommutative spaces of generic form, when the commutator between coordinates is a function of these coordinates. In this paper we discuss the mathematical framework of such a theory. The noncommutativity is treated as an external antisymmetric field satisfying the Jacobi identity. First, we propose a symplectic realization of a given Poisson manifold and construct the Darboux coordinates on the obtained symplectic manifold. Then we define the star product on a Poisson manifold and obtain the expression for the trace functional. The above ingredients are used to formulate a nonrelativistic quantum mechanics on noncommutative spaces of general form. All considered constructions are obtained as a formal series in the parameter of noncommutativity. In particular, the complete algebra of commutation relations between coordinates and conjugated momenta is a deformation of the standard Heisenberg algebra. As examples we consider a free particle and an isotropic harmonic oscillator on the rotational invariant noncommutative space.

  20. Structure of nucleosome-HMG complexes

    SciTech Connect

    Paton, A.E.

    1982-12-01

    This dissertation concentrates on the structure of HMG-nucleosome complexes, and how they differ from nucleosomes alone. The first chapter provides an introduction to chromatin and an overview of the field. The second and third chapters describe what kinds of nucleosome-HMG protein complexes form in solution, and where the HMG proteins may bind on the nucleosome. A model is proposed that locates the HMG binding sites on the nucleosome core particle. The fourth chapter describes the biophysical characterization of the complex. The methods include thermal denaturation, circular dichroism and sedimentation velocity, all done under variety of solvent conditions. These methods reveal a great deal of information on the stability and interactions of the complex. The fifth chapter describes conformational probes of the complex. These results reveal the structural transitions that occur when HMG protein binds to the nucleosome as well as the parts of the nucleosome essential for the binding reaction.

  1. Structural Studies of Protein-Surfactant Complexes

    SciTech Connect

    Chodankar, S. N.; Aswal, V. K.; Wagh, A. G.

    2008-03-17

    The structure of protein-surfactant complexes of two proteins bovine serum albumin (BSA) and lysozyme in presence of anionic surfactant sodium dodecyl sulfate (SDS) has been studied using small-angle neutron scattering (SANS). It is observed that these two proteins form different complex structures with the surfactant. While BSA protein undergoes unfolding on addition of surfactant, lysozyme does not show any unfolding even up to very high surfactant concentrations. The unfolding of BSA protein is caused by micelle-like aggregation of surfactant molecules in the complex. On the other hand, for lysozyme protein there is only binding of individual surfactant molecules to protein. Lysozyme in presence of higher surfactant concentrations has protein-surfactant complex structure coexisting with pure surfactant micelles.

  2. Stochastic transport through complex comb structures

    SciTech Connect

    Zaburdaev, V. Yu.; Popov, P. V.; Romanov, A. S.; Chukbar, K. V.

    2008-05-15

    A unified rigorous approach is used to derive fractional differential equations describing subdiffusive transport through comb structures of various geometrical complexity. A general nontrivial effect of the initial particle distribution on the subsequent evolution is exposed. Solutions having qualitative features of practical importance are given for joined structures with widely different fractional exponents.

  3. Deformation of noncommutative quantum mechanics

    NASA Astrophysics Data System (ADS)

    Jiang, Jian-Jian; Chowdhury, S. Hasibul Hassan

    2016-09-01

    In this paper, the Lie group GNC α , β , γ , of which the kinematical symmetry group GNC of noncommutative quantum mechanics (NCQM) is a special case due to fixed nonzero α, β, and γ, is three-parameter deformation quantized using the method suggested by Ballesteros and Musso [J. Phys. A: Math. Theor. 46, 195203 (2013)]. A certain family of QUE algebras, corresponding to GNC α , β , γ with two of the deformation parameters approaching zero, is found to be in agreement with the existing results of the literature on quantum Heisenberg group. Finally, we dualize the underlying QUE algebra to obtain an expression for the underlying star-product between smooth functions on GNC α , β , γ .

  4. Thermodynamics of the Schwarzschild Black Hole in Noncommutative Space

    SciTech Connect

    Perez-Payan, S.; Sabido, M.

    2009-04-20

    In this paper we study noncommutative black holes. In particular, we use a deform Schwarzschild solution in noncommutative gauge theory of gravity. By means of euclidean quantum gravity we obtain the entropy, temperatute and the time of evaporation of the noncommutative black hole.

  5. The Electronic Structure of Heavy Element Complexes

    SciTech Connect

    Bursten, Bruce E.

    2000-07-25

    The area of study is the bonding in heavy element complexes, and the application of more sophisticated electronic structure theories. Progress is recounted in several areas: (a) technological advances and current methodologies - Relativistic effects are extremely important in gaining an understanding of the electronic structure of compounds of the actinides, transactinides, and other heavy elements. Therefore, a major part of the continual benchmarking was the proper inclusion of the appropriate relativistic effects for the properties under study. (b) specific applications - These include organoactinide sandwich complexes, CO activation by actinide atoms, and theoretical studies of molecules of the transactinide elements. Finally, specific directions in proposed research are described.

  6. Robustness and structure of complex networks

    NASA Astrophysics Data System (ADS)

    Shao, Shuai

    This dissertation covers the two major parts of my PhD research on statistical physics and complex networks: i) modeling a new type of attack -- localized attack, and investigating robustness of complex networks under this type of attack; ii) discovering the clustering structure in complex networks and its influence on the robustness of coupled networks. Complex networks appear in every aspect of our daily life and are widely studied in Physics, Mathematics, Biology, and Computer Science. One important property of complex networks is their robustness under attacks, which depends crucially on the nature of attacks and the structure of the networks themselves. Previous studies have focused on two types of attack: random attack and targeted attack, which, however, are insufficient to describe many real-world damages. Here we propose a new type of attack -- localized attack, and study the robustness of complex networks under this type of attack, both analytically and via simulation. On the other hand, we also study the clustering structure in the network, and its influence on the robustness of a complex network system. In the first part, we propose a theoretical framework to study the robustness of complex networks under localized attack based on percolation theory and generating function method. We investigate the percolation properties, including the critical threshold of the phase transition pc and the size of the giant component Pinfinity. We compare localized attack with random attack and find that while random regular (RR) networks are more robust against localized attack, Erdoḧs-Renyi (ER) networks are equally robust under both types of attacks. As for scale-free (SF) networks, their robustness depends crucially on the degree exponent lambda. The simulation results show perfect agreement with theoretical predictions. We also test our model on two real-world networks: a peer-to-peer computer network and an airline network, and find that the real-world networks

  7. Noncommutative geometrical origin of the energy-momentum dispersion relation

    NASA Astrophysics Data System (ADS)

    Watcharangkool, A.; Sakellariadou, M.

    2017-01-01

    We investigate a link between the energy-momentum dispersion relation and the spectral distance in the context of a Lorentzian almost-commutative spectral geometry, defined by the product of Minkowski spacetime and an internal discrete noncommutative space. Using the causal structure, the almost-commutative manifold can be identified with a pair of four-dimensional Minkowski spacetimes embedded in a five-dimensional Minkowski geometry. Considering fermions traveling within the light cone of the ambient five-dimensional spacetime, we then derive the energy-momentum dispersion relation.

  8. Noncommutative Dirac quantization condition using the Seiberg-Witten map

    NASA Astrophysics Data System (ADS)

    Maceda, Marco; Martínez-Carbajal, Daniel

    2016-11-01

    The Dirac quantization condition (DQC) for magnetic monopoles in noncommutative space-time is analyzed. For this a noncommutative generalization of the method introduced by Wu and Yang is considered; the effects of noncommutativity are analyzed using the Seiberg-Witten map and the corresponding deformed Maxwell's equations are discussed. By using a perturbation expansion in the noncommutativity parameter θ , we show first that the DQC remains unmodified up to the first and second order. This result is then generalized to all orders in the expansion parameter for a class of noncommutative electric currents induced by the Seiberg-Witten map; these currents reduce to the Dirac delta function in the commutative limit.

  9. Bell operator and Gaussian squeezed states in noncommutative quantum mechanics

    NASA Astrophysics Data System (ADS)

    Bastos, Catarina; Bernardini, Alex E.; Bertolami, Orfeu; Dias, Nuno Costa; Prata, João Nuno

    2016-05-01

    We examine putative corrections to the Bell operator due to the noncommutativity in the phase space. Starting from a Gaussian squeezed envelope whose time evolution is driven by commutative (standard quantum mechanics) and noncommutative dynamics, respectively, we conclude that although the time-evolving covariance matrix in the noncommutative case is different from the standard case, the squeezing parameter dominates and there are no noticeable noncommutative corrections to the Bell operator. This indicates that, at least for squeezed states, the privileged states to test Bell correlations, noncommutativity versions of quantum mechanics remain as nonlocal as quantum mechanics itself.

  10. Impulse Response Operators for Structural Complexes

    DTIC Science & Technology

    1990-05-12

    systems of the complex. The statistical energy analysis (SEA) is one such a device [ 13, 14]. The rendering of SEA from equation (21) and/or (25) lies...Propagation.] 13. L. Cremer, M. Heckl, and E.E. Ungar 1973 Structure-Borne Sound (Springer Verlag). 14. R. H. Lyon 1975 Statistical Energy Analysis of

  11. Structure of Complex Verb Forms in Meiteilon

    ERIC Educational Resources Information Center

    Singh, Lourembam Surjit

    2016-01-01

    This piece of work proposes to descriptively investigate the structures of complex verbs in Meiteilon. The categorization of such verbs is based on the nature of semantic and syntactic functions of a lexeme or verbal lexeme. A lexeme or verbal lexeme in Meiteilon may have multifunctional properties in the nature of occurrence. Such lexical items…

  12. Noncommutative Geometry in M-Theory and Conformal Field Theory

    SciTech Connect

    Morariu, Bogdan

    1999-05-01

    In the first part of the thesis I will investigate in the Matrix theory framework, the subgroup of dualities of the Discrete Light Cone Quantization of M-theory compactified on tori, which corresponds to T-duality in the auxiliary Type II string theory. After a review of matrix theory compactification leading to noncommutative supersymmetric Yang-Mills gauge theory, I will present solutions for the fundamental and adjoint sections on a two-dimensional twisted quantum torus and generalize to three-dimensional twisted quantum tori. After showing how M-theory T-duality is realized in supersymmetric Yang-Mills gauge theories on dual noncommutative tori I will relate this to the mathematical concept of Morita equivalence of C*-algebras. As a further generalization, I consider arbitrary Ramond-Ramond backgrounds. I will also discuss the spectrum of the toroidally compactified Matrix theory corresponding to quantized electric fluxes on two and three tori. In the second part of the thesis I will present an application to conformal field theory involving quantum groups, another important example of a noncommutative space. First, I will give an introduction to Poisson-Lie groups and arrive at quantum groups using the Feynman path integral. I will quantize the symplectic leaves of the Poisson-Lie group SU(2)*. In this way we obtain the unitary representations of Uq(SU(2)). I discuss the X-structure of SU(2)* and give a detailed description of its leaves using various parametrizations. Then, I will introduce a new reality structure on the Heisenberg double of Funq (SL(N,C)) for q phase, which can be interpreted as the quantum phase space of a particle on the q-deformed mass-hyperboloid. I also present evidence that the above real form describes zero modes of certain non-compact WZNW-models.

  13. COMPLEX STRUCTURE IN CLASS 0 PROTOSTELLAR ENVELOPES

    SciTech Connect

    Tobin, John J.; Hartmann, Lee; Looney, Leslie W.; Chiang, Hsin-Fang

    2010-04-01

    We use archived Infrared Array Camera images from the Spitzer Space Telescope to show that many Class 0 protostars exhibit complex, irregular, and non-axisymmetric structure within their dusty envelopes. Our 8 {mu}m extinction maps probe some of the densest regions in these protostellar envelopes. Many of the systems are observed to have highly irregular and non-axisymmetric morphologies on scales {approx}>1000 AU, with a quarter of the sample exhibiting filamentary or flattened dense structures. Complex envelope structure is observed in regions spatially distinct from outflow cavities, and the densest structures often show no systematic alignment perpendicular to the cavities. These results indicate that mass ejection is not responsible for much of the irregular morphologies we detect; rather, we suggest that the observed envelope complexity is mostly the result of collapse from protostellar cores with initially non-equilibrium structures. The striking non-axisymmetry in many envelopes could provide favorable conditions for the formation of binary systems. We also note that protostars in the sample appear to be formed preferentially near the edges of clouds or bends in filaments, suggesting formation by gravitational focusing.

  14. Shadow of noncommutative geometry inspired black hole

    SciTech Connect

    Wei, Shao-Wen; Cheng, Peng; Zhong, Yi; Zhou, Xiang-Nan E-mail: pcheng14@lzu.edu.cn E-mail: zhouxn10@lzu.edu.cn

    2015-08-01

    In this paper, the shadow casted by the rotating black hole inspired by noncommutative geometry is investigated. In addition to the dimensionless spin parameter a/M{sub 0} with M{sub 0} black hole mass and inclination angle i, the dimensionless noncommutative parameter √θ/M{sub 0} is also found to affect the shape of the black hole shadow. The result shows that the size of the shadow slightly decreases with the parameter √θ/M{sub 0}, while the distortion increases with it. Compared to the Kerr black hole, the parameter √θ/M{sub 0} increases the deformation of the shadow. This may offer a way to distinguish noncommutative geometry inspired black hole from Kerr one via astronomical instruments in the near future.

  15. Non-Pauli transitions from spacetime noncommutativity.

    PubMed

    Balachandran, A P; Joseph, Anosh; Padmanabhan, Pramod

    2010-07-30

    The consideration of noncommutative spacetimes in quantum theory can be plausibly advocated from physics at the Planck scale. Typically, this noncommutativity is controlled by fixed "vectors" or "tensors" with numerical entries like θμν for the Moyal spacetime. In approaches enforcing Poincaré invariance, these deform or twist the method of (anti)symmetrization of identical particle state vectors. We argue that the Earth's rotation and movements in the cosmos are "sudden" events to Pauli-forbidden processes. This induces (twisted) bosonic components in state vectors of identical spinorial particles. These components induce non-Pauli transitions. From known limits on such transitions, we infer that the energy scale for noncommutativity is ≳10(24)  TeV. This suggests a new energy scale beyond the Planck scale.

  16. Natural discretization in noncommutative field theory

    NASA Astrophysics Data System (ADS)

    Acatrinei, Ciprian Sorin

    2015-12-01

    A discretization scheme for field theory is developed, in which the space time coordinates are assumed to be operators forming a noncommutative algebra. Generic waves without rotational symmetry are studied in (2+1) - dimensional scalar field theory with Heisenberg-type noncommutativity. In the representation chosen, the radial coordinate is naturally rendered discrete. Nonlocality along this coordinate, induced by noncommutativity, accounts for the angular dependence of the fields. A complete solution and the interpretation of its nonlocal features are given. The exact form of standing and propagating waves on such a discrete space is found in terms of finite series. A precise correspondence is established between the degree of nonlocality and the angular momentum of a field configuration. At small distance no classical singularities appear, even at the location of the sources. At large radius one recovers the usual commutative/continuum behaviour.

  17. Deconstructing Noncommutativity with a Giant Fuzzy Moose

    SciTech Connect

    Adams, Allan W.

    2001-12-05

    We argue that the world volume theories of D-branes probing orbifolds with discrete torsion develop, in the large quiver limit, new non-commutative directions. This provides an explicit ''deconstruction'' of a wide class of noncommutative theories. This also provides insight into the physical meaning of discrete torsion and its relation to the T-dual B field. We demonstrate that the strict large quiver limit reproduces the matrix theory construction of higher-dimensional D-branes, and argue that finite ''fuzzy moose'' theories provide novel regularizations of non-commutative theories and explicit string theory realizations of gauge theories on fuzzy tori. We also comment briefly on the relation to NCOS, (2,0) and little string theories.

  18. Natural discretization in noncommutative field theory

    SciTech Connect

    Acatrinei, Ciprian Sorin

    2015-12-07

    A discretization scheme for field theory is developed, in which the space time coordinates are assumed to be operators forming a noncommutative algebra. Generic waves without rotational symmetry are studied in (2+1) - dimensional scalar field theory with Heisenberg-type noncommutativity. In the representation chosen, the radial coordinate is naturally rendered discrete. Nonlocality along this coordinate, induced by noncommutativity, accounts for the angular dependence of the fields. A complete solution and the interpretation of its nonlocal features are given. The exact form of standing and propagating waves on such a discrete space is found in terms of finite series. A precise correspondence is established between the degree of nonlocality and the angular momentum of a field configuration. At small distance no classical singularities appear, even at the location of the sources. At large radius one recovers the usual commutative/continuum behaviour.

  19. Renormalization group flow for noncommutative Fermi liquids

    SciTech Connect

    Estrada-Jimenez, Sendic; Garcia-Compean, Hugo; Wu Yongshi

    2011-06-15

    Some recent studies of the AdS/CFT correspondence for condensed matter systems involve the Fermi liquid theory as a boundary field theory. Adding B-flux to the boundary D-branes leads in a certain limit to the noncommutative Fermi liquid, which calls for a field theory description of its critical behavior. As a preliminary step to more general consideration, the modification of the Landau's Fermi liquid theory due to noncommutativity of spatial coordinates is studied in this paper. We carry out the renormalization of interactions at tree level and one loop in a weakly coupled fermion system in two spatial dimensions. Channels ZS, ZS' and BCS are discussed in detail. It is shown that while the Gaussian fixed-point remains unchanged, the BCS instability is modified due to the space noncommutativity.

  20. Complex structures of dense lithium: Electronic origin

    NASA Astrophysics Data System (ADS)

    Degtyareva, V. F.

    2016-11-01

    Lithium—the lightest alkali metal exhibits unexpected structures and electronic behavior at high pressures. Like the heavier alkali metals, Li is bcc at ambient pressure and transforms first to fcc (at 7.5 GPa). The post-fcc high-pressure form Li-cI 16 (at 40-60 GPa) is similar to Na-cI 16 and related to more complex structures of heavy alkalis Rb-oC52 and Cs- oC84. The other high pressure phases for Li (oC88, oC40, oC24) observed at pressures up to 130 GPa are found only in Li. The different route of Li high-pressure structures correlates with its special electronic configuration containing the only 3 electrons (at 1s and 2s levels). Crystal structures for Li are analyzed within the model of Fermi sphere-Brillouin zone interactions. Stability of post-fcc structures for Li are supported by the Hume-Rothery arguments when new diffraction plains appear close to the Fermi level producing pseudogaps near the Fermi level and decreasing the crystal energy. The filling of Brillouin-Jones zones by electron states for a given structure defines the physical properties as optical reflectivity, electrical resistivity and superconductivity. To understand the complexity of structural and physical properties of Li above 60 GPa it is necessary to assume the valence electron band overlap with the core electrons and increase the valence electron count under compression.

  1. Braneworld cosmology and noncommutative inflation

    NASA Astrophysics Data System (ADS)

    Calcagni, Gianluca

    2005-03-01

    In this work we develop the patch formalism, an approach providing a very simple and compact description of braneworld-motivated cosmologies with nonstandard effective Friedmann equations. In particular, the Hubble parameter is assumed to depend on some power of the brane energy density, H^2 propto rho^q. The high-energy limit of Randall-Sundrum (q=2) and Gauss-Bonnet (q=2/3) braneworlds are considered, during an accelerating era triggered by a single ordinary or tachyonic scalar field. The inflationary dynamics, solutions, and spectra are provided. Using the latest results from WMAP and other experiments for estimates of cosmological observables, it is shown that future data and missions can in principle discriminate between standard four-dimensional and braneworld scenarios. The issue of non-Gaussianity is also studied within nonlinear perturbation theory. The introduction of a fundamental energy scale reinforces these results. Several classes of noncommutative inflationary models are considered and their features analyzed in a number of ways and energy regimes. Finally, we establish dual relations between inflationary, cyclic/ekpyrotic and phantom cosmologies, as well as between scalar-driven and tachyon-driven cosmologies. The exact dualities relating the four-dimensional spectra are broken in favour of their braneworld counterparts. The dual solutions display new interesting features because of the modification of the effective Friedmann equation on the brane.

  2. Structure of bacterial respiratory complex I.

    PubMed

    Berrisford, John M; Baradaran, Rozbeh; Sazanov, Leonid A

    2016-07-01

    Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. It is the largest protein assembly of respiratory chains and one of the most elaborate redox membrane proteins known. Bacterial enzyme is about half the size of mitochondrial and thus provides its important "minimal" model. Dysfunction of mitochondrial complex I is implicated in many human neurodegenerative diseases. The L-shaped complex consists of a hydrophilic arm, where electron transfer occurs, and a membrane arm, where proton translocation takes place. We have solved the crystal structures of the hydrophilic domain of complex I from Thermus thermophilus, the membrane domain from Escherichia coli and recently of the intact, entire complex I from T. thermophilus (536 kDa, 16 subunits, 9 iron-sulphur clusters, 64 transmembrane helices). The 95Å long electron transfer pathway through the enzyme proceeds from the primary electron acceptor flavin mononucleotide through seven conserved Fe-S clusters to the unusual elongated quinone-binding site at the interface with the membrane domain. Four putative proton translocation channels are found in the membrane domain, all linked by the central flexible axis containing charged residues. The redox energy of electron transfer is coupled to proton translocation by the as yet undefined mechanism proposed to involve long-range conformational changes. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.

  3. Imaging beneath complex structure: a case history

    SciTech Connect

    Gibson, B.; Larner, K.; Chambers, R.

    1983-08-01

    Migration is recognized as the essential step in converting seismic data into a representation of the earth's subsurface structure. Ironically, conventional migration often fails where migration is needed most - when the data are recorded over complex structures. In the Central American example, velocities increase nearly two-fold across an arched and thrust-faulted interface. Wave-front distortion introduced by this feature gives rise to distorted reflection from depth. Even with interval velocity known perfectly, no velocity is proper for time migrating the data here; time migration is the wrong process because it does not honor Snell's law. Depth migration of the stacked data, on the other hand, produces a reasonable image of the deeper section. The depth migration, however, leaves artifacts that could be attributed to problems that are common in structurally complicated areas: (1) departures of the stacked section from the ideal, a zero-offset section, (2) incorrect specification of velocities, and (3) loss of energy transmitted through the complex zone. For such an inhomogeneous velocity structure, shortcoming in CDP stacking are related directly to highly nonhyperbolic moveout. As with migration velocity, no proper stacking velocity can be developed for these data, even from the known interval-velocity model. Proper treatment of nonzero-offset reflection data could be accomplished by depth migration before stacking. Simple ray-theoretical correction of the complex moveouts, however, can produce a stack that is similar to the desired zero-offset section.

  4. Variable Complexity Structural Optimization of Shells

    NASA Technical Reports Server (NTRS)

    Haftka, Raphael T.; Venkataraman, Satchi

    1999-01-01

    Structural designers today face both opportunities and challenges in a vast array of available analysis and optimization programs. Some programs such as NASTRAN, are very general, permitting the designer to model any structure, to any degree of accuracy, but often at a higher computational cost. Additionally, such general procedures often do not allow easy implementation of all constraints of interest to the designer. Other programs, based on algebraic expressions used by designers one generation ago, have limited applicability for general structures with modem materials. However, when applicable, they provide easy understanding of design decisions trade-off. Finally, designers can also use specialized programs suitable for designing efficiently a subset of structural problems. For example, PASCO and PANDA2 are panel design codes, which calculate response and estimate failure much more efficiently than general-purpose codes, but are narrowly applicable in terms of geometry and loading. Therefore, the problem of optimizing structures based on simultaneous use of several models and computer programs is a subject of considerable interest. The problem of using several levels of models in optimization has been dubbed variable complexity modeling. Work under NASA grant NAG1-2110 has been concerned with the development of variable complexity modeling strategies with special emphasis on response surface techniques. In addition, several modeling issues for the design of shells of revolution were studied.

  5. Variable Complexity Structural Optimization of Shells

    NASA Technical Reports Server (NTRS)

    Haftka, Raphael T.; Venkataraman, Satchi

    1998-01-01

    Structural designers today face both opportunities and challenges in a vast array of available analysis and optimization programs. Some programs such as NASTRAN, are very general, permitting the designer to model any structure, to any degree of accuracy, but often at a higher computational cost. Additionally, such general procedures often do not allow easy implementation of all constraints of interest to the designer. Other programs, based on algebraic expressions used by designers one generation ago, have limited applicability for general structures with modem materials. However, when applicable, they provide easy understanding of design decisions trade-off. Finally, designers can also use specialized programs suitable for designing efficiently a subset of structural problems. For example, PASCO and PANDA2 are panel design codes, which calculate response and estimate failure much more efficiently than general-purpose codes, but are narrowly applicable in terms of geometry and loading. Therefore, the problem of optimizing structures based on simultaneous use of several models and computer programs is a subject of considerable interest. The problem of using several levels of models in optimization has been dubbed variable complexity modeling. Work under NASA grant NAG1-1808 has been concerned with the development of variable complexity modeling strategies with special emphasis on response surface techniques. In addition several modeling issues for the design of shells of revolution were studied.

  6. Structure of the haptoglobin-haemoglobin complex.

    PubMed

    Andersen, Christian Brix Folsted; Torvund-Jensen, Morten; Nielsen, Marianne Jensby; de Oliveira, Cristiano Luis Pinto; Hersleth, Hans-Petter; Andersen, Niels Højmark; Pedersen, Jan Skov; Andersen, Gregers Rom; Moestrup, Søren Kragh

    2012-09-20

    Red cell haemoglobin is the fundamental oxygen-transporting molecule in blood, but also a potentially tissue-damaging compound owing to its highly reactive haem groups. During intravascular haemolysis, such as in malaria and haemoglobinopathies, haemoglobin is released into the plasma, where it is captured by the protective acute-phase protein haptoglobin. This leads to formation of the haptoglobin-haemoglobin complex, which represents a virtually irreversible non-covalent protein-protein interaction. Here we present the crystal structure of the dimeric porcine haptoglobin-haemoglobin complex determined at 2.9 Å resolution. This structure reveals that haptoglobin molecules dimerize through an unexpected β-strand swap between two complement control protein (CCP) domains, defining a new fusion CCP domain structure. The haptoglobin serine protease domain forms extensive interactions with both the α- and β-subunits of haemoglobin, explaining the tight binding between haptoglobin and haemoglobin. The haemoglobin-interacting region in the αβ dimer is highly overlapping with the interface between the two αβ dimers that constitute the native haemoglobin tetramer. Several haemoglobin residues prone to oxidative modification after exposure to haem-induced reactive oxygen species are buried in the haptoglobin-haemoglobin interface, thus showing a direct protective role of haptoglobin. The haptoglobin loop previously shown to be essential for binding of haptoglobin-haemoglobin to the macrophage scavenger receptor CD163 (ref. 3) protrudes from the surface of the distal end of the complex, adjacent to the associated haemoglobin α-subunit. Small-angle X-ray scattering measurements of human haptoglobin-haemoglobin bound to the ligand-binding fragment of CD163 confirm receptor binding in this area, and show that the rigid dimeric complex can bind two receptors. Such receptor cross-linkage may facilitate scavenging and explain the increased functional affinity of

  7. Structural alignment of RNA with complex pseudoknot structure.

    PubMed

    Wong, Thomas K F; Lam, T W; Sung, Wing-Kin; Cheung, Brenda W Y; Yiu, S M

    2011-01-01

    The secondary structure of an ncRNA molecule is known to play an important role in its biological functions. Aligning a known ncRNA to a target candidate to determine the sequence and structural similarity helps in identifying de novo ncRNA molecules that are in the same family of the known ncRNA. However, existing algorithms cannot handle complex pseudoknot structures which are found in nature. In this article, we propose algorithms to handle two types of complex pseudoknots: simple non-standard pseudoknots and recursive pseudoknots. Although our methods are not designed for general pseudoknots, it already covers all known ncRNAs in both Rfam and PseudoBase databases. An evaluation of our algorithms shows that it is useful to identify ncRNA molecules in other species which are in the same family of a known ncRNA.

  8. Structure of a human translation termination complex

    PubMed Central

    Matheisl, Sarah; Berninghausen, Otto; Becker, Thomas; Beckmann, Roland

    2015-01-01

    In contrast to bacteria that have two release factors, RF1 and RF2, eukaryotes only possess one unrelated release factor eRF1, which recognizes all three stop codons of the mRNA and hydrolyses the peptidyl-tRNA bond. While the molecular basis for bacterial termination has been elucidated, high-resolution structures of eukaryotic termination complexes have been lacking. Here we present a 3.8 Å structure of a human translation termination complex with eRF1 decoding a UAA(A) stop codon. The complex was formed using the human cytomegalovirus (hCMV) stalling peptide, which perturbs the peptidyltransferase center (PTC) to silence the hydrolysis activity of eRF1. Moreover, unlike sense codons or bacterial stop codons, the UAA stop codon adopts a U-turn-like conformation within a pocket formed by eRF1 and the ribosome. Inducing the U-turn conformation for stop codon recognition rationalizes how decoding by eRF1 includes monitoring geometry in order to discriminate against sense codons. PMID:26384426

  9. Structurally robust control of complex networks

    NASA Astrophysics Data System (ADS)

    Nacher, Jose C.; Akutsu, Tatsuya

    2015-01-01

    Robust control theory has been successfully applied to numerous real-world problems using a small set of devices called controllers. However, the real systems represented by networks contain unreliable components and modern robust control engineering has not addressed the problem of structural changes on complex networks including scale-free topologies. Here, we introduce the concept of structurally robust control of complex networks and provide a concrete example using an algorithmic framework that is widely applied in engineering. The developed analytical tools, computer simulations, and real network analyses lead herein to the discovery that robust control can be achieved in scale-free networks with exactly the same order of controllers required in a standard nonrobust configuration by adjusting only the minimum degree. The presented methodology also addresses the probabilistic failure of links in real systems, such as neural synaptic unreliability in Caenorhabditis elegans, and suggests a new direction to pursue in studies of complex networks in which control theory has a role.

  10. The Structure and Dynamics of Economic Complexity

    NASA Astrophysics Data System (ADS)

    Hidalgo, Cesar A.

    2011-03-01

    Can network science help us understand the structure and evolution of the global economy? In this talk I summarize recent research that uses networks and complexity science to describe and explain the evolution of the mix of products that countries, and cities, produce and export. First, I show how to use information on the network connecting industries to locations to measure the complexity of an economy. Using these measures I demonstrate that countries tend to approach a level of income that is dictated by the complexity of their economies. Next, I study the evolution of economic complexity by showing that it is constrained by a coordination problem that countries, and cities, deal with using three different channels: First, they move to products that are close by, in the Product Space, to the products that they already do. Second, they are more likely to develop a product if a geographical neighbor has already developed it. And third, they follow the nestedness of the network connecting industries to locations. Finally, I introduce a simple model to account for the stylized facts uncovered in the previous sections.

  11. Morphologically complex protostellar envelopes : structure and kinematics

    NASA Astrophysics Data System (ADS)

    Tobin, John J.

    I present an in-depth study of protostars and their surrounding envelopes of dense gas and dust, using a multitude of observational methods to reveal new details of the star formation process. I use mid-infrared imaging from the Spitzer Space Telescope, combined with photometry spanning the near-infrared to millimeter wavelengths, to construct a model of the L1527 protostellar system. I modeled both the spectral energy distribution and resolved scattered light images to determine physical properties of the protostellar system. The nature of the apparent central point source in the Spitzer images was uncertain until high-resolution L-band imaging from the Gemini observatory resolved the point source into a disk in scattered light, having a radius of 200 AU. Protostellar envelopes are also often found to cast shadows against the 8 micron Galactic background in Spitzer imaging, enabling direct probes of envelope structure. The shadow images show that the dense envelopes around twenty-two Class 0 protostars are generally morphologically complex from 0.1 pc scales down to ˜1000 AU; they are often filamentary, and frequently non-axisymmetric. The observed envelope structure indicates a likely origin in turbulent cloud structure rather than a quasi-static/equilibrium formation. The complex envelope structure also may indicate an increased likelihood of fragmentation during collapse, forming close binaries. To further characterize these envelopes, I have observed them in the dense molecular gas tracers nthp and nht, both of which closely follow the 8 micron extinction morphology. The magnitude of the velocity gradients and envelope complexity on ˜10000 AU scales indicates that the velocity structure may reflect large-scale infall in addition to the often assumed rotation. Comparisons with three-dimensional filamentary and symmetric rotating collapse models reinforce the interpretation of velocities reflecting large-scale infall, showing that the structure of the envelope

  12. Structured analysis and modeling of complex systems

    NASA Technical Reports Server (NTRS)

    Strome, David R.; Dalrymple, Mathieu A.

    1992-01-01

    The Aircrew Evaluation Sustained Operations Performance (AESOP) facility at Brooks AFB, Texas, combines the realism of an operational environment with the control of a research laboratory. In recent studies we collected extensive data from the Airborne Warning and Control Systems (AWACS) Weapons Directors subjected to high and low workload Defensive Counter Air Scenarios. A critical and complex task in this environment involves committing a friendly fighter against a hostile fighter. Structured Analysis and Design techniques and computer modeling systems were applied to this task as tools for analyzing subject performance and workload. This technology is being transferred to the Man-Systems Division of NASA Johnson Space Center for application to complex mission related tasks, such as manipulating the Shuttle grappler arm.

  13. Strong gravitational lensing in a noncommutative black-hole spacetime

    SciTech Connect

    Ding Chikun; Kang Shuai; Chen Changyong; Chen Songbai; Jing Jiliang

    2011-04-15

    Noncommutative geometry may be a starting point to a quantum gravity. We study the influence of the spacetime noncommutative parameter on the strong field gravitational lensing in the noncommutative Schwarzschild black-hole spacetime and obtain the angular position and magnification of the relativistic images. Supposing that the gravitational field of the supermassive central object of the galaxy can be described by this metric, we estimate the numerical values of the coefficients and observables for strong gravitational lensing. In comparison to the Reissner-Norstroem black hole, we find that the influences of the spacetime noncommutative parameter is similar to those of the charge, but these influences are much smaller. This may offer a way to distinguish a noncommutative black hole from a Reissner-Norstroem black hole, and may permit us to probe the spacetime noncommutative constant {theta} by the astronomical instruments in the future.

  14. Simulating Vibrations in a Complex Loaded Structure

    NASA Technical Reports Server (NTRS)

    Cao, Tim T.

    2005-01-01

    The Dynamic Response Computation (DIRECT) computer program simulates vibrations induced in a complex structure by applied dynamic loads. Developed to enable rapid analysis of launch- and landing- induced vibrations and stresses in a space shuttle, DIRECT also can be used to analyze dynamic responses of other structures - for example, the response of a building to an earthquake, or the response of an oil-drilling platform and attached tanks to large ocean waves. For a space-shuttle simulation, the required input to DIRECT includes mathematical models of the space shuttle and its payloads, and a set of forcing functions that simulates launch and landing loads. DIRECT can accommodate multiple levels of payload attachment and substructure as well as nonlinear dynamic responses of structural interfaces. DIRECT combines the shuttle and payload models into a single structural model, to which the forcing functions are then applied. The resulting equations of motion are reduced to an optimum set and decoupled into a unique format for simulating dynamics. During the simulation, maximum vibrations, loads, and stresses are monitored and recorded for subsequent analysis to identify structural deficiencies in the shuttle and/or payloads.

  15. Exponential convergence rates for weighted sums in noncommutative probability space

    NASA Astrophysics Data System (ADS)

    Choi, Byoung Jin; Ji, Un Cig

    2016-11-01

    We study exponential convergence rates for weighted sums of successive independent random variables in a noncommutative probability space of which the weights are in a von Neumann algebra. Then we prove a noncommutative extension of the result for the exponential convergence rate by Baum, Katz and Read. As applications, we first study a large deviation type inequality for weighted sums in a noncommutative probability space, and secondly we study exponential convergence rates for weighted free additive convolution sums of probability measures.

  16. Classical mechanics in non-commutative phase space

    NASA Astrophysics Data System (ADS)

    Wei, Gao-Feng; Long, Chao-Yun; Long, Zheng-Wen; Qin, Shui-Jie; Fu, Qiang

    2008-05-01

    In this paper the laws of motion of classical particles have been investigated in a non-commutative phase space. The corresponding non-commutative relations contain not only spatial non-commutativity but also momentum non-commutativity. First, new Poisson brackets have been defined in non-commutative phase space. They contain corrections due to the non-commutativity of coordinates and momenta. On the basis of this new Poisson brackets, a new modified second law of Newton has been obtained. For two cases, the free particle and the harmonic oscillator, the equations of motion are derived on basis of the modified second law of Newton and the linear transformation (Phys. Rev. D, 2005, 72: 025010). The consistency between both methods is demonstrated. It is shown that a free particle in commutative space is not a free particle with zero-acceleration in the non-commutative phase space, but it remains a free particle with zero-acceleration in non-commutative space if only the coordinates are non-commutative. Supported by National Natural Science Foundation of China (10347003, 60666001), Planned Training Excellent Scientific and Technological Youth Foundation of Guizhou Province, China (2002,2013), Science Foundation of Guizhou Province, China, and Creativity Foundation for Graduate Guizhou University, China (2006031)

  17. Electronic Structure and Bonding in Complex Biomolecule

    NASA Astrophysics Data System (ADS)

    Ouyang, Lizhi

    2005-03-01

    For over a century vitamin B12 and its enzyme cofactor derivates have persistently attracted research efforts for their vital biological role, unique Co-C bonding, rich red-ox chemistry, and recently their candidacies as drug delivery vehicles etc. However, our understanding of this complex metalorganic molecule's efficient enzyme activated catalytic power is still controversial. We have for the first time calculated the electronic structure, Mulliken effective charge and bonding of a whole Vitamin B12 molecule without any structural simplification by first- principles approaches based on density functional theory using structures determined by high resolution X-ray diffraction. A partial density of states analysis shows excellent agreement with X-ray absorption data and has been used successfully to interpret measured optical absorption spectra. Mulliken bonding analysis of B12 and its derivatives reveal noticeable correlations between the two axial ligands which could be exploited by the enzyme to control the catalytic process. Our calculated X-ray near edge structure of B12 and its derivates using Slater's transition state theory are also in good agreement with experiments. The same approach has been applied to other B12 derivatives, ferrocene peptides, and recently DNA molecules.

  18. Noncommutative spaces and covariant formulation of statistical mechanics

    NASA Astrophysics Data System (ADS)

    Hosseinzadeh, V.; Gorji, M. A.; Nozari, K.; Vakili, B.

    2015-07-01

    We study the statistical mechanics of a general Hamiltonian system in the context of symplectic structure of the corresponding phase space. This covariant formalism reveals some interesting correspondences between properties of the phase space and the associated statistical physics. While topology, as a global property, turns out to be related to the total number of microstates, the invariant measure which assigns a priori probability distribution over the microstates is determined by the local form of the symplectic structure. As an example of a model for which the phase space has a nontrivial topology, we apply our formulation on the Snyder noncommutative space-time with de Sitter four-momentum space and analyze the results. Finally, in the framework of such a setup, we examine our formalism by studying the thermodynamical properties of a harmonic oscillator system.

  19. Paraquantum strings in noncommutative space-time

    NASA Astrophysics Data System (ADS)

    Seridi, M. A.; Belaloui, N.

    2015-10-01

    A parabosonic string is assumed to propagate in a total noncommutative target phase space. Three models are investigated: open strings, open strings between two parallel Dp-Dq branes and closed ones. This leads to a generalization of the oscillators algebra of the string and the corresponding Virasoro algebra. The mass operator is no more diagonal in the ordinary Fock space, a redefinition of this later will modify the mass spectrum, so that, neither massless vector state nor massless tensor state are present. The restoration of the photon and the graviton imposes specific forms of the noncommutativity parameter matrices, partially removes the mass degeneracy and gives new additional ones. In particular, for the D-branes, one can have a tachyon free model with a photon state when more strict conditions on these parameters are imposed, while, the match level condition of the closed string model induces the reduction of the spectrum.

  20. Hamiltonian Approach To Dp-Brane Noncommutativity

    NASA Astrophysics Data System (ADS)

    Nikolic, B.; Sazdovic, B.

    2010-07-01

    In this article we investigate Dp-brane noncommutativity using Hamiltonian approach. We consider separately open bosonic string and type IIB superstring which endpoints are attached to the Dp-brane. From requirement that Hamiltonian, as the time translation generator, has well defined derivatives in the coordinates and momenta, we obtain boundary conditions directly in the canonical form. Boundary conditions are treated as canonical constraints. Solving them we obtain initial coordinates in terms of the effective ones as well as effective momenta. Presence of momenta implies noncommutativity of the initial coordinates. Effective theory, defined as initial one on the solution of boundary conditions, is its Ω even projection, where Ω is world-sheet parity transformation Ω:σ→-σ. The effective background fields are expressed in terms of Ω even and squares of the Ω odd initial background fields.

  1. Geomechanical numerical simulations of complex geologic structures

    SciTech Connect

    Arguello, J.G.; Stone, C.M.; Lorenz, J.C.

    1996-05-01

    Ability to predict mechanical response of rock in three dimensions over the spatial and time scales of geologic interest would give the oil and gas industry the ability to reduce risk on prospects, improve pre-project initial reserve estimates, and lower operating costs. A program has recently been initiated, under the auspices of the Advanced Computational Technology Initiative (ACTI), to achieve such a computational technology breakthrough by adapting the unique advanced quasistatic finite element technology developed by Sandia to the mechanics applications important to exploration and production activities within the oil and gas industry. As a precursor to that program, in an effort to evaluate the feasibility of the approach, several complex geologic structures of interest were analyzed with the existing two-dimensional quasistatic finite element code, SANTOS, developed at Sandia. Examples are presented and discussed.

  2. Identifying community structure in complex networks

    NASA Astrophysics Data System (ADS)

    Shao, Chenxi; Duan, Yubing

    2015-07-01

    A wide variety of applications could be formulated to resolve the problem of finding all communities from a given network, ranging from social and biological network analysis to web mining and searching. In this study, we propose the concept of virtual attractive strength between each pair of node in networks, and then give the definition of community structure based on the proposed attractive strength. Furthermore, we present a community detection method by moving vertices to the clusters that produce the largest attractive strengths to them until the division of network reaches unchanged. Experimental results on synthetic and real networks indicate that the proposed approach has favorite effectiveness and fast convergence speed, which provides an efficient method for exploring and analyzing complex systems.

  3. Electronic structures of ytterbocene-imine complexes

    SciTech Connect

    Da Re, R. E.; Kuehl, C. J.; John, K. D.; Morris, D. E.

    2004-01-01

    The electronic structures of complexes of the form [(C{sub 5}Me{sub 5}){sub 2}Yb(L)]{sup +/0} (L = bipyridine, phenanthroline, terpyridine) have been probed using cyclic voltammetry and electronic spectroscopy. Remarkably, the voltammetric data reveal that the imine-based LUMO is stabilized and the redox-active metal f orbital is destabilized by ca. 1 V each upon formation of the ytterbocene-imine adduct, which is presumably responsible for the [(f){sup 13}({pi}*(L)){sup 1}] charge-transfer ground state characteristic of these complexes. The ca. 0.8 V separation between ligand-based oxidation and metal-based reduction waves for each ytterbocene adduct correlates with the energy of its optically promoted {pi}*(L)-f(Yb) charge transfer (LMCT) transition (ca. 5000 cm{sup -1}). The coupling between this LMCT excited state and the {sup 2}F{sub 7/2} ground and {sup 2}F{sub 5/2} excited states of Yb(III) leads to unusually large intensities ({var_epsilon} {approx} 1000) for the metal-localized f-f bands, which will be discussed in the context of an intensity borrowing mechanism that invokes exchange between the ligand-based {sup 2}S and metal-based {sup 2}F spin states.

  4. Sigma-Model Solitons on Noncommutative Spaces

    NASA Astrophysics Data System (ADS)

    Dabrowski, Ludwik; Landi, Giovanni; Luef, Franz

    2015-12-01

    We use results from time-frequency analysis and Gabor analysis to construct new classes of sigma-model solitons over the Moyal plane and over noncommutative tori, taken as source spaces, with a target space made of two points. A natural action functional leads to self-duality equations for projections in the source algebra. Solutions, having nontrivial topological content, are constructed via suitable Morita duality bimodules.

  5. Notes on "Quantum Gravity" and Noncommutative Geometry

    NASA Astrophysics Data System (ADS)

    Gracia-Bondía, J. M.

    I hesitated for a long time before giving shape to these notes, originally intended for preliminary reading by the attendees to the Summer School "New paths towards quantum gravity" (Holbaek Bay, Denmark, May 2008). At the end, I decide against just selling my mathematical wares, and for a survey, necessarily very selective, but taking a global phenomenological approach to its subject matter. After all, noncommutative geometry does not purport yet to solve the riddle of quantum gravity; it is more of an insurance policy against the probable failure of the other approaches. The plan is as follows: the introduction invites students to the fruitful doubts and conundrums besetting the application of even classical gravity. Next, the first experiments detecting quantum gravitational states inoculate us a healthy dose of scepticism on some of the current ideologies. In Sect. 1.3 we look at the action for general relativity as a consequence of gauge theory for quantum tensor fields. Section 1.4 briefly deals with the unimodular variants. Section 1.5 arrives at noncommutative geometry. I am convinced that, if this is to play a role in quantum gravity, commutative and noncommutative manifolds must be treated on the same footing, which justifies the place granted to the reconstruction theorem. Together with Sect. 1.3, this part constitutes the main body of the notes. Only very summarily at the end of this section do we point to some approaches to gravity within the noncommutative realm. The last section delivers a last dose of scepticism. My efforts will have been rewarded if someone from the young generation learns to mistrust current mindsets.

  6. Deformed symmetries in noncommutative and multifractional spacetimes

    NASA Astrophysics Data System (ADS)

    Calcagni, Gianluca; Ronco, Michele

    2017-02-01

    We clarify the relation between noncommutative spacetimes and multifractional geometries, two quantum-gravity-related approaches where the fundamental description of spacetime is not given by a classical smooth geometry. Despite their different conceptual premises and mathematical formalisms, both research programs allow for the spacetime dimension to vary with the probed scale. This feature and other similarities led to ask whether there is a duality between these two independent proposals. In the absence of curvature and comparing the symmetries of both position and momentum space, we show that κ -Minkowski spacetime and the commutative multifractional theory with q -derivatives are physically inequivalent but they admit several contact points that allow one to describe certain aspects of κ -Minkowski noncommutative geometry as a multifractional theory and vice versa. Contrary to previous literature, this result holds without assuming any specific measure for κ -Minkowski. More generally, no well-defined ⋆-product can be constructed from the q -theory, although the latter does admit a natural noncommutative extension with a given deformed Poincaré algebra. A similar no-go theorem may be valid for all multiscale theories with factorizable measures. Turning gravity on, we write the algebras of gravitational first-class constraints in the multifractional theories with q - and weighted derivatives and discuss their differences with respect to the deformed algebras of κ -Minkowski spacetime and of loop quantum gravity.

  7. Coherent structures in a supersonic complex nozzle

    NASA Astrophysics Data System (ADS)

    Magstadt, Andrew; Berry, Matthew; Glauser, Mark

    2016-11-01

    The jet flow from a complex supersonic nozzle is studied through experimental measurements. The nozzle's geometry is motivated by future engine designs for high-performance civilian and military aircraft. This rectangular jet has a single plane of symmetry, an additional shear layer (referred to as a wall jet), and an aft deck representative of airframe integration. The core flow operates at a Mach number of Mj , c = 1 . 6 , and the wall jet is choked (Mj , w = 1 . 0). This high Reynolds number jet flow is comprised of intense turbulence levels, an intricate shock structure, shear and boundary layers, and powerful corner vortices. In the present study, stereo PIV measurements are simultaneously sampled with high-speed pressure measurements, which are embedded in the aft deck, and far-field acoustics in the anechoic chamber at Syracuse University. Time-resolved schlieren measurements have indicated the existence of strong flow events at high frequencies, at a Strouhal number of St = 3 . 4 . These appear to result from von Kàrmàn vortex shedding within the nozzle and pervade the entire flow and acoustic domain. Proper orthogonal decomposition is applied on the current data to identify coherent structures in the jet and study the influence of this vortex street. AFOSR Turbulence and Transition Program (Grant No. FA9550-15-1-0435) with program managers Dr. I. Leyva and Dr. R. Ponnappan.

  8. Characterizing the Community Structure of Complex Networks

    PubMed Central

    Lancichinetti, Andrea; Kivelä, Mikko; Saramäki, Jari; Fortunato, Santo

    2010-01-01

    Background Community structure is one of the key properties of complex networks and plays a crucial role in their topology and function. While an impressive amount of work has been done on the issue of community detection, very little attention has been so far devoted to the investigation of communities in real networks. Methodology/Principal Findings We present a systematic empirical analysis of the statistical properties of communities in large information, communication, technological, biological, and social networks. We find that the mesoscopic organization of networks of the same category is remarkably similar. This is reflected in several characteristics of community structure, which can be used as “fingerprints” of specific network categories. While community size distributions are always broad, certain categories of networks consist mainly of tree-like communities, while others have denser modules. Average path lengths within communities initially grow logarithmically with community size, but the growth saturates or slows down for communities larger than a characteristic size. This behaviour is related to the presence of hubs within communities, whose roles differ across categories. Also the community embeddedness of nodes, measured in terms of the fraction of links within their communities, has a characteristic distribution for each category. Conclusions/Significance Our findings, verified by the use of two fundamentally different community detection methods, allow for a classification of real networks and pave the way to a realistic modelling of networks' evolution. PMID:20711338

  9. Parity-dependent non-commutative quantum mechanics

    NASA Astrophysics Data System (ADS)

    Chung, Won Sang

    2017-01-01

    In this paper, we consider the non-commutative quantum mechanics (NCQM) with parity (or space reflection) in two dimensions. Using the parity operators Ri, we construct the deformed Heisenberg algebra with parity in the non-commutative plane. We use this algebra to discuss the isotropic harmonic Hamiltonian with parity.

  10. Warped Products and Yang-Mills Equations on Noncommutative Spaces

    NASA Astrophysics Data System (ADS)

    Zampini, Alessandro

    2015-02-01

    This paper presents a non-self-dual solution of the Yang-Mills equations on a noncommutative version of the classical , so generalizing the classical meron solution first introduced by de Alfaro et al. (Phys Lett B 65:163-166, 1976). The basic tool for that is a generalization to noncommutative spaces of the classical notion of warped products between metric spaces.

  11. Noncommutative anisotropic oscillator in a homogeneous magnetic field

    NASA Astrophysics Data System (ADS)

    Nath, D.; Roy, P.

    2017-02-01

    We study anisotropic oscillator in the presence of a homogeneous magnetic field and other related systems in the noncommutative plane. Energy values as function of the noncommutative parameter θ and the magnetic field B have been obtained. Some features of the spectrum, for example, formation of energy bands etc. have been examined. The effect of anisotropy on the energy levels has also been discussed.

  12. Stabilization of Internal Space in Noncommutative Multidimensional Cosmology

    NASA Astrophysics Data System (ADS)

    Khosravi, N.; Jalalzadeh, S.; Sepangi, H. R.

    We study the cosmological aspects of a noncommutative, multidimensional universe where the matter source is assumed to be a scalar field which does not commute with the internal scale factor. We show that such noncommutativity results in the internal dimensions being stabilized.

  13. Hydrogen atom spectrum and the lamb shift in noncommutative QED.

    PubMed

    Chaichian, M; Sheikh-Jabbari, M M; Tureanu, A

    2001-03-26

    We have calculated the energy levels of the hydrogen atom as well as the Lamb shift within the noncommutative quantum electrodynamics theory. The results show deviations from the usual QED both on the classical and the quantum levels. On both levels, the deviations depend on the parameter of space/space noncommutativity.

  14. Quantum fields with noncommutative target spaces

    NASA Astrophysics Data System (ADS)

    Balachandran, A. P.; Queiroz, A. R.; Marques, A. M.; Teotonio-Sobrinho, P.

    2008-05-01

    Quantum field theories (QFT’s) on noncommutative spacetimes are currently under intensive study. Usually such theories have world sheet noncommutativity. In the present work, instead, we study QFT’s with commutative world sheet and noncommutative target space. Such noncommutativity can be interpreted in terms of twisted statistics and is related to earlier work of Oeckl [R. Oeckl, Commun. Math. Phys. 217, 451 (2001).CMPHAY0010-361610.1007/s002200100375], and others [A. P. Balachandran, G. Mangano, A. Pinzul, and S. Vaidya, Int. J. Mod. Phys. A 21, 3111 (2006)IMPAEF0217-751X10.1142/S0217751X06031764; A. P. Balachandran, A. Pinzul, and B. A. Qureshi, Phys. Lett. B 634, 434 (2006)PYLBAJ0370-269310.1016/j.physletb.2006.02.006; A. P. Balachandran, A. Pinzul, B. A. Qureshi, and S. Vaidya, arXiv:hep-th/0608138; A. P. Balachandran, T. R. Govindarajan, G. Mangano, A. Pinzul, B. A. Qureshi, and S. Vaidya, Phys. Rev. D 75, 045009 (2007)PRVDAQ0556-282110.1103/PhysRevD.75.045009; A. Pinzul, Int. J. Mod. Phys. A 20, 6268 (2005)IMPAEF0217-751X10.1142/S0217751X05029290; G. Fiore and J. Wess, Phys. Rev. D 75, 105022 (2007)PRVDAQ0556-282110.1103/PhysRevD.75.105022; Y. Sasai and N. Sasakura, Prog. Theor. Phys. 118, 785 (2007)PTPKAV0033-068X10.1143/PTP.118.785]. The twisted spectra of their free Hamiltonians has been found earlier by Carmona et al. [J. M. Carmona, J. L. Cortes, J. Gamboa, and F. Mendez, Phys. Lett. B 565, 222 (2003)PYLBAJ0370-269310.1016/S0370-2693(03)00728-7; J. M. Carmona, J. L. Cortes, J. Gamboa, and F. Mendez, J. High Energy Phys.JHEPFG1029-8479 03 (2003) 05810.1088/1126-6708/2003/03/058]. We review their derivation and then compute the partition function of one such typical theory. It leads to a deformed blackbody spectrum, which is analyzed in detail. The difference between the usual and the deformed blackbody spectrum appears in the region of high frequencies. Therefore we expect that the deformed blackbody radiation may potentially be used to compute a

  15. Entropy bound for the photon gas in noncommutative spacetime

    NASA Astrophysics Data System (ADS)

    Nozari, K.; Gorji, M. A.; Damavandi Kamali, A.; Vakili, B.

    2016-09-01

    Motivated by the doubly special relativity theories and noncommutative spacetime structures, thermodynamical properties of the photon gas in a phase space with compact spatial momentum space is studied. At the high temperature limit, the upper bounds for the internal energy and entropy are obtained which are determined by the size of the compact spatial momentum space. The maximum internal energy turns out to be of the order of the Planck energy and the entropy bound is then determined by the factor (V /lPl3) through the relevant identification of the size of the momentum space with Planck scale. The entropy bound is very similar to the case of Bekenstein-Hawking entropy of black holes and suggests that thermodynamics of black holes may be deduced from a saturated state in the framework of a full quantum gravitational statistical mechanics.

  16. Aspects of noncommutative (1+1)-dimensional black holes

    NASA Astrophysics Data System (ADS)

    Mureika, Jonas R.; Nicolini, Piero

    2011-08-01

    We present a comprehensive analysis of the spacetime structure and thermodynamics of (1+1)-dimensional black holes in a noncommutative framework. It is shown that a wider variety of solutions are possible than the commutative case considered previously in the literature. As expected, the introduction of a minimal length θ cures singularity pathologies that plague the standard two-dimensional general relativistic case, where the latter solution is recovered at large length scales. Depending on the choice of input parameters (black hole mass M, cosmological constant Λ, etc.), black hole solutions with zero, up to six, horizons are possible. The associated thermodynamics allows for the either complete evaporation, or the production of black hole remnants.

  17. A note on nonlinear σ-models in noncommutative geometry

    NASA Astrophysics Data System (ADS)

    Lee, Hyun Ho

    2016-03-01

    We study nonlinear σ-models defined on a noncommutative torus as a two-dimensional string worldsheet. We consider (i) a two-point space, (ii) a circle, (iii) a noncommutative torus, (iv) a classical group SU(2, ℂ) as examples of space-time. Based on established results, the trivial harmonic unitaries of the noncommutative chiral model known as local minima are shown not to be global minima by comparing them to the symmetric unitaries derived from instanton solutions of the noncommutative Ising model corresponding to a two-point space. In addition, a ℤ2-action on field maps is introduced to a noncommutative torus, and its action on solutions of various Euler-Lagrange equations is described.

  18. C, P, and T invariance of noncommutative gauge theories

    PubMed

    Sheikh-Jabbari

    2000-06-05

    In this paper we study the invariance of the noncommutative gauge theories under C, P, and T transformations. For the noncommutative space (when only the spatial part of straight theta is nonzero) we show that noncommutative QED (NCQED) is parity invariant. In addition, we show that under charge conjugation the theory on noncommutative R(4)(straight theta) is transformed to the theory on R(4)(-straight theta), so NCQED is a CP violating theory. The theory remains invariant under time reversal if, together with proper changes in fields, we also change straight theta by -straight theta. Hence altogether NCQED is CPT invariant. Moreover, we show that the CPT invariance holds for general noncommutative space-time.

  19. Holographic entanglement entropy for noncommutative anti-de Sitter space

    NASA Astrophysics Data System (ADS)

    Momeni, Davood; Raza, Muhammad; Myrzakulov, Ratbay

    2016-04-01

    A metric is proposed to explore the noncommutative form of the anti-de Sitter (AdS) space due to quantum effects. It has been proved that the noncommutativity in AdS space induces a single component gravitoelectric field. The holographic Ryu-Takayanagi (RT) algorithm is then applied to compute the entanglement entropy (EE) in dual CFT2. This calculation can be exploited to compute ultraviolet-infrared (UV-IR) cutoff dependent central charge of the certain noncommutative CFT2. This noncommutative computation of the EE can be interpreted in the form of the surface/state correspondence. We have shown that noncommutativity increases the dimension of the effective Hilbert space of the dual conformal field theory (CFT).

  20. Noncommutativity and Humanity — Julius Wess and his Legacy

    NASA Astrophysics Data System (ADS)

    Djordjevic, Goran S.

    2012-03-01

    A personal view on Julius Wess's human and scientific legacy in Serbia and the Balkan region is given. Motivation for using noncommutative and nonarchimedean geometry on very short distances is presented. In addition to some mathematical preliminaries, we present a short introduction in adelic quantum mechanics in a way suitable for its noncommutative generalization. We also review the basic ideas and tools embedded in q-deformed and noncommutative quantum mechanics. A rather fundamental approach, called deformation quantization, is noted. A few relations between noncommutativity and nonarchimedean spaces, as well as similarities between corresponding quantum theories, in particular, quantum cosmology are pointed out. An extended Moyal product in a frame of an adelic noncommutative quantum mechanics is also considered.

  1. Classical electrodynamics in a space with spin noncommutativity of coordinates

    NASA Astrophysics Data System (ADS)

    Vasyuta, V. M.; Tkachuk, V. M.

    2016-10-01

    We propose a relativistic Lorentz-invariant spin-noncommutative algebra. Using the Weyl ordering of noncommutative position operators, we find a mapping from a space of commutative functions into space of noncommutative functions. The Lagrange function of an electromagnetic field in the space with spin noncommutativity is constructed. In such a space electromagnetic field becomes non-abelian. A gauge transformation law of this field is also obtained. Exact nonlinear field equations of noncommutative electromagnetic field are derived from the least action principle. Within the perturbative approach we consider field of a point charge in a constant magnetic field and interaction of two plane waves. An exact solution of a plane wave propagation in a constant magnetic and electric fields is found.

  2. Hawking-Moss tunneling in non-commutative eternal inflation

    SciTech Connect

    Cai Yifu; Wang Yi E-mail: wangyi@itp.ac.cn

    2008-01-15

    The quantum behavior of non-commutative eternal inflation is quite different from the usual scenario. Unlike the usual eternal inflation, non-commutative eternal inflation has quantum fluctuation suppressed by the Hubble parameter. Because of this, we need to reconsider many conceptions of eternal inflation. In this paper we study the Hawking-Moss tunneling in non-commutative eternal inflation using the stochastic approach. We obtain a brand new form of tunneling probability for this process and find that the Hawking-Moss tunneling is more unlikely to take place in the non-commutative case than in the usual one. We also conclude that the lifetime of a metastable de Sitter vacuum in the non-commutative spacetime is longer than that in the commutative case.

  3. Doubly special relativity and canonical transformations: Comment on 'Lagrangian for doubly special relativity particle and the role of noncommutativity'

    SciTech Connect

    Garcia, J. Antonio

    2007-08-15

    The aim of this Comment is to call to the attention of double special relativity (DSR) readers a basic fact. The introduction of noncommutative structures in problems like the one addressed by Ghosh [ Phys. Rev. D 74, 084019 (2006)] is not necessary for the understanding of DSR physics. It can be described just as the relativistic free particle problem in a different parametrization.

  4. The importance of structural complexity in coral reef ecosystems

    NASA Astrophysics Data System (ADS)

    Graham, N. A. J.; Nash, K. L.

    2013-06-01

    The importance of structural complexity in coral reefs has come to the fore with the global degradation of reef condition; however, the limited scale and replication of many studies have restricted our understanding of the role of complexity in the ecosystem. We qualitatively and quantitatively (where sufficient standardised data were available) assess the literature regarding the role of structural complexity in coral reef ecosystems. A rapidly increasing number of publications have studied the role of complexity in reef ecosystems over the past four decades, with a concomitant increase in the diversity of methods used to quantify structure. Quantitative analyses of existing data indicate a strong negative relationship between structural complexity and algal cover, which may reflect the important role complexity plays in enhancing herbivory by reef fishes. The cover of total live coral and branching coral was positively correlated with structural complexity. These habitat attributes may be creating much of the structure, resulting in a collinear relationship; however, there is also evidence of enhanced coral recovery from disturbances where structural complexity is high. Urchin densities were negatively correlated with structural complexity; a relationship that may be driven by urchins eroding reef structure or by their gregarious behaviour when in open space. There was a strong positive relationship between structural complexity and fish density and biomass, likely mediated through density-dependent competition and refuge from predation. More variable responses were found when assessing individual fish families, with all families examined displaying a positive relationship to structural complexity, but only half of these relationships were significant. Although only corroborated with qualitative data, structural complexity also seems to have a positive effect on two ecosystem services: tourism and shoreline protection. Clearly, structural complexity is an

  5. Laplace-Runge-Lenz vector in quantum mechanics in noncommutative space

    SciTech Connect

    Gáliková, Veronika; Kováčik, Samuel; Prešnajder, Peter

    2013-12-15

    The main point of this paper is to examine a “hidden” dynamical symmetry connected with the conservation of Laplace-Runge-Lenz vector (LRL) in the hydrogen atom problem solved by means of non-commutative quantum mechanics (NCQM). The basic features of NCQM will be introduced to the reader, the key one being the fact that the notion of a point, or a zero distance in the considered configuration space, is abandoned and replaced with a “fuzzy” structure in such a way that the rotational invariance is preserved. The main facts about the conservation of LRL vector in both classical and quantum theory will be reviewed. Finally, we will search for an analogy in the NCQM, provide our results and their comparison with the QM predictions. The key notions we are going to deal with are non-commutative space, Coulomb-Kepler problem, and symmetry.

  6. Complex Convective Thermal Fluxes and Vorticity Structure

    NASA Astrophysics Data System (ADS)

    Redondo, Jose M.; Tellez, Jackson; Sotillos, Laura; Lopez Gonzalez-Nieto, Pilar; Sanchez, Jesus M.; Furmanek, Petr; Diez, Margarita

    2015-04-01

    Local Diffusion and the topological structure of vorticity and velocity fields is measured in the transition from a homogeneous linearly stratified fluid to a cellular or layered structure by means of convective cooling and/or heating[1,2]. Patterns arise by setting up a convective flow generated by an array of Thermoelectric devices (Peltier/Seebeck cells) these are controlled by thermal PID generating a buoyant heat flux [2]. The experiments described here investigate high Prandtl number mixing using brine and fresh water in order to form density interfaces and low Prandtl number mixing with temperature gradients. The set of dimensionless parameters define conditions of numeric and small scale laboratory modeling of environmental flows. Fields of velocity, density and their gradients were computed and visualized [3,4]. When convective heating and cooling takes place the combination of internal waves and buoyant turbulence is much more complicated if the Rayleigh and Reynolds numbers are high in order to study entrainment and mixing. Using ESS and selfsimilarity structures in the velocity and vorticity fieds and intermittency [3,5] that forms in the non-homogeneous flow is related to mixing and stiring. The evolution of the mixing fronts are compared and the topological characteristics of the merging of plumes and jets in different configurations presenting detailed comparison of the evolution of RM and RT, Jets and Plumes in overall mixing. The relation between structure functions, fractal analysis and spectral analysis can be very useful to determine the evolution of scales. Experimental and numerical results on the advance of a mixing or nonmixing front occurring at a density interface due to body forces [6]and gravitational acceleration are analyzed considering the fractal and spectral structure of the fronts like in removable plate experiments for Rayleigh-Taylor flows. The evolution of the turbulent mixing layer and its complex configuration is studied

  7. Structure, dynamics, assembly, and evolution of protein complexes.

    PubMed

    Marsh, Joseph A; Teichmann, Sarah A

    2015-01-01

    The assembly of individual proteins into functional complexes is fundamental to nearly all biological processes. In recent decades, many thousands of homomeric and heteromeric protein complex structures have been determined, greatly improving our understanding of the fundamental principles that control symmetric and asymmetric quaternary structure organization. Furthermore, our conception of protein complexes has moved beyond static representations to include dynamic aspects of quaternary structure, including conformational changes upon binding, multistep ordered assembly pathways, and structural fluctuations occurring within fully assembled complexes. Finally, major advances have been made in our understanding of protein complex evolution, both in reconstructing evolutionary histories of specific complexes and in elucidating general mechanisms that explain how quaternary structure tends to evolve. The evolution of quaternary structure occurs via changes in self-assembly state or through the gain or loss of protein subunits, and these processes can be driven by both adaptive and nonadaptive influences.

  8. Noncommutative cosmological model in the presence of a phantom fluid

    NASA Astrophysics Data System (ADS)

    Oliveira-Neto, G.; Vaz, A. R.

    2017-03-01

    We study noncommutative classical Friedmann-Robertson-Walker cosmological models. The constant curvature of the spatial sections can be positive (k=1), negative (k=-1) or zero (k=0). The matter is represented by a perfect fluid with negative pressure, phantom fluid, which satisfies the equation of state p =α ρ, with α < -1, where p is the pressure and ρ is the energy density. We use Schutz's formalism in order to write the perfect fluid Hamiltonian. The noncommutativity is introduced by nontrivial Poisson brackets between few variables of the models. In order to recover a description in terms of commutative variables, we introduce variables transformations that depend on a noncommutative parameter (γ). The main motivation for the introduction of the noncommutativity is trying to explain the present accelerated expansion of the universe. We obtain the dynamical equations for these models and solve them. The solutions have four constants: γ, a parameter associated with the fluid energy C, k, α and the initial conditions of the models variables. For each value of α, we obtain different equations of motion. Then, we compare the evolution of the universe in the noncommutative models with the corresponding commutative ones (γ → 0). The results show that γ is very useful for describing an accelerating universe. We also obtain estimates for the noncommutative parameter γ . Then, using those values of γ, in one of the noncommutative cosmological models with a specific value of α, we compute the amount of time those universes would take to reach the big rip.

  9. Pair creation in noncommutative space-time

    NASA Astrophysics Data System (ADS)

    Hamil, B.; Chetouani, L.

    2016-09-01

    By taking two interactions, the Volkov plane wave and a constant electromagnetic field, the probability related to the process of pair creation from the vacuum is exactly and analytically determined via the Schwinger method in noncommutative space-time. For the plane wave, it is shown that the probability is simply null and for the electromagnetic wave it is found that the expression of the probability has a similar form to that obtained by Schwinger in a commutative space-time. For a certain critical value of H, the probability is simply equal to 1.

  10. Thermal transport in a noncommutative hydrodynamics

    SciTech Connect

    Geracie, M. Son, D. T.

    2015-03-15

    We find the hydrodynamic equations of a system of particles constrained to be in the lowest Landau level. We interpret the hydrodynamic theory as a Hamiltonian system with the Poisson brackets between the hydrodynamic variables determined from the noncommutativity of space. We argue that the most general hydrodynamic theory can be obtained from this Hamiltonian system by allowing the Righi-Leduc coefficient to be an arbitrary function of thermodynamic variables. We compute the Righi-Leduc coefficient at high temperatures and show that it satisfies the requirements of particle-hole symmetry, which we outline.

  11. Noncommutative q -photon-added coherent states

    NASA Astrophysics Data System (ADS)

    Dey, Sanjib; Hussin, Véronique

    2016-05-01

    We construct the photon-added coherent states of a noncommutative harmonic oscillator associated to a q -deformed oscillator algebra. Various nonclassical properties of the corresponding system are explored, first, by studying two different types of higher-order quadrature squeezing, namely, the Hillery type and the Hong-Mandel type, and second, by testing the sub-Poissonian nature of photon statistics in higher order with the help of the correlation function and the Mandel parameter. Also, we compare the behavior of different types of quadrature and photon number squeezing of our system with those of the ordinary harmonic oscillator by considering the same set of parameters.

  12. Lie algebra type noncommutative phase spaces are Hopf algebroids

    NASA Astrophysics Data System (ADS)

    Meljanac, Stjepan; Škoda, Zoran; Stojić, Martina

    2016-11-01

    For a noncommutative configuration space whose coordinate algebra is the universal enveloping algebra of a finite-dimensional Lie algebra, it is known how to introduce an extension playing the role of the corresponding noncommutative phase space, namely by adding the commuting deformed derivatives in a consistent and nontrivial way; therefore, obtaining certain deformed Heisenberg algebra. This algebra has been studied in physical contexts, mainly in the case of the kappa-Minkowski space-time. Here, we equip the entire phase space algebra with a coproduct, so that it becomes an instance of a completed variant of a Hopf algebroid over a noncommutative base, where the base is the enveloping algebra.

  13. Structurally simple complexes of CO2.

    PubMed

    Murphy, Luke J; Robertson, Katherine N; Kemp, Richard A; Tuononen, Heikki M; Clyburne, Jason A C

    2015-03-07

    The ability to bind CO2 through the formation of low-energy, easily-broken, bonds could prove invaluable in a variety of chemical contexts. For example, weak bonds to CO2 would greatly decrease the cost of the energy-intensive sorbent-regeneration step common to most carbon capture technologies. Furthermore, exploration of this field could lead to the discovery of novel CO2 chemistry. Reduction of complexed carbon dioxide might generate chemical feedstocks for the preparation of value-added products, particularly transportation fuels or fuel precursors. Implementation on a large scale could help to drastically reduce CO2 concentrations in the atmosphere. However, literature examples of weakly bonded complexes of CO2 are relatively few and true coordination complexes to a 'naked' CO2 fragment are nearly unheard of. In this review article, a variety of complexes of CO2 featuring diverse binding modes and reactivity will be examined. Topics covered include: (A) inclusion complexes of CO2 in porous materials. (B) Zwitterionic carbamates produced from the reaction of CO2 with polyamines. (C) Carbamate salts produced from reaction of CO2 with two equivalents of an amine. (D) Insertion products of CO2 into acid-base adducts (e.g., metal complexes). (E) Lewis acid-base activated CO2, such as frustrated Lewis pair complexes. (F) Simple base-CO2 adducts, wherein the base-CO2 bond is the only interaction formed. Complexes in the last category are of particular interest, and include imidazol-2-carboxylates (N-heterocyclic carbene adducts of CO2) as well as a few other examples that lie outside NHC chemistry.

  14. The Hawking-Page crossover in noncommutative anti-deSitter space

    NASA Astrophysics Data System (ADS)

    Nicolini, Piero; Torrieri, Giorgio

    2011-08-01

    We study the problem of a Schwarzschild-anti-deSitter black hole in a non-commutative geometry framework, thought to be an effective description of quantum-gravitational spacetime. As a first step we derive the noncommutative geometry inspired Schwarzschild-anti-deSitter solution. After studying the horizon structure, we find that the curvature singularity is smeared out by the noncommutative fluctuations. On the thermodynamics side, we show that the black hole temperature, instead of a divergent behavior at small scales, admits a maximum value. This fact implies an extension of the Hawking-Page transition into a van der Waals-like phase diagram, with a critical point at a critical cosmological constant size in Plank units and a smooth crossover thereafter. We speculate that, in the gauge-string dictionary, this corresponds to the confinement "critical point" in number of colors at finite number of flavors, a highly non-trivial parameter that can be determined through lattice simulations.

  15. Nonclassicality versus entanglement in a noncommutative space

    NASA Astrophysics Data System (ADS)

    Dey, Sanjib; Fring, Andreas; Hussin, Véronique

    2017-01-01

    Nonclassicality is an interesting property of light having applications in many different contexts of quantum optics, quantum information and computation. Nonclassical states produce substantial amount of reduced noise in optical communications. Furthermore, they often behave as sources of entangled quantum states, which are the most elementary requirement for quantum teleportation. We study various nonclassical properties of coherent states and Schrödinger cat states in a setting of noncommutative space resulting from the generalized uncertainty relation, first, in a complete analytical fashion and, later, by computing their entanglement entropies, which in turn provide supporting arguments behind our analytical results. By using standard theoretical frameworks, they are shown to produce considerably improved squeezing and nonclassicality and, hence, significantly higher amount of entanglement in comparison to the usual quantum mechanical models. Both the nonclassicality and the entanglement can be enhanced further by increasing the noncommutativity of the underlying space. In addition, we find as a by-product some rare explicit minimum uncertainty quadrature and number squeezed states, i.e., ideal squeezed states.

  16. Scalar field theory on noncommutative Snyder spacetime

    SciTech Connect

    Battisti, Marco Valerio; Meljanac, Stjepan

    2010-07-15

    We construct a scalar field theory on the Snyder noncommutative space-time. The symmetry underlying the Snyder geometry is deformed at the co-algebraic level only, while its Poincare algebra is undeformed. The Lorentz sector is undeformed at both the algebraic and co-algebraic level, but the coproduct for momenta (defining the star product) is non-coassociative. The Snyder-deformed Poincare group is described by a non-coassociative Hopf algebra. The definition of the interacting theory in terms of a nonassociative star product is thus questionable. We avoid the nonassociativity by the use of a space-time picture based on the concept of the realization of a noncommutative geometry. The two main results we obtain are (i) the generic (namely, for any realization) construction of the co-algebraic sector underlying the Snyder geometry and (ii) the definition of a nonambiguous self-interacting scalar field theory on this space-time. The first-order correction terms of the corresponding Lagrangian are explicitly computed. The possibility to derive Noether charges for the Snyder space-time is also discussed.

  17. Noncommutative accelerated multidimensional universe dominated by quintessence

    NASA Astrophysics Data System (ADS)

    El-Nabulsi, Ahmad Rami

    2010-04-01

    Noncommutative Geometry recently attracted growing interest of cosmologists, mainly after the greatest success of unifying the forces of nature into a single gravitational spectral action in a purely algebraic way, rather than as being an entirely new formalism. In the present work, we discuss a multidimensional Friedmann-Robertson-Walker flat universe in which the perfect fluid has a Gaussian profile in time and depends on a fundamental minimal length sqrt{θ} like ρ= ρ(0)exp (- t 2/4 θ) for some positive constant ρ(0). This special form is motivated by a more recent noncommutative inflationary cosmological model, which was found to be able to drive the universe through a bounce without the need of any scalar field. Furthermore, we conjecture that the generalized equation of state has the special form p= ω a m ρ- ρ,( ω, m)∈ℝ where a( t) is the scale factor. It was found that the expansion of the multidimensional universe accelerates in time and is dominated for very large time by quintessence. Many additional consequences are revealed and discussed in some detail.

  18. Constraining spacetime noncommutativity with primordial nucleosynthesis

    SciTech Connect

    Horvat, Raul; Trampetic, Josip

    2009-04-15

    We discuss a constraint on the scale {lambda}{sub NC} of noncommutative (NC) gauge field theory arising from consideration of the big bang nucleosynthesis of light elements. The propagation of neutrinos in the NC background described by an antisymmetric tensor {theta}{sup {mu}}{sup {nu}} does result in a tree-level vectorlike coupling to photons in a generation-independent manner, raising thus a possibility to have an appreciable contribution of three light right-handed (RH) fields to the energy density of the Universe at nucleosynthesis time. Considering elastic scattering processes of the RH neutrinos off charged plasma constituents at a given cosmological epoch, we obtain for a conservative limit on an effective number of additional doublet neutrinos {delta}N{sub {nu}}=1, a bound {lambda}{sub NC} > or approx. 3 TeV. With a more stringent requirement, {delta}N{sub {nu}} < or approx. 0.2, the bound is considerably improved, {lambda}{sub NC} > or approx. 10{sup 3} TeV. For our bounds the {theta} expansion of the NC action stays always meaningful, since the decoupling temperature of the RH species is perseveringly much less than the inferred bound for the scale of noncommutativity.

  19. What Makes Reading Difficult: The Complexity of Structures.

    ERIC Educational Resources Information Center

    Schmidt, Eunice L.

    The original version of the "Helen Keller Story" and a linguistically more complex version of it were used to test the hypothesis that reading comprehension is affected by the complexity of linguistic structures. Complexity was measured by four readability measures, the mean number of words per T-unit, and the Schmidt-Kittrell Linguistic…

  20. Atomic structure of the Y complex of the nuclear pore.

    PubMed

    Kelley, Kotaro; Knockenhauer, Kevin E; Kabachinski, Greg; Schwartz, Thomas U

    2015-05-01

    The nuclear pore complex (NPC) is the principal gateway for transport into and out of the nucleus. Selectivity is achieved through the hydrogel-like core of the NPC. The structural integrity of the NPC depends on ~15 architectural proteins, which are organized in distinct subcomplexes to form the >40-MDa ring-like structure. Here we present the 4.1-Å crystal structure of a heterotetrameric core element ('hub') of the Y complex, the essential NPC building block, from Myceliophthora thermophila. Using the hub structure together with known Y-complex fragments, we built the entire ~0.5-MDa Y complex. Our data reveal that the conserved core of the Y complex has six rather than seven members. Evolutionarily distant Y-complex assemblies share a conserved core that is very similar in shape and dimension, thus suggesting that there are closely related architectural codes for constructing the NPC in all eukaryotes.

  1. Gelled Complex Fluids: Combining Unique Structures with Mechanical Stability.

    PubMed

    Stubenrauch, Cosima; Gießelmann, Frank

    2016-03-01

    Gelled complex fluids are soft materials in which the microstructure of the complex fluid is combined with the mechanical stability of a gel. To obtain a gelled complex fluid one either adds a gelator to a complex fluid or replaces the solvent in a gel by a complex fluid. The most prominent example of a "natural" gelled complex fluid is the cell. There are various strategies by which one can form a gelled complex fluid; one such strategy is orthogonal self-assembly, that is, the independent but simultaneous formation of two coexisting self-assembled structures within one system. The aim of this Review is to describe the structure and potential applications of various man-made gelled complex fluids and to clarify whether or not the respective system is formed by orthogonal self-assembly.

  2. Noncommutative analogue Aharonov-Bohm effect and superresonance

    NASA Astrophysics Data System (ADS)

    Anacleto, M. A.; Brito, F. A.; Passos, E.

    2013-06-01

    We consider the idea of modeling a rotating acoustic black hole by an idealized draining bathtub vortex which is a planar circulating flow phenomenon with a sink at the origin. We find the acoustic metric for this phenomenon from a noncommutative Abelian Higgs model. As such the acoustic metric not only describes a rotating acoustic black hole but also inherits the noncommutative characteristic of the spacetime. We address the issues of superresonance and analogue Aharonov-Bohm (AB) effect in this background. We mainly show that the scattering of planar waves by a draining bathtub vortex leads to a modified AB effect and due to spacetime noncommutativity, the phase shift persists even in the limit where the parameters associated with the circulation and draining vanish. Finally, we also find that the analogue AB effect and superresonance are competing phenomena at a noncommutative spacetime.

  3. Exact master equation for a noncommutative Brownian particle

    SciTech Connect

    Costa Dias, Nuno Nuno Prata, Joao

    2009-01-15

    We derive the Hu-Paz-Zhang master equation for a Brownian particle linearly coupled to a bath of harmonic oscillators on the plane with spatial noncommutativity. The results obtained are exact to all orders in the noncommutative parameter. As a by-product we derive some miscellaneous results such as the equilibrium Wigner distribution for the reservoir of noncommutative oscillators, the weak coupling limit of the master equation and a set of sufficient conditions for strict purity decrease of the Brownian particle. Finally, we consider a high-temperature Ohmic model and obtain an estimate for the time scale of the transition from noncommutative to ordinary quantum mechanics. This scale is considerably smaller than the decoherence scale.

  4. Phase-space noncommutative formulation of Ozawa's uncertainty principle

    NASA Astrophysics Data System (ADS)

    Bastos, Catarina; Bernardini, Alex E.; Bertolami, Orfeu; Costa Dias, Nuno; Prata, João Nuno

    2014-08-01

    Ozawa's measurement-disturbance relation is generalized to a phase-space noncommutative extension of quantum mechanics. It is shown that the measurement-disturbance relations have additional terms for backaction evading quadrature amplifiers and for noiseless quadrature transducers. Several distinctive features appear as a consequence of the noncommutative extension: measurement interactions which are noiseless, and observables which are undisturbed by a measurement, or of independent intervention in ordinary quantum mechanics, may acquire noise, become disturbed by the measurement, or no longer be an independent intervention in noncommutative quantum mechanics. It is also found that there can be states which violate Ozawa's universal noise-disturbance trade-off relation, but verify its noncommutative deformation.

  5. On the non-commutative CP{sup 1} model

    SciTech Connect

    Lechtenfeld, Olaf; Maceda, Marco

    2010-07-12

    We present some results on the moduli space for the charge two-soliton solution of the non-commutative CP{sup 1} model. The associated Kaehler potential and its relation to the commutative case are discussed.

  6. Strong Planck constraints on braneworld and non-commutative inflation

    SciTech Connect

    Calcagni, Gianluca; Kuroyanagi, Sachiko; Ohashi, Junko; Tsujikawa, Shinji E-mail: skuro@rs.tus.ac.jp E-mail: shinji@rs.kagu.tus.ac.jp

    2014-03-01

    We place observational likelihood constraints on braneworld and non-commutative inflation for a number of inflaton potentials, using Planck, WMAP polarization and BAO data. Both braneworld and non-commutative scenarios of the kind considered here are limited by the most recent data even more severely than standard general-relativity models. At more than 95 % confidence level, the monomial potential V(φ)∝φ{sup p} is ruled out for p ≥ 2 in the Randall-Sundrum (RS) braneworld cosmology and, for p > 0, also in the high-curvature limit of the Gauss-Bonnet (GB) braneworld and in the infrared limit of non-commutative inflation, due to a large scalar spectral index. Some parameter values for natural inflation, small-varying inflaton models and Starobinsky inflation are allowed in all scenarios, although some tuning is required for natural inflation in a non-commutative spacetime.

  7. Structure of complexes between aluminum chloride and other chlorides, 2: Alkali-(chloroaluminates). Gaseous complexes

    NASA Technical Reports Server (NTRS)

    Hargittai, M.

    1980-01-01

    The structural chemistry of complexes between aluminum chloride and other metal chlorides is important both for practice and theory. Condensed-phase as well as vapor-phase complexes are of interest. Structural information on such complexes is reviewed. The first emphasis is given to the molten state because of its practical importance. Aluminum chloride forms volatile complexes with other metal chlorides and these vapor-phase complexes are dealt with in the second part. Finally, the variations in molecular shape and geometrical parameters are summarized.

  8. Calculus structure on the Lie conformal algebra complex and the variational complex

    SciTech Connect

    De Sole, Alberto; Hekmati, Pedram; Kac, Victor G.

    2011-05-15

    We construct a calculus structure on the Lie conformal algebra cochain complex. By restricting to degree one chains, we recover the structure of a g-complex introduced in [A. De Sole and V. G. Kac, Commun. Math. Phys. 292, 667 (2009)]. A special case of this construction is the variational calculus, for which we provide explicit formulas.

  9. Wedge-local quantum fields on a nonconstant noncommutative spacetime

    SciTech Connect

    Much, A.

    2012-08-15

    Within the framework of warped convolutions we deform the massless free scalar field. The deformation is performed by using the generators of the special conformal transformations. The investigation shows that the deformed field turns out to be wedge-local. Furthermore, it is shown that the spacetime induced by the deformation with the special conformal operators is nonconstant noncommutative. The noncommutativity is obtained by calculating the deformed commutator of the coordinates.

  10. Non-commutativity and Local Indistinguishability of Quantum States

    PubMed Central

    Ma, Teng; Zhao, Ming-Jing; Wang, Yao-Kun; Fei, Shao-Ming

    2014-01-01

    We study the local indistinguishability problem of quantum states. By introducing an easily calculated quantity, non-commutativity, we present an criterion which is both necessary and sufficient for the local indistinguishability of a complete set of pure orthogonal product states. A constructive distinguishing procedure to obtain the concrete local measurements and classical communications is given. The non-commutativity of ensembles can be also used to characterize the quantumness for classical-quantum or quantum-classical correlated states. PMID:25208830

  11. Spectral functionals, nonholonomic Dirac operators, and noncommutative Ricci flows

    SciTech Connect

    Vacaru, Sergiu I.

    2009-07-15

    We formulate a noncommutative generalization of the Ricci flow theory in the framework of spectral action approach to noncommutative geometry. Grisha Perelman's functionals are generated as commutative versions of certain spectral functionals defined by nonholonomic Dirac operators and corresponding spectral triples. We derive the formulas for spectral averaged energy and entropy functionals and state the conditions when such values describe (non)holonomic Riemannian configurations.

  12. Fractional Zero-Point Angular Momenta in Noncommutative Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Liu, Si-Jia; Zhang, Yu-Fei; Long, Zheng-Wen; Jing, Jian

    2016-09-01

    The charged particle confined by a harmonic potential in a noncommutative planar phase space interacting with a homogeneous dynamical magnetic field and Aharonov-Bohm potentials is studied. We find that the canonical orbital angular momenta of the reduced models, which are obtained by setting the mass and a dimensionless parameter to zero, take fractional values. These fractional angular momenta are not only determined by the flux inside the thin long solenoid but also affected by the noncommutativities of phase space.

  13. Background independent noncommutative gravity from Fedosov quantization of endomorphism bundle

    NASA Astrophysics Data System (ADS)

    Dobrski, Michał

    2017-04-01

    A model of noncommutative gravity is constructed by means of Fedosov deformation quantization of an endomorphism bundle. The fields describing noncommutativity—symplectic form and symplectic connection—are dynamical, and the resulting theory is coordinate covariant and background independent. Its interpretation in terms of a Seiberg–Witten map is provided. Also, a new action for ordinary (commutative) general relativity is given, which in the present context appears as a commutative limit of noncommutative theory.

  14. Cosmology and the noncommutative approach to the standard model

    SciTech Connect

    Nelson, William; Sakellariadou, Mairi

    2010-04-15

    We study cosmological consequences of the noncommutative approach to the standard model of particle physics. Neglecting the nonminimal coupling of the Higgs field to the curvature, noncommutative corrections to Einstein's equations are present only for inhomogeneous and anisotropic space-times. Considering the nonminimal coupling however, corrections are obtained even for background cosmologies. Links with dilatonic gravity as well as chameleon cosmology are briefly discussed, and potential experimental consequences are mentioned.

  15. Organizational Structure and Complex Problem Solving

    ERIC Educational Resources Information Center

    Becker, Selwyn W.; Baloff, Nicholas

    1969-01-01

    The problem-solving efficiency of different organization structures is discussed in relation to task requirements and the appropriate organizational behavior, to group adaptation to a task over time, and to various group characteristics. (LN)

  16. Noncommutative minisuperspace, gravity-driven acceleration, and kinetic inflation

    NASA Astrophysics Data System (ADS)

    Rasouli, S. M. M.; Moniz, Paulo Vargas

    2014-10-01

    In this paper, we introduce a noncommutative version of the Brans-Dicke (BD) theory and obtain the Hamiltonian equations of motion for a spatially flat Friedmann-Lemaître-Robertson-Walker universe filled with a perfect fluid. We focus on the case where the scalar potential as well as the ordinary matter sector are absent. Then, we investigate gravity-driven acceleration and kinetic inflation in this noncommutative BD cosmology. In contrast to the commutative case, in which the scale factor and BD scalar field are in a power-law form, in the noncommutative case the power-law scalar factor is multiplied by a dynamical exponential warp factor. This warp factor depends on the noncommutative parameter as well as the momentum conjugate associated to the BD scalar field. We show that the BD scalar field and the scale factor effectively depend on the noncommutative parameter. For very small values of this parameter, we obtain an appropriate inflationary solution, which can overcome problems within BD standard cosmology in a more efficient manner. Furthermore, a graceful exit from an early acceleration epoch towards a decelerating radiation epoch is provided. For late times, due to the presence of the noncommutative parameter, we obtain a zero acceleration epoch, which can be interpreted as the coarse-grained explanation.

  17. In situ structural analysis of the human nuclear pore complex.

    PubMed

    von Appen, Alexander; Kosinski, Jan; Sparks, Lenore; Ori, Alessandro; DiGuilio, Amanda L; Vollmer, Benjamin; Mackmull, Marie-Therese; Banterle, Niccolo; Parca, Luca; Kastritis, Panagiotis; Buczak, Katarzyna; Mosalaganti, Shyamal; Hagen, Wim; Andres-Pons, Amparo; Lemke, Edward A; Bork, Peer; Antonin, Wolfram; Glavy, Joseph S; Bui, Khanh Huy; Beck, Martin

    2015-10-01

    Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a formidable challenge and requires in situ structural biology approaches. Of approximately 30 nucleoporins (Nups), 15 are structured and form the Y and inner-ring complexes. These two major scaffolding modules assemble in multiple copies into an eight-fold rotationally symmetric structure that fuses the inner and outer nuclear membranes to form a central channel of ~60 nm in diameter. The scaffold is decorated with transport-channel Nups that often contain phenylalanine-repeat sequences and mediate the interaction with cargo complexes. Although the architectural arrangement of parts of the Y complex has been elucidated, it is unclear how exactly it oligomerizes in situ. Here we combine cryo-electron tomography with mass spectrometry, biochemical analysis, perturbation experiments and structural modelling to generate, to our knowledge, the most comprehensive architectural model of the human nuclear pore complex to date. Our data suggest previously unknown protein interfaces across Y complexes and to inner-ring complex members. We show that the transport-channel Nup358 (also known as Ranbp2) has a previously unanticipated role in Y-complex oligomerization. Our findings blur the established boundaries between scaffold and transport-channel Nups. We conclude that, similar to coated vesicles, several copies of the same structural building block--although compositionally identical--engage in different local sets of interactions and conformations.

  18. Structural Determination of Certain Novel ER Complexes

    DTIC Science & Technology

    2005-09-01

    and Parker, T. M. (1992). Hydrophobicity-induced pK shifts in elastin protein-based polymers . Biopolymers 32, 373-379. Webb, P., Nguyen, P., and...between the aligned H12 from different complex struc- Chemicals, Materials, and Plasmids tures (OHT-ER and GW-ER) were calculated using a python script...buffer consisting of 1.5%-2% ethylene were used. 100 nM of GW7604 were added to the cells 18-24 hr imine polymer , 100 mM trisodium citrate (pH 5.6-5.7

  19. Does Structural Complexity Necessarily Imply Processing Difficulty?

    ERIC Educational Resources Information Center

    Gayraud, Frederique; Martinie, Bruno

    2008-01-01

    Our goal is to establish a link between the time needed to plan a sentence containing an embedded clause and the structure of this sentence. Contrary to a traditional monolithic conception of subordination, three types of embeddings were considered, depending on their degree of syntactic integration: subcategorized, modifier and pseudo-embedded…

  20. Nanoscale structure of protamine/DNA complexes for gene delivery

    NASA Astrophysics Data System (ADS)

    Motta, Simona; Brocca, Paola; Del Favero, Elena; Rondelli, Valeria; Cantù, Laura; Amici, Augusto; Pozzi, Daniela; Caracciolo, Giulio

    2013-02-01

    Understanding the internal packing of gene carriers is a key-factor to realize both gene protection during transport and de-complexation at the delivery site. Here, we investigate the structure of complexes formed by DNA fragments and protamine, applied in gene delivery. We found that complexes are charge- and size-tunable aggregates, depending on the protamine/DNA ratio, hundred nanometers in size. Their compactness and fractal structure depend on the length of the DNA fragments. Accordingly, on the local scale, the sites of protamine/DNA complexation assume different morphologies, seemingly displaying clumping ability for the DNA network only for shorter DNA fragments.

  1. Structure, dynamics and function of nuclear pore complexes

    PubMed Central

    D’Angelo, M. A.; Hetzer, M. W.

    2009-01-01

    Nuclear pore complexes are large aqueous channels that penetrate the nuclear envelope, connecting the nuclear interior with the cytoplasm. Until recently, these macromolecular complexes were viewed as static structures whose only function was to control the molecular trafficking between the two compartments. It has now become evident that this simplistic scenario is inaccurate and that nuclear pore complexes are highly dynamic multiprotein assemblies involved in diverse cellular processes ranging from the organization of the cytoskeleton to gene expression. In this review, we will discuss the most recent developments in the nuclear pore complex field, focusing in the assembly, disassembly, maintenance and function of this macromolecular structure. PMID:18786826

  2. Complexity and dynamics of topological and community structure in complex networks

    NASA Astrophysics Data System (ADS)

    Berec, Vesna

    2017-01-01

    Complexity is highly susceptible to variations in the network dynamics, reflected on its underlying architecture where topological organization of cohesive subsets into clusters, system's modular structure and resulting hierarchical patterns, are cross-linked with functional dynamics of the system. Here we study connection between hierarchical topological scales of the simplicial complexes and the organization of functional clusters - communities in complex networks. The analysis reveals the full dynamics of different combinatorial structures of q-th-dimensional simplicial complexes and their Laplacian spectra, presenting spectral properties of resulting symmetric and positive semidefinite matrices. The emergence of system's collective behavior from inhomogeneous statistical distribution is induced by hierarchically ordered topological structure, which is mapped to simplicial complex where local interactions between the nodes clustered into subcomplexes generate flow of information that characterizes complexity and dynamics of the full system.

  3. Thermodynamics of a Charged Particle in a Noncommutative Plane in a Background Magnetic Field

    NASA Astrophysics Data System (ADS)

    Halder, Aslam; Gangopadhyay, Sunandan

    2017-03-01

    Landau system in noncommutative space has been considered. To take into account the issue of gauge invariance in noncommutative space, we incorporate the Seiberg-Witten map in our analysis. Generalised Bopp-shift transformation is then used to map the noncommutative system to its commutative equivalent system. In particular we have computed the partition function of the system and from this we obtained the susceptibility of the Landau system and found that the result gets modified by the spatial noncommutative parameter θ. We also investigate the de Hass-van Alphen effect in noncommutative space and observe that the oscillation of the magnetization and the susceptibility gets noncommutative corrections. Interestingly, the susceptibility in the noncommutative scenario is non-zero in the range of the magnetic field greater than the threshold value which is in contrast to its commutative counterpart. The results obtained are valid upto all orders in the noncommutative parameter θ.

  4. Reinforcing Visual Grouping Cues to Communicate Complex Informational Structure.

    PubMed

    Bae, Juhee; Watson, Benjamin

    2014-12-01

    In his book Multimedia Learning [7], Richard Mayer asserts that viewers learn best from imagery that provides them with cues to help them organize new information into the correct knowledge structures. Designers have long been exploiting the Gestalt laws of visual grouping to deliver viewers those cues using visual hierarchy, often communicating structures much more complex than the simple organizations studied in psychological research. Unfortunately, designers are largely practical in their work, and have not paused to build a complex theory of structural communication. If we are to build a tool to help novices create effective and well structured visuals, we need a better understanding of how to create them. Our work takes a first step toward addressing this lack, studying how five of the many grouping cues (proximity, color similarity, common region, connectivity, and alignment) can be effectively combined to communicate structured text and imagery from real world examples. To measure the effectiveness of this structural communication, we applied a digital version of card sorting, a method widely used in anthropology and cognitive science to extract cognitive structures. We then used tree edit distance to measure the difference between perceived and communicated structures. Our most significant findings are: 1) with careful design, complex structure can be communicated clearly; 2) communicating complex structure is best done with multiple reinforcing grouping cues; 3) common region (use of containers such as boxes) is particularly effective at communicating structure; and 4) alignment is a weak structural communicator.

  5. Spacetime singularity resolution in Snyder noncommutative space

    NASA Astrophysics Data System (ADS)

    Gorji, M. A.; Nozari, K.; Vakili, B.

    2014-04-01

    Inspired by quantum gravity proposals, we construct a deformed phase space which supports the UV and IR cutoffs. We show that the Liouville theorem is satisfied in the deformed phase space which allows us to formulate the thermodynamics of the early universe in the semiclassical regime. Applying the proposed method to the Snyder noncommutative space, we find a temperature dependent equation of state which opens a new window for the natural realization of inflation as a phase transition from the quantum gravity regime to the standard radiation dominated era. Also, we obtain finite energy and entropy densities for the Universe when at least the weak energy condition is satisfied. We show that there is a minimum size for the Universe which is proportional to the Planck length and consequently the big bang singularity is removed.

  6. Cosmological power spectrum in a noncommutative spacetime

    NASA Astrophysics Data System (ADS)

    Kothari, Rahul; Rath, Pranati K.; Jain, Pankaj

    2016-09-01

    We propose a generalized star product that deviates from the standard one when the fields are considered at different spacetime points by introducing a form factor in the standard star product. We also introduce a recursive definition by which we calculate the explicit form of the generalized star product at any number of spacetime points. We show that our generalized star product is associative and cyclic at linear order. As a special case, we demonstrate that our recursive approach can be used to prove the associativity of standard star products for same or different spacetime points. The introduction of a form factor has no effect on the standard Lagrangian density in a noncommutative spacetime because it reduces to the standard star product when spacetime points become the same. We show that the generalized star product leads to physically consistent results and can fit the observed data on hemispherical anisotropy in the cosmic microwave background radiation.

  7. A non-commuting stabilizer formalism

    SciTech Connect

    Ni, Xiaotong; Van den Nest, Maarten; Buerschaper, Oliver

    2015-05-15

    We propose a non-commutative extension of the Pauli stabilizer formalism. The aim is to describe a class of many-body quantum states which is richer than the standard Pauli stabilizer states. In our framework, stabilizer operators are tensor products of single-qubit operators drawn from the group 〈αI, X, S〉, where α = e{sup iπ/4} and S = diag(1, i). We provide techniques to efficiently compute various properties related to bipartite entanglement, expectation values of local observables, preparation by means of quantum circuits, parent Hamiltonians, etc. We also highlight significant differences compared to the Pauli stabilizer formalism. In particular, we give examples of states in our formalism which cannot arise in the Pauli stabilizer formalism, such as topological models that support non-Abelian anyons.

  8. A Structurally Characterized Organometallic Plutonium(IV) Complex.

    PubMed

    Apostolidis, Christos; Walter, Olaf; Vogt, Jochen; Liebing, Phil; Maron, Laurent; Edelmann, Frank T

    2017-03-30

    The blood-red plutonocene complex Pu(1,3-COT'')(1,4-COT'') (4; COT''=η(8) -bis(trimethylsilyl)cyclooctatetraenyl) has been synthesized by oxidation of the anionic sandwich complex Li[Pu(1,4-COT'')2 ] (3) with anhydrous cobalt(II) chloride. The first crystal structure determination of an organoplutonium(IV) complex revealed an asymmetric sandwich structure for 4 where one COT'' ring is 1,3-substituted while the other retains the original 1,4-substitution pattern. The electronic structure of 4 has been elucidated by a computational study, revealing a probable cause for the unexpected silyl group migration.

  9. Toward structural elucidation of the gamma-secretase complex

    SciTech Connect

    Li, H.; Wolfe, M. S.; Selkoe, D. J.

    2009-03-11

    {gamma}-Secretase is an intramembrane protease complex that mediates the Notch signaling pathway and the production of amyloid {beta}-proteins. As such, this enzyme has emerged as an important target for development of novel therapeutics for Alzheimer disease and cancer. Great progress has been made in the identification and characterization of the membrane complex and its biological functions. One major challenge now is to illuminate the structure of this fascinating and important protease at atomic resolution. Here, we review recent progress on biochemical and biophysical probing of the structure of the four-component complex and discuss obstacles and potential pathways toward elucidating its detailed structure.

  10. Toward structural elucidation of the γ-secretase complex

    PubMed Central

    Li, Huilin; Wolfe, Michael S.; Selkoe, Dennis J.

    2009-01-01

    γ-Secretase is an intramembrane protease complex that mediates the Notch signaling pathway and the production of amyloid β-proteins. As such, this enzyme has emerged as an important target for development of novel therapeutics for Alzheimer disease and cancer. Great progress has been made in the identification and characterization of the membrane complex and its biological functions. One major challenge now is to illuminate the structure of this fascinating and important protease at atomic resolution. Here, we review recent progress on biochemical and biophysical probing of the structure of the four-component complex and discuss barriers and potential pathways toward elucidating its detailed structure. PMID:19278647

  11. Structure and function of complex brain networks.

    PubMed

    Sporns, Olaf

    2013-09-01

    An increasing number of theoretical and empirical studies approach the function of the human brain from a network perspective. The analysis of brain networks is made feasible by the development of new imaging acquisition methods as well as new tools from graph theory and dynamical systems. This review surveys some of these methodological advances and summarizes recent findings on the architecture of structural and functional brain networks. Studies of the structural connectome reveal several modules or network communities that are interlinked by hub regions mediating communication processes between modules. Recent network analyses have shown that network hubs form a densely linked collective called a "rich club," centrally positioned for attracting and dispersing signal traffic. In parallel, recordings of resting and task-evoked neural activity have revealed distinct resting-state networks that contribute to functions in distinct cognitive domains. Network methods are increasingly applied in a clinical context, and their promise for elucidating neural substrates of brain and mental disorders is discussed.

  12. Classical limits of quantum mechanics on a non-commutative configuration space

    SciTech Connect

    Benatti, Fabio; Gouba, Laure

    2013-06-15

    We consider a model of non-commutative quantum mechanics given by two harmonic oscillators over a non-commutative two dimensional configuration space. We study possible ways of removing the non-commutativity based on the classical limit context known as anti-Wick quantization. We show that removal of non-commutativity from the configuration space and from the canonical operators is not commuting operation.

  13. Structural and dynamical properties of complex networks

    NASA Astrophysics Data System (ADS)

    Ghoshal, Gourab

    Recent years have witnessed a substantial amount of interest within the physics community in the properties of networks. Techniques from statistical physics coupled with the widespread availability of computing resources have facilitated studies ranging from large scale empirical analysis of the worldwide web, social networks, biological systems, to the development of theoretical models and tools to explore the various properties of these systems. Following these developments, in this dissertation, we present and solve for a diverse set of new problems, investigating the structural and dynamical properties of both model and real world networks. We start by defining a new metric to measure the stability of network structure to disruptions, and then using a combination of theory and simulation study its properties in detail on artificially generated networks; we then compare our results to a selection of networks from the real world and find good agreement in most cases. In the following chapter, we propose a mathematical model that mimics the structure of popular file-sharing websites such as Flickr and CiteULike and demonstrate that many of its properties can solved exactly in the limit of large network size. The remaining part of the dissertation primarily focuses on the dynamical properties of networks. We first formulate a model of a network that evolves under the addition and deletion of vertices and edges, and solve for the equilibrium degree distribution for a variety of cases of interest. We then consider networks whose structure can be manipulated by adjusting the rules by which vertices enter and leave the network. We focus in particular on degree distributions and show that, with some mild constraints, it is possible by a suitable choice of rules to arrange for the network to have any degree distribution we desire. In addition we define a simple local algorithm by which appropriate rules can be implemented in practice. Finally, we conclude our

  14. Structure and function of complex brain networks

    PubMed Central

    Sporns, Olaf

    2013-01-01

    An increasing number of theoretical and empirical studies approach the function of the human brain from a network perspective. The analysis of brain networks is made feasible by the development of new imaging acquisition methods as well as new tools from graph theory and dynamical systems. This review surveys some of these methodological advances and summarizes recent findings on the architecture of structural and functional brain networks. Studies of the structural connectome reveal several modules or network communities that are interlinked by hub regions mediating communication processes between modules. Recent network analyses have shown that network hubs form a densely linked collective called a “rich club,” centrally positioned for attracting and dispersing signal traffic. In parallel, recordings of resting and task-evoked neural activity have revealed distinct resting-state networks that contribute to functions in distinct cognitive domains. Network methods are increasingly applied in a clinical context, and their promise for elucidating neural substrates of brain and mental disorders is discussed. PMID:24174898

  15. Microbial mediation of complex subterranean mineral structures

    PubMed Central

    Tisato, Nicola; Torriani, Stefano F. F.; Monteux, Sylvain; Sauro, Francesco; De Waele, Jo; Tavagna, Maria Luisa; D’Angeli, Ilenia M.; Chailloux, Daniel; Renda, Michel; Eglinton, Timothy I.; Bontognali, Tomaso R. R.

    2015-01-01

    Helictites—an enigmatic type of mineral structure occurring in some caves—differ from classical speleothems as they develop with orientations that defy gravity. While theories for helictite formation have been forwarded, their genesis remains equivocal. Here, we show that a remarkable suite of helictites occurring in Asperge Cave (France) are formed by biologically-mediated processes, rather than abiotic processes as had hitherto been proposed. Morphological and petro-physical properties are inconsistent with mineral precipitation under purely physico-chemical control. Instead, microanalysis and molecular-biological investigation reveals the presence of a prokaryotic biofilm intimately associated with the mineral structures. We propose that microbially-influenced mineralization proceeds within a gliding biofilm which serves as a nucleation site for CaCO3, and where chemotaxis influences the trajectory of mineral growth, determining the macroscopic morphology of the speleothems. The influence of biofilms may explain the occurrence of similar speleothems in other caves worldwide, and sheds light on novel biomineralization processes. PMID:26510667

  16. When complex neuronal structures may not matter

    PubMed Central

    Otopalik, Adriane G; Sutton, Alexander C; Banghart, Matthew; Marder, Eve

    2017-01-01

    Much work has explored animal-to-animal variability and compensation in ion channel expression. Yet, little is known regarding the physiological consequences of morphological variability. We quantify animal-to-animal variability in cable lengths (CV = 0.4) and branching patterns in the Gastric Mill (GM) neuron, an identified neuron type with highly-conserved physiological properties in the crustacean stomatogastric ganglion (STG) of Cancer borealis. We examined passive GM electrotonic structure by measuring the amplitudes and apparent reversal potentials (Erevs) of inhibitory responses evoked with focal glutamate photo-uncaging in the presence of TTX. Apparent Erevs were relatively invariant across sites (mean CV ± SD = 0.04 ± 0.01; 7–20 sites in each of 10 neurons), which ranged between 100–800 µm from the somatic recording site. Thus, GM neurons are remarkably electrotonically compact (estimated λ > 1.5 mm). Electrotonically compact structures, in consort with graded transmission, provide an elegant solution to observed morphological variability in the STG. DOI: http://dx.doi.org/10.7554/eLife.23508.001 PMID:28165322

  17. Microbial mediation of complex subterranean mineral structures.

    PubMed

    Tisato, Nicola; Torriani, Stefano F F; Monteux, Sylvain; Sauro, Francesco; De Waele, Jo; Tavagna, Maria Luisa; D'Angeli, Ilenia M; Chailloux, Daniel; Renda, Michel; Eglinton, Timothy I; Bontognali, Tomaso R R

    2015-10-29

    Helictites--an enigmatic type of mineral structure occurring in some caves--differ from classical speleothems as they develop with orientations that defy gravity. While theories for helictite formation have been forwarded, their genesis remains equivocal. Here, we show that a remarkable suite of helictites occurring in Asperge Cave (France) are formed by biologically-mediated processes, rather than abiotic processes as had hitherto been proposed. Morphological and petro-physical properties are inconsistent with mineral precipitation under purely physico-chemical control. Instead, microanalysis and molecular-biological investigation reveals the presence of a prokaryotic biofilm intimately associated with the mineral structures. We propose that microbially-influenced mineralization proceeds within a gliding biofilm which serves as a nucleation site for CaCO3, and where chemotaxis influences the trajectory of mineral growth, determining the macroscopic morphology of the speleothems. The influence of biofilms may explain the occurrence of similar speleothems in other caves worldwide, and sheds light on novel biomineralization processes.

  18. Microbial mediation of complex subterranean mineral structures

    NASA Astrophysics Data System (ADS)

    Tisato, Nicola; Torriani, Stefano F. F.; Monteux, Sylvain; Sauro, Francesco; de Waele, Jo; Tavagna, Maria Luisa; D'Angeli, Ilenia M.; Chailloux, Daniel; Renda, Michel; Eglinton, Timothy I.; Bontognali, Tomaso R. R.

    2015-10-01

    Helictites—an enigmatic type of mineral structure occurring in some caves—differ from classical speleothems as they develop with orientations that defy gravity. While theories for helictite formation have been forwarded, their genesis remains equivocal. Here, we show that a remarkable suite of helictites occurring in Asperge Cave (France) are formed by biologically-mediated processes, rather than abiotic processes as had hitherto been proposed. Morphological and petro-physical properties are inconsistent with mineral precipitation under purely physico-chemical control. Instead, microanalysis and molecular-biological investigation reveals the presence of a prokaryotic biofilm intimately associated with the mineral structures. We propose that microbially-influenced mineralization proceeds within a gliding biofilm which serves as a nucleation site for CaCO3, and where chemotaxis influences the trajectory of mineral growth, determining the macroscopic morphology of the speleothems. The influence of biofilms may explain the occurrence of similar speleothems in other caves worldwide, and sheds light on novel biomineralization processes.

  19. Remarkable luminescence properties of lanthanide complexes with asymmetric dodecahedron structures.

    PubMed

    Miyata, Kohei; Nakagawa, Tetsuya; Kawakami, Ryuhei; Kita, Yuki; Sugimoto, Katsufumi; Nakashima, Takuya; Harada, Takashi; Kawai, Tsuyoshi; Hasegawa, Yasuchika

    2011-01-10

    The distorted coordination structures and luminescence properties of novel lanthanide complexes with oxo-linked bidentate phosphane oxide ligands--4,5-bis(diphenylphosphoryl)-9,9-dimethylxanthene (xantpo), 4,5-bis(di-tert-butylphosphoryl)-9,9-dimethylxanthene (tBu-xantpo), and bis[(2-diphenylphosphoryl)phenyl] ether (dpepo)--and low-vibrational frequency hexafluoroacetylacetonato (hfa) ligands are reported. The lanthanide complexes exhibit characteristic square antiprism and trigonal dodecahedron structures with eight-coordinated oxygen atoms. The luminescence properties of these complexes are characterized by their emission quantum yields, emission lifetimes, and their radiative and nonradiative rate constants. Lanthanide complexes with dodecahedron structures offer markedly high emission quantum yields (Eu: 55-72 %, Sm: 2.4-5.0 % in [D(6)]acetone) due to enhancement of the electric dipole transition and suppression of vibrational relaxation. These remarkable luminescence properties are elucidated in terms of their distorted coordination structures.

  20. Toward understanding the structure of the vertebrate nuclear pore complex.

    PubMed

    Beck, Martin; Glavy, Joseph S

    2014-01-01

    Nuclear pore complexes are large macromolecular assemblies that facilitate the nucleocytoplasmic exchange of macromolecules. Because of their intricate composition, membrane association, and sheer size, the integration of various, complementary structure determination approaches is a prerequisite for elucidating their structure. We have recently employed such an integrated strategy to analyze the scaffold structure of the cytoplasmic and nuclear rings of the human nuclear pore complex. In this extra view, we highlight two specific aspects of this work: the power of electron microscopy for bridging different resolution regimes and the importance of post-translational modifications for regulating nucleoporin interactions. We review recent technological developments and give a perspective toward future structure determination approaches.

  1. Mesoscopic hydrothermodynamics of complex-structured materials

    NASA Astrophysics Data System (ADS)

    Vasconcellos, Áurea R.; Silva, A. A. P.; Luzzi, Roberto; Casas-Vázquez, J.; Jou, David

    2013-10-01

    Some experimental results in the study of disordered systems, polymeric fluids, solutions of micelles and surfactants, ionic-glass conductors, and others show a hydrodynamic behavior labeled “anomalous” with properties described by some kind of fractional power laws in place of the standard ones. This is a consequence of the fractal-like structure that is present in these systems of which we do not have a detailed description, thus impairing the application of the conventional ensemble formalism of statistical mechanics. In order to obtain a physical picture of the phenomenon for making predictions which may help with technological and industrial decisions, one may resort to different styles (so-called nonconventional) in statistical mechanics. In that way can be introduced a theory for handling such impaired situations, a nonconventional mesoscopic hydrothermodynamics (MHT). We illustrate the question presenting an application in a contracted description of such nonconventional MHT, consisting in the use of the Renyi approach to derive a set of coupled nonstandard evolution equations, one for the density, a nonconventional Maxwell-Cattaneo equation, which in a limiting case goes over a non-Fickian diffusion equation, and other for the velocity in fluids under forced flow. For illustration the theory is applied to the study of the hydrodynamic motion in several soft-matter systems under several conditions such as streaming flow appearing in electrophoretic techniques and flow generated by harmonic forces arising in optical traps. The equivalence with Lévy processes is discussed and comparison with experiment is done.

  2. The Structure Inventory of the Nuclear Pore Complex.

    PubMed

    Schwartz, Thomas U

    2016-05-22

    The nuclear pore complex (NPC) is the principal gateway for molecular exchange between nucleus and cytoplasm across the nuclear envelope. Due to its sheer size of estimated 50-112MDa and its complex buildup from about 500-1000 individual proteins, it is a difficult object to study for structural biologists. Here, I review the extensive ensemble of high-resolution structures of the building blocks of the NPC. Concurrent with the increase in size and complexity, these latest, large structures and assemblies can now be used as the basis for hybrid approaches, primarily in combination with cryo-electron microscopic analysis, generating the first structure-based assembly models of the NPC. Going forward, the structures will be critically important for a detailed analysis of the NPC, including function, evolution, and assembly.

  3. Calculus structure on the Lie conformal algebra complex and the variational complex

    NASA Astrophysics Data System (ADS)

    De Sole, Alberto; Hekmati, Pedram; Kac, Victor G.

    2011-05-01

    We construct a calculus structure on the Lie conformal algebra cochain complex. By restricting to degree one chains, we recover the structure of a {mathfrak g}-complex introduced in [A. De Sole and V. G. Kac, Commun. Math. Phys. 292, 667 (2009), 10.1007/s00220-009-0886-1]. A special case of this construction is the variational calculus, for which we provide explicit formulas.

  4. Photonic crystals, light manipulation, and imaging in complex nematic structures

    NASA Astrophysics Data System (ADS)

    Ravnik, Miha; Å timulak, Mitja; Mur, Urban; Čančula, Miha; Čopar, Simon; Žumer, Slobodan

    2016-03-01

    Three selected approaches for manipulation of light by complex nematic colloidal and non-colloidal structures are presented using different own custom developed theoretical and modelling approaches. Photonic crystals bands of distorted cholesteric liquid crystal helix and of nematic colloidal opals are presented, also revealing distinct photonic modes and density of states. Light propagation along half-integer nematic disclinations is shown with changes in the light polarization of various winding numbers. As third, simulated light transmission polarization micrographs of nematic torons are shown, offering a new insight into the complex structure characterization. Finally, this work is a contribution towards using complex soft matter in optics and photonics for advanced light manipulation.

  5. Modeling of Protein Binary Complexes Using Structural Mass Spectrometry Data

    SciTech Connect

    Amisha Kamal,J.; Chance, M.

    2008-01-01

    In this article, we describe a general approach to modeling the structure of binary protein complexes using structural mass spectrometry data combined with molecular docking. In the first step, hydroxyl radical mediated oxidative protein footprinting is used to identify residues that experience conformational reorganization due to binding or participate in the binding interface. In the second step, a three-dimensional atomic structure of the complex is derived by computational modeling. Homology modeling approaches are used to define the structures of the individual proteins if footprinting detects significant conformational reorganization as a function of complex formation. A three-dimensional model of the complex is constructed from these binary partners using the ClusPro program, which is composed of docking, energy filtering, and clustering steps. Footprinting data are used to incorporate constraints--positive and/or negative--in the docking step and are also used to decide the type of energy filter--electrostatics or desolvation--in the successive energy-filtering step. By using this approach, we examine the structure of a number of binary complexes of monomeric actin and compare the results to crystallographic data. Based on docking alone, a number of competing models with widely varying structures are observed, one of which is likely to agree with crystallographic data. When the docking steps are guided by footprinting data, accurate models emerge as top scoring. We demonstrate this method with the actin/gelsolin segment-1 complex. We also provide a structural model for the actin/cofilin complex using this approach which does not have a crystal or NMR structure.

  6. Preparation and Structural Properties of InIII–H Complexes

    PubMed Central

    Sickerman, Nathaniel S.; Henry, Renée M.; Ziller, Joseph W.

    2013-01-01

    The use of the tripodal ligands tris[(N'-tert-butylureaylato)-N-ethyl]aminato ([H3buea]3−) and the sulfonamide-based N,N',N"-[2,2',2"-nitrilotris(ethane-2,1-diyl)]tris(2,4,6-trimethylbenzene-sulfonamidato) ([MST]3−) has led to the synthesis of two structurally distinct In(III)–OH complexes. The first example of a five-coordinate indium(III) complex with a terminal hydroxide ligand, K[InIIIH3buea(OH)], was prepared by addition of In(OAc)3 and water to a deprotonated solution of H6buea. X-ray diffraction analysis, as well as FTIR and 1H NMR spectroscopic methods, provided evidence for the formation of a monomeric In(III)–OH complex. The complex contains an intramolecular hydrogen bonding (H-bonding) network involving the In(III)–OH unit and [H3buea]3− ligand, which aided in isolation of the complex. Isotope labeling studies verified the source of the hydroxo ligand as water. Treatment of the [InIIIMST] complex with a mixture of 15-crown-5 ether and NaOH led to isolation of the complex [15-crown-5⊃NaI-(μ-OH)-InIIIMST], whose solid-state structure was confirmed using X-ray diffraction methods. Nuclear magnetic resonance studies on this complex suggest it retains its heterobimetallic structure in solution. PMID:25309019

  7. On the complexity and the information content of cosmic structures

    NASA Astrophysics Data System (ADS)

    Vazza, F.

    2017-03-01

    The emergence of cosmic structure is commonly considered one of the most complex phenomena in nature. However, this complexity has never been defined nor measured in a quantitative and objective way. In this work, we propose a method to measure the information content of cosmic structure and to quantify the complexity that emerges from it, based on Information Theory. The emergence of complex evolutionary patterns is studied with a statistical symbolic analysis of the datastream produced by state-of-the-art cosmological simulations of forming galaxy clusters. This powerful approach allows us to measure how many bits of information is necessary to predict the evolution of energy fields in a statistical way, and it offers a simple way to quantify when, where and how the cosmic gas behaves in complex ways. The most complex behaviours are found in the peripheral regions of galaxy clusters, where supersonic flows drive shocks and large energy fluctuations over a few tens of million years. Describing the evolution of magnetic energy requires at least twice as large amount of bits as required for the other energy fields. When radiative cooling and feedback from galaxy formation are considered, the cosmic gas is overall found to double its degree of complexity. In the future, Cosmic Information Theory can significantly increase our understanding of the emergence of cosmic structure as it represents an innovative framework to design and analyse complex simulations of the Universe in a simple, yet powerful way.

  8. Structure and Dynamics of Antigenic Peptides in Complex with TAP

    PubMed Central

    Lehnert, Elisa; Tampé, Robert

    2017-01-01

    The transporter associated with antigen processing (TAP) selectively translocates antigenic peptides into the endoplasmic reticulum. Loading onto major histocompatibility complex class I molecules and proofreading of these bound epitopes are orchestrated within the macromolecular peptide-loading complex, which assembles on TAP. This heterodimeric ABC-binding cassette (ABC) transport complex is therefore a major component in the adaptive immune response against virally or malignantly transformed cells. Its pivotal role predestines TAP as a target for infectious diseases and malignant disorders. The development of therapies or drugs therefore requires a detailed comprehension of structure and function of this ABC transporter, but our knowledge about various aspects is still insufficient. This review highlights recent achievements on the structure and dynamics of antigenic peptides in complex with TAP. Understanding the binding mode of antigenic peptides in the TAP complex will crucially impact rational design of inhibitors, drug development, or vaccination strategies. PMID:28194151

  9. Structural and evolutionary versatility in protein complexes with uneven stoichiometry.

    PubMed

    Marsh, Joseph A; Rees, Holly A; Ahnert, Sebastian E; Teichmann, Sarah A

    2015-03-16

    Proteins assemble into complexes with diverse quaternary structures. Although most heteromeric complexes of known structure have even stoichiometry, a significant minority have uneven stoichiometry--that is, differing numbers of each subunit type. To adopt this uneven stoichiometry, sequence-identical subunits must be asymmetric with respect to each other, forming different interactions within the complex. Here we first investigate the occurrence of uneven stoichiometry, demonstrating that it is common in vitro and is likely to be common in vivo. Next, we elucidate the structural determinants of uneven stoichiometry, identifying six different mechanisms by which it can be achieved. Finally, we study the frequency of uneven stoichiometry across evolution, observing a significant enrichment in bacteria compared with eukaryotes. We show that this arises due to a general increased tendency for bacterial proteins to self-assemble and form homomeric interactions, even within the context of a heteromeric complex.

  10. Stability analysis of lower dimensional gravastars in noncommutative geometry

    NASA Astrophysics Data System (ADS)

    Banerjee, Ayan; Hansraj, Sudan

    2016-11-01

    The Bañados et al. (Phys. Rev. Lett 69:1849, 1992), black hole solution is revamped from the Einstein field equations in (2 + 1)-dimensional anti-de Sitter spacetime, in a context of noncommutative geometry (Phys. Rev. D 87:084014, 2013). In this article, we explore the exact gravastar solutions in three-dimensional anti-de Sitter space given in the same geometry. As a first step we derive BTZ solution assuming the source of energy density as point-like structures in favor of smeared objects, where the particle mass M, is diffused throughout a region of linear size √{α } and is described by a Gaussian function of finite width rather than a Dirac delta function. We matched our interior solution to an exterior BTZ spacetime at a junction interface situated outside the event horizon. Furthermore, a stability analysis is carried out for the specific case when χ < 0. 214 under radial perturbations about the static equilibrium solutions. To give theoretical support we are also trying to explore their physical properties and characteristics.

  11. Noncommutative quantum mechanics in a time-dependent background

    NASA Astrophysics Data System (ADS)

    Dey, Sanjib; Fring, Andreas

    2014-10-01

    We investigate a quantum mechanical system on a noncommutative space for which the structure constant is explicitly time dependent. Any autonomous Hamiltonian on such a space acquires a time-dependent form in terms of the conventional canonical variables. We employ the Lewis-Riesenfeld method of invariants to construct explicit analytical solutions for the corresponding time-dependent Schrödinger equation. The eigenfunctions are expressed in terms of the solutions of variants of the nonlinear Ermakov-Pinney equation and discussed in detail for various types of background fields. We utilize the solutions to verify a generalized version of Heisenberg's uncertainty relations for which the lower bound becomes a time-dependent function of the background fields. We study the variance for various states, including standard Glauber coherent states with their squeezed versions and Gaussian Klauder coherent states resembling a quasiclassical behavior. No type of coherent state appears to be optimal in general with regard to achieving minimal uncertainties, as this feature turns out to be background field dependent.

  12. Structural evaluation of crystalline ternary γ-cyclodextrin complex.

    PubMed

    Higashi, Kenjirou; Ideura, Saori; Waraya, Haruka; Moribe, Kunikazu; Yamamoto, Keiji

    2011-01-01

    The structure of a crystalline γ-cyclodextrin (γ-CD) ternary complex containing salicylic acid (SA) and flurbiprofen (FBP) prepared by sealed heating was investigated. FBP/γ-CD inclusion complex was prepared by coprecipitation; its molar ratio was determined as 1/1. Powder X-ray diffraction measurements showed that the molecular packing of γ-CD changed from hexagonal to monoclinic columnar form by sealed heating of SA with dried FBP/γ-CD inclusion complex, indicating ternary complex formation. The stoichiometry of SA/FBP/γ-CD was estimated as 2/1/1. Solid-state transformation of γ-CD molecular packing upon water vapor adsorption and desorption was irreversible for this ternary complex, in contrast to the reversible transition for the FBP/γ-CD inclusion complex. The ternary complex contained one FBP molecule in the cavity of γ-CD and two SA molecules in the intermolecular space between neighboring γ-CD column stacks. Infrared and (13) C solid-state NMR spectroscopies revealed that the molecular states of SA and FBP changed upon ternary complex formation. In the complex, dimer FBP molecules were sandwiched between two γ-CD molecules whereas each monomer SA molecule was present in the intermolecular space of γ-CD. Ternary complex formation was also observed for other drug-guest systems using naproxen and ketoprofen. Thus, the complex can be used to formulate variety of drugs.

  13. Instantons, quivers and noncommutative Donaldson-Thomas theory

    NASA Astrophysics Data System (ADS)

    Cirafici, Michele; Sinkovics, Annamaria; Szabo, Richard J.

    2011-12-01

    We construct noncommutative Donaldson-Thomas invariants associated with abelian orbifold singularities by analyzing the instanton contributions to a six-dimensional topological gauge theory. The noncommutative deformation of this gauge theory localizes on noncommutative instantons which can be classified in terms of three-dimensional Young diagrams with a colouring of boxes according to the orbifold group. We construct a moduli space for these gauge field configurations which allows us to compute its virtual numbers via the counting of representations of a quiver with relations. The quiver encodes the instanton dynamics of the noncommutative gauge theory, and is associated to the geometry of the singularity via the generalized McKay correspondence. The index of BPS states which compute the noncommutative Donaldson-Thomas invariants is realized via topological quantum mechanics based on the quiver data. We illustrate these constructions with several explicit examples, involving also higher rank Coulomb branch invariants and geometries with compact divisors, and connect our approach with other ones in the literature.

  14. Statistical energy analysis of complex structures, phase 2

    NASA Technical Reports Server (NTRS)

    Trudell, R. W.; Yano, L. I.

    1980-01-01

    A method for estimating the structural vibration properties of complex systems in high frequency environments was investigated. The structure analyzed was the Materials Experiment Assembly, (MEA), which is a portion of the OST-2A payload for the space transportation system. Statistical energy analysis (SEA) techniques were used to model the structure and predict the structural element response to acoustic excitation. A comparison of the intial response predictions and measured acoustic test data is presented. The conclusions indicate that: the SEA predicted the response of primary structure to acoustic excitation over a wide range of frequencies; and the contribution of mechanically induced random vibration to the total MEA is not significant.

  15. Repression and activation by multiprotein complexes that alter chromatin structure.

    PubMed

    Kingston, R E; Bunker, C A; Imbalzano, A N

    1996-04-15

    Recent studies have provided strong evidence that macromolecular complexes are used in the cell to remodel chromatin structure during activation and to create an inaccessible structure during repression, Although there is not yet any rigorous demonstration that modification of chromatin structure plays a direct, causal role in either activation or repression, there is sufficient smoke to indicate the presence of a blazing inferno nearby. It is clear that complexes that remodel chromatin are tractable in vitro; hopefully this will allow the establishment of systems that provide a direct analysis of the role that remodeling might play in activation. These studies indicate that establishment of functional systems to corroborate the elegant genetic studies on repression might also be tractable. As the mechanistic effects of these complexes are sorted out, it will become important to understand how the complexes are regulated. In many of the instances discussed above, the genes whose products make up these complexes were identified in genetic screens for effects on developmental processes. This implies a regulation of the activity of these complexes in response to developmental cues and further implies that the work to fully understand these complexes will occupy a generation of scientists.

  16. The Ccr4-Not Complex: Architecture and Structural Insights.

    PubMed

    Collart, Martine A; Panasenko, Olesya O

    2017-01-01

    The Ccr4-Not complex is an essential multi-subunit protein complex that plays a fundamental role in eukaryotic mRNA metabolism and has a multitude of different roles that impact eukaryotic gene expression . It has a conserved core of three Not proteins, the Ccr4 protein, and two Ccr4 associated factors, Caf1 and Caf40. A fourth Not protein, Not4, is conserved, but is only a stable subunit of the complex in yeast. Certain subunits have been duplicated during evolution, with functional divergence, such as Not3 in yeast, and Ccr4 or Caf1 in human. However the complex includes only one homolog for each protein. In addition, species-specific subunits are part of the complex, such as Caf130 in yeast or Not10 and Not11 in human. Two conserved catalytic functions are associated with the complex, deadenylation and ubiquitination . The complex adopts an L-shaped structure, in which different modules are bound to a large Not1 scaffold protein. In this chapter we will summarize our current knowledge of the architecture of the complex and of the structure of its constituents.

  17. Geometric modeling of subcellular structures, organelles, and multiprotein complexes.

    PubMed

    Feng, Xin; Xia, Kelin; Tong, Yiying; Wei, Guo-Wei

    2012-12-01

    Recently, the structure, function, stability, and dynamics of subcellular structures, organelles, and multiprotein complexes have emerged as a leading interest in structural biology. Geometric modeling not only provides visualizations of shapes for large biomolecular complexes but also fills the gap between structural information and theoretical modeling, and enables the understanding of function, stability, and dynamics. This paper introduces a suite of computational tools for volumetric data processing, information extraction, surface mesh rendering, geometric measurement, and curvature estimation of biomolecular complexes. Particular emphasis is given to the modeling of cryo-electron microscopy data. Lagrangian-triangle meshes are employed for the surface presentation. On the basis of this representation, algorithms are developed for surface area and surface-enclosed volume calculation, and curvature estimation. Methods for volumetric meshing have also been presented. Because the technological development in computer science and mathematics has led to multiple choices at each stage of the geometric modeling, we discuss the rationales in the design and selection of various algorithms. Analytical models are designed to test the computational accuracy and convergence of proposed algorithms. Finally, we select a set of six cryo-electron microscopy data representing typical subcellular complexes to demonstrate the efficacy of the proposed algorithms in handling biomolecular surfaces and explore their capability of geometric characterization of binding targets. This paper offers a comprehensive protocol for the geometric modeling of subcellular structures, organelles, and multiprotein complexes.

  18. A deformation quantization theory for noncommutative quantum mechanics

    SciTech Connect

    Costa Dias, Nuno; Prata, Joao Nuno; Gosson, Maurice de; Luef, Franz

    2010-07-15

    We show that the deformation quantization of noncommutative quantum mechanics previously considered by Dias and Prata ['Weyl-Wigner formulation of noncommutative quantum mechanics', J. Math. Phys. 49, 072101 (2008)] and Bastos, Dias, and Prata ['Wigner measures in non-commutative quantum mechanics', e-print arXiv:math-ph/0907.4438v1; Commun. Math. Phys. (to appear)] can be expressed as a Weyl calculus on a double phase space. We study the properties of the star-product thus defined and prove a spectral theorem for the star-genvalue equation using an extension of the methods recently initiated by de Gosson and Luef ['A new approach to the *-genvalue equation', Lett. Math. Phys. 85, 173-183 (2008)].

  19. Noncommutative topology and the world’s simplest index theorem

    PubMed Central

    van Erp, Erik

    2010-01-01

    In this article we outline an approach to index theory on the basis of methods of noncommutative topology. We start with an explicit index theorem for second-order differential operators on 3-manifolds that are Fredholm but not elliptic. This low-brow index formula is expressed in terms of winding numbers. We then proceed to show how it is derived as a special case of an index theorem for hypoelliptic operators on contact manifolds. Finally, we discuss the noncommutative topology that is employed in the proof of this theorem. The article is intended to illustrate that noncommutative topology can be a powerful tool for proving results in classical analysis and geometry. PMID:20418506

  20. k-Inflation in noncommutative space-time

    NASA Astrophysics Data System (ADS)

    Feng, Chao-Jun; Li, Xin-Zhou; Liu, Dao-Jun

    2015-02-01

    The power spectra of the scalar and tensor perturbations in the noncommutative k-inflation model are calculated in this paper. In this model, all the modes created when the stringy space-time uncertainty relation is satisfied, and they are generated inside the sound/Hubble horizon during inflation for the scalar/tensor perturbations. It turns out that a linear term describing the noncommutative space-time effect contributes to the power spectra of the scalar and tensor perturbations. Confronting the general noncommutative k-inflation model with latest results from Planck and BICEP2, and taking and as free parameters, we find that it is well consistent with observations. However, for the two specific models, i.e. the tachyon and DBI inflation models, it is found that the DBI model is not favored, while the tachyon model lies inside the contour, when the e-folding number is assumed to be around.

  1. Black hole evaporation in a noncommutative charged Vaidya model

    SciTech Connect

    Sharif, M. Javed, W.

    2012-06-15

    We study the black hole evaporation and Hawking radiation for a noncommutative charged Vaidya black hole. For this purpose, we determine a spherically symmetric charged Vaidya model and then formulate a noncommutative Reissner-Nordstroem-like solution of this model, which leads to an exact (t - r)-dependent metric. The behavior of the temporal component of this metric and the corresponding Hawking temperature are investigated. The results are shown in the form of graphs. Further, we examine the tunneling process of charged massive particles through the quantum horizon. We find that the tunneling amplitude is modified due to noncommutativity. Also, it turns out that the black hole evaporates completely in the limits of large time and horizon radius. The effect of charge is to reduce the temperature from a maximum value to zero. We note that the final stage of black hole evaporation is a naked singularity.

  2. Structural dependence of Mn complexation by siderophores: Donor group dependence on complex stability and reactivity

    NASA Astrophysics Data System (ADS)

    Harrington, James M.; Parker, Dorothy L.; Bargar, John R.; Jarzecki, Andrzej A.; Tebo, Bradley M.; Sposito, Garrison; Duckworth, Owen W.

    2012-07-01

    Siderophores traditionally have been viewed as solely being involved in the biogeochemical cycling of Fe(III). This paradigm, however, ignores the diverse roles siderophores may play in the cycling of other trace metals, such as Mn, Co, Mo, and V. Recent work has shown that siderophores form complexes with high stability constants with Mn(III), which are in some cases higher than that of the corresponding Fe(III) complex. Herein, we report on a structural analysis of the dissolved Fe(III)- and Mn(III)-siderophore complexes of rhizoferrin and two pyoverdin-type siderophores using X-ray spectroscopic techniques. Additionally, the stability constants of the Mn(III)-pyoverdinPaA and Mn(III)-rhizoferrin complexes have been quantified as log β111 = 47.5 ± 0.3 and log β110 = 29.8 ± 0.3, respectively. Comparisons of thermodynamic stability and solution structures of Fe(III)- and Mn(III)-complexes with a variety of siderophores demonstrate the relationship between donor group identity, siderophore structure, and strength of complex formation. Rhizoferrin and two mixed-moiety pyoverdins bind with a higher affinity for Mn(III) than Fe(III), possibly because of binding moiety composition which makes them better able to accommodate Jahn-Teller distortion. In contrast, Fe(III) forms complexes of higher relative stability with siderophores that contain hydroxamate and catecholate moieties, more rigid donor groups that form five-membered chelate rings.

  3. Surprise maximization reveals the community structure of complex networks

    PubMed Central

    Aldecoa, Rodrigo; Marín, Ignacio

    2013-01-01

    How to determine the community structure of complex networks is an open question. It is critical to establish the best strategies for community detection in networks of unknown structure. Here, using standard synthetic benchmarks, we show that none of the algorithms hitherto developed for community structure characterization perform optimally. Significantly, evaluating the results according to their modularity, the most popular measure of the quality of a partition, systematically provides mistaken solutions. However, a novel quality function, called Surprise, can be used to elucidate which is the optimal division into communities. Consequently, we show that the best strategy to find the community structure of all the networks examined involves choosing among the solutions provided by multiple algorithms the one with the highest Surprise value. We conclude that Surprise maximization precisely reveals the community structure of complex networks. PMID:23320141

  4. Quantum dynamics of simultaneously measured non-commuting observables

    NASA Astrophysics Data System (ADS)

    Hacohen-Gourgy, Shay; Martin, Leigh S.; Flurin, Emmanuel; Ramasesh, Vinay V.; Whaley, K. Birgitta; Siddiqi, Irfan

    2016-10-01

    In quantum mechanics, measurements cause wavefunction collapse that yields precise outcomes, whereas for non-commuting observables such as position and momentum Heisenberg’s uncertainty principle limits the intrinsic precision of a state. Although theoretical work has demonstrated that it should be possible to perform simultaneous non-commuting measurements and has revealed the limits on measurement outcomes, only recently has the dynamics of the quantum state been discussed. To realize this unexplored regime, we simultaneously apply two continuous quantum non-demolition probes of non-commuting observables to a superconducting qubit. We implement multiple readout channels by coupling the qubit to multiple modes of a cavity. To control the measurement observables, we implement a ‘single quadrature’ measurement by driving the qubit and applying cavity sidebands with a relative phase that sets the observable. Here, we use this approach to show that the uncertainty principle governs the dynamics of the wavefunction by enforcing a lower bound on the measurement-induced disturbance. Consequently, as we transition from measuring identical to measuring non-commuting observables, the dynamics make a smooth transition from standard wavefunction collapse to localized persistent diffusion and then to isotropic persistent diffusion. Although the evolution of the state differs markedly from that of a conventional measurement, information about both non-commuting observables is extracted by keeping track of the time ordering of the measurement record, enabling quantum state tomography without alternating measurements. Our work creates novel capabilities for quantum control, including rapid state purification, adaptive measurement, measurement-based state steering and continuous quantum error correction. As physical systems often interact continuously with their environment via non-commuting degrees of freedom, our work offers a way to study how notions of contemporary

  5. Effective action for noncommutative Bianchi I model

    SciTech Connect

    Rosenbaum, M.; Vergara, J. D.; Minzoni, A. A.

    2013-06-12

    Quantum Mechanics, as a mini-superspace of Field Theory has been assumed to provide physically relevant information on quantum processes in Field Theory. In the case of Quantum Gravity this would imply using Cosmological models to investigate quantum processes at distances of the order of the Planck scale. However because of the Stone-von Neuman Theorem, it is well known that quantization of Cosmological models by the Wheeler-DeWitt procedure in the context of a Heisenberg-Weyl group with piecewise continuous parameters leads irremediably to a volume singularity. In order to avoid this information catastrophe it has been suggested recently the need to introduce in an effective theory of the quantization some form of reticulation in 3-space. On the other hand, since in the geometry of the General Relativistic formulation of Gravitation space can not be visualized as some underlying static manifold in which the physical system evolves, it would be interesting to investigate whether the effective reticulation which removes the singularity in such simple cosmologies as the Bianchi models has a dynamical origin manifested by a noncommutativity of the generators of the Heisenberg-Weyl algebra, as would be expected from an operational point of view at the Planck length scale.

  6. Effective action for noncommutative Bianchi I model

    NASA Astrophysics Data System (ADS)

    Rosenbaum, M.; Vergara, J. D.; Minzoni, A. A.

    2013-06-01

    Quantum Mechanics, as a mini-superspace of Field Theory has been assumed to provide physically relevant information on quantum processes in Field Theory. In the case of Quantum Gravity this would imply using Cosmological models to investigate quantum processes at distances of the order of the Planck scale. However because of the Stone-von Neuman Theorem, it is well known that quantization of Cosmological models by the Wheeler-DeWitt procedure in the context of a Heisenberg-Weyl group with piecewise continuous parameters leads irremediably to a volume singularity. In order to avoid this information catastrophe it has been suggested recently the need to introduce in an effective theory of the quantization some form of reticulation in 3-space. On the other hand, since in the geometry of the General Relativistic formulation of Gravitation space can not be visualized as some underlying static manifold in which the physical system evolves, it would be interesting to investigate whether the effective reticulation which removes the singularity in such simple cosmologies as the Bianchi models has a dynamical origin manifested by a noncommutativity of the generators of the Heisenberg-Weyl algebra, as would be expected from an operational point of view at the Planck length scale.

  7. Navigation signal structure based on complex carrier modulation

    NASA Astrophysics Data System (ADS)

    Xu, Ying; Yuan, Hong

    2011-06-01

    Signal structure design is an important part of satellite navigation system research, which directly affects navigation performance. Signal performance parameters are analyzed and performances of BPSK modulated signals and BOC modulated signals are compared. Aiming at requirements of high navigation precision and high anti-jamming ability, a new navigation signal structure based on complex carrier modulation is proposed and performances of the signal are researched with different parameters. A synchronization algorithm is put forward according to the signal characteristics, and the synchronization performance is qualitatively analyzed. Next, the applications of the complex carrier modulated signal are discussed, which include anti-jamming, navigation enhancement, power combing and so on. Simulations and analysis show that the proposed navigation signal structure based on complex carrier modulation has good navigation capabilities and anti-jamming abilities, which deserves further study.

  8. Stoichiometry and structure of a lantibiotic maturation complex

    PubMed Central

    Reiners, Jens; Abts, André; Clemens, Rebecca; Smits, Sander H. J.; Schmitt, Lutz

    2017-01-01

    Lantibiotics are ribosomally synthesized antimicrobial peptides secreted by mainly Gram-positive bacteria. Class 1 lantibiotics mature via two modification steps introduced by a modification LanBC complex. For the lantibiotic nisin, the dehydratase NisB catalyzes the dehydration of serine and threonine residues in the so-called core peptide. Second, five (methyl)-lanthionine rings are introduced in a regio- and stereospecific manner by the cyclase NisC. Here, we characterized the assembly of the NisBC complex in vitro, which is only formed in the presence of the substrate. The complex is composed of a NisB dimer, a monomer of NisC and one prenisin molecule. Interestingly, the presence of the last lanthionine ring prevented complex formation. This stoichiometry was verified by small-angle X-ray scattering measurements, which revealed the first structural glimpse of a LanBC complex in solution. PMID:28169337

  9. Noncommutative scalar field minimally coupled to nonsymmetric gravity

    SciTech Connect

    Kouadik, S.; Sefai, D.

    2012-06-27

    We construct a non-commutative non symmetric gravity minimally coupled model (the star product only couples matter). We introduce the action for the system considered namely a non-commutative scalar field propagating in a nontrivial gravitational background. We expand the action in powers of the anti-symmetric field and the graviton to second order adopting the assumption that the scalar is weekly coupled to the graviton. We compute the one loop radiative corrections to the self-energy of a scalar particle.

  10. Infinite volume of noncommutative black hole wrapped by finite surface

    NASA Astrophysics Data System (ADS)

    Zhang, Baocheng; You, Li

    2017-02-01

    The volume of a black hole under noncommutative spacetime background is found to be infinite, in contradiction with the surface area of a black hole, or its Bekenstein-Hawking (BH) entropy, which is well-known to be finite. Our result rules out the possibility of interpreting the entropy of a black hole by counting the number of modes wrapped inside its surface if the final evaporation stage can be properly treated. It implies the statistical interpretation for the BH entropy can be independent of the volume, provided spacetime is noncommutative. The effect of radiation back reaction is found to be small and doesn't influence the above conclusion.

  11. Curvature and geometric modules of noncommutative spheres and tori

    SciTech Connect

    Arnlind, Joakim

    2014-04-15

    When considered as submanifolds of Euclidean space, the Riemannian geometry of the round sphere and the Clifford torus may be formulated in terms of Poisson algebraic expressions involving the embedding coordinates, and a central object is the projection operator, projecting tangent vectors in the ambient space onto the tangent space of the submanifold. In this note, we point out that there exist noncommutative analogues of these projection operators, which implies a very natural definition of noncommutative tangent spaces as particular projective modules. These modules carry an induced connection from Euclidean space, and we compute its scalar curvature.

  12. Noncommutative geometry modified non-Gaussianities of cosmological perturbation

    SciTech Connect

    Fang Kejie; Xue Wei; Chen Bin

    2008-03-15

    We investigate the noncommutative effect on the non-Gaussianities of primordial cosmological perturbation. In the lowest order of string length and slow-roll parameter, we find that in the models with small speed of sound the noncommutative modifications could be observable if assuming a relatively low string scale. In particular, the dominant modification of the non-Gaussianity estimator f{sub NL} could reach O(1) in Dirac-Born-Infeld (DBI) inflation and K-inflation. The corrections are sensitive to the speed of sound and the choice of string length scale. Moreover the shapes of the corrected non-Gaussianities are distinct from that of ordinary ones.

  13. Complex quantum networks as structured environments: engineering and probing

    NASA Astrophysics Data System (ADS)

    Nokkala, Johannes; Galve, Fernando; Zambrini, Roberta; Maniscalco, Sabrina; Piilo, Jyrki

    2016-05-01

    We consider structured environments modeled by bosonic quantum networks and investigate the probing of their spectral density, structure, and topology. We demonstrate how to engineer a desired spectral density by changing the network structure. Our results show that the spectral density can be very accurately detected via a locally immersed quantum probe for virtually any network configuration. Moreover, we show how the entire network structure can be reconstructed by using a single quantum probe. We illustrate our findings presenting examples of spectral densities and topology probing for networks of genuine complexity.

  14. Complex quantum networks as structured environments: engineering and probing

    PubMed Central

    Nokkala, Johannes; Galve, Fernando; Zambrini, Roberta; Maniscalco, Sabrina; Piilo, Jyrki

    2016-01-01

    We consider structured environments modeled by bosonic quantum networks and investigate the probing of their spectral density, structure, and topology. We demonstrate how to engineer a desired spectral density by changing the network structure. Our results show that the spectral density can be very accurately detected via a locally immersed quantum probe for virtually any network configuration. Moreover, we show how the entire network structure can be reconstructed by using a single quantum probe. We illustrate our findings presenting examples of spectral densities and topology probing for networks of genuine complexity. PMID:27230125

  15. Protein-complex structure completion using IPCAS (Iterative Protein Crystal structure Automatic Solution).

    PubMed

    Zhang, Weizhe; Zhang, Hongmin; Zhang, Tao; Fan, Haifu; Hao, Quan

    2015-07-01

    Protein complexes are essential components in many cellular processes. In this study, a procedure to determine the protein-complex structure from a partial molecular-replacement (MR) solution is demonstrated using a direct-method-aided dual-space iterative phasing and model-building program suite, IPCAS (Iterative Protein Crystal structure Automatic Solution). The IPCAS iteration procedure involves (i) real-space model building and refinement, (ii) direct-method-aided reciprocal-space phase refinement and (iii) phase improvement through density modification. The procedure has been tested with four protein complexes, including two previously unknown structures. It was possible to use IPCAS to build the whole complex structure from one or less than one subunit once the molecular-replacement method was able to give a partial solution. In the most challenging case, IPCAS was able to extend to the full length starting from less than 30% of the complex structure, while conventional model-building procedures were unsuccessful.

  16. Self-Assembly of Structures with Addressable Complexity.

    PubMed

    Jacobs, William M; Frenkel, Daan

    2016-03-02

    The self-assembly of structures with "addressable complexity", where every component is distinct and is programmed to occupy a specific location within a target structure, is a promising route to engineering materials with precisely defined morphologies. Because systems with many components are inherently complicated, one might assume that the chances of successful self-assembly are extraordinarily small. Yet recent advances suggest otherwise: addressable structures with hundreds of distinct building blocks have been designed and assembled with nanometer precision. Despite this remarkable success, it is often challenging to optimize a self-assembly reaction to ensure that the intended structure is kinetically accessible. In this Perspective, we focus on the prediction of kinetic pathways for self-assembly and implications for the design of robust experimental protocols. The development of general principles to predict these pathways will enable the engineering of complex materials using a much wider range of building blocks than is currently possible.

  17. Quantum groups, non-commutative differential geometry and applications

    SciTech Connect

    Schupp, Peter

    1993-12-09

    The topic of this thesis is the development of a versatile and geometrically motivated differential calculus on non-commutative or quantum spaces, providing powerful but easy-to-use mathematical tools for applications in physics and related sciences. A generalization of unitary time evolution is proposed and studied for a simple 2-level system, leading to non-conservation of microscopic entropy, a phenomenon new to quantum mechanics. A Cartan calculus that combines functions, forms, Lie derivatives and inner derivations along general vector fields into one big algebra is constructed for quantum groups and then extended to quantum planes. The construction of a tangent bundle on a quantum group manifold and an BRST type approach to quantum group gauge theory are given as further examples of applications. The material is organized in two parts: Part I studies vector fields on quantum groups, emphasizing Hopf algebraic structures, but also introducing a ``quantum geometric`` construction. Using a generalized semi-direct product construction we combine the dual Hopf algebras A of functions and U of left-invariant vector fields into one fully bicovariant algebra of differential operators. The pure braid group is introduced as the commutant of {Delta}(U). It provides invariant maps A {yields} U and thereby bicovariant vector fields, casimirs and metrics. This construction allows the translation of undeformed matrix expressions into their less obvious quantum algebraic counter parts. We study this in detail for quasitriangular Hopf algebras, giving the determinant and orthogonality relation for the ``reflection`` matrix. Part II considers the additional structures of differential forms and finitely generated quantum Lie algebras -- it is devoted to the construction of the Cartan calculus, based on an undeformed Cartan identity.

  18. Structural Changes in the Antennapedia Complex of Drosophila Pseudoobscura

    PubMed Central

    Randazzo, F. M.; Seeger, M. A.; Huss, C. A.; Sweeney, M. A.; Cecil, J. K.; Kaufman, T. C.

    1993-01-01

    The discovery of the striking positional conservation between the Antennapedia and Bithorax homeotic gene complexes (ANT-C and BX-C) in Drosophila melanogaster and the murine Hox and human HOX clusters has had a substantial impact on our understanding of the evolution of development and its genetic regulation. Structural differences do exist among the mammalian Hox complexes and the ANT-C in D. melanogaster. To gain further insight into the evolutionary changes among these complexes, the ANT-C was cloned in the closely related species, Drosophila pseudoobscura. The overall structure of the ANT-C in D. pseudoobscura is highly similar to its D. melanogaster counterpart; however, two differences in the organization of the ANT-C have been identified. First, the z2 gene, a member of the ANT-C in D. melanogaster, is not present in the D. pseudoobscura ANT-C and is possibly absent from the D. pseudoobscura genome. Second, the orientation of the Deformed gene is inverted in D. pseudoobscura, providing it with a 5' to 3' direction of transcription identical to the remaining ANT-C homeobox genes with the exception of fushi tarazu. These differences demonstrate that subtle changes can occur in ANT-C structure during relatively short periods of evolutionary divergence, although the fundamental organization of the complex is conserved. These observations and others suggest that the complex is not absolutely rigid but that selective pressures have maintained this organization of genes for some functional reason that remains elusive. PMID:8099892

  19. Purple Bacterial Light-harvesting Complexes: From Dreams to Structures.

    PubMed

    Cogdell, Richard J; Hashimoto, Hideki; Gardiner, Alastair T

    2004-01-01

    This paper describes the main stages involved in the research efforts designed to try and understand the structure and function of purple bacterial antenna complexes. Wherever possible the work has been illustrated by pictures of the major people who carried it out.

  20. Structure, Agency, Complexity Theory and Interdisciplinary Research in Education Studies

    ERIC Educational Resources Information Center

    Smith, John A.

    2013-01-01

    This article argues that Education Studies needs to develop its existing interdisciplinarity understanding of structures and agencies by giving greater attention to the modern process theories of self-organisation in the physical, biological, psychological and social sciences, sometimes given the umbrella term "complexity theory". The…

  1. Fitting Meta-Analytic Structural Equation Models with Complex Datasets

    ERIC Educational Resources Information Center

    Wilson, Sandra Jo; Polanin, Joshua R.; Lipsey, Mark W.

    2016-01-01

    A modification of the first stage of the standard procedure for two-stage meta-analytic structural equation modeling for use with large complex datasets is presented. This modification addresses two common problems that arise in such meta-analyses: (a) primary studies that provide multiple measures of the same construct and (b) the correlation…

  2. Argument Structure of Tsou: Simplex and Complex Predicates

    ERIC Educational Resources Information Center

    Lin, Gujing

    2010-01-01

    This thesis investigates the argument structure of Tsou, a Formosan language within the Austronesian family. The investigation studies both simplex and complex predicates as well as describes the valency groupings and alignment patterns emerging from various clausal configurations. Assuming the stance that language description should respect…

  3. Hybrid Structural Model of the Complete Human ESCRT-0 Complex

    SciTech Connect

    Ren, Xuefeng; Kloer, Daniel P.; Kim, Young C.; Ghirlando, Rodolfo; Saidi, Layla F.; Hummer, Gerhard; Hurley, James H.

    2009-03-31

    The human Hrs and STAM proteins comprise the ESCRT-0 complex, which sorts ubiquitinated cell surface receptors to lysosomes for degradation. Here we report a model for the complete ESCRT-0 complex based on the crystal structure of the Hrs-STAM core complex, previously solved domain structures, hydrodynamic measurements, and Monte Carlo simulations. ESCRT-0 expressed in insect cells has a hydrodynamic radius of R{sub H} = 7.9 nm and is a 1:1 heterodimer. The 2.3 {angstrom} crystal structure of the ESCRT-0 core complex reveals two domain-swapped GAT domains and an antiparallel two-stranded coiled-coil, similar to yeast ESCRT-0. ESCRT-0 typifies a class of biomolecular assemblies that combine structured and unstructured elements, and have dynamic and open conformations to ensure versatility in target recognition. Coarse-grained Monte Carlo simulations constrained by experimental R{sub H} values for ESCRT-0 reveal a dynamic ensemble of conformations well suited for diverse functions.

  4. Chlorine Nuclear Quadrupole Hyperfine Structure in the Vinyl - Chloride Complex

    NASA Astrophysics Data System (ADS)

    Leung, Helen O.; Marshall, Mark D.; Messinger, Joseph P.

    2015-06-01

    The microwave spectrum of the vinyl chloride--hydrogen chloride complex, presented at last year's symposium, is greatly complicated by the presence of two chlorine nuclei as well as an observed, but not fully explained tunneling motion. Indeed, although it was possible at that time to demonstrate conclusively that the complex is nonplanar, the chlorine nuclear quadrupole hyperfine splitting in the rotational spectrum resisted analysis. With higher resolution, Balle-Flygare Fourier transform microwave spectra, the hyperfine structure has been more fully resolved, but appears to be perturbed for some rotational transitions. It appears that knowledge of the quadrupole coupling constants will provide essential information regarding the structure of the complex, specifically the location of the hydrogen atom in HCl. Our progress towards obtaining values for these constants will be presented.

  5. One Single Static Measurement Predicts Wave Localization in Complex Structures.

    PubMed

    Lefebvre, Gautier; Gondel, Alexane; Dubois, Marc; Atlan, Michael; Feppon, Florian; Labbé, Aimé; Gillot, Camille; Garelli, Alix; Ernoult, Maxence; Mayboroda, Svitlana; Filoche, Marcel; Sebbah, Patrick

    2016-08-12

    A recent theoretical breakthrough has brought a new tool, called the localization landscape, for predicting the localization regions of vibration modes in complex or disordered systems. Here, we report on the first experiment which measures the localization landscape and demonstrates its predictive power. Holographic measurement of the static deformation under uniform load of a thin plate with complex geometry provides direct access to the landscape function. When put in vibration, this system shows modes precisely confined within the subregions delineated by the landscape function. Also the maxima of this function match the measured eigenfrequencies, while the minima of the valley network gives the frequencies at which modes become extended. This approach fully characterizes the low frequency spectrum of a complex structure from a single static measurement. It paves the way for controlling and engineering eigenmodes in any vibratory system, especially where a structural or microscopic description is not accessible.

  6. Structural and functional clusters of complex brain networks

    NASA Astrophysics Data System (ADS)

    Zemanová, Lucia; Zhou, Changsong; Kurths, Jürgen

    2006-12-01

    Recent research using the complex network approach has revealed a rich and complicated network topology in the cortical connectivity of mammalian brains. It is of importance to understand the implications of such complex network structures in the functional organization of the brain activities. Here we study this problem from the viewpoint of dynamical complex networks. We investigate synchronization dynamics on the corticocortical network of the cat by modeling each node (cortical area) of the network with a sub-network of interacting excitable neurons. We find that the network displays clustered synchronization behavior, and the dynamical clusters coincide with the topological community structures observed in the anatomical network. Our results provide insights into the relationship between the global organization and the functional specialization of the brain cortex.

  7. 2. View, structures in Systems Integration Laboratory complex, looking north. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. View, structures in Systems Integration Laboratory complex, looking north. The Components Test Laboratory (T-27) is located in the immediate foreground. Immediately uphill to the left of T-27 is the Boiler Chiller Plant (T-28H). To the left of T-28H is the Oxidizer Conditioning Structure (T-28D). Behind the T-28D is the Long-Term Oxidizer Silo (T-28B). The twin gantry structure at the left is the Systems Integration Laboratory (T-28). - Air Force Plant PJKS, Systems Integration Laboratory, Waterton Canyon Road & Colorado Highway 121, Lakewood, Jefferson County, CO

  8. Complex Nano-Scale Structures for Unprecedented Properties in Steels

    DOE PAGES

    Caballero, Francisca G.; Poplawsky, Jonathan D.; Yen, Hung Wei; ...

    2016-11-01

    Processing bulk nanoscrystalline materials for structural applications still poses a rather large challenge, particularly in achieving an industrially viable process. In this context, recent work has proved that complex nanoscale steel structures can be formed by solid reaction at low temperatures. These nanocrystalline bainitic steels present the highest strength ever recorded, unprecedented ductility, fatigue on par with commercial bearing steels and exceptional rolling-sliding wear performances. In this paper, a description of the characteristics and significance of these remarkable structures in the context of the atomic mechanism of transformation is provided.

  9. Fuzzy Physics: A Brief Overview of Noncommutative Geometry in Physics

    NASA Astrophysics Data System (ADS)

    Maceda, Marco

    2011-10-01

    Noncommutative geometry (NCG) is a mathematical tool which has been used in the search for a quantum theory of gravity. However, its application is not limited to this field. In this brief note we present different uses of NCG in Theoretical Physics.

  10. A perspective on non-commutative quantum gravity

    NASA Astrophysics Data System (ADS)

    Martins, Rachel A. D.

    2015-06-01

    In this paper, we present some of the concepts underlying a program of non-commutative quantum gravity and recall some of the results. This program includes a novel approach to spectral triple categorification and also a precise connection between Fell bundles and Connes' non-commutative geometry. Motivated by topics in quantization of the non-commutative standard model and introduction of algebraic techniques and concepts into quantum gravity (following for example Crane, Baez and Barrett), we define spectral C*-categories, which are deformed spectral triples in a sense made precise. This definition gives to representations of a C*-category on a small category of Hilbert spaces and bounded linear maps, the interpretation of a topological quantum field theory. The construction passes two mandatory tests: (i) there is a classical limit theorem reproducing a Riemannian spin manifold manifesting Connes' and Schücker's non-commutative counterpart of Einstein's equivalence principle, and (ii) there is consistency with the experimental fermion mass matrix. We also present an algebra invariant taking the form of a partition function arising from a C*-bundle dynamical system in connection with C*-subalgebra theory.

  11. Curved noncommutative tori as Leibniz quantum compact metric spaces

    SciTech Connect

    Latrémolière, Frédéric

    2015-12-15

    We prove that curved noncommutative tori are Leibniz quantum compact metric spaces and that they form a continuous family over the group of invertible matrices with entries in the image of the quantum tori for the conjugation by modular conjugation operator in the regular representation, when this group is endowed with a natural length function.

  12. The left spectrum, the Levitzki radical, and noncommutative schemes.

    PubMed Central

    Rosenberg, A L

    1990-01-01

    This note contains a brief exposition of the basics of a noncommutative version of affine, quasi-affine, and projective algebraic geometry. In this version, to any associative ring (with unity) a quasi-affine (resp. affine) left scheme is assigned. The notion of the left spectrum of a ring plays the key role. PMID:11607114

  13. 3D quantum gravity and effective noncommutative quantum field theory.

    PubMed

    Freidel, Laurent; Livine, Etera R

    2006-06-09

    We show that the effective dynamics of matter fields coupled to 3D quantum gravity is described after integration over the gravitational degrees of freedom by a braided noncommutative quantum field theory symmetric under a kappa deformation of the Poincaré group.

  14. Noncommuting observables in quantum detection and estimation theory

    NASA Technical Reports Server (NTRS)

    Helstrom, C. W.

    1971-01-01

    In quantum detection theory, the optimum detection operators must commute; admitting simultaneous approximate measurement of noncommuting observables cannot yield a lower Bayes cost. In addition, the lower bounds on mean square errors of parameter estimates, predicted by the quantum mechanical Cramer-Rao inequality, cannot be reduced by such means.

  15. Effects of the Noncommutative Standard Model in WW Scattering

    SciTech Connect

    Conley, John A.; Hewett, JoAnne L.

    2008-12-02

    We examine W pair production in the Noncommutative Standard Model constructed with the Seiberg-Witten map. Consideration of partial wave unitarity in the reactions WW {yields} WW and e{sup +}e{sup -} {yields} WW shows that the latter process is more sensitive and that tree-level unitarity is violated when scattering energies are of order a TeV and the noncommutative scale is below about a TeV. We find that WW production at the LHC is not sensitive to scales above the unitarity bounds. WW production in e{sup +}e{sup -} annihilation, however, provides a good probe of such effects with noncommutative scales below 300-400 GeV being excluded at LEP-II, and the ILC being sensitive to scales up to 10-20 TeV. In addition, we find that the ability to measure the helicity states of the final state W bosons at the ILC provides a diagnostic tool to determine and disentangle the different possible noncommutative contributions.

  16. Slavnov-Taylor identities for noncommutative QED{sub 4}

    SciTech Connect

    Charneski, B.; Gomes, M.; Silva, A. J. da; Mariz, T.; Nascimento, J. R.

    2010-05-15

    In this work we present an analysis of the one-loop Slavnov-Taylor identities in noncommutative QED{sub 4}. The vectorial fermion-photon and the triple photon vertex functions were studied, with the conclusion that no anomalies arise.

  17. Structural Architecture of SNP Effects on Complex Traits

    PubMed Central

    Gamazon, Eric R.; Cox, Nancy J.; Davis, Lea K.

    2014-01-01

    Despite the discovery of copy-number variation (CNV) across the genome nearly 10 years ago, current SNP-based analysis methodologies continue to collapse the homozygous (i.e., A/A), hemizygous (i.e., A/0), and duplicative (i.e., A/A/A) genotype states, treating the genotype variable as irreducible or unaltered by other colocalizing forms of genetic (e.g., structural) variation. Our understanding of common, genome-wide CNVs suggests that the canonical genotype construct might belie the enormous complexity of the genome. Here we present multiple analyses of several phenotypes and provide methods supporting a conceptual shift that embraces the structural dimension of genotype. We comprehensively investigate the impact of the structural dimension of genotype on (1) GWAS methods, (2) interpretation of rare LOF variants, (3) characterization of genomic architecture, and (4) implications for mapping loci involved in complex disease. Taken together, these results argue for the inclusion of a structural dimension and suggest that some portion of the “missing” heritability might be recovered through integration of the structural dimension of SNP effects on complex traits. PMID:25307299

  18. Informational Complexity and Functional Activity of RNA Structures

    PubMed Central

    Carothers, James M.; Oestreich, Stephanie C.; Davis, Jonathan H.

    2004-01-01

    Very little is known about the distribution of functional DNA, RNA, and protein molecules in sequence space. The question of how the number and complexity of distinct solutions to a particular biochemical problem varies with activity is an important aspect of this general problem. Here we present a comparison of the structures and activities of eleven distinct GTP-binding RNAs (aptamers). By experimentally measuring the amount of information required to specify each optimal binding structure, we show that defining a structure capable of 10-fold tighter binding requires approximately 10 additional bits of information. This increase in information content is equivalent to specifying the identity of five additional nucleotide positions and corresponds to an ∼1000-fold decrease in abundance in a sample of random sequences. We observe a similar relationship between structural complexity and activity in a comparison of two catalytic RNAs (ribozyme ligases), raising the possibility of a general relationship between the complexity of RNA structures and their functional activity. Describing how information varies with activity in other heteropolymers, both biological and synthetic, may lead to an objective means of comparing their functional properties. This approach could be useful in predicting the functional utility of novel heteropolymers. PMID:15099096

  19. Significance tests for functional data with complex dependence structure

    PubMed Central

    Lahiri, Soumen N.; Carroll, Raymond J.

    2015-01-01

    We propose an L2-norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a multilevel structure of the form groups–clusters or subjects–units, where the unit-level profiles are spatially correlated within the cluster, and the cluster-level data are independent. Orthogonal series expansions are used to approximate the group mean functions and the test statistic is estimated using the basis coefficients. The asymptotic null distribution of the test statistic is developed, under mild regularity conditions. To our knowledge this is the first work that studies hypothesis testing, when data have such complex multilevel functional and spatial structure. Two small-sample alternatives, including a novel block bootstrap for functional data, are proposed, and their performance is examined in simulation studies. The paper concludes with an illustration of a motivating experiment. PMID:26023253

  20. Structure of the Rigor Actin-Tropomyosin-Myosin Complex

    PubMed Central

    Behrmann, Elmar; Müller, Mirco; Penczek, Pawel A.; Mannherz, Hans Georg; Manstein, Dietmar J.; Raunser, Stefan

    2014-01-01

    The interaction of myosin with actin filaments is the central feature of muscle contraction and cargo movement along actin filaments of the cytoskeleton. Myosin converts the chemical energy stored in ATP into force and movement along actin filaments. Myosin binding to actin induces conformational changes that are coupled to the nucleotide-binding pocket and amplified by a specialized region of the motor domain for efficient force generation. Tropomyosin plays a key role in regulating the productive interaction between myosins and actin. Here, we report the 8 Å resolution structure of the actin-tropomyosin-myosin complex determined by cryo electron microscopy. The pseudo-atomic model of the complex obtained from fitting crystal structures into the map defines the large actin-myosin-tropomyosin interface and the molecular interactions between the proteins in detail and allows us to propose a structural model for tropomyosin dependent myosin binding to actin and actin-induced nucleotide release from myosin. PMID:22817895

  1. Geometric and electronic structures of potassium-adsorbed rubrene complexes

    SciTech Connect

    Li, Tsung-Lung; Lu, Wen-Cai

    2015-06-28

    The geometric and electronic structures of potassium-adsorbed rubrene complexes are studied in this article. It is found that the potassium-rubrene (K{sub 1}RUB) complexes inherit the main symmetry characteristics from their pristine counterparts and are thus classified into D{sub 2}- and C{sub 2h}-like complexes according to the relative orientations of the four phenyl side groups. The geometric structures of K{sub 1}RUB are governed by two general effects on the total energy: Deformation of the carbon frame of the pristine rubrene increases the total energy, while proximity of the potassium ion to the phenyl ligands decreases the energy. Under these general rules, the structures of D{sub 2}- and C{sub 2h}-like K{sub 1}RUB, however, exhibit their respective peculiarities. These peculiarities can be illustrated by their energy profiles of equilibrium structures. For the potassium adsorption-sites, the D{sub 2}-like complexes show minimum-energy basins, whereas the C{sub 2h}-like ones have single-point minimum-energies. If the potassium atom ever has the energy to diffuse from the minimum-energy site, the potassium diffusion path on the D{sub 2}-like complexes is most likely along the backbone in contrast to the C{sub 2h}-like ones. Although the electronic structures of the minimum-energy structures of D{sub 2}- and C{sub 2h}-like K{sub 1}RUB are very alike, decompositions of their total spectra reveal insights into the electronic structures. First, the spectral shapes are mainly determined by the facts that, in comparison with the backbone carbons, the phenyl carbons have more uniform chemical environments and far less contributions to the electronic structures around the valence-band edge. Second, the electron dissociated from the potassium atom mainly remains on the backbone and has little effects on the electronic structures of the phenyl groups. Third, the two phenyls on the same side of the backbone as the potassium atom have more similar chemical environments

  2. Solution structures of antimalarial drug-heme complexes.

    PubMed

    Leed, Alison; DuBay, Kateri; Ursos, Lyann M B; Sears, Devin; De Dios, Angel C; Roepe, Paul D

    2002-08-13

    Paramagnetic metal centers [such as Fe(III) found within ferriprotoporphyrin IX heme (FPIX)] exert through space effects on the relaxation rate of nearby proton spins that depend critically on the metal-proton distance. We have measured these effects for all protons of several antimalarial drugs that bind to FPIX by systematically varying the drug:heme molar ratio in high field NMR experiments. These measurements allow us to determine precise FPIX Fe-drug H distances for the solution structures of noncovalent complexes formed between FPIX mu-oxo dimers and the antimalarial drugs chloroquine (CQ), quinine (QN), and quinidine (QD). Using these distances, we then performed distance restraint calculations to determine the lowest-energy solution structures of these complexes. Structures were solved for neutral, monoprotic (+1), and diprotic (+2) forms of the drugs. Analysis of these structures allows us to visualize for the first time the stereospecific differences between QN and QD binding to FPIX and the differences in populations of QN and QD solution structures upon changes in digestive vacuolar pH for drug resistant malarial parasites [Dzekunov, S. M., et al. (2000) Mol. Biochem. Parasitol. 110, 107-124]. The data indicate a previously unrecognized key role for the CQ aliphatic chain in stabilizing FPIX-CQ complexes, and suggest how lengthening or shortening the chain might perturb stability. We also define FPIX:drug stoichiometries of 2:1 for the complexes formed at physiological FPIX concentrations, in contrast to the 4:1 and 5:1 stoichiometries previously determined at higher FPIX concentrations [Dorn, A., et al. (1998) Biochem. Pharmacol. 55, 727-736]. These atomic resolution antimalarial drug-heme structures should help elucidate how these drugs inhibit formation of hemozoin during metabolism of heme within the malarial parasite Plasmodium falciparum and assist ongoing development of strategies for circumventing antimalarial drug resistance.

  3. Structural Allostery and Binding of the Transferring Receptor Complex

    SciTech Connect

    Xu,G.; Liu, R.; Zak, O.; Aisen, P.; Chance, M.

    2005-01-01

    The structural allostery and binding interface for the human serum transferrin (Tf){center_dot}transferrin receptor (TfR) complex were identified using radiolytic footprinting and mass spectrometry. We have determined previously that the transferrin C-lobe binds to the receptor helical domain. In this study we examined the binding interactions of full-length transferrin with receptor and compared these data with a model of the complex derived from cryoelectron microscopy (cryo-EM) reconstructions. The footprinting results provide the following novel conclusions. First, we report characteristic oxidations of acidic residues in the C-lobe of native Tf and basic residues in the helical domain of TfR that were suppressed as a function of complex formation; this confirms ionic interactions between these protein segments as predicted by cryo-EM data and demonstrates a novel method for detecting ion pair interactions in the formation of macromolecular complexes. Second, the specific side-chain interactions between the C-lobe and N-lobe of transferrin and the corresponding interactions sites on the transferrin receptor predicted from cryo-EM were confirmed in solution. Last, the footprinting data revealed allosteric movements of the iron binding C- and N-lobes of Tf that sequester iron as a function of complex formation; these structural changes promote tighter binding of the metal ion and facilitate efficient ion transport during endocytosis.

  4. Three-dimensional structure of the {gamma}-secretase complex

    SciTech Connect

    Ogura, Toshihiko; Mio, Kazuhiro; Hayashi, Ikuo; Miyashita, Hiroyuki; Iwastubo, Takeshi; Fukuda, Rie; Kopan, Raphael |; Kodama, Tatsuhiko; Hamakubo, Takao; Tomita, Taisuke . E-mail: taisuke@mol.f.u-tokyo.ac.jp; Sato, Chikara . E-mail: ti-sato@aist.go.jp

    2006-05-05

    {gamma}-Secretase belongs to an atypical class of aspartic proteases that hydrolyzes peptide bonds within the transmembrane domain of substrates, including amyloid-{beta} precursor protein and Notch. {gamma}-Secretase is comprised of presenilin, nicastrin, APH-1, and PEN-2 which form a large multimeric membrane protein complex, the three-dimensional structure of which is unknown. To gain insight into the structure of this complex enzyme, we purified functional {gamma}-secretase complex reconstituted in Sf9 cells and analyzed it using negative stain electron microscopy and 3D reconstruction techniques. Analysis of 2341 negatively stained particle images resulted in the three-dimensional representation of {gamma}-secretase at a resolution of 48 A. The structure occupies a volume of 560 x 320 x 240 A and resembles a flat heart comprised of two oppositely faced, dimpled domains. A low density space containing multiple pores resides between the domains. Some of the dimples in the putative transmembrane region may house the catalytic site. The large dimensions are consistent with the observation that {gamma}-secretase activity resides within a high molecular weight complex.

  5. Structure, bonding, and reactivity of reactant complexes and key intermediates.

    PubMed

    Soriano, Elena; Marco-Contelles, José

    2011-01-01

    Complexes of Pt and Au (gold(III) and cationic gold(I)) have shown an exceptional ability to promote a variety of organic transformations of unsaturated precursors due to their peculiar Lewis acid properties: the alkynophilic character of these soft metals and the π-acid activation of unsaturated groups promotes the intra- or intermolecular attack of a nucleophile. In this chapter we summarize the computational data reported on the structure, bonding, and reactivity of the reactant π-complexes and also on the key intermediate species.

  6. Vacuum structure of the Higgs complex singlet-doublet model

    NASA Astrophysics Data System (ADS)

    Ferreira, P. M.

    2016-11-01

    The complex singlet-doublet model is a popular theory to account for dark matter and electroweak baryogenesis, wherein the Standard Model particle content is supplemented by a complex scalar gauge singlet, with certain discrete symmetries imposed. The scalar potential which results thereof can have seven different types of minima at tree level, which may coexist for specific choices of parameters. There is therefore the possibility that a given minimum is not global but rather a local one, and may tunnel to a deeper extremum, thus causing vacuum instability. This rich vacuum structure is explained and discussed in detail.

  7. Noncommutative correction to the Cornell potential in heavy-quarkonium atoms

    NASA Astrophysics Data System (ADS)

    Mirjalili, A.; Taki, M.

    2016-02-01

    We investigate the effect of space-time noncommutativity on the Cornell potential in heavy-quarkonium systems. It is known that the space-time noncommutativity can create bound states, and we therefore consider the noncommutative geometry of the space-time as a correction in quarkonium models. Furthermore, we take the experimental hyperfine measurements of the bottomium ground state as an upper limit on the noncommutative energy correction and derive the maximum possible value of the noncommutative parameter θ, obtaining θ ≤ 37.94 · 10-34 m2. Finally, we use our model to calculate the maximum value of the noncommutative energy correction for energy levels of charmonium and bottomium in 1S and 2S levels. The energy correction as a binding effect in quarkonium system is smaller for charmonium than for bottomium, as expected.

  8. STRIPAK complexes: structure, biological function, and involvement in human diseases.

    PubMed

    Hwang, Juyeon; Pallas, David C

    2014-02-01

    The mammalian striatin family consists of three proteins, striatin, S/G2 nuclear autoantigen, and zinedin. Striatin family members have no intrinsic catalytic activity, but rather function as scaffolding proteins. Remarkably, they organize multiple diverse, large signaling complexes that participate in a variety of cellular processes. Moreover, they appear to be regulatory/targeting subunits for the major eukaryotic serine/threonine protein phosphatase 2A. In addition, striatin family members associate with germinal center kinase III kinases as well as other novel components, earning these assemblies the name striatin-interacting phosphatase and kinase (STRIPAK) complexes. Recently, there has been a great increase in functional and mechanistic studies aimed at identifying and understanding the roles of STRIPAK and STRIPAK-like complexes in cellular processes of multiple organisms. These studies have identified novel STRIPAK and STRIPAK-like complexes and have explored their roles in specific signaling pathways. Together, the results of these studies have sparked increased interest in striatin family complexes because they have revealed roles in signaling, cell cycle control, apoptosis, vesicular trafficking, Golgi assembly, cell polarity, cell migration, neural and vascular development, and cardiac function. Moreover, STRIPAK complexes have been connected to clinical conditions, including cardiac disease, diabetes, autism, and cerebral cavernous malformation. In this review, we discuss the expression, localization, and protein domain structure of striatin family members. Then we consider the diverse complexes these proteins and their homologs form in various organisms, emphasizing what is known regarding function and regulation. Finally, we explore possible roles of striatin family complexes in disease, especially cerebral cavernous malformation.

  9. Crystal structure of human nuclear pore complex component NUP43.

    PubMed

    Xu, Chao; Li, Zhihong; He, Hao; Wernimont, Amy; Li, Yanjun; Loppnau, Peter; Min, Jinrong

    2015-10-24

    Nuclear pore complexes (NPC) form nuclear pores that cross the nuclear envelope and allow molecules to transport between the nucleus and the cytoplasm. We solved the crystal structure of human Nup43 (hNUP43), an important component in the Nup107 subcomplex of NPC. hNup43 adopts a seven-bladed β-propeller fold. We confirmed by ITC that neither human Nup37 (hNup37) nor human Nup133 (hNup133) interacts with hNup43. We demonstrated by analytical gel filtration that the human Nup85-Seh1L binary complex recruits hNup43 to form a ternary complex. Based on amino acid sequence analysis, we predicted the hNup85-hSeh1L binding surface of hNup43.

  10. Polyacrylic acids-bovine serum albumin complexation: Structure and dynamics.

    PubMed

    Othman, Mohamed; Aschi, Adel; Gharbi, Abdelhafidh

    2016-01-01

    The study of the mixture of BSA with polyacrylic acids at different masses versus pH allowed highlighting the existence of two regimes of weak and strong complexation. These complexes were studied in diluted regime concentration, by turbidimetry, dynamic light scattering (DLS), zeta-potential measurements and nuclear magnetic resonance (NMR). We have followed the pH effect on the structure and properties of the complex. This allowed refining the interpretation of the phase diagram and understanding the observed phenomena. The NMR measurements allowed probing the dynamics of the constituents versus the pH. The computational method was used to precisely determine the electrostatic potential of BSA and how the polyelectrolyte binds to it at different pH.

  11. Parallel Structural Evolution of Mitochondrial Ribosomes and OXPHOS Complexes.

    PubMed

    van der Sluis, Eli O; Bauerschmitt, Heike; Becker, Thomas; Mielke, Thorsten; Frauenfeld, Jens; Berninghausen, Otto; Neupert, Walter; Herrmann, Johannes M; Beckmann, Roland

    2015-04-09

    The five macromolecular complexes that jointly mediate oxidative phosphorylation (OXPHOS) in mitochondria consist of many more subunits than those of bacteria, yet, it remains unclear by which evolutionary mechanism(s) these novel subunits were recruited. Even less well understood is the structural evolution of mitochondrial ribosomes (mitoribosomes): while it was long thought that their exceptionally high protein content would physically compensate for their uniquely low amount of ribosomal RNA (rRNA), this hypothesis has been refuted by structural studies. Here, we present a cryo-electron microscopy structure of the 73S mitoribosome from Neurospora crassa, together with genomic and proteomic analyses of mitoribosome composition across the eukaryotic domain. Surprisingly, our findings reveal that both structurally and compositionally, mitoribosomes have evolved very similarly to mitochondrial OXPHOS complexes via two distinct phases: A constructive phase that mainly acted early in eukaryote evolution, resulting in the recruitment of altogether approximately 75 novel subunits, and a reductive phase that acted during metazoan evolution, resulting in gradual length-reduction of mitochondrially encoded rRNAs and OXPHOS proteins. Both phases can be well explained by the accumulation of (slightly) deleterious mutations and deletions, respectively, in mitochondrially encoded rRNAs and OXPHOS proteins. We argue that the main role of the newly recruited (nuclear encoded) ribosomal- and OXPHOS proteins is to provide structural compensation to the mutationally destabilized mitochondrially encoded components. While the newly recruited proteins probably provide a selective advantage owing to their compensatory nature, and while their presence may have opened evolutionary pathways toward novel mitochondrion-specific functions, we emphasize that the initial events that resulted in their recruitment was nonadaptive in nature. Our framework is supported by population genetic

  12. Upper-mantle structures beneath USArray derived from waveform complexity

    NASA Astrophysics Data System (ADS)

    Sun, Daoyuan; Helmberger, Don

    2011-01-01

    Tomographic imaging of the crust and upper mantle beneath the western United States has greatly improved with the addition of USArray data. These models display many detailed images of both fast and slow blobs penetrating into the transition zone. To study such features, we apply a newly developed technique, called MultiPath Detector analysis, to the SH waveform data. The method simulates each observed body waveform by performing a decomposition; by [S(t)+C×S(t-ΔLR)]/2, where S(t) is the synthetics for a reference model. Time separation ΔLR and amplitude ratio C are needed to obtain a high cross-correlation between a simulated waveform and data. The travel time of the composite waveform relative to the reference model synthetics is defined as ΔT. A simulated annealing algorithm is used to determine the parameters ΔLR and C. We also record the amplitude ratio (Amp) between the synthetics for the reference model relative to the data. Generally, large ΔLR values are associated with low Amp's. Whereas the conventional tomography yields a travel time correction (ΔT), our analysis yields an extra parameter (ΔLR), which describes the waveform complexity. With the array, we can construct a mapping of the gradient of ΔLR with complexity patterns. A horizontal structure introduces waveform complexity along the distance profile (in-plane multipathing). An azimuthally orientation ΔLR pattern indicates a vertical structure with out-of-plane multipathing. Using such maps generated from artificial data, we can easily recognize features produced by dipping fast structures and slow structures (DSS). Many of these features display organized waveform complexity that are distinctly directional indicative of dipping sharp-edges. Here, we process the array data for events arriving from various azimuths and construct maps of multipathing patterns. The similarity between tomographic features and complexity maps is striking. When features are dipping such as the slab structures

  13. Integrated structural analysis of the human nuclear pore complex scaffold.

    PubMed

    Bui, Khanh Huy; von Appen, Alexander; DiGuilio, Amanda L; Ori, Alessandro; Sparks, Lenore; Mackmull, Marie-Therese; Bock, Thomas; Hagen, Wim; Andrés-Pons, Amparo; Glavy, Joseph S; Beck, Martin

    2013-12-05

    The nuclear pore complex (NPC) is a fundamental component of all eukaryotic cells that facilitates nucleocytoplasmic exchange of macromolecules. It is assembled from multiple copies of about 30 nucleoporins. Due to its size and complex composition, determining the structure of the NPC is an enormous challenge, and the overall architecture of the NPC scaffold remains elusive. In this study, we have used an integrated approach based on electron tomography, single-particle electron microscopy, and crosslinking mass spectrometry to determine the structure of a major scaffold motif of the human NPC, the Nup107 subcomplex, in both isolation and integrated into the NPC. We show that 32 copies of the Nup107 subcomplex assemble into two reticulated rings, one each at the cytoplasmic and nuclear face of the NPC. This arrangement may explain how changes of the diameter are realized that would accommodate transport of huge cargoes.

  14. The nuclear pore complex: understanding its function through structural insight.

    PubMed

    Beck, Martin; Hurt, Ed

    2017-02-01

    Nuclear pore complexes (NPCs) fuse the inner and outer nuclear membranes to form channels across the nuclear envelope. They are large macromolecular assemblies with a complex composition and diverse functions. Apart from facilitating nucleocytoplasmic transport, NPCs are involved in chromatin organization, the regulation of gene expression and DNA repair. Understanding the molecular mechanisms underlying these functions has been hampered by a lack of structural knowledge about the NPC. The recent convergence of crystallographic and biochemical in vitro analysis of nucleoporins (NUPs), the components of the NPC, with cryo-electron microscopic imaging of the entire NPC in situ has provided first pseudo-atomic view of its central core and revealed that an unexpected network of short linear motifs is an important spatial organization principle. These breakthroughs have transformed the way we understand NPC structure, and they provide an important base for functional investigations, including the elucidation of the molecular mechanisms underlying clinically manifested mutations of the nucleocytoplasmic transport system.

  15. Emergence of hierarchical structural complexities in nanoparticles and their assembly

    NASA Astrophysics Data System (ADS)

    Zeng, Chenjie; Chen, Yuxiang; Kirschbaum, Kristin; Lambright, Kelly J.; Jin, Rongchao

    2016-12-01

    We demonstrate that nanoparticle self-assembly can reach the same level of hierarchy, complexity, and accuracy as biomolecules. The precise assembly structures of gold nanoparticles (246 gold core atoms with 80 p-methylbenzenethiolate surface ligands) at the atomic, molecular, and nanoscale levels were determined from x-ray diffraction studies. We identified the driving forces and rules that guide the multiscale assembly behavior. The protecting ligands self-organize into rotational and parallel patterns on the nanoparticle surface via C-Hṡṡṡπ interaction, and the symmetry and density of surface patterns dictate directional packing of nanoparticles into crystals with orientational, rotational, and translational orders. Through hierarchical interactions and symmetry matching, the simple building blocks evolve into complex structures, representing an emergent phenomenon in the nanoparticle system.

  16. Pair production of Dirac particles in a -dimensional noncommutative space-time

    NASA Astrophysics Data System (ADS)

    Ousmane Samary, Dine; N'Dolo, Emanonfi Elias; Hounkonnou, Mahouton Norbert

    2014-11-01

    This work addresses the computation of the probability of fermionic particle pair production in -dimensional noncommutative Moyal space. Using Seiberg-Witten maps, which establish relations between noncommutative and commutative field variables, up to the first order in the noncommutative parameter , we derive the probability density of vacuum-vacuum pair production of Dirac particles. The cases of constant electromagnetic, alternating time-dependent, and space-dependent electric fields are considered and discussed.

  17. Fractional angular momentum in noncommutative generalized Chern-Simons quantum mechanics

    NASA Astrophysics Data System (ADS)

    Zhang, Xi-Lun; Sun, Yong-Li; Wang, Qing; Long, Zheng-Wen; Jing, Jian

    2016-07-01

    The noncommutative generalized Chern-Simons quantum mechanics, i.e., the Chern-Simons quantum mechanics on the noncommutative plane in the presence of Aharonov-Bohm magnetic vector potentials, is studied in this paper. We focus our attention on the canonical orbital angular momentum and show that there are two different approaches to produce the fractional angular momentum in the noncommutative generalized Chern-Simons quantum mechanics.

  18. Retroviral integrase protein and intasome nucleoprotein complex structures

    PubMed Central

    Grawenhoff, Julia; Engelman, Alan N

    2017-01-01

    Retroviral replication proceeds through the integration of a DNA copy of the viral RNA genome into the host cellular genome, a process that is mediated by the viral integrase (IN) protein. IN catalyzes two distinct chemical reactions: 3’-processing, whereby the viral DNA is recessed by a di- or trinucleotide at its 3’-ends, and strand transfer, in which the processed viral DNA ends are inserted into host chromosomal DNA. Although IN has been studied as a recombinant protein since the 1980s, detailed structural understanding of its catalytic functions awaited high resolution structures of functional IN-DNA complexes or intasomes, initially obtained in 2010 for the spumavirus prototype foamy virus (PFV). Since then, two additional retroviral intasome structures, from the α-retrovirus Rous sarcoma virus (RSV) and β-retrovirus mouse mammary tumor virus (MMTV), have emerged. Here, we briefly review the history of IN structural biology prior to the intasome era, and then compare the intasome structures of PFV, MMTV and RSV in detail. Whereas the PFV intasome is characterized by a tetrameric assembly of IN around the viral DNA ends, the newer structures harbor octameric IN assemblies. Although the higher order architectures of MMTV and RSV intasomes differ from that of the PFV intasome, they possess remarkably similar intasomal core structures. Thus, retroviral integration machineries have adapted evolutionarily to utilize disparate IN elements to construct convergent intasome core structures for catalytic function. PMID:28289517

  19. Ultrathin conformal coating for complex magneto-photonic structures.

    PubMed

    Pascu, Oana; Caicedo, José Manuel; López-García, Martín; Canalejas, Víctor; Blanco, Álvaro; López, Cefe; Arbiol, Jordi; Fontcuberta, Josep; Roig, Anna; Herranz, Gervasi

    2011-11-01

    We report on an extremely fast and versatile synthetic approach, based on microwave assisted sol-gel chemistry, that allows a conformal nanometric coating of intricate three-dimensional structures. Using this methodology, we have achieved a conformal coverage of large areas of three-dimensional opals with a superparamagnetic manganese ferrite layer, yielding magneto-photonic crystals with excellent quality. The use of a ternary oxide for the ultrathin coating demonstrates the potential of this methodology to realize three-dimensional structures with complex materials that may find applications beyond photonics, such as energy, sensing or catalysis.

  20. 1. View, structures in Systems Integration Laboratory complex, looking northwest. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. View, structures in Systems Integration Laboratory complex, looking northwest. The twin gantry structure in the center is the Systems Integration Laboratory (T-28). To its immediate left in the foreground is a truck well, concrete retaining wall, piping, and stack associated with the oxidizer vault storage area. To the immediate right of T-28 is the concrete Signal Transfer Building (T-28A). At the extreme right is the Long-Term Hydrazine Silo (T-28E). - Air Force Plant PJKS, Systems Integration Laboratory, Waterton Canyon Road & Colorado Highway 121, Lakewood, Jefferson County, CO

  1. Block-structured grids for complex aerodynamic configurations: Current status

    NASA Technical Reports Server (NTRS)

    Vatsa, Veer N.; Sanetrik, Mark D.; Parlette, Edward B.

    1995-01-01

    The status of CFD methods based on the use of block-structured grids for analyzing viscous flows over complex configurations is examined. The objective of the present study is to make a realistic assessment of the usability of such grids for routine computations typically encountered in the aerospace industry. It is recognized at the very outset that the total turnaround time, from the moment the configuration is identified until the computational results have been obtained and postprocessed, is more important than just the computational time. Pertinent examples will be cited to demonstrate the feasibility of solving flow over practical configurations of current interest on block-structured grids.

  2. Structure and function analysis of protein-nucleic acid complexes

    NASA Astrophysics Data System (ADS)

    Kuznetsova, S. A.; Oretskaya, T. S.

    2016-05-01

    The review summarizes published data on the results and achievements in the field of structure and function analysis of protein-nucleic acid complexes by means of main physical and biochemical methods, including X-ray diffraction, nuclear magnetic resonance spectroscopy, electron and atomic force microscopy, small-angle X-ray and neutron scattering, footprinting and cross-linking. Special attention is given to combined approaches. The advantages and limitations of each method are considered, and the prospects of their application for wide-scale structural studies in vivo are discussed. The bibliography includes 145 references.

  3. Structural complexity and the quality of stepfather-stepchild relationships.

    PubMed

    Clingempeel, W G; Ievoli, R; Brand, E

    1984-12-01

    This research examined the effects of structural complexity and sex of stepchild on the quality of stepfather-stepchild relationships. Sixteen simple stepfather families (the wife had custody of a child from a previous marriage, but the stepfather has no biological children) and 16 complex stepfather families (the wife had custody of a child from a previous marriage, and the stepfather was a noncustodial biological parent) with half of each type (N = 8) having a male and half having a female, 9-12-year-old target child participated in a multimethod-multimeasure assessment of the stepfather-stepchild relationship. Families were recruited from marriage license records, and data collection was accomplished in a single three-and-a-half-hour home visit. Dependent variables included: (a) questionnaire measures of love and detachment relationship dimensions independently obtained from parents, stepparents, and (step)children, and (b) proportions of positive and negative stepparent and stepchild communication behaviors derived from videotaped interaction tasks. Findings revealed that simple and complex stepfather families did not differ on any questionnaire or behavioral measures. Girls, however, engaged in a lower proportion of positive verbal and greater proportion of negative problem-solving behaviors toward their stepfathers than boys did. Stepfathers did not differ on proportions of communication behaviors emitted toward boys and girls. No sex-of-child differences were obtained on the questionnaire measures. Directions for future research on structural complexity and stepfather families are discussed.

  4. DNA complexes with Ni nanoparticles: structural and functional properties

    NASA Astrophysics Data System (ADS)

    Tatarinova, Olga N.; Smirnov, Igor P.; Safenkova, Irina V.; Varizhuk, Anna M.; Pozmogova, Galina E.

    2012-10-01

    Supramolecular complexes of biopolymers based on magnetic nanoparticles play an important role in creation of biosensors, implementation of theragnostic and gene therapeutic methods and biosafety evaluation. We investigated the impact of DNA interactions with nanoparticles of nickel (nNi) on the integrity and functionality of DNA. Data obtained by mass spectrometry, electrophoresis, TEM and AFM microscopy techniques, bacterial transformation, and real-time PCR provide evidence that ssDNA and plasmid DNA (pDNA) efficiently form complexes with nNi. AFM data suggest that the complexes are necklace-type structures, in which nanoparticles are randomly distributed along the DNA chains, rather than highly entangled clot-type structures. After desorption, observed DNA characteristics in bioanalytical and biological systems remain unchanged. Only supercoiled pDNA was nicked, but remained, as well as a plasmid-nNi complex, active in expression vector assays. These results are very important for creation of new methods of DNA immobilization and controlled manipulation.

  5. Control of cerium oxidation state through metal complex secondary structures

    SciTech Connect

    Levin, Jessica R.; Dorfner, Walter L.; Carroll, Patrick J.; Schelter, Eric J.

    2015-08-11

    A series of alkali metal cerium diphenylhydrazido complexes, Mx(py)y[Ce(PhNNPh)4], M = Li, Na, and K, x = 4 (Li and Na) or 5 (K), and y = 4 (Li), 8 (Na), or 7 (K), were synthesized to probe how a secondary coordination sphere would modulate electronic structures at a cerium cation. The resulting electronic structures of the heterobimetallic cerium diphenylhydrazido complexes were found to be strongly dependent on the identity of the alkali metal cations. When M = Li+ or Na+, the cerium(III) starting material was oxidized with concomitant reduction of 1,2-diphenylhydrazine to aniline. Reduction of 1,2-diphenylhydrazine was not observed when M = K+, and the complex remained in the cerium(III) oxidation state. Oxidation of the cerium(III) diphenylhydrazido complex to the Ce(IV) diphenylhydrazido one was achieved through a simple cation exchange reaction of the alkali metals. As a result, UV-Vis spectroscopy, FTIR spectroscopy, electrochemistry, magnetic susceptibility, and DFT studies were used to probe the oxidation state and the electronic changes that occurred at the metal centre.

  6. Control of cerium oxidation state through metal complex secondary structures

    DOE PAGES

    Levin, Jessica R.; Dorfner, Walter L.; Carroll, Patrick J.; ...

    2015-08-11

    A series of alkali metal cerium diphenylhydrazido complexes, Mx(py)y[Ce(PhNNPh)4], M = Li, Na, and K, x = 4 (Li and Na) or 5 (K), and y = 4 (Li), 8 (Na), or 7 (K), were synthesized to probe how a secondary coordination sphere would modulate electronic structures at a cerium cation. The resulting electronic structures of the heterobimetallic cerium diphenylhydrazido complexes were found to be strongly dependent on the identity of the alkali metal cations. When M = Li+ or Na+, the cerium(III) starting material was oxidized with concomitant reduction of 1,2-diphenylhydrazine to aniline. Reduction of 1,2-diphenylhydrazine was not observedmore » when M = K+, and the complex remained in the cerium(III) oxidation state. Oxidation of the cerium(III) diphenylhydrazido complex to the Ce(IV) diphenylhydrazido one was achieved through a simple cation exchange reaction of the alkali metals. As a result, UV-Vis spectroscopy, FTIR spectroscopy, electrochemistry, magnetic susceptibility, and DFT studies were used to probe the oxidation state and the electronic changes that occurred at the metal centre.« less

  7. Structure of the ESCRT-II endosomal trafficking complex.

    PubMed

    Hierro, Aitor; Sun, Ji; Rusnak, Alexander S; Kim, Jaewon; Prag, Gali; Emr, Scott D; Hurley, James H

    2004-09-09

    The multivesicular-body (MVB) pathway delivers transmembrane proteins and lipids to the lumen of the endosome. The multivesicular-body sorting pathway has crucial roles in growth-factor-receptor downregulation, developmental signalling, regulation of the immune response and the budding of certain enveloped viruses such as human immunodeficiency virus. Ubiquitination is a signal for sorting into the MVB pathway, which also requires the functions of three protein complexes, termed ESCRT-I, -II and -III (endosomal sorting complex required for transport). Here we report the crystal structure of the core of the yeast ESCRT-II complex, which contains one molecule of the Vps protein Vps22, the carboxy-terminal domain of Vps36 and two molecules of Vps25, and has the shape of a capital letter 'Y'. The amino-terminal coiled coil of Vps22 and the flexible linker leading to the ubiquitin-binding NZF domain of Vps36 both protrude from the tip of one branch of the 'Y'. Vps22 and Vps36 form nearly equivalent interactions with the two Vps25 molecules at the centre of the 'Y'. The structure suggests how ubiquitinated cargo could be passed between ESCRT components of the MVB pathway through the sequential transfer of ubiquitinated cargo from one complex to the next.

  8. Optimal structure of complex networks for minimizing traffic congestion.

    PubMed

    Zhao, Liang; Cupertino, Thiago Henrique; Park, Kwangho; Lai, Ying-Cheng; Jin, Xiaogang

    2007-12-01

    To design complex networks to minimize traffic congestion, it is necessary to understand how traffic flow depends on network structure. We study data packet flow on complex networks, where the packet delivery capacity of each node is not fixed. The optimal configuration of capacities to minimize traffic congestion is derived and the critical packet generating rate is determined, below which the network is at a free flow state but above which congestion occurs. Our analysis reveals a direct relation between network topology and traffic flow. Optimal network structure, free of traffic congestion, should have two features: uniform distribution of load over all nodes and small network diameter. This finding is confirmed by numerical simulations. Our analysis also makes it possible to theoretically compare the congestion conditions for different types of complex networks. In particular, we find that network with low critical generating rate is more susceptible to congestion. The comparison has been made on the following complex-network topologies: random, scale-free, and regular.

  9. Control of complex networks requires both structure and dynamics

    NASA Astrophysics Data System (ADS)

    Gates, Alexander J.; Rocha, Luis M.

    2016-04-01

    The study of network structure has uncovered signatures of the organization of complex systems. However, there is also a need to understand how to control them; for example, identifying strategies to revert a diseased cell to a healthy state, or a mature cell to a pluripotent state. Two recent methodologies suggest that the controllability of complex systems can be predicted solely from the graph of interactions between variables, without considering their dynamics: structural controllability and minimum dominating sets. We demonstrate that such structure-only methods fail to characterize controllability when dynamics are introduced. We study Boolean network ensembles of network motifs as well as three models of biochemical regulation: the segment polarity network in Drosophila melanogaster, the cell cycle of budding yeast Saccharomyces cerevisiae, and the floral organ arrangement in Arabidopsis thaliana. We demonstrate that structure-only methods both undershoot and overshoot the number and which sets of critical variables best control the dynamics of these models, highlighting the importance of the actual system dynamics in determining control. Our analysis further shows that the logic of automata transition functions, namely how canalizing they are, plays an important role in the extent to which structure predicts dynamics.

  10. Potassium under pressure: Electronic origin of complex structures

    NASA Astrophysics Data System (ADS)

    Degtyareva, V. F.

    2014-10-01

    Recent high-pressure X-ray diffraction studies of alkali metals revealed unusual complex structures that follow the body-centred and face-centred cubic structures on compression. The structural sequence of potassium under compression to 1 Mbar is as follows: bcc-fcc-h-g (tI19*), hP4-oP8-tI4-oC16. We consider configurations of Brillouin-Jones zones and the Fermi surface within a nearly-free-electron model in order to analyze the importance of these configurations for the crystal structure stability. Formation of Brillouin zone planes close to the Fermi surface is related to opening an energy gap at these planes and reduction of crystal energy. Under pressure, this mechanism becomes more important leading to appearance of complex low-symmetry structures. The stability of the post-fcc phases in K is attributed to the changes in the valence electron configuration under strong compression.

  11. Methods for SAXS-Based Structure Determination of Biomolecular Complexes

    DOE PAGES

    Yang, Sichun

    2014-05-30

    Measurements from small-angle X-ray scattering (SAXS) are highly informative to determine the structures of bimolecular complexes in solution. Here, we describe current and recent SAXS-driven developments, with an emphasis on computational modeling. In particular, accurate methods to computing one theoretical scattering profile from a given structure model are discussed, with a key focus on structure factor coarse-graining and hydration contribution. Methods for reconstructing topological structures from an experimental SAXS profile are currently under active development. We report on several modeling tools designed for conformation generation that make use of either atomic-level or coarse-grained representations. Furthermore, since large, flexible biomolecules canmore » adopt multiple well-defined conformations, a traditional single-conformation SAXS analysis is inappropriate, so we also discuss recent methods that utilize the concept of ensemble optimization, weighing in on the SAXS contributions of a heterogeneous mixture of conformations. These tools will ultimately posit the usefulness of SAXS data beyond a simple space-filling approach by providing a reliable structure characterization of biomolecular complexes under physiological conditions.« less

  12. Structure sensitive normal coordinate analysis of metal-diethyldithiocarbamate - complexes

    NASA Astrophysics Data System (ADS)

    Mikosch, H.; Bauer, G.; Kellner, R.; Trendafilova, N. S.; St. Nikolov, G.

    1986-03-01

    Symmetry changes in the course of dissolution are assumed to produce frequency shifts in molecular spectra of N, N-Disubstituted Dithiocarbamates. Using (mass-weighted) cartesian coordinates it is possible to calculate eigenvalues both for the site- and the molecular symmetry. Calculated shifts for Cu- and Zn- complexes are of the same order of magnitude as experimental results and calculation of frequencies even for assumed structures is possible.

  13. 18-crown-6-sodium cholate complex: thermochemistry, structure, and stability.

    PubMed

    Mihelj, Tea; Tomašić, Vlasta; Biliškov, Nikola

    2014-06-03

    18-Crown-6, one of the most relevant crown ethers, and sodium cholate, a steroidal surfactant classified as a natural bile salt, are components of a novel, synthesized coordination complex: 18-crown-6-sodium cholate (18C6·NaCh). Like crown ethers, bile salts act as building blocks in supramolecular chemistry to design new functionalized materials with a desired structure and properties. In order to obtain thermal behavior of this 1:1 coordination complex, thermogravimetry and differential thermal analysis were used, as well as microscopic observations and differential scanning calorimetry. Temperature dependent infrared (IR) spectroscopy gave a detailed view into phase transitions. The structures during thermal treatment were observed with powder X-ray diffraction, and molecular models of the phases were made. Hard, glassy, colorless compound 18C6·NaCh goes through crystalline-crystalline polymorphic phase transitions at higher temperatures. The room temperature phase is indexed to a triclinic lattice, while in the high temperature phases molecules take randomly one of the two different configurations in the unit cell, resulting in the 2-fold symmetry. The formation of cholesteric liquid crystalline phase occurs simultaneously with partial decomposition, followed by the isotropization with simultaneous and complete decomposition at much higher temperature, as obtained by IR. The results provide valuable information about the relationship between molecular structure, thermal properties, and stability of the complex, indicating the importance of an appropriate choice of cation, amphiphilic, and crown ether unit in order to synthesize compounds with desired behavior.

  14. DMS Footprinting of Structured RNAs and RNA-Protein Complexes

    PubMed Central

    Tijerina, Pilar; Mohr, Sabine; Russell, Rick

    2008-01-01

    We describe a protocol in which dimethyl sulfate (DMS) modification of the base-pairing faces of unpaired adenosine and cytidine nucleotides is used for structural analysis of RNAs and RNA-protein complexes (RNPs). The protocol is optimized for RNAs of small to moderate size (≤500 nucleotides). The RNA or RNP is first exposed to DMS under conditions that promote formation of the folded structure or complex, as well as ‘control’ conditions that do not allow folding or complex formation. The positions and extents of modification are then determined by primer extension, polyacrylamide gel electrophoresis (PAGE), and quantitative analysis. From changes in the extent of modification upon folding or protein binding (appearance of a ‘footprint’), it is possible to detect local changes in RNA secondary and tertiary structure, as well as the formation of RNA-protein contacts. This protocol takes 1.5–3 days to complete, depending on the type of analysis used. PMID:17948004

  15. Complexation of Flavonoids with Iron: Structure and Optical Signatures

    NASA Astrophysics Data System (ADS)

    Ren, Jun; Meng, Sheng; Lekka, Ch. E.; Kaxiras, Efthimios

    2008-03-01

    Flavonoids exhibit antioxidant behavior believed to be related to their metal ion chelation ability. We investigate the complexation mechanism of several flavonoids, quercetin, luteolin, galangin, kaempferol and chrysin with iron, the most abundant type of metal ions in the body, through first- principles electronic structure calculations based on Density Functional Theory (DFT). We find that the most likely chelation site for Fe is the 3-hydroxyl-4-carbonyl group, followed by 4- carbonyl-5-hydroxyl group and the 3'-4' hydroxyl (if present) for all the flavonoid molecules studied. Three quercetin molecules are required to saturate the bonds of a single Fe ion by forming six orthogonal Fe-O bonds, though the binding energy per molecule is highest for complexes consisting of two quercetin molecules and one Fe atom, in agreement with experiment. Optical absorption spectra calculated with time- dependent DFT serve as signatures to identify various complexes. For the iron-quercetin complexes, we find a redshift of the first absorbance peak upon complexation in good agreement with experiment; this behavior is explained by the narrowing of the optical gap of quercetin due to Fe(d)--O(p) orbital hybridization.

  16. Realization of Cohen-Glashow very special relativity on noncommutative space-time.

    PubMed

    Sheikh-Jabbari, M M; Tureanu, A

    2008-12-31

    We show that the Cohen-Glashow very special relativity (VSR) theory [A. G. Cohen and S. L. Glashow, Phys. Rev. Lett. 97, 021601 (2006)] can be realized as the part of the Poincaré symmetry preserved on a noncommutative Moyal plane with lightlike noncommutativity. Moreover, we show that the three subgroups relevant to VSR can also be realized in the noncommutative space-time setting. For all of these three cases, the noncommutativity parameter theta(mu upsilon) should be lightlike (theta(mu upsilon) theta mu upsilon = 0). We discuss some physical implications of this realization of the Cohen-Glashow VSR.

  17. Complexity of Soils Porous Structure: A Simple Question

    NASA Astrophysics Data System (ADS)

    Benito, R. M.; Cardenas, J. P.; Santiago, A.; Borondo, F.; Losada, J. C.; Tarquis, A. M.; Grupo de Sistemas Complejos

    2011-12-01

    In the last decades scientist have realized that soil processes are implicated the biggest global challenges facing humanity such as soil aeration, sequestration or emission of greenhouse gasses, volatilization of volatile organic chemicals among other phenomena. Progress in these challenges will depend on being able to understand the integrated behavior of soil as a system, and dealing with the complexity in describing soil in these terms. In this work we focus in one of the critical soil issues: soil structure and pore connectivity. A quantitative and explicit characterization of soil structure is difficult because of the complexity of the pore space. We proposed a model to attempt to capture the complexity of the system in which we interpret porous soils as heterogeneous networks, where pores are represented by nodes and the links representing flows between them. Pore properties such as position and size are described by fixed states in a metric space, while an affinity function is introduced to bias the attachment probabilities of links according to these properties taking in account soil texture. These types of models are named as Heterogeneous Preferential Attachment (HPA). We perform an analytical study of the degree distributions in the soil model and show that under reasonable conditions all the model variants yield a multiscaling behavior in the connectivity degrees, leaving an empirically testable signature of heterogeneity in the topology of pore networks. With the aim to study in more detail topological properties of these networks, for different real soils samples an analysis of the community structure have been applied and studied depending on the values of the parameters of the porous soil model used. The detection of communities of pores, as groups densely connected with only sparser connections between groups, could contribute to understand the mechanisms of the diffusion phenomena in soils. References Cardenas, J. P. Cardenas, A. M. Tarquis, J. C

  18. Crystal Structure of LGR4-Rspo1 Complex

    PubMed Central

    Xu, Jin-Gen; Huang, Chunfeng; Yang, Zhengfeng; Jin, Mengmeng; Fu, Panhan; Zhang, Ni; Luo, Jian; Li, Dali; Liu, Mingyao; Zhou, Yan; Zhu, Yongqun

    2015-01-01

    Leucine-rich repeat G-protein-coupled receptors (LGRs) are a unique class of G-protein-coupled receptors characterized by a large extracellular domain to recognize ligands and regulate many important developmental processes. Among the three groups of LGRs, group B members (LGR4–6) recognize R-spondin family proteins (Rspo1–4) to stimulate Wnt signaling. In this study, we successfully utilized the “hybrid leucine-rich repeat technique,” which fused LGR4 with the hagfish VLR protein, to obtain two recombinant human LGR4 proteins, LGR415 and LGR49. We determined the crystal structures of ligand-free LGR415 and the LGR49-Rspo1 complex. LGR4 exhibits a twisted horseshoe-like structure. Rspo1 adopts a flat and β-fold architecture and is bound in the concave surface of LGR4 in the complex through electrostatic and hydrophobic interactions. All the Rspo1-binding residues are conserved in LGR4–6, suggesting that LGR4–6 bind R-spondins through an identical surface. Structural analysis of our LGR4-Rspo1 complex with the previously determined LGR4 and LGR5 structures revealed that the concave surface of LGR4 is the sole binding site for R-spondins, suggesting a one-site binding model of LGR4–6 in ligand recognition. The molecular mechanism of LGR4–6 is distinct from the two-step mechanism of group A receptors LGR1–3 and the multiple-interface binding model of group C receptors LGR7–8, suggesting LGRs utilize the divergent mechanisms for ligand recognition. Our structures, together with previous reports, provide a comprehensive understanding of the ligand recognition by LGRs. PMID:25480784

  19. Bio-inspired Fabrication of Complex Hierarchical Structure in Silicon.

    PubMed

    Gao, Yang; Peng, Zhengchun; Shi, Tielin; Tan, Xianhua; Zhang, Deqin; Huang, Qiang; Zou, Chuanping; Liao, Guanglan

    2015-08-01

    In this paper, we developed a top-down method to fabricate complex three dimensional silicon structure, which was inspired by the hierarchical micro/nanostructure of the Morpho butterfly scales. The fabrication procedure includes photolithography, metal masking, and both dry and wet etching techniques. First, microscale photoresist grating pattern was formed on the silicon (111) wafer. Trenches with controllable rippled structures on the sidewalls were etched by inductively coupled plasma reactive ion etching Bosch process. Then, Cr film was angled deposited on the bottom of the ripples by electron beam evaporation, followed by anisotropic wet etching of the silicon. The simple fabrication method results in large scale hierarchical structure on a silicon wafer. The fabricated Si structure has multiple layers with uniform thickness of hundreds nanometers. We conducted both light reflection and heat transfer experiments on this structure. They exhibited excellent antireflection performance for polarized ultraviolet, visible and near infrared wavelengths. And the heat flux of the structure was significantly enhanced. As such, we believe that these bio-inspired hierarchical silicon structure will have promising applications in photovoltaics, sensor technology and photonic crystal devices.

  20. Probing the complex ionic structure of warm dense carbon

    NASA Astrophysics Data System (ADS)

    Kraus, Dominik

    2014-10-01

    The carbon phase diagram at extreme pressure conditions has received broad interest for modeling planetary interiors and high energy density laboratory experiments. Numerous theoretical models and simulations have recently been performed but critical experimental data at the phase boundaries and of the microscopic physical properties remain very scarce. In this work, we present novel experimental observations of the complex ion structure in warm dense carbon at pressures from 20 to 220 GPa and temperatures of several thousand Kelvins. Our experiments employ powerful x-ray sources at kilo-joule class laser facilities and at the Linac Coherent Light Source to perform spectrally and angularly resolved x-ray scattering from shock-compressed graphite samples; the absolute static ion structure factor is directly measured by resolving the ratio of elastically and inelastically scattered radiation. Using different types of graphite and varying drive laser intensity, we were able to probe conditions below and above the melting line, resolving the shock-induced graphite-to-diamond and graphite-to-liquid transitions on nanosecond time scale. Our results confirm a complex ionic structure predicted by QMD simulations and demonstrate the importance of chemical bonds at extreme conditions similar to those found in the interiors of giant planets. The evidence presented here thus provides a firmer ground for modeling the evolution and current structure of carbon-bearing icy giants like Neptune, Uranus, and a number of extra-solar planets.

  1. Crystal structure of a nuclear actin ternary complex.

    PubMed

    Cao, Tingting; Sun, Lingfei; Jiang, Yuxiang; Huang, Shanjin; Wang, Jiawei; Chen, Zhucheng

    2016-08-09

    Actin polymerizes and forms filamentous structures (F-actin) in the cytoplasm of eukaryotic cells. It also exists in the nucleus and regulates various nucleic acid transactions, particularly through its incorporation into multiple chromatin-remodeling complexes. However, the specific structure of actin and the mechanisms that regulate its polymeric nature inside the nucleus remain unknown. Here, we report the crystal structure of nuclear actin (N-actin) complexed with actin-related protein 4 (Arp4) and the helicase-SANT-associated (HSA) domain of the chromatin remodeler Swr1. The inner face and barbed end of N-actin are sequestered by interactions with Arp4 and the HSA domain, respectively, which prevents N-actin from polymerization and binding to many actin regulators. The two major domains of N-actin are more twisted than those of globular actin (G-actin), and its nucleotide-binding pocket is occluded, freeing N-actin from binding to and regulation by ATP. These findings revealed the salient structural features of N-actin that distinguish it from its cytoplasmic counterpart and provide a rational basis for its functions and regulation inside the nucleus.

  2. Structural characterization of polymorphs and molecular complexes of finasteride

    NASA Astrophysics Data System (ADS)

    Wawrzycka, Irena; Stȩpniak, Krystyna; Matyjaszczyk, Sławomir; Kozioł, Anna E.; Lis, Tadeusz; Abboud, Khalil A.

    1999-01-01

    The molecular structure of finasteride, 17 β-( N-tert-butylcarbamoyl)-4-aza-5 α-androst-1-en-3-one, and structures of three related crystalline forms have been determined by X-ray analysis. The rigid steroid skeleton of the molecule adopts a half-chair/chair/chair/half-chair conformation. Two peptide groups, one cyclic (lactam) in the ring A and a second being a part of the substituent at C17, are the main factors influencing intermolecular contacts. Different hydrogen-bond interactions of these hydrophilic groups are observed in the crystal structures. An infinite ribbon of finasteride molecules is formed between lactam groups in the orthorhombic homomolecular crystal ( 1) obtained from an ethanol solution. The linear molecular complex finasteride-acetic acid ( 1a) is connected by hydrogen bonds between the lactam of finasteride and the carboxyl group of acetic acid. The crystallization from an ethyl acetate solution gives a complex structure of bis-finasteride monohydrate ethyl acetate clathrate ( 1b) with guest molecule disordered in channels. Crystals of a second (monoclinic) finasteride polymorph ( 2) were obtained during thermal decomposition of 1a, and sublimation of 1, 1a and 1b. Two polymorphic forms show different IR spectra.

  3. Crystal structure of a nuclear actin ternary complex

    PubMed Central

    Cao, Tingting; Sun, Lingfei; Jiang, Yuxiang; Huang, Shanjin; Wang, Jiawei; Chen, Zhucheng

    2016-01-01

    Actin polymerizes and forms filamentous structures (F-actin) in the cytoplasm of eukaryotic cells. It also exists in the nucleus and regulates various nucleic acid transactions, particularly through its incorporation into multiple chromatin-remodeling complexes. However, the specific structure of actin and the mechanisms that regulate its polymeric nature inside the nucleus remain unknown. Here, we report the crystal structure of nuclear actin (N-actin) complexed with actin-related protein 4 (Arp4) and the helicase-SANT–associated (HSA) domain of the chromatin remodeler Swr1. The inner face and barbed end of N-actin are sequestered by interactions with Arp4 and the HSA domain, respectively, which prevents N-actin from polymerization and binding to many actin regulators. The two major domains of N-actin are more twisted than those of globular actin (G-actin), and its nucleotide-binding pocket is occluded, freeing N-actin from binding to and regulation by ATP. These findings revealed the salient structural features of N-actin that distinguish it from its cytoplasmic counterpart and provide a rational basis for its functions and regulation inside the nucleus. PMID:27457955

  4. Cyclodextrins in pharmaceutical formulations I: structure and physicochemical properties, formation of complexes, and types of complex.

    PubMed

    Jambhekar, Sunil S; Breen, Philip

    2016-02-01

    Cyclodextrins are cyclic oligosaccharides that have been recognized as pharmaceutical adjuvants for the past 20 years. The molecular structure of these glucose derivatives, which approximates a truncated cone, bucket, or torus, generates a hydrophilic exterior surface and a nonpolar interior cavity. Cyclodextrins can interact with appropriately sized drug molecules to yield an inclusion complex. These noncovalent inclusion complexes offer a variety of advantages over the noncomplexed form of a drug. Cyclodextrins are primarily used to enhance the aqueous solubility, physical chemical stability, and bioavailability of drugs. Their other applications include preventing drug-drug interactions, converting liquid drugs into microcrystalline powders, minimizing gastrointestinal and ocular irritation, and reducing or eliminating unpleasant taste and smell. Here, we discuss the physical chemical properties of various cyclodextrins, including the effects of substitutions on these properties. Additionally, we report on the regulatory status of their use, commercial products containing cyclodextrins, toxicological considerations, and the forces involved in complex formation. We also highlight the types of complex formed and discuss the methods used to determine the types of complex present.

  5. The structure of the O2-N2O complex.

    PubMed

    Salmon, Steven R; Lane, Joseph R

    2015-09-28

    We have investigated the lowest energy structures and interaction energies of the oxygen nitrous oxide complex (O2-N2O) using explicitly correlated coupled cluster theory. We find that the intermolecular potential energy surface of O2-N2O is very flat, with two minima of comparable energy separated by a low energy first order saddle point. Our results are able to conclusively distinguish between the two sets of experimental geometric parameters for O2-N2O that were previously determined from rotationally resolved infrared spectra. The global minimum structure of O2-N2O is therefore found to be planar with a distorted slipped parallel structure. Finally, we show that the very flat potential energy surface of O2-N2O is problematic when evaluating vibrational frequencies with a numerical Hessian and that consideration should be given as to whether results might change if the step-size is varied.

  6. Structural Complexity and Phonon Physics in 2D Arsenenes.

    PubMed

    Carrete, Jesús; Gallego, Luis J; Mingo, Natalio

    2017-03-15

    In the quest for stable 2D arsenic phases, four different structures have been recently claimed to be stable. We show that, due to phonon contributions, the relative stability of those structures differs from previous reports and depends crucially on temperature. We also show that one of those four phases is in fact mechanically unstable. Furthermore, our results challenge the common assumption of an inverse correlation between structural complexity and thermal conductivity. Instead, a richer picture emerges from our results, showing how harmonic interactions, anharmonicity, and symmetries all play a role in modulating thermal conduction in arsenenes. More generally, our conclusions highlight how vibrational properties are an essential element to be carefully taken into account in theoretical searches for new 2D materials.

  7. Complex Dynamic Flows in Solar Flare Sheet Structures

    NASA Technical Reports Server (NTRS)

    McKenzie, David E.; Reeves, Katharine K.; Savage, Sabrina

    2012-01-01

    Observations of high-energy emission from solar flares often reveal the presence of large sheet-like structures, sometimes extending over a space comparable to the Sun's radius. Given that these structures are found between a departing coronal mass ejection and the post-eruption flare arcade, it is natural to associate the structure with a current sheet; though the relationship is unclear. Moreover, recent high-resolution observations have begun to reveal that the motions in this region are highly complex, including reconnection outflows, oscillations, and apparent wakes and eddies. We present a detailed first look at the complicated dynamics within this supra-arcade plasma, and consider implications for the interrelationship between the plasma and its embedded magnetic field.

  8. Measuring robustness of community structure in complex networks

    NASA Astrophysics Data System (ADS)

    Li, Hui-Jia; Wang, Hao; Chen, Luonan

    2014-12-01

    The theory of community structure is a powerful tool for real networks, which can simplify their topological and functional analysis considerably. However, since community detection methods have random factors and real social networks derived from complex systems always contain error edges, evaluating the robustness of community structure is an urgent and important task. In this letter, we employ the critical threshold of resolution parameter in Hamiltonian function, γC , to measure the robustness of a network. According to spectral theory, a rigorous proof shows that the index we proposed is inversely proportional to robustness of community structure. Furthermore, by utilizing the co-evolution model, we provides a new efficient method for computing the value of γC . The research can be applied to broad clustering problems in network analysis and data mining due to its solid mathematical basis and experimental effects.

  9. The Bow City structure, southern Alberta, Canada: The deep roots of a complex impact structure?

    NASA Astrophysics Data System (ADS)

    Glombick, Paul; Schmitt, Douglas R.; Xie, Wei; Bown, Todd; Hathway, Ben; Banks, Christopher

    2014-05-01

    Geological and geophysical evidence is presented for a newly discovered, probable remnant complex impact structure. The structure, located near Bow City, southern Alberta, has no obvious morphological expression at surface. The geometry of the structure in the shallow subsurface, mapped using downhole geophysical well logs, is a semicircular structural depression approximately 8 km in diameter with a semicircular uplifted central region. Detailed subsurface mapping revealed evidence of localized duplication of stratigraphic section in the central uplift area and omission of strata within the surrounding annular region. Field mapping of outcrop confirmed an inlier of older rocks present within the center of the structure. Evidence of deformation along the eastern margin of the central uplift includes thrust faulting, folding, and steeply dipping bedding. Normal faults were mapped along the northern margin of the annular region. Isopach maps reveal that structural thickening and thinning were accommodated primarily within the Belly River Group. Evidence from legacy 2-D seismic data is consistent with the subsurface mapping and reveals additional insight into the geometry of the structure, including a series of listric normal faults in the annular region and complex faulting within the central uplift. The absence of any ejecta blanket, breccia, suevite, or melt sheet (based on available data) is consistent with the Bow City structure being the remnant of a deeply eroded, complex impact structure. Accordingly, the Bow City structure may provide rare access and insight into zones of deformation remaining beneath an excavated transient crater in stratified siliciclastic target rocks.

  10. Exceptional structural and mechanical flexibility of the nuclear pore complex.

    PubMed

    Liashkovich, Ivan; Meyring, Anne; Kramer, Armin; Shahin, Victor

    2011-03-01

    Nuclear pore complexes (NPCs) mediate all transport between the cytosol and the nucleus and therefore take centre stage in physiology. While transport through NPCs has been extensively investigated little is known about their structural and barley anything about their mechanical flexibility. Structural and mechanical flexibility of NPCs, however, are presumably of key importance. Like the cell and the cell nucleus, NPCs themselves are regularly exposed to physiological mechanical forces. Besides, NPCs reveal striking transport properties which are likely to require fairly high structural flexibility. The NPC transports up to 1,000 molecules per second through a physically 9 nm wide channel which repeatedly opens to accommodate macromolecules significantly larger than its physical diameter. We hypothesised that NPCs possess remarkable structural and mechanical stability. Here, we tested this hypothesis at the single NPC level using the nano-imaging and probing approach atomic force microscopy (AFM). AFM presents the NPC as a highly flexible structure. The NPC channel dilates by striking 35% on exposure to trans-cyclohexane-1,2-diol (TCHD), which is known to transiently collapse the hydrophobic phase in the NPC channel like receptor-cargo complexes do in transit. It constricts again to its initial size after TCHD removal. AFM-based nano-indentation measurements show that the 50 nm long NPC basket can astonishingly be squeezed completely into the NPC channel on exposure to incremental mechanical loads but recovers its original vertical position within the nuclear envelope plane when relieved. We conclude that the NPC possesses exceptional structural and mechanical flexibility which is important to fulfilling its functions.

  11. Manufacturing of a 3D complex hyperstable Cesic structure

    NASA Astrophysics Data System (ADS)

    Kroedel, Matthias; Courteau, Pascal; Poupinet, Anne; Sarri, Giuseppe

    2007-09-01

    Global astrometry requires extremely stable materials for instrument structures, such as optical benches. Cesic®, developed by ECM and Thales Alenia Space for mirrors and high stability structures, offers an excellent compromise in terms of structural strength, stability and very high lightweight capability, with a coefficient of thermal expansion that is virtually zero at cryogenic T°. The High-Stability Optical Bench (HSOB) GAIA study, realized by Thales Alenia Space under ESA contract, aimed to design, develop and test a full-scale representative of the HSOB bench, made entirely of Cesic®. The bench has been equipped with SAGEIS-CSO laser metrology system MOUSE1, a Michelson interferometer composed of integrated optics with nm-resolution. The HSOB bench has been submitted to a homogeneous T° step under vacuum to characterize 3-D expansion behavior of its two arms. The quite negligible interarm differential, measured with a nm-range reproducibility, demonstrates that a complete 3-D structure made of Cesic® has the same CTE homogeneity as do characterization samples, fully in line with the stringent GAIA requirements (1ppm at 120K). This demonstrates that Cesic® properties at cryogenic temperatures are fully appropriate to the manufacturing of complex highly stable optical structures. This successful study confirms ECM's and Thales Alenia Space's ability to design and manufacture monolithic lightweight highly stable optical structures, based on inner-cell triangular design made possible by the unique Cesic® manufacturing process.

  12. Structural Mechanism for Cargo Recognition by the Retromer Complex.

    PubMed

    Lucas, María; Gershlick, David C; Vidaurrazaga, Ander; Rojas, Adriana L; Bonifacino, Juan S; Hierro, Aitor

    2016-12-01

    Retromer is a multi-protein complex that recycles transmembrane cargo from endosomes to the trans-Golgi network and the plasma membrane. Defects in retromer impair various cellular processes and underlie some forms of Alzheimer's disease and Parkinson's disease. Although retromer was discovered over 15 years ago, the mechanisms for cargo recognition and recruitment to endosomes have remained elusive. Here, we present an X-ray crystallographic analysis of a four-component complex comprising the VPS26 and VPS35 subunits of retromer, the sorting nexin SNX3, and a recycling signal from the divalent cation transporter DMT1-II. This analysis identifies a binding site for canonical recycling signals at the interface between VPS26 and SNX3. In addition, the structure highlights a network of cooperative interactions among the VPS subunits, SNX3, and cargo that couple signal-recognition to membrane recruitment.

  13. Noncommutative geometry and the primordial dipolar imaginary power spectrum

    NASA Astrophysics Data System (ADS)

    Jain, Pankaj; Rath, Pranati K.

    2015-03-01

    We argue that noncommutative space-times lead to an anisotropic dipolar imaginary primordial power spectrum. We define a new product rule, which allows us to consistently extract the power spectrum in such space-times. The precise nature of the power spectrum depends on the model of noncommutative geometry. We assume a simple dipolar model which has a power dependence on the wave number, , with a spectral index, . We show that such a spectrum provides a good description of the observed dipole modulation in the cosmic microwave background radiation (CMBR) data with . We extract the parameters of this model from the data. The dipole modulation is related to the observed hemispherical anisotropy in the CMBR data, which might represent the first signature of quantum gravity.

  14. q -deformed noncommutative cat states and their nonclassical properties

    NASA Astrophysics Data System (ADS)

    Dey, Sanjib

    2015-02-01

    We study several classical-like properties of q -deformed nonlinear coherent states as well as nonclassical behaviors of q -deformed version of the Schrödinger cat states in noncommutative space. Coherent states in q -deformed space are found to be minimum uncertainty states together with the squeezed photon distributions unlike the ordinary systems, where the photon distributions are always Poissonian. Several advantages of utilizing cat states in noncommutative space over the standard quantum mechanical spaces have been reported here. For instance, the q -deformed parameter has been utilized to improve the squeezing of the quadrature beyond the ordinary case. Most importantly, the parameter provides an extra degree of freedom by which we achieve both quadrature squeezed and number squeezed cat states at the same time in a single system, which is impossible to achieve from ordinary cat states.

  15. Noncommutative QED+QCD and the {beta} function for QED

    SciTech Connect

    Ettefaghi, M. M.; Haghighat, M.; Mohammadi, R.

    2010-11-15

    QED based on {theta}-unexpanded noncomutative space-time in contrast with the noncommutative QED based on {theta}-expanded U(1) gauge theory via the Seiberg-Witten map is one-loop renormalizable. Meanwhile it suffers from asymptotic freedom that is not in agreement with the experiment. We show that the QED part of the U{sub *}(3)xU{sub *}(1) gauge group as an appropriate gauge group for the noncommutative QED+QCD is not only one-loop renormalizable but also has a {beta} function that can be positive, negative and even zero. In fact the {beta} function depends on the mixing parameter {delta}{sub 13} as a free parameter and it will be equal to its counterpart in the ordinary QED for {delta}{sub 13}=0.367{pi}.

  16. Temporal Structure and Complexity Affect Audio-Visual Correspondence Detection

    PubMed Central

    Denison, Rachel N.; Driver, Jon; Ruff, Christian C.

    2013-01-01

    Synchrony between events in different senses has long been considered the critical temporal cue for multisensory integration. Here, using rapid streams of auditory and visual events, we demonstrate how humans can use temporal structure (rather than mere temporal coincidence) to detect multisensory relatedness. We find psychophysically that participants can detect matching auditory and visual streams via shared temporal structure for crossmodal lags of up to 200 ms. Performance on this task reproduced features of past findings based on explicit timing judgments but did not show any special advantage for perfectly synchronous streams. Importantly, the complexity of temporal patterns influences sensitivity to correspondence. Stochastic, irregular streams – with richer temporal pattern information – led to higher audio-visual matching sensitivity than predictable, rhythmic streams. Our results reveal that temporal structure and its complexity are key determinants for human detection of audio-visual correspondence. The distinctive emphasis of our new paradigms on temporal patterning could be useful for studying special populations with suspected abnormalities in audio-visual temporal perception and multisensory integration. PMID:23346067

  17. Synthesis and structure of didysprosium complexes with a tetraketone

    NASA Astrophysics Data System (ADS)

    Yang, Luqin; Yang, Rudong

    1996-06-01

    Two novel didysprosium (Dy 2) complexes of 1,5-bis(1'-phenyl-3'-methyl-5'-pyrazolone-4')-1,5-pentanedione (H 2L), Dy 2L 3·2H 2O and Dy 2L 3·5DMF (DMF = dimethylformamide), have been synthesized. The crystal structure of Dy 2L 3·5DMF was determined by X-ray diffraction. Crystals are triclinic, space group P1¯, with a = 16.99(1), b = 17.970(9), c = 18.28(1) Å, α = 110.36(4), β = 101.47(6), γ = 111.11(5)°, V = 4533(9) Å 3, Mr = 2017.91, Z = 2, D x = 1.48 g cm -3, μ = 17.22 cm -1, F(000) = 2056, R = 0.074 with 3804 reflections used in the refinement. In the complex, each L bonds two dysprosium atoms with its two β-diketone groups. Two DMF solvent molecules bond to each dysprosium ion. The coordination number of the two dysprosium ions is eight. The eight oxygen atoms around the dysprosium ion make up a distorted square antiprism coordination polyhedron. The resonance structures of coordinated β-diketonates are also discussed. Different lanthanide ions may stabilize the specific structure.

  18. Structure and stability of oligomer/α-cyclodextrin inclusion complexes.

    NASA Astrophysics Data System (ADS)

    Hunt, Marcus; Villar, Silvia; Gomez, Marian; Tonelli, Alan; Balik, Maury

    2007-03-01

    Cyclomaltohexaose (α-cyclodextrin, α-CD) can form inclusion complexes (ICs) with polymer molecules in the columnar crystal in which α-CD molecules stack to form a molecular tube. Complementary water vapor sorption and wide-angle X-ray diffractomery (WAXD) were performed on oligomer/α-CD ICs to probe their structures and stabilities. To discern the effect of guest molecule hydrophobicity on water adsorption isotherms, polyethylene glycol (PEG, MW = 600 g/mol) and hexatriacontane (HTC) guests were used. Sorption isotherms for PEG/α-CD IC are similar to those obtained for pure α-CD and PEG, suggesting the presence of dethreaded PEG in the sample. WAXD collected before and after water vapor sorption of PEG/α-CD IC indicated a partial conversion from columnar to cage crystal structure, the thermodynamically preferred structure for pure α-CD, due to dethreading of PEG. This behavior does not occur for HTC/α-CD IC. Sorption isotherms collected at 20, 30, 40 and 50 C allowed the calculation of differential heats of adsorption and integral entropies of adsorbed water, while solid-state ^13C NMR suggested a dramatic increase in HTC and α-CD mobilities upon complexation.

  19. Brain structural correlates of complex sentence comprehension in children

    PubMed Central

    Fengler, Anja; Meyer, Lars; Friederici, Angela D.

    2015-01-01

    Prior structural imaging studies found initial evidence for the link between structural gray matter changes and the development of language performance in children. However, previous studies generally only focused on sentence comprehension. Therefore, little is known about the relationship between structural properties of brain regions relevant to sentence processing and more specific cognitive abilities underlying complex sentence comprehension. In this study, whole-brain magnetic resonance images from 59 children between 5 and 8 years were assessed. Scores on a standardized sentence comprehension test determined grammatical proficiency of our participants. A confirmatory factory analysis corroborated a grammar-relevant and a verbal working memory-relevant factor underlying the measured performance. Voxel-based morphometry of gray matter revealed that while children's ability to assign thematic roles is positively correlated with gray matter probability (GMP) in the left inferior temporal gyrus and the left inferior frontal gyrus, verbal working memory-related performance is positively correlated with GMP in the left parietal operculum extending into the posterior superior temporal gyrus. Since these areas are known to be differentially engaged in adults’ complex sentence processing, our data suggest a specific correspondence between children's GMP in language-relevant brain regions and differential cognitive abilities that guide their sentence comprehension. PMID:26468613

  20. Brain structural correlates of complex sentence comprehension in children.

    PubMed

    Fengler, Anja; Meyer, Lars; Friederici, Angela D

    2015-10-01

    Prior structural imaging studies found initial evidence for the link between structural gray matter changes and the development of language performance in children. However, previous studies generally only focused on sentence comprehension. Therefore, little is known about the relationship between structural properties of brain regions relevant to sentence processing and more specific cognitive abilities underlying complex sentence comprehension. In this study, whole-brain magnetic resonance images from 59 children between 5 and 8 years were assessed. Scores on a standardized sentence comprehension test determined grammatical proficiency of our participants. A confirmatory factory analysis corroborated a grammar-relevant and a verbal working memory-relevant factor underlying the measured performance. Voxel-based morphometry of gray matter revealed that while children's ability to assign thematic roles is positively correlated with gray matter probability (GMP) in the left inferior temporal gyrus and the left inferior frontal gyrus, verbal working memory-related performance is positively correlated with GMP in the left parietal operculum extending into the posterior superior temporal gyrus. Since these areas are known to be differentially engaged in adults' complex sentence processing, our data suggest a specific correspondence between children's GMP in language-relevant brain regions and differential cognitive abilities that guide their sentence comprehension.

  1. Changes in protein structure at the interface accompanying complex formation

    PubMed Central

    Chakravarty, Devlina; Janin, Joël; Robert, Charles H.; Chakrabarti, Pinak

    2015-01-01

    Protein interactions are essential in all biological processes. The changes brought about in the structure when a free component forms a complex with another molecule need to be characterized for a proper understanding of molecular recognition as well as for the successful implementation of docking algorithms. Here, unbound (U) and bound (B) forms of protein structures from the Protein–Protein Interaction Affinity Database are compared in order to enumerate the changes that occur at the interface atoms/residues in terms of the solvent-accessible surface area (ASA), secondary structure, temperature factors (B factors) and disorder-to-order transitions. It is found that the interface atoms optimize contacts with the atoms in the partner protein, which leads to an increase in their ASA in the bound interface in the majority (69%) of the proteins when compared with the unbound interface, and this is independent of the root-mean-square deviation between the U and B forms. Changes in secondary structure during the transition indicate a likely extension of helices and strands at the expense of turns and coils. A reduction in flexibility during complex formation is reflected in the decrease in B factors of the interface residues on going from the U form to the B form. There is, however, no distinction in flexibility between the interface and the surface in the monomeric structure, thereby highlighting the potential problem of using B factors for the prediction of binding sites in the unbound form for docking another protein. 16% of the proteins have missing (disordered) residues in the U form which are observed (ordered) in the B form, mostly with an irregular conformation; the data set also shows differences in the composition of interface and non-interface residues in the disordered polypeptide segments as well as differences in their surface burial. PMID:26594372

  2. Changes in protein structure at the interface accompanying complex formation.

    PubMed

    Chakravarty, Devlina; Janin, Joël; Robert, Charles H; Chakrabarti, Pinak

    2015-11-01

    Protein interactions are essential in all biological processes. The changes brought about in the structure when a free component forms a complex with another molecule need to be characterized for a proper understanding of molecular recognition as well as for the successful implementation of docking algorithms. Here, unbound (U) and bound (B) forms of protein structures from the Protein-Protein Interaction Affinity Database are compared in order to enumerate the changes that occur at the interface atoms/residues in terms of the solvent-accessible surface area (ASA), secondary structure, temperature factors (B factors) and disorder-to-order transitions. It is found that the interface atoms optimize contacts with the atoms in the partner protein, which leads to an increase in their ASA in the bound interface in the majority (69%) of the proteins when compared with the unbound interface, and this is independent of the root-mean-square deviation between the U and B forms. Changes in secondary structure during the transition indicate a likely extension of helices and strands at the expense of turns and coils. A reduction in flexibility during complex formation is reflected in the decrease in B factors of the interface residues on going from the U form to the B form. There is, however, no distinction in flexibility between the interface and the surface in the monomeric structure, thereby highlighting the potential problem of using B factors for the prediction of binding sites in the unbound form for docking another protein. 16% of the proteins have missing (disordered) residues in the U form which are observed (ordered) in the B form, mostly with an irregular conformation; the data set also shows differences in the composition of interface and non-interface residues in the disordered polypeptide segments as well as differences in their surface burial.

  3. Crystal structure of eukaryotic ribosome and its complexes with inhibitors.

    PubMed

    Yusupova, Gulnara; Yusupov, Marat

    2017-03-19

    A high-resolution structure of the eukaryotic ribosome has been determined and has led to increased interest in studying protein biosynthesis and regulation of biosynthesis in cells. The functional complexes of the ribosome crystals obtained from bacteria and yeast have permitted researchers to identify the precise residue positions in different states of ribosome function. This knowledge, together with electron microscopy studies, enhances our understanding of how basic ribosome processes, including mRNA decoding, peptide bond formation, mRNA, and tRNA translocation and cotranslational transport of the nascent peptide, are regulated. In this review, we discuss the crystal structure of the entire 80S ribosome from yeast, which reveals its eukaryotic-specific features, and application of X-ray crystallography of the 80S ribosome for investigation of the binding mode for distinct compounds known to inhibit or modulate the protein-translation function of the ribosome. We also refer to a challenging aspect of the structural study of ribosomes, from higher eukaryotes, where the structures of major distinctive features of higher eukaryote ribosome-the high-eukaryote-specific long ribosomal RNA segments (about 1MDa)-remain unresolved. Presently, the structures of the major part of these high-eukaryotic expansion ribosomal RNA segments still remain unresolved.This article is part of the themed issue 'Perspectives on the ribosome'.

  4. Dynamic heteroleptic metal-phenanthroline complexes: from structure to function.

    PubMed

    Saha, Manik Lal; Neogi, Subhadip; Schmittel, Michael

    2014-03-14

    Dynamically heteroligated metal centres are auspicious platforms to access multicomponent supramolecular systems, the latter showing unique structures, amazing properties and even emergent functions. The great potential of heteroleptic complexes has materialised after the development of appropriate strategies that warrant quantitative formation in spite of the dynamic character. In this perspective, we discuss our endeavours at developing various heteroleptic self-assembly protocols based on sterically bulky 2,9-diarylphenanthrolines and our work toward self-sorted multicomponent architectures and assemblies with new and useful functions.

  5. Non-Poissonian intermittent fluorescence from complex structured environments

    SciTech Connect

    Budini, Adrian A.

    2006-06-15

    We characterize the photon-counting statistics of single-chromophore systems submitted to continuous laser radiation and embedded in a complex structured environment able to induce strong non-Markovian effects in the decay dynamics. In the weak-laser-excitation regime, the photon-emission process can be described through a delay function. We demonstrate that the dynamics, by itself, is able to develop a non-Poissonian intermittent fluorescence phenomenon where the bright and dark intervals are characterized by probability distributions that may depart from an exponential one.

  6. Long tailed cage amines: Synthesis, metal complexation, and structure

    SciTech Connect

    Dittrich, Birger; Harrowfield, Jack M.; Koutsantonis, George A.; Nealon, Gareth L.; Skelton, Brian W.

    2011-12-09

    The generation of amphiphiles derived from macrobicyclic hexamines of the 'sarcophagine' class can be prepared through efficient and selective reactions involving the reductive alkylation, using long-chain aldehydes, of amino-functionalized sarcophagines when bound to Cu(II) or Mg(II). The Mg(II) pathway is particularly convenient for the ultimate isolation of the free ligands, which can then be used to form metalloamphiphiles with a variety of metal ions. Structural studies have been made of one of the free (protonated) ligands and some of their complexes.

  7. Structure and spectroscopy of hydrated neptunyl(VI) nitrate complexes.

    PubMed

    Lindqvist-Reis, Patric; Apostolidis, Christos; Walter, Olaf; Marsac, Remi; Banik, Nidhu Lal; Skripkin, Mikhail Yu; Rothe, Jörg; Morgenstern, Alfred

    2013-11-21

    Complexation between hexavalent neptunium and nitrate was studied in aqueous nitric acid solution using optical absorption, vibrational and X-ray absorption spectroscopies. Distributions of aqueous [NpO2](2+), [NpO2(NO3)](+) and [NpO2(NO3)2] species were obtained as a function of nitric acid concentration between 0 and 14 M. The crystal structure of [NpO2(NO3)2(H2O)2]·H2O was determined.

  8. Structural and Electronic Investigations of Complex Intermetallic Compounds

    SciTech Connect

    Ko, Hyunjin

    2008-01-01

    In solid state chemistry, numerous investigations have been attempted to address the relationships between chemical structure and physical properties. Such questions include: (1) How can we understand the driving forces of the atomic arrangements in complex solids that exhibit interesting chemical and physical properties? (2) How do different elements distribute themselves in a solid-state structure? (3) Can we develop a chemical understanding to predict the effects of valence electron concentration on the structures and magnetic ordering of systems by both experimental and theoretical means? Although these issues are relevant to various compound classes, intermetallic compounds are especially interesting and well suited for a joint experimental and theoretical effort. For intermetallic compounds, the questions listed above are difficult to answer since many of the constituent atoms simply do not crystallize in the same manner as in their separate, elemental structures. Also, theoretical studies suggest that the energy differences between various structural alternatives are small. For example, Al and Ga both belong in the same group on the Periodic Table of Elements and share many similar chemical properties. Al crystallizes in the fcc lattice with 4 atoms per unit cell and Ga crystallizes in an orthorhombic unit cell lattice with 8 atoms per unit cell, which are both fairly simple structures (Figure 1). However, when combined with Mn, which itself has a very complex cubic crystal structure with 58 atoms per unit cell, the resulting intermetallic compounds crystallize in a completely different fashion. At the 1:1 stoichiometry, MnAl forms a very simple tetragonal lattice with two atoms per primitive unit cell, while MnGa crystallizes in a complicated rhombohedral unit cell with 26 atoms within the primitive unit cell. The mechanisms influencing the arrangements of atoms in numerous crystal structures have been studied theoretically by calculating electronic

  9. Canonical quantum gravity on noncommutative space-time

    NASA Astrophysics Data System (ADS)

    Kober, Martin

    2015-06-01

    In this paper canonical quantum gravity on noncommutative space-time is considered. The corresponding generalized classical theory is formulated by using the Moyal star product, which enables the representation of the field quantities depending on noncommuting coordinates by generalized quantities depending on usual coordinates. But not only the classical theory has to be generalized in analogy to other field theories. Besides, the necessity arises to replace the commutator between the gravitational field operator and its canonical conjugated quantity by a corresponding generalized expression on noncommutative space-time. Accordingly the transition to the quantum theory has also to be performed in a generalized way and leads to extended representations of the quantum theoretical operators. If the generalized representations of the operators are inserted to the generalized constraints, one obtains the corresponding generalized quantum constraints including the Hamiltonian constraint as dynamical constraint. After considering quantum geometrodynamics under incorporation of a coupling to matter fields, the theory is transferred to the Ashtekar formalism. The holonomy representation of the gravitational field as it is used in loop quantum gravity opens the possibility to calculate the corresponding generalized area operator.

  10. Regular black holes and noncommutative geometry inspired fuzzy sources

    NASA Astrophysics Data System (ADS)

    Kobayashi, Shinpei

    2016-05-01

    We investigated regular black holes with fuzzy sources in three and four dimensions. The density distributions of such fuzzy sources are inspired by noncommutative geometry and given by Gaussian or generalized Gaussian functions. We utilized mass functions to give a physical interpretation of the horizon formation condition for the black holes. In particular, we investigated three-dimensional BTZ-like black holes and four-dimensional Schwarzschild-like black holes in detail, and found that the number of horizons is related to the space-time dimensions, and the existence of a void in the vicinity of the center of the space-time is significant, rather than noncommutativity. As an application, we considered a three-dimensional black hole with the fuzzy disc which is a disc-shaped region known in the context of noncommutative geometry as a source. We also analyzed a four-dimensional black hole with a source whose density distribution is an extension of the fuzzy disc, and investigated the horizon formation condition for it.

  11. Can noncommutativity affect the whole history of the universe?

    NASA Astrophysics Data System (ADS)

    Monerat, G. A.; Corrêa Silva, E. V.; Neves, C.; Oliveira-Neto, G.; Rezende Rodrigues, L. G.; Silva de Oliveira, M.

    We study a classical, noncommutative (NC), Friedmann-Robertson-Walker (FRW) cosmological model. The spatial sections may have positive, negative or zero constant curvatures. The matter content is a generic perfect fluid. The initial noncommutativity between some canonical variables is rewritten, such that, we end up with commutative variables and a NC parameter. Initially, we derive the scale factor dynamic equations for the general situation, without specifying the perfect fluid or the curvature of the spatial sections. Next, we consider two concrete situations: a radiation perfect fluid and dust. We study all possible scale factor behaviors, for both cases. We compare them with the corresponding commutative cases and one with the other. We obtain, some cases, where the NC model predicts a scale factor expansion which may describe the present expansion of our universe. Those cases are not present in the corresponding commutative models. Finally, we compare our model with another NC model, where the noncommutativity is between different canonical variables. We show that, in general, it leads to a scale factor behavior that is different from our model.

  12. Frequency and Complexity of De Novo Structural Mutation in Autism

    PubMed Central

    Brandler, William M.; Antaki, Danny; Gujral, Madhusudan; Noor, Amina; Rosanio, Gabriel; Chapman, Timothy R.; Barrera, Daniel J.; Lin, Guan Ning; Malhotra, Dheeraj; Watts, Amanda C.; Wong, Lawrence C.; Estabillo, Jasper A.; Gadomski, Therese E.; Hong, Oanh; Fajardo, Karin V. Fuentes; Bhandari, Abhishek; Owen, Renius; Baughn, Michael; Yuan, Jeffrey; Solomon, Terry; Moyzis, Alexandra G.; Maile, Michelle S.; Sanders, Stephan J.; Reiner, Gail E.; Vaux, Keith K.; Strom, Charles M.; Zhang, Kang; Muotri, Alysson R.; Akshoomoff, Natacha; Leal, Suzanne M.; Pierce, Karen; Courchesne, Eric; Iakoucheva, Lilia M.; Corsello, Christina; Sebat, Jonathan

    2016-01-01

    Genetic studies of autism spectrum disorder (ASD) have established that de novo duplications and deletions contribute to risk. However, ascertainment of structural variants (SVs) has been restricted by the coarse resolution of current approaches. By applying a custom pipeline for SV discovery, genotyping, and de novo assembly to genome sequencing of 235 subjects (71 affected individuals, 26 healthy siblings, and their parents), we compiled an atlas of 29,719 SV loci (5,213/genome), comprising 11 different classes. We found a high diversity of de novo mutations, the majority of which were undetectable by previous methods. In addition, we observed complex mutation clusters where combinations of de novo SVs, nucleotide substitutions, and indels occurred as a single event. We estimate a high rate of structural mutation in humans (20%) and propose that genetic risk for ASD is attributable to an elevated frequency of gene-disrupting de novo SVs, but not an elevated rate of genome rearrangement. PMID:27018473

  13. Frequency and Complexity of De Novo Structural Mutation in Autism.

    PubMed

    Brandler, William M; Antaki, Danny; Gujral, Madhusudan; Noor, Amina; Rosanio, Gabriel; Chapman, Timothy R; Barrera, Daniel J; Lin, Guan Ning; Malhotra, Dheeraj; Watts, Amanda C; Wong, Lawrence C; Estabillo, Jasper A; Gadomski, Therese E; Hong, Oanh; Fajardo, Karin V Fuentes; Bhandari, Abhishek; Owen, Renius; Baughn, Michael; Yuan, Jeffrey; Solomon, Terry; Moyzis, Alexandra G; Maile, Michelle S; Sanders, Stephan J; Reiner, Gail E; Vaux, Keith K; Strom, Charles M; Zhang, Kang; Muotri, Alysson R; Akshoomoff, Natacha; Leal, Suzanne M; Pierce, Karen; Courchesne, Eric; Iakoucheva, Lilia M; Corsello, Christina; Sebat, Jonathan

    2016-04-07

    Genetic studies of autism spectrum disorder (ASD) have established that de novo duplications and deletions contribute to risk. However, ascertainment of structural variants (SVs) has been restricted by the coarse resolution of current approaches. By applying a custom pipeline for SV discovery, genotyping, and de novo assembly to genome sequencing of 235 subjects (71 affected individuals, 26 healthy siblings, and their parents), we compiled an atlas of 29,719 SV loci (5,213/genome), comprising 11 different classes. We found a high diversity of de novo mutations, the majority of which were undetectable by previous methods. In addition, we observed complex mutation clusters where combinations of de novo SVs, nucleotide substitutions, and indels occurred as a single event. We estimate a high rate of structural mutation in humans (20%) and propose that genetic risk for ASD is attributable to an elevated frequency of gene-disrupting de novo SVs, but not an elevated rate of genome rearrangement.

  14. Finding community structures in complex networks using mixed integer optimisation

    NASA Astrophysics Data System (ADS)

    Xu, G.; Tsoka, S.; Papageorgiou, L. G.

    2007-11-01

    The detection of community structure has been used to reveal the relationships between individual objects and their groupings in networks. This paper presents a mathematical programming approach to identify the optimal community structures in complex networks based on the maximisation of a network modularity metric for partitioning a network into modules. The overall problem is formulated as a mixed integer quadratic programming (MIQP) model, which can then be solved to global optimality using standard optimisation software. The solution procedure is further enhanced by developing special symmetry-breaking constraints to eliminate equivalent solutions. It is shown that additional features such as minimum/maximum module size and balancing among modules can easily be incorporated in the model. The applicability of the proposed optimisation-based approach is demonstrated by four examples. Comparative results with other approaches from the literature show that the proposed methodology has superior performance while global optimum is guaranteed.

  15. Towards reconciling structure and function in the nuclear pore complex

    PubMed Central

    Aebi, Ueli; Fahrenkrog, Birthe

    2008-01-01

    The spatial separation between the cytoplasm and the cell nucleus necessitates the continuous exchange of macromolecular cargo across the double-membraned nuclear envelope. Being the only passageway in and out of the nucleus, the nuclear pore complex (NPC) has the principal function of regulating the high throughput of nucleocytoplasmic transport in a highly selective manner so as to maintain cellular order and function. Here, we present a retrospective review of the evidence that has led to the current understanding of both NPC structure and function. Looking towards the future, we contemplate on how various outstanding effects and nanoscopic characteristics ought to be addressed, with the goal of reconciling structure and function into a single unified picture of the NPC. PMID:18228033

  16. Structure and gating of the nuclear pore complex

    NASA Astrophysics Data System (ADS)

    Eibauer, Matthias; Pellanda, Mauro; Turgay, Yagmur; Dubrovsky, Anna; Wild, Annik; Medalia, Ohad

    2015-06-01

    Nuclear pore complexes (NPCs) perforate the nuclear envelope and allow the exchange of macromolecules between the nucleus and the cytoplasm. To acquire a deeper understanding of this transport mechanism, we analyse the structure of the NPC scaffold and permeability barrier, by reconstructing the Xenopus laevis oocyte NPC from native nuclear envelopes up to 20 Å resolution by cryo-electron tomography in conjunction with subtomogram averaging. In addition to resolving individual protein domains of the NPC constituents, we propose a model for the architecture of the molecular gate at its central channel. Furthermore, we compare and contrast this native NPC structure to one that exhibits reduced transport activity and unveil the spatial properties of the NPC gate.

  17. Structural permeability of complex networks to control signals

    PubMed Central

    Lo Iudice, Francesco; Garofalo, Franco; Sorrentino, Francesco

    2015-01-01

    Many biological, social and technological systems can be described as complex networks. The goal of affecting their behaviour has motivated recent work focusing on the relationship between the network structure and its propensity to be controlled. While this work has provided insight into several relevant problems, a comprehensive approach to address partial and complete controllability of networks is still lacking. Here, we bridge this gap by developing a framework to maximize the diffusion of the control signals through a network, while taking into account physical and economic constraints that inevitably arise in applications. This approach allows us to introduce the network permeability, a unified metric of the propensity of a network to be controllable. The analysis of the permeability of several synthetic and real networks enables us to extract some structural features that deepen our quantitative understanding of the ease with which specific controllability requirements can be met. PMID:26391186

  18. Contaminant Organic Complexes: Their Structure and Energetics in Surface Decontamination

    SciTech Connect

    Samuel Traina; Shankar Sharma

    2005-07-12

    The Department of Energy has a goal of decontaminating an estimated 180,000 metric tons of metal wastes in various surplus facilities. Uranium (U) and other radioactive actinides and lanthanides are embedded within the mixed oxide structures of the passivity layers of corroded iron and steel. These toxic metals can be dissolved out of the surface layers by a naturally occurring bacterial siderophore called Desferrioxamine B (DFB). DFB is a trihydroxamate ligand with one amine and three hydroxamate groups, which chelates with metals through hydroxamate coordination. Complexation of DFB with U can be utilized in decontamination strategy of the passivity layers. Therefore, we have been studying reactions of uranyl U(VI) with zerovalent iron (Fe0) followed by dissolution by DFB. The objectives were to determine the structure and speciation of solution and solid phases of U and to assess the effectiveness of DVB in U dissolution.

  19. Structure and gating of the nuclear pore complex.

    PubMed

    Eibauer, Matthias; Pellanda, Mauro; Turgay, Yagmur; Dubrovsky, Anna; Wild, Annik; Medalia, Ohad

    2015-06-26

    Nuclear pore complexes (NPCs) perforate the nuclear envelope and allow the exchange of macromolecules between the nucleus and the cytoplasm. To acquire a deeper understanding of this transport mechanism, we analyse the structure of the NPC scaffold and permeability barrier, by reconstructing the Xenopus laevis oocyte NPC from native nuclear envelopes up to 20 Å resolution by cryo-electron tomography in conjunction with subtomogram averaging. In addition to resolving individual protein domains of the NPC constituents, we propose a model for the architecture of the molecular gate at its central channel. Furthermore, we compare and contrast this native NPC structure to one that exhibits reduced transport activity and unveil the spatial properties of the NPC gate.

  20. Structural complexities in the active layers of organic electronics.

    PubMed

    Lee, Stephanie S; Loo, Yueh-Lin

    2010-01-01

    The field of organic electronics has progressed rapidly in recent years. However, understanding the direct structure-function relationships between the morphology in electrically active layers and the performance of devices composed of these materials has proven difficult. The morphology of active layers in organic electronics is inherently complex, with heterogeneities existing across multiple length scales, from subnanometer to micron and millimeter range. A major challenge still facing the organic electronics community is understanding how the morphology across all of the length scales in active layers collectively determines the device performance of organic electronics. In this review we highlight experiments that have contributed to the elucidation of structure-function relationships in organic electronics and also point to areas in which knowledge of such relationships is still lacking. Such knowledge will lead to the ability to select active materials on the basis of their inherent properties for the fabrication of devices with prespecified characteristics.

  1. The structure and proteolytic processing of Cbln1 complexes.

    PubMed

    Bao, Dashi; Pang, Zhen; Morgan, James I

    2005-11-01

    The hexadecapeptide cerebellin is present in the brains of many vertebrate species and is derived from a larger protein, Cbln1 (cerebellin 1 precursor protein). Although cerebellin has features of a neuropeptide, Cbln1 belongs to the C1q/tumor necrosis factor superfamily of secreted proteins, suggesting that it is the biologically active molecule and the proteolytic events that generate cerebellin serve another function. Therefore, we assessed whether Cbln1 undergoes proteolytic processing and determined what consequences the cleavage events necessary to produce cerebellin have on the structure of Cbln1. Substantial degradation of Cbln1 was evident in the synaptic compartment of cerebellum and lysates of cultured cerebellar neurons and cells transfected with Cbln1 expression vectors. However, only uncleaved Cbln1 containing the cerebellin motif was released and assembled into hexameric complexes. Using yeast two hybrid and mammalian expression systems we show that the cleavages required to produce cerebellin influence the subunit stoichiometry of Cbln1 complexes. Cleavage at the N-terminus of the cerebellin sequence in Cbln1 yields trimeric complexes by separating the trimer-mediating C-terminal C1q domain from conserved N-terminal cysteine residues that mediate higher order oligomerization. Cleavage at the C-terminus of the cerebellin motif disrupts the C1q domain and abolishes subunit interactions. Functional implications of these data are discussed.

  2. Structure of the nocturnal boundary layer over a complex terrain

    SciTech Connect

    Parker, M.J. ); Raman, S. . Dept. of Marine, Earth and Atmospheric Sciences)

    1992-01-01

    The complex nature of the nocturnal boundary layer (NBL) has been shown extensively in the literature Project STABLE was conducted in 1988 to study NBL turbulence and diffusion over the complex terrain of the Savannah River Site (SRS) near Augusta, Georgia. The third night of the study was particularly interesting because of the unusual phenomena observed in the structure of the NBL. Further analyses of microscale and mesoscale data from this night are presented using data from SRS network of eight 61 m towers over 900 km{sup 2}, from six launches of an instrumented tethersonde, from permanent SRL meteorological instrumentation at seven levels of the 304 m (1,000 ft) WJBF-TV tower near SRS, and additional data collected at 36 m (CC) by North Carolina State University (NCSU) including a one dimensional sonic anemometer, fine wire thermocouple, and a three dimensional propeller anemometer. Also, data from the nearby Plant Vogtle nuclear power plant observation tower and the National Weather Service at Augusta's Bush Field (AGS) are presented. The passage of a mesoscale phenomenon, defined as a microfront (with an explanation of the nomenclature used), and a vertical composite schematic of the NBL which shows dual low level wind maxima, dual inversions, and a persistent, elevated turbulent layer over a complex terrain are described.

  3. Structure of the nocturnal boundary layer over a complex terrain

    SciTech Connect

    Parker, M.J.; Raman, S.

    1992-08-01

    The complex nature of the nocturnal boundary layer (NBL) has been shown extensively in the literature Project STABLE was conducted in 1988 to study NBL turbulence and diffusion over the complex terrain of the Savannah River Site (SRS) near Augusta, Georgia. The third night of the study was particularly interesting because of the unusual phenomena observed in the structure of the NBL. Further analyses of microscale and mesoscale data from this night are presented using data from SRS network of eight 61 m towers over 900 km{sup 2}, from six launches of an instrumented tethersonde, from permanent SRL meteorological instrumentation at seven levels of the 304 m (1,000 ft) WJBF-TV tower near SRS, and additional data collected at 36 m (CC) by North Carolina State University (NCSU) including a one dimensional sonic anemometer, fine wire thermocouple, and a three dimensional propeller anemometer. Also, data from the nearby Plant Vogtle nuclear power plant observation tower and the National Weather Service at Augusta`s Bush Field (AGS) are presented. The passage of a mesoscale phenomenon, defined as a microfront (with an explanation of the nomenclature used), and a vertical composite schematic of the NBL which shows dual low level wind maxima, dual inversions, and a persistent, elevated turbulent layer over a complex terrain are described.

  4. Seiberg-Witten map and quantum phase effects for neutral Dirac particle on noncommutative plane

    NASA Astrophysics Data System (ADS)

    Ma, Kai; Wang, Jian-Hua; Yang, Huan-Xiong

    2016-05-01

    We provide a new approach to study the noncommutative effects on the neutral Dirac particle with anomalous magnetic or electric dipole moment on the noncommutative plane. The advantages of this approach are demonstrated by investigating the noncommutative corrections on the Aharonov-Casher and He-McKellar-Wilkens effects. This approach is based on the effective U (1) gauge symmetry for the electrodynamics of spin on the two dimensional space. The Seiberg-Witten map for this symmetry is then employed when we study the noncommutative corrections. Because the Seiberg-Witten map preserves the gauge symmetry, the noncommutative corrections can be defined consistently with the ordinary phases. Based on this approach we find the noncommutative corrections on the Aharonov-Casher and He-McKellar-Wilkens phases consist of two terms. The first one depends on the beam particle velocity and consistence with the previous results. However the second term is velocity-independent and then completely new. Therefore our results indicate it is possible to investigate the noncommutative space by using ultra-cold neutron interferometer in which the velocity-dependent term is negligible. Furthermore, both these two terms are proportional to the ratio between the noncommutative parameter θ and the cross section Ae/m of the electrical/magnetic charged line enclosed by the trajectory of beam particles. Therefore the experimental sensitivity can be significantly enhanced by reducing the cross section of the charge line Ae/m.

  5. Noncommutative Integrability of the Klein-Gordon and Dirac Equations in (2+1)-Dimensional Spacetime

    NASA Astrophysics Data System (ADS)

    Breev, A. I.; Shapovalov, A. V.

    2017-03-01

    Noncommutative integration of the Klein-Gordon and Dirac relativistic wave equations in (2+1)-dimensional Minkowski space is considered. It is shown that for all non-Abelian subalgebras of the (2+1)-dimensional Poincaré algebra the condition of noncommutative integrability is satisfied.

  6. Two crystal structures of the leupeptin-trypsin complex.

    PubMed Central

    Kurinov, I. V.; Harrison, R. W.

    1996-01-01

    Three-dimensional structures of trypsin with the reversible inhibitor leupeptin have been determined in two different crystal forms. The first structure was determined at 1.7 A resolution with R-factor = 17.7% in the trigonal crystal space group P3(1)21, with unit cell dimensions of a = b = 55.62 A, c = 110.51 A. The second structure was determined at a resolution of 1.8 A with R-factor = 17.5% in the orthorhombic space group P2(1)2(1)2(1), with unit cell dimensions of a = 63.69 A, b = 69.37 A, c = 63.01 A. The overall protein structure is very similar in both crystal forms, with RMS difference for main-chain atoms of 0.27 A. The leupeptin backbone forms four hydrogen bonds with trypsin and a fifth hydrogen bond interaction is mediated by a water molecule. The aldehyde carbonyl of leupeptin forms a covalent bond of 1.42 A length with side-chain oxygen of Ser-195 in the active site. The reaction of trypsin with leupeptin proceeds through the formation of stable tetrahedral complex in which the hemiacetal oxygen atom is pointing out of the oxyanion hole and forming a hydrogen bond with His-57. PMID:8845765

  7. Synthesis and structure of 6-aminofulvene-2-aldiminate complexes.

    PubMed

    Willcocks, Alexander M; Gilbank, Alexander; Richards, Stephen P; Brayshaw, Simon K; Kingsley, Andrew J; Odedra, Raj; Johnson, Andrew L

    2011-02-07

    We report here a synthetic route to bis(N,N'-aryl)-6-aminofulvene-2-aldimine (AFA) ligand systems, specifically Ph(2)-AFAH and Dip(2)-AFAH. The synthesis and structural characterization of a series of Cu(I) complexes [(Ph(2)-AFA)Cu(CNPh)(2)] (2), [(Ph(2)-AFA)Cu(CN(i)Pr)] (3), and [(Dip(2)-AFA)Cu(CN(i)Pr)] (4), from the reaction of the corresponding lithiated AFA systems with Cu-Cl derivatives are reported; notably in the case of [(Ph(2)-AFA)Cu(CNPh)(2)] studies have revealed the existence of two structural isomers (2a and 2b), both of which can be isolated and structurally characterized. Density functional theory (DFT) calculations suggest that the two crystal forms are comparatively close in energy, and geometry optimization reveals a convergence of these two forms to a geometry that more closely resembles the solid-state structure of isomer 2b, having a CH···π interaction. The reactions of the AFA compounds Ph(2)-AFAH and Dip(2)-AFAH with ZnMe(2) and AlMe(3) have also been investigated, and the results of these reactions are described here.

  8. Crystal Structure of Baculovirus RNA Triphosphatase Complexed with Phosphate

    SciTech Connect

    Changela, Anita; Martin, Alexandra; Shuman, Stewart; Mondragon, Alfonso

    2010-03-05

    Baculovirus RNA 5'-triphosphatase (BVP) exemplifies a family of RNA-specific cysteine phosphatases that includes the RNA triphosphatase domains of metazoan and plant mRNA capping enzymes. Here we report the crystal structure of BVP in a phosphate-bound state at 1.5 {angstrom} resolution. BVP adopts the characteristic cysteine-phosphatase {alpha}/{beta} fold and binds two phosphate ions in the active site region, one of which is proposed to mimic the phosphate of the product complex after hydrolysis of the covalent phosphoenzyme intermediate. The crystal structure highlights the role of backbone amides and side chains of the P-loop motif {sup 118}HCTHGXNRT{sup 126} in binding the cleavable phosphate and stabilizing the transition state. Comparison of the BVP structure to the apoenzyme of mammalian RNA triphosphatase reveals a concerted movement of the Arg-125 side chain (to engage the phosphate directly) and closure of an associated surface loop over the phosphate in the active site. The structure highlights a direct catalytic role of Asn-124, which is the signature P-loop residue of the RNA triphosphatase family and a likely determinant of the specificity of BVP for hydrolysis of phosphoanhydride linkages.

  9. Structural and Operational Complexity of the Geobacter Sulfurreducens Genome

    SciTech Connect

    Qiu, Yu; Cho, Byung-Kwan; Park, Young S.; Lovley, Derek R.; Palsson, Bernhard O.; Zengler, Karsten

    2010-06-30

    Prokaryotic genomes can be annotated based on their structural, operational, and functional properties. These annotations provide the pivotal scaffold for understanding cellular functions on a genome-scale, such as metabolism and transcriptional regulation. Here, we describe a systems approach to simultaneously determine the structural and operational annotation of the Geobacter sulfurreducens genome. Integration of proteomics, transcriptomics, RNA polymerase, and sigma factor-binding information with deep-sequencing-based analysis of primary 59-end transcripts allowed for a most precise annotation. The structural annotation is comprised of numerous previously undetected genes, noncoding RNAs, prevalent leaderless mRNA transcripts, and antisense transcripts. When compared with other prokaryotes, we found that the number of antisense transcripts reversely correlated with genome size. The operational annotation consists of 1453 operons, 22% of which have multiple transcription start sites that use different RNA polymerase holoenzymes. Several operons with multiple transcription start sites encoded genes with essential functions, giving insight into the regulatory complexity of the genome. The experimentally determined structural and operational annotations can be combined with functional annotation, yielding a new three-level annotation that greatly expands our understanding of prokaryotic genomes.

  10. Structural and operational complexity of the Geobacter sulfurreducens genome

    PubMed Central

    Qiu, Yu; Cho, Byung-Kwan; Park, Young Seoub; Lovley, Derek; Palsson, Bernhard Ø.; Zengler, Karsten

    2010-01-01

    Prokaryotic genomes can be annotated based on their structural, operational, and functional properties. These annotations provide the pivotal scaffold for understanding cellular functions on a genome-scale, such as metabolism and transcriptional regulation. Here, we describe a systems approach to simultaneously determine the structural and operational annotation of the Geobacter sulfurreducens genome. Integration of proteomics, transcriptomics, RNA polymerase, and sigma factor-binding information with deep-sequencing-based analysis of primary 5′-end transcripts allowed for a most precise annotation. The structural annotation is comprised of numerous previously undetected genes, noncoding RNAs, prevalent leaderless mRNA transcripts, and antisense transcripts. When compared with other prokaryotes, we found that the number of antisense transcripts reversely correlated with genome size. The operational annotation consists of 1453 operons, 22% of which have multiple transcription start sites that use different RNA polymerase holoenzymes. Several operons with multiple transcription start sites encoded genes with essential functions, giving insight into the regulatory complexity of the genome. The experimentally determined structural and operational annotations can be combined with functional annotation, yielding a new three-level annotation that greatly expands our understanding of prokaryotic genomes. PMID:20592237

  11. Structure and Assembly Pathway of the Ribosome Quality Control Complex

    PubMed Central

    Shao, Sichen; Brown, Alan; Santhanam, Balaji; Hegde, Ramanujan S.

    2015-01-01

    Summary During ribosome-associated quality control, stalled ribosomes are split into subunits and the 60S-housed nascent polypeptides are poly-ubiquitinated by Listerin. How this low-abundance ubiquitin ligase targets rare stall-generated 60S among numerous empty 60S is unknown. Here, we show that Listerin specificity for nascent chain-60S complexes depends on nuclear export mediator factor (NEMF). The 3.6 Å cryo-EM structure of a nascent chain-containing 60S-Listerin-NEMF complex revealed that NEMF makes multiple simultaneous contacts with 60S and peptidyl-tRNA to sense nascent chain occupancy. Structural and mutational analyses showed that ribosome-bound NEMF recruits and stabilizes Listerin’s N-terminal domain, while Listerin’s C-terminal RWD domain directly contacts the ribosome to position the adjacent ligase domain near the nascent polypeptide exit tunnel. Thus, highly specific nascent chain targeting by Listerin is imparted by the avidity gained from a multivalent network of context-specific individually weak interactions, highlighting a new principle of client recognition during protein quality control. PMID:25578875

  12. Emergence of complex behaviour from simple circuit structures.

    PubMed

    Kaufman, Marcelle; Thomas, René

    2003-02-01

    The set of (feedback) circuits of a complex system is the machinery that allows the system to be aware of the levels of its crucial constituents. Circuits can be identified without ambiguity from the elements of the Jacobian matrix of the system. There are two types of circuits: positive if they comprise an even number of negative interactions, negative if this number is odd. The two types of circuits play deeply different roles: negative circuits are required for homeostasis, with or without oscillations, positive circuits are required for multistationarity, and hence, in biology, for differentiation and memory. In non-linear systems, a circuit can positive or negative (an 'ambiguous circuit', depending on the location in phase space. Full circuits are those circuits (or unions of disjoint circuits) that imply all the variables of the system. There is a tight relation between circuits and steady states. Each full circuit, if isolated, generates steady state(s) whose nature (eigenvalues) is determined by the structure of the circuit. Multistationarity requires the presence of at least two full circuits of opposite Eisenfeld signs, or else, an ambiguous circuit. We show how a significant part of the dynamical behaviour of a system can be predicted by a mere examination of its Jacobian matrix. We also show how extremely complex dynamics can be generated by such simple logical structures as a single (full and ambiguous) circuit.

  13. Perspective: Explicitly correlated electronic structure theory for complex systems

    NASA Astrophysics Data System (ADS)

    Grüneis, Andreas; Hirata, So; Ohnishi, Yu-ya; Ten-no, Seiichiro

    2017-02-01

    The explicitly correlated approach is one of the most important breakthroughs in ab initio electronic structure theory, providing arguably the most compact, accurate, and efficient ansatz for describing the correlated motion of electrons. Since Hylleraas first used an explicitly correlated wave function for the He atom in 1929, numerous attempts have been made to tackle the significant challenges involved in constructing practical explicitly correlated methods that are applicable to larger systems. These include identifying suitable mathematical forms of a correlated wave function and an efficient evaluation of many-electron integrals. R12 theory, which employs the resolution of the identity approximation, emerged in 1985, followed by the introduction of novel correlation factors and wave function ansätze, leading to the establishment of F12 theory in the 2000s. Rapid progress in recent years has significantly extended the application range of explicitly correlated theory, offering the potential of an accurate wave-function treatment of complex systems such as photosystems and semiconductors. This perspective surveys explicitly correlated electronic structure theory, with an emphasis on recent stochastic and deterministic approaches that hold significant promise for applications to large and complex systems including solids.

  14. Brain structural complexity and life course cognitive change.

    PubMed

    Mustafa, Nazahah; Ahearn, Trevor S; Waiter, Gordon D; Murray, Alison D; Whalley, Lawrence J; Staff, Roger T

    2012-07-02

    Fractal measures such as fractal dimension (FD) can quantify the structural complexity of the brain. These have been used in clinical neuroscience to investigate brain development, ageing and in studies of psychiatric and neurological disorders. Here, we examined associations between the FD of white matter and cognitive changes across the life course in the absence of detectable brain disease. The FD was calculated from segmented cerebral white matter MR images in 217 subjects aged about 68years, in whom archived intelligence scores from age 11years were available. Cognitive test scores of fluid and crystallised intelligence were obtained at the time of MR imaging. Significant differences were found (intracranial volume, brain volume, white matter volume and Raven's Progressive Matrices score) between men and women at age 68years and novel associations were found between FD and measures of cognitive change over the life course from age 11 to 68years. Those with greater FD were found to have greater than expected fluid abilities at age 68years than predicted by their childhood intelligence and less cognitive decline from age 11 to 68years. These results are consistent with other reports that FD measures of cortical structural complexity increase across the early life course during maturation of the cerebral cortex and add new data to support an association between FD and cognitive ageing.

  15. Structure of a bacterial RNA polymerase holoenzyme open promoter complex

    DOE PAGES

    Bae, Brian; Feklistov, Andrey; Lass-Napiorkowska, Agnieszka; ...

    2015-09-08

    Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 Å-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the -10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstreammore » of the -10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Additionally a RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and σA dissociation.« less

  16. Structural genomic variation in childhood epilepsies with complex phenotypes

    PubMed Central

    Helbig, Ingo; Swinkels, Marielle E M; Aten, Emmelien; Caliebe, Almuth; van 't Slot, Ruben; Boor, Rainer; von Spiczak, Sarah; Muhle, Hiltrud; Jähn, Johanna A; van Binsbergen, Ellen; van Nieuwenhuizen, Onno; Jansen, Floor E; Braun, Kees P J; de Haan, Gerrit-Jan; Tommerup, Niels; Stephani, Ulrich; Hjalgrim, Helle; Poot, Martin; Lindhout, Dick; Brilstra, Eva H; Møller, Rikke S; Koeleman, Bobby PC

    2014-01-01

    A genetic contribution to a broad range of epilepsies has been postulated, and particularly copy number variations (CNVs) have emerged as significant genetic risk factors. However, the role of CNVs in patients with epilepsies with complex phenotypes is not known. Therefore, we investigated the role of CNVs in patients with unclassified epilepsies and complex phenotypes. A total of 222 patients from three European countries, including patients with structural lesions on magnetic resonance imaging (MRI), dysmorphic features, and multiple congenital anomalies, were clinically evaluated and screened for CNVs. MRI findings including acquired or developmental lesions and patient characteristics were subdivided and analyzed in subgroups. MRI data were available for 88.3% of patients, of whom 41.6% had abnormal MRI findings. Eighty-eight rare CNVs were discovered in 71 out of 222 patients (31.9%). Segregation of all identified variants could be assessed in 42 patients, 11 of which were de novo. The frequency of all structural variants and de novo variants was not statistically different between patients with or without MRI abnormalities or MRI subcategories. Patients with dysmorphic features were more likely to carry a rare CNV. Genome-wide screening methods for rare CNVs may provide clues for the genetic etiology in patients with a broader range of epilepsies than previously anticipated, including in patients with various brain anomalies detectable by MRI. Performing genome-wide screens for rare CNVs can be a valuable contribution to the routine diagnostic workup in patients with a broad range of childhood epilepsies. PMID:24281369

  17. Using Machine Learning to Accelerate Complex Atomic Structure Elucidation

    NASA Astrophysics Data System (ADS)

    Brouwer, William; Calderin, Lazaro; Sofo, Jorge

    2012-02-01

    Workers in various scientific disciplines seek to develop chemical models for extended and molecular systems. The modeling process revolves around the gradual refinement of model assumptions, through comparison of experimental and computational results. Solid state Nuclear Magnetic Resonance (NMR) is one such experimental technique, providing great insight into chemical order over Angstrom length scales. However, interpretation of spectra for complex materials is difficult, often requiring intensive simulations. Similarly, working forward from the model in order to produce experimental quantities via ab initio is computationally demanding. The work involved in these two significant steps, compounded by the need to iterate back and forth, drastically slows the discovery process for new materials. There is thus great motivation for the derivation of structural models directly from complex experimental data, the subject of this work. Using solid state NMR experimental datasets, in conjunction with ab initio calculations of measurable NMR parameters, a network of machine learning kernels are trained to rapidly yield structural details, on the basis of input NMR spectra. Results for an environmentally relevant material will be presented, and directions for future work.

  18. A new Cu–cysteamine complex: structure and optical properties

    SciTech Connect

    Ma, Lun; Chen, Wei; Schatte, Gabriele; Wang, Wei; Joly, Alan G.; Huang, Yining; Sammynaiken, Ramaswami; Hossu, Marius

    2014-06-07

    Here we report the structure and optical properties of a new Cu–cysteamine complex (Cu–Cy) with a formula of Cu3Cl(SR)2 (R ¼ CH2CH2NH2). This Cu–Cy has a different structure from a previous Cu–Cy complex, in which both thio and amine groups from cysteamine bond with copper ions. Single-crystal X-ray diffraction and solid-state nuclear magnetic resonance results show that the oxidation state of copper in Cu3Cl(SR)2 is +1 rather than +2. Further, Cu3Cl(SR)2 has been observed to show intense photoluminescence and X-ray excited luminescence. More interesting is that Cu3Cl(SR)2 particles can produce singlet oxygen under irradiation by light or X-ray. This indicates that Cu3Cl(SR)2 is a new photosensitizer that can be used for deep cancer treatment as X-ray can penetrate soft tissues. All these findings mean that Cu3Cl(SR)2 is a new material with potential applications for lighting, radiation detection and cancer treatment.

  19. Structure of a bacterial RNA polymerase holoenzyme open promoter complex

    SciTech Connect

    Bae, Brian; Feklistov, Andrey; Lass-Napiorkowska, Agnieszka; Landick, Robert; Darst, Seth A.

    2015-09-08

    Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 Å-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the -10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstream of the -10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Additionally a RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and σA dissociation.

  20. Bipyrimidine ruthenium(II) arene complexes: structure, reactivity and cytotoxicity.

    PubMed

    Betanzos-Lara, Soledad; Novakova, Olga; Deeth, Robert J; Pizarro, Ana M; Clarkson, Guy J; Liskova, Barbora; Brabec, Viktor; Sadler, Peter J; Habtemariam, Abraha

    2012-10-01

    The synthesis and characterization of complexes [(η(6)-arene)Ru(N,N')X][PF(6)], where arene is para-cymene (p-cym), biphenyl (bip), ethyl benzoate (etb), hexamethylbenzene (hmb), indane (ind) or 1,2,3,4-tetrahydronaphthalene (thn), N,N' is 2,2'-bipyrimidine (bpm) and X is Cl, Br or I, are reported, including the X-ray crystal structures of [(η(6)-p-cym)Ru(bpm)I][PF(6)], [(η(6)-bip)Ru(bpm)Cl][PF(6)], [(η(6)-bip)Ru(bpm)I][PF(6)] and [(η(6)-etb)Ru(bpm)Cl][PF(6)]. Complexes in which N,N' is 1,10-phenanthroline (phen), 1,10-phenanthroline-5,6-dione or 4,7-diphenyl-1,10-phenanthroline (bathophen) were studied for comparison. The Ru(II) arene complexes undergo ligand-exchange reactions in aqueous solution at 310 K; their half-lives for hydrolysis range from 14 to 715 min. Density functional theory calculations on [(η(6)-p-cym)Ru(bpm)Cl][PF(6)], [(η(6)-p-cym)Ru(bpm)Br][PF(6)], [(η(6)-p-cym)Ru(bpm)I][PF(6)], [(η(6)-bip)Ru(bpm)Cl][PF(6)], [(η(6)-bip)Ru(bpm)Br][PF(6)] and [(η(6)-bip)Ru(bpm)I][PF(6)] suggest that aquation occurs via an associative pathway and that the reaction is thermodynamically favourable when the leaving ligand is I > Br ≈ Cl. pK (a)* values for the aqua adducts of the complexes range from 6.9 to 7.32. A binding preference for 9-ethylguanine (9-EtG) compared with 9-ethyladenine (9-EtA) was observed for [(η(6)-p-cym)Ru(bpm)Cl][PF(6)], [(η(6)-hmb)Ru(bpm)Cl](+), [(η(6)-ind)Ru(bpm)Cl](+), [(η(6)-thn)Ru(bpm)Cl](+), [(η(6)-p-cym)Ru(phen)Cl](+) and [(η(6)-p-cym)Ru(bathophen)Cl](+) in aqueous solution at 310 K. The X-ray crystal structure of the guanine complex [(η(6)-p-cym)Ru(bpm)(9-EtG-N7)][PF(6)](2) shows multiple hydrogen bonding. Density functional theory calculations show that the 9-EtG adducts of all complexes are thermodynamically preferred compared with those of 9-EtA. However, the bmp complexes are inactive towards A2780 human ovarian cancer cells. Calf thymus DNA interactions for [(η(6)-p-cym)Ru(bpm)Cl][PF(6)] and [(η(6)-p

  1. On the dimension of complex responses in nonlinear structural vibrations

    NASA Astrophysics Data System (ADS)

    Wiebe, R.; Spottswood, S. M.

    2016-07-01

    The ability to accurately model engineering systems under extreme dynamic loads would prove a major breakthrough in many aspects of aerospace, mechanical, and civil engineering. Extreme loads frequently induce both nonlinearities and coupling which increase the complexity of the response and the computational cost of finite element models. Dimension reduction has recently gained traction and promises the ability to distill dynamic responses down to a minimal dimension without sacrificing accuracy. In this context, the dimensionality of a response is related to the number of modes needed in a reduced order model to accurately simulate the response. Thus, an important step is characterizing the dimensionality of complex nonlinear responses of structures. In this work, the dimensionality of the nonlinear response of a post-buckled beam is investigated. Significant detail is dedicated to carefully introducing the experiment, the verification of a finite element model, and the dimensionality estimation algorithm as it is hoped that this system may help serve as a benchmark test case. It is shown that with minor modifications, the method of false nearest neighbors can quantitatively distinguish between the response dimension of various snap-through, non-snap-through, random, and deterministic loads. The state-space dimension of the nonlinear system in question increased from 2-to-10 as the system response moved from simple, low-level harmonic to chaotic snap-through. Beyond the problem studied herein, the techniques developed will serve as a prescriptive guide in developing fast and accurate dimensionally reduced models of nonlinear systems, and eventually as a tool for adaptive dimension-reduction in numerical modeling. The results are especially relevant in the aerospace industry for the design of thin structures such as beams, panels, and shells, which are all capable of spatio-temporally complex dynamic responses that are difficult and computationally expensive to

  2. Mesomorphic structures of protonated surfactant-encapsulated polyoxometalate complexes.

    PubMed

    Yin, Shengyan; Li, Wen; Wang, Jinfeng; Wu, Lixin

    2008-04-03

    Keggin-type heteropolyanions, H(3)PW(12)O(40) (HPW), Na(3)PW(12)O(40) (NaPW), H(4)SiW(12)O(40) (HSiW) and K(4)SiW(12)O(40) (KSiW), were encapsulated by a cationic surfactant, di[12-(4'-octyloxy-4-azophenyl)dodecyloxy]dimethylam monium bromide (L), through the replacement of counterions. The resulting surfactant-encapsulated polyoxometalate complexes were characterized by UV-vis, Raman, and NMR spectra in detail. The measurement results indicated that some azobenzene groups of the surfactant were protonated in the complexes HL/HPW (HL is the abbreviation of the protonated surfactant), HL/NaPW, and HL/HSiW during the process of encapsulation, whereas the protonation was not observed in L/KSiW. The thermotropic liquid crystal properties of these complexes were investigated by differential scanning calorimetry, polarized optical microscopy and variable-temperature X-ray diffraction. Interestingly, different smectic mesophases were observed between the protonated HL/HSiW and the non-protonated L/KSiW, which suggests that the protonation of azobenzene groups in HL/HSiW plays a key role in the liquid crystalline organization. However, protonated HL/HPW and HL/NaPW exhibit a similar smectic B phase to that of the de-protonated one, L/HPW. A competitive balance between the phase separation and the volume minimization of surfactants was proposed to explain the self-organized liquid crystal structures of these protonated and non-protonated complexes. To the best of our knowledge, the present investigation provides a specific example for protonated hybrid materials with stable liquid crystal properties.

  3. Special relativity as a noncommutative geometry: Lessons for deformed special relativity

    SciTech Connect

    Girelli, Florian; Livine, Etera R.

    2010-04-15

    Deformed special relativity (DSR) is obtained by imposing a maximal energy to special relativity and deforming the Lorentz symmetry (more exactly, the Poincare symmetry) to accommodate this requirement. One can apply the same procedure in the context of Galilean relativity by imposing a maximal speed (the speed of light). Effectively, one deforms the Galilean group and this leads to a noncommutative space structure, together with the deformations of composition of speed and conservation of energy momentum. In doing so, one runs into most of the ambiguities that one stumbles onto in the DSR context. However, this time, special relativity is there to tell us what is the underlying physics, in such a way we can understand and interpret these ambiguities. We use these insights to comment on the physics of DSR.

  4. Fixed-point and implicit/inverse function theorems for free noncommutative functions

    NASA Astrophysics Data System (ADS)

    Abduvalieva, Gulnara K.

    We establish a fixed-point theorem for mappings of square matrices of all sizes which respect the matrix sizes and direct sums of matrices. The conclusions are stronger if such a mapping is a free noncommutative function, i.e., if it respects matrix similarities. As a special case, we obtain the corresponding version of the Banach Contraction Mapping Theorem. This result is then applied to prove the existence and uniqueness of a solution of the initial value problem for ODEs in noncommutative spaces. As a by-product of the ideas developed in this paper, we establish a noncommutative version of the principle of nested closed sets. We prove the implicit function theorem and the inverse function theorem in two different settings: for free noncommutative functions over operator spaces and for free noncommutative functions on the set of nilpotent matrices.

  5. Light transport and lasing in complex photonic structures

    NASA Astrophysics Data System (ADS)

    Liew, Seng Fatt

    Complex photonic structures refer to composite optical materials with dielectric constant varying on length scales comparable to optical wavelengths. Light propagation in such heterogeneous composites is greatly different from homogeneous media due to scattering of light in all directions. Interference of these scattered light waves gives rise to many fascinating phenomena and it has been a fast growing research area, both for its fundamental physics and for its practical applications. In this thesis, we have investigated the optical properties of photonic structures with different degree of order, ranging from periodic to random. The first part of this thesis consists of numerical studies of the photonic band gap (PBG) effect in structures from 1D to 3D. From these studies, we have observed that PBG effect in a 1D photonic crystal is robust against uncorrelated disorder due to preservation of long-range positional order. However, in higher dimensions, the short-range positional order alone is sufficient to form PBGs in 2D and 3D photonic amorphous structures (PASS). We have identified several parameters including dielectric filling fraction and degree of order that can be tuned to create a broad isotropic PBG. The largest PBG is produced by the dielectric networks due to local uniformity in their dielectric constant distribution. In addition, we also show that deterministic aperiodic structures (DASs) such as the golden-angle spiral and topological defect structures can support a wide PBG and their optical resonances contain unexpected features compared to those in photonic crystals. Another growing research field based on complex photonic structures is the study of structural color in animals and plants. Previous studies have shown that non-iridescent color can be generated from PASs via single or double scatterings. For better understanding of the coloration mechanisms, we have measured the wavelength-dependent scattering length from the biomimetic samples. Our

  6. Confinement Effects on the Structure of Complex Fluids

    NASA Astrophysics Data System (ADS)

    Kim, Mahn

    2009-03-01

    Actin is a key component of the protein complex responsible for producing contractile force in skeletal muscle. Filamentous actin, called F-actin, is a two-stranded helical protofilament with a diameter of ˜8nm and a contour length of ˜10m. The experimental results show that the persistence length of the F-actin is 4 -20 m. One of interesting problems is to find the structure of a semiflexible filament in a confined space [1], such as a channel width less than the persistence length. The other interesting problem is to find the surface treatment effect on the liquid crystal structure in a confined space. The boundary conditions imposed by the walls of the microchannel generate the spatial patterning of defect domains in a smectic liquid crystal [2] and the formation of a large-area ordered structure [3] by using the structure of smectic liquid in the microchannels. We found that the F-actin undergoes a transition from a 2D randomly oriented regime to a 1D biaxially confined regime with the effective persistence length. We were able to generate defect domains that are nearly uniformly arranged in 2D ordered patterns by controlling the surface hydrophobicity. Furthermore, the formation of a large-area ordered structure of toric focal conic domains was generated. This work was done with C. R. Safinya's group at UCSB and Hee-Tae Jung's group at KAIST. [4pt] [1] M.C Choi at. al, Macromolecules 2005,38, 9882-9884[0pt] [2] M. C. Choi at. al, PNAS 2004, 101, 17340-17344[0pt] [3] D. K. Yoon at. al, Nature Materials, 2007, 6, 866-870

  7. 75 FR 61857 - Statement on Sound Practices Concerning Elevated Risk Complex Structured Finance Activities

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-06

    ... Office of Thrift Supervision Statement on Sound Practices Concerning Elevated Risk Complex Structured... concerning the following information collection. Title of Proposal: Statement on Sound Practices Concerning...: Statement on Sound Practices Concerning Elevated Risk Complex Structured Finance Activities describes...

  8. Complex Dynamic Flows in Solar Flare Sheet Structures

    NASA Astrophysics Data System (ADS)

    McKenzie, David Eugene; Reeves, K. K.; Savage, S. L.

    2012-05-01

    Observations of high-energy emission from solar flares often reveal the presence of large sheet-like structures, sometimes extending over a space comparable to the Sun's radius. Given that these structures are found between a departing coronal mass ejection and the post-eruption flare arcade, it is natural to associate the structure with a current sheet; though the relationship is unclear. Moreover, recent high-resolution observations have begun to reveal that the motions in this region are highly complex, including reconnection outflows, oscillations, and apparent wakes and eddies. We present a detailed first look at the complicated dynamics within this supra-arcade plasma, and consider implications for the interrelationship between the plasma and its embedded magnetic field. This work is supported by NASA under contract SP02H3901R from Lockheed-Martin to MSU (DMcK), contract SP02H1701R from Lockheed-Martin to SAO (KKR), and contract NNM07AB07C with the Harvard-Smithsonian Astrophysical Observatory. SLS is supported via a NASA/GSFC NPP appointment administered by Oak Ridge Associated Universities and under the mentorship of G. Holman.

  9. Structural basis of complement membrane attack complex formation

    PubMed Central

    Serna, Marina; Giles, Joanna L.; Morgan, B. Paul; Bubeck, Doryen

    2016-01-01

    In response to complement activation, the membrane attack complex (MAC) assembles from fluid-phase proteins to form pores in lipid bilayers. MAC directly lyses pathogens by a ‘multi-hit' mechanism; however, sublytic MAC pores on host cells activate signalling pathways. Previous studies have described the structures of individual MAC components and subcomplexes; however, the molecular details of its assembly and mechanism of action remain unresolved. Here we report the electron cryo-microscopy structure of human MAC at subnanometre resolution. Structural analyses define the stoichiometry of the complete pore and identify a network of interaction interfaces that determine its assembly mechanism. MAC adopts a ‘split-washer' configuration, in contrast to the predicted closed ring observed for perforin and cholesterol-dependent cytolysins. Assembly precursors partially penetrate the lipid bilayer, resulting in an irregular β-barrel pore. Our results demonstrate how differences in symmetric and asymmetric components of the MAC underpin a molecular basis for pore formation and suggest a mechanism of action that extends beyond membrane penetration. PMID:26841837

  10. Structural basis of complement membrane attack complex formation.

    PubMed

    Serna, Marina; Giles, Joanna L; Morgan, B Paul; Bubeck, Doryen

    2016-02-04

    In response to complement activation, the membrane attack complex (MAC) assembles from fluid-phase proteins to form pores in lipid bilayers. MAC directly lyses pathogens by a 'multi-hit' mechanism; however, sublytic MAC pores on host cells activate signalling pathways. Previous studies have described the structures of individual MAC components and subcomplexes; however, the molecular details of its assembly and mechanism of action remain unresolved. Here we report the electron cryo-microscopy structure of human MAC at subnanometre resolution. Structural analyses define the stoichiometry of the complete pore and identify a network of interaction interfaces that determine its assembly mechanism. MAC adopts a 'split-washer' configuration, in contrast to the predicted closed ring observed for perforin and cholesterol-dependent cytolysins. Assembly precursors partially penetrate the lipid bilayer, resulting in an irregular β-barrel pore. Our results demonstrate how differences in symmetric and asymmetric components of the MAC underpin a molecular basis for pore formation and suggest a mechanism of action that extends beyond membrane penetration.

  11. Cryo-electron tomography for structural characterization of macromolecular complexes.

    PubMed

    Cope, Julia; Heumann, John; Hoenger, Andreas

    2011-08-01

    Cryo-electron tomography (cryo-ET) is an emerging 3-D reconstruction technology that combines the principles of tomographic 3-D reconstruction with the unmatched structural preservation of biological matter embedded in vitreous ice. Cryo-ET is particularly suited to investigating cell-biological samples and large macromolecular structures that are too polymorphic to be reconstructed by classical averaging-based 3-D reconstruction procedures. This unit aims to make cryo-ET accessible to newcomers and discusses the specialized equipment required, as well as relevant advantages and hurdles associated with sample preparation by vitrification and cryo-ET. Protocols describe specimen preparation, data recording and 3-D data reconstruction for cryo-ET, with a special focus on macromolecular complexes. A step-by-step procedure for specimen vitrification by plunge freezing is provided, followed by the general practicalities of tilt-series acquisition for cryo-ET, including advice on how to select an area appropriate for acquiring a tilt series. A brief introduction to the underlying computational reconstruction principles applied in tomography is described, along with instructions for reconstructing a tomogram from cryo-tilt series data. Finally, a method is detailed for extracting small subvolumes containing identical macromolecular structures from tomograms for alignment and averaging as a means to increase the signal-to-noise ratio and eliminate missing wedge effects inherent in tomographic reconstructions.

  12. Local structure studies of some cobalt (II) complexes using extended X-ray absorption fine structure

    NASA Astrophysics Data System (ADS)

    Mishra, Ashutosh; Ninama, Samrath; Trivedi, Apurva

    2014-09-01

    Extended X-ray Absorption Fine Structure (EXAFS) analysis of Cobalt (II) complex as a ligand of 2 -methyl-3-[(bis-aniline(R) phenyl]-3H-l,5 benzodiazepine for finding local structure using conventional method .The Co(II) complexes were prepared by chemical root method. The EXAFS spectra were recorded at Cobalt K-edge i.e.; 7709 eV using Dispersive EXFAS beam line at 2.5GeV Indus-2 Synchrotron Radiation Source(SRS) at RRCAT, Indore, India. The recorded EXAFS data were analysed using the computer software Athena for determine the nearest neighbouring distances (bond lengths) of these complexes with conventional methods and it compared with Fourier transform(FT) analysis. The Fourier Transform convert EXAFS data signal into r-space or k-space. This is useful for visualizing the major contributions to the EXAFS spectrum.

  13. Structural development of the western Makran Accretionary Complex, Offshore Iran

    NASA Astrophysics Data System (ADS)

    Burberry, C. M.; Jackson, C. A.

    2013-12-01

    The Makran Accretionary Complex (MAC), which straddles the southern offshore regions of Iran and Pakistan, is a fold-thrust system bound by the Murray Ridge and Ornach Nal Fault to the east, and the Minab Fault System (MFS) to the west. It is c. 1000 km wide and the frontal c. 125 km of the system is submerged beneath the Gulf of Oman. Relatively little is known about this system, despite the fact that constitutes a large portion of the Central Tethyan Orogen and is one of the largest accretionary complexes in the world. We use offshore 2D seismic reflection data to investigate the structural style and evolution of the Iranian segment of the MAC. The MAC is divided into two morphologically distinct domains: (i) a northern domain (Domain 1), which is located landward of a prominant break-in-slope on the seabed and is characterised by a series of normal fault-bound sub-basins that are approximately 50 km wide, and which contain numerous, unconformity-bound seismic units; and (ii) a southern domain (Domain 2), which is located basinward of the prominent seabed slope break, and is characterised by alternating ridges and troughs. Seismic data indicate that these structures are laterally continuous (over 100 km long) north-dipping thrust faults, which are overlain by south-verging, non-cylindrical, fault-propagation folds. Towards the western end of the study area, immediately offshore of the prominent onshore trace of the MFS, there is no single structure that can be reliably interpreted as the offshore extension of the MFS. Instead, a series of oblique-slip faults with thrust and strike-slip components are identified, spanning a zone that is c. 40 km wide. In the north and close to the coastline, the faults are dominantly strike-slip, whereas further south, closer to the deformation front, the thrust-sense component is more important. Irrespective of their slip sense, faults in this zone have a similar N-S strike to the onshore trace of the MFS. In addition, the basin

  14. Electrical resistance of complex two-dimensional structures of loops

    NASA Astrophysics Data System (ADS)

    Gomes, M. A. F.; Hora, R. R.; Brito, V. P.

    2011-06-01

    This work presents a study of the dc electrical resistance of a recently discovered hierarchical two-dimensional system which has a complex topology consisting of a distribution of disordered macroscopic loops with no characteristic size and a distribution of several types of contacts between loops. In addition to its intrinsic interest in the important context of low-dimensional systems and crumpled systems, the structures under study are of relevance in a number of areas including soft condensed matter and packing of DNA in viral capsids. In the particular case discussed here, the loops are made of layers of graphite with a height of tens of nanometers deposited on a substrate of cellulose. Experiments with these systems indicate an anomalous electrical resistance of sub-diffusive type. The results reported here are explained with scaling arguments and computer simulation. A comparison with the dc electrical properties of percolation clusters is made, and some other experimental issues as future prospects are commented.

  15. Protection of cooled blades of complex internal structure

    NASA Technical Reports Server (NTRS)

    Glamiche, P.

    1977-01-01

    The problem of general protection of cooled blades of complex internal structure was solved by a method called SF technique which makes possible the protection of both external and internal surfaces, as well as those of the orifices of cooling air, whatever their diameter. The SF method is most often applied in the case of pack process, at controlled or high activity; it can be of use on previously uncoated parts, but also on pieces already coated by a thermochemical, chemical or PVD method. The respective thickness of external and internal coatings may be precisely predetermined, no parasitic particle being liable to remain inside the parts after application of the protecting treatment. Results obtained to date by application of this method are illustrated by the presentation and examination of a various selection of advanced turbo engines.

  16. Encoding techniques for complex information structures in connectionist systems

    NASA Technical Reports Server (NTRS)

    Barnden, John; Srinivas, Kankanahalli

    1990-01-01

    Two general information encoding techniques called relative position encoding and pattern similarity association are presented. They are claimed to be a convenient basis for the connectionist implementation of complex, short term information processing of the sort needed in common sense reasoning, semantic/pragmatic interpretation of natural language utterances, and other types of high level cognitive processing. The relationships of the techniques to other connectionist information-structuring methods, and also to methods used in computers, are discussed in detail. The rich inter-relationships of these other connectionist and computer methods are also clarified. The particular, simple forms are discussed that the relative position encoding and pattern similarity association techniques take in the author's own connectionist system, called Conposit, in order to clarify some issues and to provide evidence that the techniques are indeed useful in practice.

  17. Hybrid Direct Write Lithographic Strategies for Complex Hierarchical Structures

    NASA Astrophysics Data System (ADS)

    Singer, Jonathan P.

    With the number of alternative lithographic techniques for high resolution and 3D patterning rapidly increasing, there is a need to identify a set of scalable techniques which balances the ability to arbitrarily control every detail of a target pattern and to produce these complex patterns at a high rate. It is in this way that metamaterial devices put forward on a lab scale for applications such as phononics, photonics, and plasmonics can be realized in the industrial scale. This thesis, in approaching this challenge, utilizes combinations of patterning techniques, leveraging the ability for "large" scale alternative lithographic techniques, such as interference lithography or self-assembly, to create the same nanostructured morphology over a large area combined with laser direct write. The process of drawing a single line or isolated voxel can result in a hierarchical pattern defined by the latent motif of the larger-scale technique. The net resuh is to shift the burden of high resolution patterning from the direct write to the large scale technique, effectively decoupling the correlation between the level of detail and the patterning speed and control. More specifically, the following combinations with laser direct writing were investigated: (1) proximity field nanopatterning for the predefinition of diffraction-order-defined 3D resonators which were applied as "stand-up" plasmodic microresonators, (2) dewetting to conduct development-free 2D patterning of isolated sub-micron lines, and, via overlap effects, nanoscale ( <1 00 nm) gratings, (3) block copolymer self-assembly to initiate the simultaneous annealing and alignment of near-equilibrium microdomains from a metastable starting morphology, and (4) interference lithography to fabricate 3D sub-micron periodic and quasiperiodic hierarchical structures with controllable positioning and tunable fill fraction that has potential for applications to microphotonics. In conjunction with the experimental components

  18. Solving structures of protein complexes by molecular replacement with Phaser

    SciTech Connect

    McCoy, Airlie J.

    2007-01-01

    Four case studies in using maximum-likelihood molecular replacement, as implemented in the program Phaser, to solve structures of protein complexes are described. Molecular replacement (MR) generally becomes more difficult as the number of components in the asymmetric unit requiring separate MR models (i.e. the dimensionality of the search) increases. When the proportion of the total scattering contributed by each search component is small, the signal in the search for each component in isolation is weak or non-existent. Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components with a ‘tree search with pruning’ approach. This method, as implemented in the automated search procedure of the program Phaser, has been very successful in solving many previously intractable MR problems. However, there are a number of cases in which the automated search procedure of Phaser is suboptimal or encounters difficulties. These include cases where there are a large number of copies of the same component in the asymmetric unit or where the components of the asymmetric unit have greatly varying B factors. Two case studies are presented to illustrate how Phaser can be used to best advantage in the standard ‘automated MR’ mode and two case studies are used to show how to modify the automated search strategy for problematic cases.

  19. Structure of the guide-strand-containing argonaute silencing complex

    SciTech Connect

    Wang, Yanli; Sheng, Gang; Juranek, Stefan; Tuschl, Thomas; Patel, Dinshaw J.

    2009-01-15

    The slicer activity of the RNA-induced silencing complex is associated with argonaute, the RNase H-like PIWI domain of which catalyses guide-strand-mediated sequence-specific cleavage of target messenger RNA. Here we report on the crystal structure of Thermus thermophilus argonaute bound to a 5'-phosphorylated 21-base DNA guide strand, thereby identifying the nucleic-acid-binding channel positioned between the PAZ- and PIWI-containing lobes, as well as the pivot-like conformational changes associated with complex formation. The bound guide strand is anchored at both of its ends, with the solvent-exposed Watson-Crick edges of stacked bases 2 to 6 positioned for nucleation with the mRNA target, whereas two critically positioned arginines lock bases 10 and 11 at the cleavage site into an unanticipated orthogonal alignment. Biochemical studies indicate that key amino acid residues at the active site and those lining the 5'-phosphate-binding pocket made up of the Mid domain are critical for cleavage activity, whereas alterations of residues lining the 2-nucleotide 3'-end-binding pocket made up of the PAZ domain show little effect.

  20. Integrated quality assurance for assembly and testing of complex structures

    NASA Astrophysics Data System (ADS)

    von Kopylow, Christoph; Bothe, Thorsten; Elandaloussi, Frank; Kalms, Michael; Jüptner, Werner

    2005-11-01

    Modern production processes are directed by properties of the components to be manufactured. These components have different sizes, functionalities, high assembly complexity and high security requirements. The increasing requirements during the manufacturing of complex products like cars and aircrafts demand new solutions for the quality assurance - especially for the production at different places. The main focus is to find a measurement strategy that is cost effective, flexible and adaptive. That means a clear definition of the measurement problem, the measurement with adapted resolution, the data preparation and evaluation and support during measurement and utilisation of the results directly in the production. In this paper we describe flexible measurement devices on example of three different techniques: fringe projection, fringe reflection and shearography. These techniques allow the detection of surface and subsurface defects like bumps, dents and delaminations with high resolution. The defects can be optically mapped onto the object's surface. Results are demonstrated with big components taken from automotive and aircraft production. We will point out the most important adaptations of the systems to realize miniaturized, robust and mobile devices for the quality assurance in an industrial environment. Additionally the implementation into a Mobile Maintenance and Control structure is demonstrated.

  1. Behavioral pattern identification for structural health monitoring in complex systems

    NASA Astrophysics Data System (ADS)

    Gupta, Shalabh

    Estimation of structural damage and quantification of structural integrity are critical for safe and reliable operation of human-engineered complex systems, such as electromechanical, thermofluid, and petrochemical systems. Damage due to fatigue crack is one of the most commonly encountered sources of structural degradation in mechanical systems. Early detection of fatigue damage is essential because the resulting structural degradation could potentially cause catastrophic failures, leading to loss of expensive equipment and human life. Therefore, for reliable operation and enhanced availability, it is necessary to develop capabilities for prognosis and estimation of impending failures, such as the onset of wide-spread fatigue crack damage in mechanical structures. This dissertation presents information-based online sensing of fatigue damage using the analytical tools of symbolic time series analysis ( STSA). Anomaly detection using STSA is a pattern recognition method that has been recently developed based upon a fixed-structure, fixed-order Markov chain. The analysis procedure is built upon the principles of Symbolic Dynamics, Information Theory and Statistical Pattern Recognition. The dissertation demonstrates real-time fatigue damage monitoring based on time series data of ultrasonic signals. Statistical pattern changes are measured using STSA to monitor the evolution of fatigue damage. Real-time anomaly detection is presented as a solution to the forward (analysis) problem and the inverse (synthesis) problem. (1) the forward problem - The primary objective of the forward problem is identification of the statistical changes in the time series data of ultrasonic signals due to gradual evolution of fatigue damage. (2) the inverse problem - The objective of the inverse problem is to infer the anomalies from the observed time series data in real time based on the statistical information generated during the forward problem. A computer-controlled special

  2. Paradigms of Complexity: Fractals and Structures in the Sciences

    NASA Astrophysics Data System (ADS)

    Novak, Miroslav M.

    The Table of Contents for the book is as follows: * Preface * The Origin of Complexity (invited talk) * On the Existence of Spatially Uniform Scaling Laws in the Climate System * Multispectral Backscattering: A Fractal-Structure Probe * Small-Angle Multiple Scattering on a Fractal System of Point Scatterers * Symmetric Fractals Generated by Cellular Automata * Bispectra and Phase Correlations for Chaotic Dynamical Systems * Self-Organized Criticality Models of Neural Development * Altered Fractal and Irregular Heart Rate Behavior in Sick Fetuses * Extract Multiple Scaling in Long-Term Heart Rate Variability * A Semi-Continous Box Counting Method for Fractal Dimension Measurement of Short Single Dimension Temporal Signals - Preliminary Study * A Fractional Brownian Motion Model of Cracking * Self-Affine Scaling Studies on Fractography * Coarsening of Fractal Interfaces * A Fractal Model of Ocean Surface Superdiffusion * Stochastic Subsurface Flow and Transport in Fractal Fractal Conductivity Fields * Rendering Through Iterated Function Systems * The σ-Hull - The Hull Where Fractals Live - Calculating a Hull Bounded by Log Spirals to Solve the Inverse IFS-Problem by the Detected Orbits * On the Multifractal Properties of Passively Convected Scalar Fields * New Statistical Textural Transforms for Non-Stationary Signals: Application to Generalized Mutlifractal Analysis * Laplacian Growth of Parallel Needles: Their Mullins-Sekerka Instability * Entropy Dynamics Associated with Self-Organization * Fractal Properties in Economics (invited talk) * Fractal Approach to the Regional Seismic Event Discrimination Problem * Fractal and Topological Complexity of Radioactive Contamination * Pattern Selection: Nonsingular Saffman-Taylor Finger and Its Dynamic Evolution with Zero Surface Tension * A Family of Complex Wavelets for the Characterization of Singularities * Stabilization of Chaotic Amplitude Fluctuations in Multimode, Intracavity-Doubled Solid-State Lasers * Chaotic

  3. Sulfonate complexes of actinide ions: structural diversity in uranyl complexes with 2-sulfobenzoate.

    PubMed

    Thuéry, Pierre

    2013-01-07

    The reaction of uranyl nitrate hexahydrate with 2-sulfobenzoate (SB(2-)) in the presence of various amines gave the series of complexes [UO(2)(SB)(H(2)O)] (1), [UO(2)(SB)(H(2)O)](2)·pyz (2), [2,2'-bipyH](2)[UO(2)(SB)(2)(H(2)O)]·4H(2)O (3), [4,4'-bipyH(2)](2)[UO(2)(SB)(2)](2) (4), [4,4'-bipyH](2)[(UO(2))(2)(SB)(3)(H(2)O)]·4H(2)O (5), [NMe(4)](2)[(UO(2))(2)(SB)(3)(H(2)O)(1.15)]·1.35H(2)O (6), [NMe(4)](2)[(UO(2))(3)(SB)(2)O(2)] (7), and [H(2)DABCO](2)[(UO(2))(5)(SB)(4)O(2)(OH)(2)]·4H(2)O (8), where pyz = pyrazine, bipy = bipyridine, and DABCO = 1,4-diazabicyclo[2.2.2]octane, with all compounds but 5 having been obtained under hydrothermal conditions. The crystal structures of these complexes display a common motif in which uranyl is chelated by the carboxylate and sulfonate groups of SB, giving a seven-membered ring. Structure-directing effects due to the amine and the presence in 7 and 8 of additional μ(3)-oxo or μ(2)-hydroxo bridges result in much structural variety, with different bridging by the carboxylate and sulfonate groups giving rise to zero- (3, 4), one- (1, 5-8), or two-dimensional (2) assemblies. Some unusual uranyl secondary building units are observed, such as the pentanuclear [(UO(2))(5)O(2)(OH)(2)] discrete motif. Addition of 3d-block metal cations (Cu(2+), Ni(2+)) in the presence of nitrogen donors gave the heterometallic molecular complex [UO(2)Cu(SB)(2)(2,2'-bipy)(2)](2)·2H(2)O (9), the heterogeneous compound [Cu(4,4'-bipy)(H(2)O)(3)](2)[UO(2)(SB)(2)](2)·2H(2)O (10), in which molecular uranyl dimers are encompassing copper-containing chains, and the heterometallic one-dimensional polymers [(UO(2))(2)Cu(2)(SB)(4)(bipym)(H(2)O)(4)] (11) and [UO(2)Ni(SB)(2)(bipym)(H(2)O)(2)]·3H(2)O (12), where bipym = bipyrimidine. The latter two complexes display two different arrangements: in 11, bipym bridges two [UO(2)Cu(SB)(2)] chains to give a ladderlike assembly, while the uranyl cations are merely decorating species in 12. In contrast to those of

  4. Complex structure of spatially resolved high-order-harmonic spectra

    NASA Astrophysics Data System (ADS)

    Catoire, F.; Ferré, A.; Hort, O.; Dubrouil, A.; Quintard, L.; Descamps, D.; Petit, S.; Burgy, F.; Mével, E.; Mairesse, Y.; Constant, E.

    2016-12-01

    We investigate the spatiospectral coupling appearing in the spatially resolved high-order-harmonic spectra generated in gases. When ionization is weak, harmonic generation in the far field often exhibits rings surrounding a central spot centered on each odd harmonics in the spatiospectral domain. The nature of these structures is debated. They could stem from interferences between the emission of short and long trajectories, or could be the signature of the temporal and spatial dependence of the longitudinal phase matching of long trajectories (Maker fringes). We conducted spectrally and spatially resolved measurements of the harmonic spectra as a function of pressure, intensity, and ellipticity. In addition, we performed calculations where only a single emission plane is included (i.e., omitting deliberately the longitudinal phase matching), reproducing the features experimentally observed. This study has been completed by the spatiospectral coupling when strong ionization occurs leading to complex patterns which have been compared to calculations using the same model and also show good agreement. We conclude that many spatiospectral structures of the harmonic spectrum can be interpreted in terms of spatial and temporal transverse coherence of the emitting medium without resorting to longitudinal phase matching or quantum phase interference between short and long trajectories.

  5. Analysis and representation of complex structures in separated flows

    NASA Technical Reports Server (NTRS)

    Helman, James; Hesselink, Lambertus

    1991-01-01

    We discuss our recent work on extraction and visualization of topological information in separated fluid flow data sets. As with scene analysis, an abstract representation of a large data set can greatly facilitate the understanding of complex, high-level structures. When studying flow topology, such a representation can be produced by locating and characterizing critical points in the velocity field and generating the associated stream surfaces. In 3D flows, the surface topology serves as the starting point. The 2D tangential velocity field near the surface of the body is examined for critical points. The tangential velocity field is integrated out along the principal directions of certain classes of critical points to produce curves depicting the topology of the flow near the body. The points and curves are linked to form a skeleton representing the 2D vector field topology. This skeleton provides a basis for analyzing the 3D structures associated with the flow separation. The points along the separation curves in the skeleton are used to start tangent curve integrations. Integration origins are successively refined to produce stream surfaces. The map of the global topology is completed by generating those stream surfaces associated with 3D critical points.

  6. Structure of unsaturated rhamnogalacturonyl hydrolase complexed with substrate

    SciTech Connect

    Itoh, Takafumi; Ochiai, Akihito; Mikami, Bunzo; Hashimoto, Wataru; Murata, Kousaku . E-mail: kmurata@kais.kyoto-u.ac.jp

    2006-09-08

    Bacillus subtilis strain 168 YteR has been identified as a novel enzyme 'unsaturated rhamnogalacturonyl hydrolase' classified in glycoside hydrolase family 105. This enzyme acts specifically on unsaturated rhamnogalacturonan (RG) produced from plant cell wall RG type-I treated with RG lyases, releasing unsaturated galacturonic acid ({delta}GalA) from the substrate. The most likely candidate catalytic residue is Asp-143. Here, we show the structure of D143N in complex with unsaturated RG disaccharide (substrate) determined at 1.9 A resolution by X-ray crystallography. This structural feature directly contributes to the postulation of the enzyme reaction mechanism. YteR triggers the hydration of vinyl ether group in {delta}GalA, but not of glycoside bond, by using Asp-143 as a general acid and base catalyst. Asp-143 donates proton to the double bond of {delta}GalA as an acid catalyst and also deprotonates a water molecule as a base catalyst. Deprotonated water molecule attacks the C5 atom of {delta}GalA.

  7. Complex central structures suggest complex evolutionary paths for barred S0 galaxies

    NASA Astrophysics Data System (ADS)

    Dullo, Bililign T.; Martínez-Lombilla, Cristina; Knapen, Johan H.

    2016-11-01

    We investigate three barred lenticular galaxies (NGC 2681, NGC 3945 and NGC 4371), which were previously reported to have complex central structures but without a detailed structural analysis of these galaxies' high-resolution data. We have therefore performed four- to six-component (pseudo-)bulge/disc/bar/ring/point source) decompositions of the composite (Hubble Space Telescope plus ground-based) surface brightness profiles. We find that NGC 2681 hosts three bars, while NGC 3945 and NGC 4371 are double- and single-barred galaxies, respectively, in agreement with past isophotal analysis. We find that the bulges in these galaxies are compact, and have Sérsic indices of n ˜ 2.2-3.6 and stellar masses of M* ˜ 0.28 × 1010-1.1 × 1010 M⊙. NGC 3945 and NGC 4371 have intermediate-scale `pseudo-bulges' that are well described by a Sérsic model with low n ≲ 0.5 instead of an exponential (n = 1) profile as done in the past. We measure emission line fluxes enclosed within nine different elliptical apertures, finding that NGC 2681 has a low-ionization nuclear emission region (LINER)-type emission inside R ˜ 3 arcsec, but the emission line due to star formation is significant when aperture size is increased. In contrast, NGC 3945 and NGC 4371 have composite (active galactic nucleus plus star-forming)- and LINER-type emissions inside and outside R ˜ 2 arcsec, respectively. Our findings suggest that the three galaxies have experienced a complex evolutionary path. The bulges appear to be consequences of an earlier violent merging event while subsequent disc formation via gas accretion and bar-driven perturbations may account for the build-up of pseudo-bulges, bars, rings and point sources.

  8. From Lorentzian to Galilean (2+1) gravity: Drinfelʼd doubles, quantization and noncommutative spacetimes

    NASA Astrophysics Data System (ADS)

    Ballesteros, Ángel; Herranz, Francisco J.; Naranjo, Pedro

    2014-12-01

    It is shown that the canonical classical r-matrix arising from the Drinfel'd double (DD) structure underlying the two-fold centrally extended (2+1) Galilean and Newton-Hooke (NH) Lie algebras (with either zero or non-zero cosmological constant Λ, respectively) originates as a well-defined non-relativistic contraction of a specific class of canonical r-matrices associated with the DD structure of the (2+1) (anti)-de Sitter Lie algebra. The full quantum group structure associated with such (2+1) Galilean and NH DD is presented, and the corresponding noncommutative spacetimes are shown to contain a commuting ‘absolute time’ coordinate {{\\hat{x}}0} together with two noncommutative space coordinates ({{\\hat{x}}1},{{\\hat{x}}2}), whose commutator is a function of the cosmological constant Λ and of the (central) ‘quantum time’ coordinate {{\\hat{x}}0}. Thus, the Chern-Simons approach to Galilean (2+1) gravity can be consistently understood as the appropriate non-relativistic limit of the Lorentzian theory, and their associated quantum group symmetries (which do not fall into the family of so-called kappa-deformations) can also be derived from the (anti)-de Sitter quantum doubles through a well-defined quantum group contraction procedure.

  9. Structure of the F–actin–tropomyosin complex

    PubMed Central

    von der Ecken, Julian; Müller, Mirco; Lehman, William; Manstein, Dietmar J.; Penczek, Pawel A.; Raunser, Stefan

    2015-01-01

    Filamentous actin (F-actin) is the major protein of muscle thin filaments, and actin microfilaments are the main component of the eukaryotic cytoskeleton. Mutations in different actin isoforms lead to early-onset autosomal dominant non-syndromic hearing loss1, familial thoracic aortic aneurysms and dissections2, and multiple variations of myopathies3. In striated muscle fibres, the binding of myosin motors to actin filaments is mainly regulated by tropomyosin and troponin4,5. Tropomyosin also binds to F-actin in smooth muscle and in non-muscle cells and stabilizes and regulates the filaments there in the absence of troponin6. Although crystal structures for monomeric actin (G-actin) are available7, a high-resolution structure of F-actin is still missing, hampering our understanding of how disease-causing mutations affect the function of thin muscle filaments and microfilaments. Here we report the three-dimensional structure of F-actin at a resolution of 3.7 ångstroms in complex with tropomyosin at a resolution of 6.5ångstroms, determined by electron cryomicroscopy. The structure reveals that the D-loop is ordered and acts as a central region for hydrophobic and electrostatic interactions that stabilize the F-actin filament. We clearly identify the density corresponding to ADP and Mg2+ and explain the possible effect of prominent disease-causing mutants. A comparison of F-actin with G-actin reveals the conformational changes during filament formation and identifies the D-loop as their key mediator. We also confirm that negatively charged tropomyosin interacts with a positively charged groove on F-actin. Comparison of the position of tropomyosin in F-actin–tropomyosin with its position in our previously determined actin–tropomyosin–myosin structure8 reveals a myosin-induced transition of tropomyosin. Our results allow us to understand the role of individual mutations in the genesis of actin- and tropomyosin-related diseases and will serve as a strong

  10. Space-Time Diffeomorphisms in Noncommutative Gauge Theories

    NASA Astrophysics Data System (ADS)

    Rosenbaum, Marcos; Vergara, J. David; Juarez, L. Román

    2008-07-01

    In previous work [Rosenbaum M. et al., J. Phys. A: Math. Theor. 40 (2007), 10367-10382] we have shown how for canonical parametrized field theories, where space-time is placed on the same footing as the other fields in the theory, the representation of space-time diffeomorphisms provides a very convenient scheme for analyzing the induced twisted deformation of these diffeomorphisms, as a result of the space-time noncommutativity. However, for gauge field theories (and of course also for canonical geometrodynamics) where the Poisson brackets of the constraints explicitely depend on the embedding variables, this Poisson algebra cannot be connected directly with a representation of the complete Lie algebra of space-time diffeomorphisms, because not all the field variables turn out to have a dynamical character [Isham C.J., Kuchar K.V., Ann. Physics 164 (1985), 288-315, 316-333]. Nonetheless, such an homomorphic mapping can be rec! uperated by first modifying the original action and then adding additional constraints in the formalism in order to retrieve the original theory, as shown by Kuchar and Stone for the case of the parametrized Maxwell field in [Kuchar K.V., Stone S.L., Classical Quantum Gravity 4 (1987), 319-328]. Making use of a combination of all of these ideas, we are therefore able to apply our canonical reparametrization approach in order to derive the deformed Lie algebra of the noncommutative space-time diffeomorphisms as well as to consider how gauge transformations act on the twisted algebras of gauge and particle fields. Thus, hopefully, adding clarification on some outstanding issues in the literature concerning the symmetries for gauge theories in noncommutative space-times.

  11. Noncommutative Independence from the Braid Group {mathbb{B}_{infty}}

    NASA Astrophysics Data System (ADS)

    Gohm, Rolf; Köstler, Claus

    2009-07-01

    We introduce ‘braidability’ as a new symmetry for infinite sequences of noncommutative random variables related to representations of the braid group {mathbb{B}_{infty}} . It provides an extension of exchangeability which is tied to the symmetric group {mathbb{S}_{infty}} . Our key result is that braidability implies spreadability and thus conditional independence, according to the noncommutative extended de Finetti theorem [Kös08]. This endows the braid groups {mathbb{B}n} with a new intrinsic (quantum) probabilistic interpretation. We underline this interpretation by a braided extension of the Hewitt-Savage Zero-One Law. Furthermore we use the concept of product representations of endomorphisms [Goh04] with respect to certain Galois type towers of fixed point algebras to show that braidability produces triangular towers of commuting squares and noncommutative Bernoulli shifts. As a specific case we study the left regular representation of {mathbb{B}_{infty}} and the irreducible subfactor with infinite Jones index in the non-hyperfinite I I 1-factor L {(mathbb{B}_{infty})} related to it. Our investigations reveal a new presentation of the braid group {mathbb{B}_{infty}} , the ‘square root of free generator presentation’ {mathbb{F}^{1/2}_{infty}} . These new generators give rise to braidability while the squares of them yield a free family. Hence our results provide another facet of the strong connection between subfactors and free probability theory [GJS07]; and we speculate about braidability as an extension of (amalgamated) freeness on the combinatorial level.

  12. The Seiberg-Witten map for noncommutative gauge theories

    SciTech Connect

    Cerchiai, B.L.; Pasqua, A.F.; Zumino, B.

    2002-06-26

    The Seiberg-Witten map for noncommutative Yang-Mills theories is studied and methods for its explicit construction are discussed which are valid for any gauge group. In particular the use of the evolution equation is described in some detail and its relation to the cohomological approach is elucidated. Cohomological methods which are applicable to gauge theories requiring the Batalin-Vilkoviskii antifield formalism are briefly mentioned. Also, the analogy of the Weyl-Moyal star product with the star product of opestring field theory and possible ramifications of this analogy are briefly mentioned.

  13. Noncommuting observables in quantum detection and estimation theory

    NASA Technical Reports Server (NTRS)

    Helstrom, C. W.; Kennedy, R. S.

    1974-01-01

    Basing decisions and estimates on simultaneous approximate measurements of noncommuting observables in a quantum receiver is shown to be equivalent to measuring commuting projection operators on a large Hilbert space than that of the receiver itself. The quantum-mechanical Cramer-Rao inequalities derived from right logarithmic derivatives and symmetrized logarithmic derivatives of the density operator are compared, and it is shown that the latter give superior lower bounds on the error variances of individual unbiased estimates of arrival time and carrier frequency of a coherent signal. For a suitably weighted sum of the error variances of simultaneous estimates of these, the former yield the superior lower bound under some conditions.

  14. Noncommuting observables in quantum detection and estimation theory

    NASA Technical Reports Server (NTRS)

    Helstrom, C. W.

    1972-01-01

    Basing decisions and estimates on simultaneous approximate measurements of noncommuting observables in a quantum receiver is shown to be equivalent to measuring commuting projection operators on a larger Hilbert space than that of the receiver itself. The quantum-mechanical Cramer-Rao inequalities derived from right logarithmic derivatives and symmetrized logarithmic derivatives of the density operator are compared, and it is shown that the latter give superior lower bounds on the error variances of individual unbiased estimates of arrival time and carrier frequency of a coherent signal. For a suitably weighted sum of the error variances of simultaneous estimates of these, the former yield the superior lower bound under some conditions.

  15. Samples of noncommutative products in certain differential equations

    NASA Astrophysics Data System (ADS)

    Légaré, M.

    2010-11-01

    A set of associative noncommutative products is considered in different differential equations of the ordinary and partial types. A method of separation of variables is considered for a large set of those systems. The products involved include for example some * products and some products based on Nijenhuis tensors, which are embedded in the differential equations of the Laplace/Poisson, Lax and Schrödinger styles. A comment on the *-products of Reshetikhin-Jambor-Sykora type is also given in relation to *-products of Vey type.

  16. Noncommutative geometry, Grand Symmetry and twisted spectral triple

    NASA Astrophysics Data System (ADS)

    Devastato, Agostino

    2015-08-01

    In the noncommutative geometry approach to the standard model we discuss the possibility to derive the extra scalar field sv - initially suggested by particle physicist to stabilize the electroweak vacuum - from a “grand algebra” that contains the usual standard model algebra. We introduce the Connes-Moscovici twisted spectral triples for the Grand Symmetry model, to cure a technical problem, that is the appearance, together with the field sv, of unbounded vectorial terms. The twist makes these terms bounded, and also permits to understand the breaking making the computation of the Higgs mass compatible with the 126 GeV experimental value.

  17. Cosmological perturbations of a perfect fluid and noncommutative variables

    SciTech Connect

    De Felice, Antonio; Gerard, Jean-Marc; Suyama, Teruaki

    2010-03-15

    We describe the linear cosmological perturbations of a perfect fluid at the level of an action, providing thus an alternative to the standard approach based only on the equations of motion. This action is suited not only to perfect fluids with a barotropic equation of state, but also to those for which the pressure depends on two thermodynamical variables. By quantizing the system we find that (1) some perturbation fields exhibit a noncommutativity quite analogous to the one observed for a charged particle moving in a strong magnetic field, (2) local curvature and pressure perturbations cannot be measured simultaneously, (3) ghosts appear if the null energy condition is violated.

  18. Perturbative Chern-Simons theory on noncommutative Bbb R3

    NASA Astrophysics Data System (ADS)

    Bichl, Andreas A.; Grimstrup, Jesper M.; Putz, Volkmar; Schweda, Manfred

    2000-07-01

    A U(N) Chern-Simons theory on non-commutative Bbb R3 is constructed as a θ-deformed field theory. The model is characterized by two symmetries: the BRST-symmetry and the topological linear vector supersymmetry. It is shown that the theory is finite and θ-independent at the one-loop level and that the calculations respect the restriction of the topological supersymmetry. Thus the topological θ-deformed Chern-Simons theory is an example of a model which is non singular in the limit θ→0.

  19. Enhanced seismic depth imaging of complex fault-fold structures

    NASA Astrophysics Data System (ADS)

    Kirtland Grech, Maria Graziella

    Synthetic seismic data were acquired over numerical and physical models, representing fault-fold structures encountered in the Canadian Rocky Mountain Foothills, to investigate which migration algorithm produces the best image in such complex environments. Results showed that pre-stack depth migration from topography with the known velocity model yielded the optimum migrated image. Errors in the positioning of a target underneath a dipping antisotropic overburden were also studied using multicomponent data. The largest error was observed on P-wave data where anisotropy was highest at 18%. For an overburden thickness of 1500 m, the target was imaged 300 m updip from the true location. Field data from a two-dimensional surface seismic line and a multioffset vertical seismic profile (VSP) from the Foothills of southern Alberta, Canada, were processed using a flow designed to yield an optimum depth image. Traveltime inversion of the first arrivals from all the shots from the multioffset VSP revealed that the Mesozoic shale strata in the area exhibit seismic velocity anisotropy. The anisotropy parameters, ε and delta, were calculated to be 0.1 and 0.05 respectively. Anisotropic pre-stack depth migration code for VSP and surface seismic data, which uses a modified version of a raytracer developed in this thesis for the computation of traveltime tables, was also developed. The algorithm was then used in a new method for integrated VSP and surface seismic depth imaging. Results from the migration of synthetic and field data show that the resulting integrated image is superior to that obtained from the migration of either data set alone or to that obtained from the conventional "splicing" approach. The combination of borehole and surface seismic data for anisotropy analysis, velocity model building, and depth migration, yielded a robust image even when the geology was complex, thus permitting a more accurate interpretation of the exploration target.

  20. Brain: a complex adaptive structure at multiple levels

    NASA Astrophysics Data System (ADS)

    Klein, Bradley G.

    2001-10-01

    The human brain is comprised of over 100 billion neurons organized into tracts, nuclei, circuits and systems. This provides innumerable elegant abilities that rely on the nervous system to act as a complex adaptive structure (CAS). This property is apparent with respect to overall function, the function of individual neurons and the function of sensory and motor systems. At the overall functional level, the nervous system monitors the environments and can alter that environment. Alterations such as turning on a light switch or changing the diameter of neural vasculature, can improve the performance or chance for survival of the nervous system. Individual neurons can alter the activity of their electrogenic pumps, their rate of transmitter synthesis, their neurotransmitter release and their receptor density in order to maintain optimal functioning in a circuit following changes in their micro-environment. At the systems level, the visual system adjusts the orientation of the eyes or pupillary diameter to receive the highest quality visual information. In the motor system, the myotatic reflex maintains muscle position in the face of changing load, and the gain of the muscle organ responsible for the myotatic reflex can also be automatically adjusted. Internal homeostasis, essential for optimal performance of the nervous system, can be achieved through complex behavioral actions such as feeding. The hypothalamus plays an important role in such behaviors and in the type of sensorimotor integration responsible for the CAS nature of overall nervous system function. Thinking about the CAS characteristics of the nervous system may lead to development of non-biological CAS prostheses for the brain.

  1. Joint probabilities of noncommuting observables and the Einstein-Podolsky-Rosen question in Wiener-Siegel quantum theory

    SciTech Connect

    Warnock, R.L.

    1996-02-01

    Ordinary quantum theory is a statistical theory without an underlying probability space. The Wiener-Siegel theory provides a probability space, defined in terms of the usual wave function and its ``stochastic coordinates``; i.e., projections of its components onto differentials of complex Wiener processes. The usual probabilities of quantum theory emerge as measures of subspaces defined by inequalities on stochastic coordinates. Since each point {alpha} of the probability space is assigned values (or arbitrarily small intervals) of all observables, the theory gives a pseudo-classical or ``hidden-variable`` view in which normally forbidden concepts are allowed. Joint probabilities for values of noncommuting variables are well-defined. This paper gives a brief description of the theory, including a new generalization to incorporate spin, and reports the first concrete calculation of a joint probability for noncommuting components of spin of a single particle. Bohm`s form of the Einstein-Podolsky-Rosen Gedankenexperiment is discussed along the lines of Carlen`s paper at this Congress. It would seem that the ``EPR Paradox`` is avoided, since to each {alpha} the theory assigns opposite values for spin components of two particles in a singlet state, along any axis. In accordance with Bell`s ideas, the price to pay for this attempt at greater theoretical detail is a disagreement with usual quantum predictions. The disagreement is computed and found to be large.

  2. The complex planetary synchronization structure of the solar system

    NASA Astrophysics Data System (ADS)

    Scafetta, N.

    2014-01-01

    The complex planetary synchronization structure of the solar system, which since Pythagoras of Samos (ca. 570-495 BC) is known as the music of the spheres, is briefly reviewed from the Renaissance up to contemporary research. Copernicus' heliocentric model from 1543 suggested that the planets of our solar system form a kind of mutually ordered and quasi-synchronized system. From 1596 to 1619 Kepler formulated preliminary mathematical relations of approximate commensurabilities among the planets, which were later reformulated in the Titius-Bode rule (1766-1772), which successfully predicted the orbital position of Ceres and Uranus. Following the discovery of the ~ 11 yr sunspot cycle, in 1859 Wolf suggested that the observed solar variability could be approximately synchronized with the orbital movements of Venus, Earth, Jupiter and Saturn. Modern research has further confirmed that (1) the planetary orbital periods can be approximately deduced from a simple system of resonant frequencies; (2) the solar system oscillates with a specific set of gravitational frequencies, and many of them (e.g., within the range between 3 yr and 100 yr) can be approximately constructed as harmonics of a base period of ~ 178.38 yr; and (3) solar and climate records are also characterized by planetary harmonics from the monthly to the millennial timescales. This short review concludes with an emphasis on the contribution of the author's research on the empirical evidences and physical modeling of both solar and climate variability based on astronomical harmonics. The general conclusion is that the solar system works as a resonator characterized by a specific harmonic planetary structure that also synchronizes the Sun's activity and the Earth's climate. The special issue Pattern in solar variability, their planetary origin and terrestrial impacts (Mörner et al., 2013) further develops the ideas about the planetary-solar-terrestrial interaction with the personal contribution of 10

  3. Structural reorganization of the interleukin-7 signaling complex

    SciTech Connect

    McElroy, Craig A.; Holland, Paul J.; Zhao, Peng; Lim, Jae-Min; Wells, Lance; Eisenstein, Edward; Walsh, Scott T.R.

    2012-06-29

    We report here an unliganded receptor structure in the common gamma-chain ({gamma}{sub c}) family of receptors and cytokines. The crystal structure of the unliganded form of the interleukin-7 alpha receptor (IL-7R{alpha}) extracellular domain (ECD) at 2.15 {angstrom} resolution reveals a homodimer forming an 'X' geometry looking down onto the cell surface with the C termini of the two chains separated by 110 {angstrom} and the dimer interface comprising residues critical for IL-7 binding. Further biophysical studies indicate a weak association of the IL-7R{alpha} ECDs but a stronger association between the {gamma}{sub c}/IL-7R{alpha} ECDs, similar to previous studies of the full-length receptors on CD4{sup +} T cells. Based on these and previous results, we propose a molecular mechanism detailing the progression from the inactive IL-7R{alpha} homodimer and IL-7R{alpha}-{gamma}{sub c} heterodimer to the active IL-7-IL-7R{alpha}-{gamma}{sub c} ternary complex whereby the two receptors undergo at least a 90{sup o} rotation away from the cell surface, moving the C termini of IL-7R{alpha} and {gamma}{sub c} from a distance of 110 {angstrom} to less than 30 {angstrom} at the cell surface. This molecular mechanism can be used to explain recently discovered IL-7- and {gamma}{sub c}-independent gain-of-function mutations in IL-7R{alpha} from B- and T-cell acute lymphoblastic leukemia patients. The mechanism may also be applicable to other {gamma}{sub c} receptors that form inactive homodimers and heterodimers independent of their cytokines.

  4. Editors' preface for the topical issue on Seven papers on Noncommutative Geometry and Operator Algebras

    NASA Astrophysics Data System (ADS)

    Guido, Daniele; Landi, Giovanni; Vassout, Stéphane

    2016-07-01

    This topical issue grew out of the International Conference "Noncommutative Geometry and Applications" held 16-21 June 2014 at Villa Mondragone, Frascati (Roma). The main purpose of the conference was to have a unified view of different incarnations of noncommutative geometry and its applications. The seven papers collected in the present topical issue represent a good sample of the topics covered at the workshop. The conference itself was one of the climaxes of the Franco-Italian project GREFI-GENCO, which was initiated in 2007 by CNRS and INDAM to promote and enhance collaboration and exchanges between French and Italian researchers in the area of noncommutative geometry.

  5. Photon-neutrino interaction in θ-exact covariant noncommutative field theory

    NASA Astrophysics Data System (ADS)

    Horvat, R.; Kekez, D.; Schupp, P.; Trampetić, J.; You, J.

    2011-08-01

    Photon-neutrino interactions arise quite naturally in noncommutative field theories. Such couplings are absent in ordinary field theory and imply experimental lower bounds on the energy scale ΛNC˜|θ|-2 of noncommutativity. Using nonperturbative methods and a Seiberg-Witten map based covariant approach to noncommutative gauge theory, we obtain θ-exact expressions for the interactions, thereby eliminating previous restrictions to low-energy phenomena. We discuss implications for plasmon decay, neutrino charge radii, big bang nucleosynthesis, and ultrahigh energy cosmic rays. Our results behave reasonably throughout all interaction energy scales, thus facilitating further phenomenological applications.

  6. Symmetry breaking in noncommutative finite temperature λphi4 theory with a nonuniform ground state

    NASA Astrophysics Data System (ADS)

    Hernández, J. M.; Ramírez, C.; Sánchez, M.

    2014-05-01

    We consider the CJT effective action at finite temperature for a noncommutative real scalar field theory, with noncommutativity among space and time variables. We study the solutions of a stripe type nonuniform background, which depends on space and time. The analysis in the first approximation shows that such solutions appear in the planar limit, but also under normal anisotropic noncommutativity. Further we show that the transition from the uniform ordered phase to the non uniform one is first order and that the critical temperature depends on the nonuniformity of the ground state.

  7. From structure of the complex to understanding of the biology

    PubMed Central

    Rossmann, Michael G.; Arisaka, Fumio; Battisti, Anthony J.; Bowman, Valorie D.; Chipman, Paul R.; Fokine, Andrei; Hafenstein, Susan; Kanamaru, Shuji; Kostyuchenko, Victor A.; Mesyanzhinov, Vadim V.; Shneider, Mikhail M.; Morais, Marc C.; Leiman, Petr G.; Palermo, Laura M.; Parrish, Colin R.; Xiao, Chuan

    2007-01-01

    The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy (cryo-EM) single-particle reconstructions. Both techniques lean heavily on imposing icosahedral symmetry, thereby obscuring any deviation from the assumed symmetry. However, tailed bacteriophages have icosahedral or prolate icosahedral heads that have one obvious unique vertex where the genome can enter for DNA packaging and exit when infecting a host cell. The presence of the tail allows cryo-EM reconstructions in which the special vertex is used to orient the head in a unique manner. Some very large dsDNA icosahedral viruses also develop special vertices thought to be required for infecting host cells. Similarly, preliminary cryo-EM data for the small ssDNA canine parvovirus complexed with receptor suggests that these viruses, previously considered to be accurately icosahedral, might have some asymmetric properties that generate one preferred receptor-binding site on the viral surface. Comparisons are made between rhinoviruses that bind receptor molecules uniformly to all 60 equivalent binding sites, canine parvovirus, which appears to have a preferred receptor-binding site, and bacteriophage T4, which gains major biological advantages on account of its unique vertex and tail organelle. PMID:17164521

  8. Microstructure-based modelling of multiphase materials and complex structures

    NASA Astrophysics Data System (ADS)

    Werner, Ewald; Wesenjak, Robert; Fillafer, Alexander; Meier, Felix; Krempaszky, Christian

    2016-09-01

    Micromechanical approaches are frequently employed to monitor local and global field quantities and their evolution under varying mechanical and/or thermal loading scenarios. In this contribution, an overview on important methods is given that are currently used to gain insight into the deformational and failure behaviour of multiphase materials and complex structures. First, techniques to represent material microstructures are reviewed. It is common to either digitise images of real microstructures or generate virtual 2D or 3D microstructures using automated procedures (e.g. Voronoï tessellation) for grain generation and colouring algorithms for phase assignment. While the former method allows to capture exactly all features of the microstructure at hand with respect to its morphological and topological features, the latter method opens up the possibility for parametric studies with respect to the influence of individual microstructure features on the local and global stress and strain response. Several applications of these approaches are presented, comprising low and high strain behaviour of multiphase steels, failure and fracture behaviour of multiphase materials and the evolution of surface roughening of the aluminium top metallisation of semiconductor devices.

  9. Fitting meta-analytic structural equation models with complex datasets.

    PubMed

    Wilson, Sandra Jo; Polanin, Joshua R; Lipsey, Mark W

    2016-06-01

    A modification of the first stage of the standard procedure for two-stage meta-analytic structural equation modeling for use with large complex datasets is presented. This modification addresses two common problems that arise in such meta-analyses: (a) primary studies that provide multiple measures of the same construct and (b) the correlation coefficients that exhibit substantial heterogeneity, some of which obscures the relationships between the constructs of interest or undermines the comparability of the correlations across the cells. One component of this approach is a three-level random effects model capable of synthesizing a pooled correlation matrix with dependent correlation coefficients. Another component is a meta-regression that can be used to generate covariate-adjusted correlation coefficients that reduce the influence of selected unevenly distributed moderator variables. A non-technical presentation of these techniques is given, along with an illustration of the procedures with a meta-analytic dataset. Copyright © 2016 John Wiley & Sons, Ltd.

  10. Crystal structure of a dimeric β-diketiminate magnesium complex

    PubMed Central

    MacNeil, Connor S.; Johnson, Kevin R. D.; Hayes, Paul G.; Boeré, René T.

    2016-01-01

    The solid-state structure of a dimeric β-diketiminate magnesium(II) complex is discussed. The compound, di-μ-iodido-bis­[(­{4-amino-1,5-bis­[2,6-bis­(propan-2-yl)phen­yl]pent-3-en-2-yl­idene}aza­nido-κ2 N,N′)magnesium(II)] toluene sesquisolvate, [Mg2(C29H41N2)2I2]·1.5C7H8, crystallizes as two independent mol­ecules, each with 2/m crystallographic site symmetry, located at Wyckoff sites 2c and 2d. These have symmetry-equivalent magnesium atoms bridged by μ-iodide ligands with very similar Mg—I distances. The two Mg atoms are located slightly below (∼0.5 Å) the least-squares plane defined by N–C—C–N atoms in the ligand scaffold, and are approximately tetra­hedrally coordinated. One and one-half toluene solvent mol­ecules are disordered with respect to mirror-site symmetry at Wyckoff sites 4i and 2a, respectively. In the former case, two toluene mol­ecules inter­act in an off-center parallel stacking arrangement; the shortest C to C′ (π–π) distance of 3.72 (1) Å was measured for this inter­action. PMID:27980823

  11. Solution structures of stromelysin complexed to thiadiazole inhibitors.

    PubMed Central

    Stockman, B. J.; Waldon, D. J.; Gates, J. A.; Scahill, T. A.; Kloosterman, D. A.; Mizsak, S. A.; Jacobsen, E. J.; Belonga, K. L.; Mitchell, M. A.; Mao, B.; Petke, J. D.; Goodman, L.; Powers, E. A.; Ledbetter, S. R.; Kaytes, P. S.; Vogeli, G.; Marshall, V. P.; Petzold, G. L.; Poorman, R. A.

    1998-01-01

    Unregulated or overexpressed matrix metalloproteinases (MMPs), including stromelysin, collagenase, and gelatinase. have been implicated in several pathological conditions including arthritis and cancer. Small-molecule MMP inhibitors may have therapeutic value in the treatment of these diseases. In this regard, the solution structures of two stromelysin/ inhibitor complexes have been investigated using 1H, 13C, and 15N NMR spectroscopy. Both-inhibitors are members of a novel class of matrix metalloproteinase inhibitor that contain a thiadiazole group and that interact with stromelysin in a manner distinct from other classes of inhibitors. The inhibitors coordinate the catalytic zinc atom through their exocyclic sulfur atom, with the remainder of the ligand extending into the S1-S3 side of the active site. The binding of inhibitor containing a protonated or fluorinated aromatic ring was investigated using 1H and 19F NMR spectroscopy. The fluorinated ring was found to have a reduced ring-flip rate compared to the protonated version. A strong, coplanar interaction between the fluorinated ring of the inhibitor and the aromatic ring of Tyr155 is proposed to account for the reduced ring-flip rate and for the increase in binding affinity observed for the fluorinated inhibitor compared to the protonated inhibitor. Binding interactions observed for the thiadiazole class of ligands have implications for the design of matrix metalloproteinase inhibitors. PMID:9827994

  12. Measuring the significance of community structure in complex networks

    NASA Astrophysics Data System (ADS)

    Hu, Yanqing; Nie, Yuchao; Yang, Hua; Cheng, Jie; Fan, Ying; di, Zengru

    2010-12-01

    Many complex systems can be represented as networks, and separating a network into communities could simplify functional analysis considerably. Many approaches have recently been proposed to detect communities, but a method to determine whether the detected communities are significant is still lacking. In this paper, an index to evaluate the significance of communities in networks is proposed based on perturbation of the network. In contrast to previous approaches, the network is disturbed gradually, and the index is defined by integrating all of the similarities between the community structures before and after perturbation. Moreover, by taking the null model into account, the index eliminates scale effects. Thus, it can evaluate and compare the significance of communities in different networks. The method has been tested in many artificial and real-world networks. The results show that the index is in fact independent of the size of the network and the number of communities. With this approach, clear communities are found to always exist in social networks, but significant communities cannot be found in protein interactions and metabolic networks.

  13. Unsaturated platinum-rhenium cluster complexes. Synthesis, structures and reactivity.

    PubMed

    Adams, Richard D; Captain, Burjor; Smith, Mark D; Beddie, Chad; Hall, Michael B

    2007-05-09

    Two new compounds PtRe3(CO)12(PBut3)(micro-H)3, 9, and PtRe2(CO)9(PBut3)(micro-H)2, 10, were obtained from the reaction of Pt(PBut3)2 with Re3(CO)12(micro-H3), 8, at room temperature. Compound 9 contains a butterfly cluster of four metals formed by the insertion of the platinum atom from a Pt(PBut3) group into one of the hydride-bridged metal-metal bonds of 8. The three hydrido ligands are bridging ligands across each of three new Pt-Re bonds. Compound 10 contains a triangular PtRe2 cluster with two hydrido ligands; one bridges a Pt-Re bond, and the other bridges the Re-Re bond. The new compound Pt2Re2(CO)7(PBut3)2(micro-H)2, 11, was obtained from the reaction of 8 with Pt(PBut3)2 in hexane at reflux. Compound 11 was also obtained from 10 by reaction with an additional quantity of Pt(PBut3)2. Compound 11 contains a tetrahedral cluster of four metal atoms with two dynamically active hydrido ligands. A CO ligand on one of the two platinum atoms also exchanges between the two platinum atoms rapidly on the NMR time scale. Compound 11 is electronically unsaturated and was found to add hydrogen at room temperature to form the tetrahydrido cluster complex, Pt2Re2(CO)7(PBut3)2(micro-H)4, 12. Compound 12 has a structure similar to 11 but contains one triply bridging hydrido ligand, two edge bridging hydrido ligands, and one terminal hydrido ligand on one of the two platinum atoms. A kinetic isotope effect D/H of 1.5(1) was determined for the addition of H2 to 11. Hydrogen can be eliminated from 12 by heating to 97 degrees C or by the application of UV-vis irradiation at room temperature. Compound 12 adds CO at room temperature to yield the complex Pt2Re2(CO)8(PBut3)2(micro-H)4, 13, which contains a planar cluster of four metal atoms with a Pt-Pt bond and four edge bridging hydrido ligands. Compounds 11 and 12 react with Pt(PBut3)2 to yield the known five metal cluster complexes Pt3Re2(CO)6(PBut3)3(micro-H)2, 14, and Pt3Re2(CO)6(PBut3)3(micro-H)4, 15, respectively. Density

  14. Evaluation of structural and functional properties of chitosan-chlorogenic acid complexes.

    PubMed

    Wei, Zihao; Gao, Yanxiang

    2016-05-01

    The objectives of the present study were to first synthesize chitosan-chlorogenic acid (CA) covalent complex and then compare structural and functional properties between chitosan-CA covalent complex and physical complex. First, chitosan-CA covalent complex was synthesized and its total phenolic content was as high as 276.5 ± 6.2 mg/g. Then structural and functional properties of chitosan-CA covalent and physical complexes were analyzed. The covalent reaction induced formation of both amide and ester bonds in chitosan. Data of X-ray diffraction (XRD) and scanning electron microscopy (SEM) indicated that the complexations of CA changed crystallinity and morphology of chitosan, and covalent complexation induced a larger change of physical structure than physical complexation. In terms of functional properties, chitosan-CA covalent complex exhibited better thermal stability than physical complex in terms of antioxidant activity, and the viscosity of chitosan was significantly increased by covalent modification.

  15. On the scalar curvature for the noncommutative four torus

    NASA Astrophysics Data System (ADS)

    Fathizadeh, Farzad

    2015-06-01

    The scalar curvature for noncommutative four tori TΘ 4 , where their flat geometries are conformally perturbed by a Weyl factor, is computed by making the use of a noncommutative residue that involves integration over the 3-sphere. This method is more convenient since it does not require the rearrangement lemma and it is advantageous as it explains the simplicity of the final functions of one and two variables, which describe the curvature with the help of a modular automorphism. In particular, it readily allows to write the function of two variables as the sum of a finite difference and a finite product of the one variable function. The curvature formula is simplified for dilatons of the form sp, where s is a real parameter and p ∈ C ∞ ( TΘ 4 ) is an arbitrary projection, and it is observed that, in contrast to the two dimensional case studied by Connes and Moscovici, J. Am. Math. Soc. 27(3), 639-684 (2014), unbounded functions of the parameter s appear in the final formula. An explicit formula for the gradient of the analog of the Einstein-Hilbert action is also calculated.

  16. Collisional family structure within the Nysa-Polana complex

    NASA Astrophysics Data System (ADS)

    Dykhuis, Melissa J.; Greenberg, Richard

    2015-05-01

    The Nysa-Polana complex is a group of low-inclination asteroid families in the inner main belt, bounded in semimajor axis by the Mars-crossing region and the Jupiter 3:1 mean-motion resonance. This group is important as the most likely source region for the target of the OSIRIS-REx mission, (101955) Bennu; however, family membership in the region is complicated by the presence of several dynamically overlapping families with a range of surface reflectance properties. The large S-type structure in the region appears to be associated with the parent body (135) Hertha, and displays an (eP,aP) correlation consistent with a collision event near true anomaly of ∼180° with ejecta velocity vej ∼ 285m /s . The ejecta distribution from a collision with these orbital properties is predicted to have a maximum semimajor axis dispersion of δaej = 0.005 ± 0.008AU , which constitutes only a small fraction (7%) of the observed semimajor axis dispersion, the rest of which is attributed to the Yarkovsky effect. The age of the family is inferred from the Yarkovsky dispersion to be 300-50+60 My. Objects in a smaller cluster that overlaps the large Hertha family in proper orbital element space have reflectance properties more consistent with the X-type (135) Hertha than the surrounding S-type family. These objects form a distinct Yarkovsky "V" signature in (aP, H) space, consistent with a more recent collision, which appears to also be dynamically connected to (135) Hertha. Production of two families with different reflectance properties from a single parent could result from the partial differentiation of the parent, shock darkening effects, or other causes. The Nysa-Polana complex also contains a low-albedo family associated with (142) Polana (called "New Polana" by Walsh et al. (Walsh, K.J. et al. [2013]. Icarus 225, 283-297)), and two other low-albedo families associated with (495) Eulalia. The second Eulalia family may be a high-aP , low-eP , low-iP component of the first

  17. Luminescence modulations of rhenium tricarbonyl complexes induced by structural variations.

    PubMed

    Bertrand, Hélène C; Clède, Sylvain; Guillot, Régis; Lambert, François; Policar, Clotilde

    2014-06-16

    Octahedral d(6) low-spin Re(I) tricarbonyl complexes are of considerable interest as noninvasive imaging probes and have been deeply studied owing to their biological stability, low toxicity, large Stokes shifts, and long luminescence lifetimes. We reported recently the bimodal IR and luminescence imaging of a Re(I) tricarbonyl complex with a Pyta ligand (4-(2-pyridyl)-1,2,3-triazole) in cells and labeled such metal-carbonyl complexes SCoMPIs for single-core multimodal probes for imaging. Re(I) tricarbonyl complexes have unique photophysical properties allowing for their unequivocal detection in cells but also present some weaknesses such as a very low luminescence quantum yield in aqueous medium. Further optimizations would thus be desirable. We therefore developed new Re(I) tricarbonyl complexes prepared from different ancillary ligands. Complexes with benzothiadiazole-triazole ligands show interesting luminescent quantum yields in acetonitrile and may constitute valuable luminescent metal complexes in organic media. A series of complexes with bidentate 1-(2-quinolinyl)-1,2,3-triazole (Taquin) and 1-(2-pyridyl)-1,2,3-triazole (Tapy) ligands bearing various 4-substituted alkyl side chains has been designed and synthesized with efficient procedures. Their photophysical properties have been characterized in acetonitrile and in a H2O/DMSO (98/2) mixture and compared with those of the parent Quinta- and Pyta-based complexes. Tapy complexes bearing long alkyl chains show impressive enhancement of their luminescent properties relative to the parent Pyta complex. Theoretical calculations have been performed to further characterize this new class of rhenium tricarbonyl complexes. Preliminary cellular imaging studies in MDA-MB231 breast cancer cells reveal a strong increase in the luminescence signal in cells incubated with the Tapy complex substituted with a C12 alkyl chain. This study points out the interesting potential of the Tapy ligand in coordination chemistry

  18. Structural biology. Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli.

    PubMed

    Jackson, Ryan N; Golden, Sarah M; van Erp, Paul B G; Carter, Joshua; Westra, Edze R; Brouns, Stan J J; van der Oost, John; Terwilliger, Thomas C; Read, Randy J; Wiedenheft, Blake

    2014-09-19

    Clustered regularly interspaced short palindromic repeats (CRISPRs) are essential components of RNA-guided adaptive immune systems that protect bacteria and archaea from viruses and plasmids. In Escherichia coli, short CRISPR-derived RNAs (crRNAs) assemble into a 405-kilodalton multisubunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Here we present the 3.24 angstrom resolution x-ray crystal structure of Cascade. Eleven proteins and a 61-nucleotide crRNA assemble into a seahorse-shaped architecture that binds double-stranded DNA targets complementary to the crRNA-guide sequence. Conserved sequences on the 3' and 5' ends of the crRNA are anchored by proteins at opposite ends of the complex, whereas the guide sequence is displayed along a helical assembly of six interwoven subunits that present five-nucleotide segments of the crRNA in pseudo-A-form configuration. The structure of Cascade suggests a mechanism for assembly and provides insights into the mechanisms of target recognition.

  19. Phase-space noncommutative extension of the Robertson-Schrödinger formulation of Ozawa's uncertainty principle

    NASA Astrophysics Data System (ADS)

    Bastos, Catarina; Bernardini, Alex E.; Bertolami, Orfeu; Dias, Nuno Costa; Prata, João Nuno

    2015-03-01

    We revisit Ozawa's uncertainty principle (OUP) in the framework of noncommutative (NC) quantum mechanics. We derive a matrix version of OUP accommodating any NC structure in the phase space, and compute NC corrections to lowest order for two measurement interactions, namely the backaction evading quadrature amplifier and noiseless quadrature transducers. These NC corrections alter the nature of the measurement interaction, as a noiseless interaction may acquire noise, and an interaction of independent intervention may become dependent on the object system. However the most striking result is that noncommutativity may lead to a violation of the OUP itself. The NC corrections for the backaction evading quadrature amplifier reveal a new term which may potentially be amplified in such a way that the violation of the OUP becomes experimentally testable. On the other hand, the NC corrections to the noiseless quadrature transducer shows an incompatibility of this model with NC quantum mechanics. We discuss the implications of this incompatibility for NC quantum mechanics and for Ozawa's uncertainty principle.

  20. Explicit derivation of Yang-Mills self-dual solutions on non-commutative harmonic space

    NASA Astrophysics Data System (ADS)

    Belhaj, A.; Hssaini, M.; Sahraoui, E. M.; Saidi, E. H.

    2001-06-01

    We develop the non-commutative harmonic space (NHS) analysis to study the problem of solving the nonlinear constraint equations of non-commutative Yang-Mills self-duality in four dimensions. We show that this space, denoted also as NHS(η,θ), has two SU(2) isovector deformations η(ij) and θ(ij) parametrizing, respectively, two non-commutative harmonic subspaces NHS(η,0) and NHS(0, θ) used to study the self-dual and anti self-dual non-commutative Yang-Mills solutions. We reformulate the Yang-Mills self-dual constraint equations on NHS(η,0) by extending the idea of harmonic analyticity to linearize them. We then give a perturbative self-dual solution recovering the ordinary one. Finally, we present the explicit computation of an exact self-dual solution.

  1. Topological expansion of the Bethe ansatz, and non-commutative algebraic geometry

    NASA Astrophysics Data System (ADS)

    Eynard, B.; Marchal, O.

    2009-03-01

    In this article, we define a non-commutative deformation of the ``symplectic invariants'' (introduced in [13]) of an algebraic hyperelliptic plane curve. The necessary condition for our definition to make sense is a Bethe ansatz. The commutative limit reduces to the symplectic invariants, i.e. algebraic geometry, and thus we define non-commutative deformations of some algebraic geometry quantities. In particular our non-commutative Bergman kernel satisfies a Rauch variational formula. Those non-commutative invariants are inspired from the large N expansion of formal non-hermitian matrix models. Thus they are expected to be related to the enumeration problem of discrete non-orientable surfaces of arbitrary topologies.

  2. Path-integral action of a particle in the noncommutative plane.

    PubMed

    Gangopadhyay, Sunandan; Scholtz, Frederik G

    2009-06-19

    Noncommutative quantum mechanics can be viewed as a quantum system represented in the space of Hilbert-Schmidt operators acting on noncommutative configuration space. Taking this as a departure point, we formulate a coherent state approach to the path-integral representation of the transition amplitude. From this we derive an action for a particle moving in the noncommutative plane and in the presence of an arbitrary potential. We find that this action is nonlocal in time. However, this nonlocality can be removed by introducing an auxilary field, which leads to a second class constrained system that yields the noncommutative Heisenberg algebra upon quantization. Using this action, the propagator of the free particle and harmonic oscillator are computed explicitly.

  3. The Kaehler Potential of the Non-commutative CP{sup 1} model

    SciTech Connect

    Lechtenfeld, Olaf; Maceda, Marco

    2010-12-07

    We present some results on the moduli space for the charge two-soliton solution of the non-commutative CP{sup 1} model. The associated Kaehler potential and its relation to the commutative case are discussed.

  4. Landau-like Atomic Problem on a Non-commutative Phase Space

    NASA Astrophysics Data System (ADS)

    Mamat, Jumakari; Dulat, Sayipjamal; Mamatabdulla, Hekim

    2016-06-01

    We study the motion of a neutral particle in symmetric gauge and in the framework of non-commutative Quantum Mechanics. Starting from the corresponding Hamiltonian we derive the eigenfunction and eigenvalues.

  5. Noncanonical phase-space noncommutativity and the Kantowski-Sachs singularity for black holes

    NASA Astrophysics Data System (ADS)

    Bastos, Catarina; Bertolami, Orfeu; Dias, Nuno Costa; Prata, João Nuno

    2011-07-01

    We consider a cosmological model based upon a noncanonical noncommutative extension of the Heisenberg-Weyl algebra to address the thermodynamical stability and the singularity problem of black holes whose interior are described by the Kantowski-Sachs metric and modeled by a noncommutative extension of the Wheeler-DeWitt equation. We compute the temperature and entropy of these black holes and compare the results with the Hawking values. We observe that it is actually the noncommutativity in the momentum sector that allows for the existence of a minimum in the potential, which is the key to apply the Feynman-Hibbs procedure. It is shown that this noncommutative model generates a nonunitary dynamics that predicts a vanishing probability in the neighborhood of the singularity. This result effectively regularizes the Kantowski-Sachs singularity and generalizes a similar result, previously obtained for the case of Schwarzschild black holes.

  6. O (θ ) Feynman rules for quadrilinear gauge boson couplings in the noncommutative standard model

    NASA Astrophysics Data System (ADS)

    Sajadi, Seyed Shams; Boroun, G. R.

    2017-02-01

    We examine the electroweak gauge sector of the noncommutative standard model and, in particular, obtain the O (θ ) Feynman rules for all quadrilinear gauge boson couplings. Surprisingly, an electroweak-chromodynamics mixing appears in the gauge sector of the noncommutative standard model, where the photon as well as the neutral weak boson is coupled directly to three gluons. The phenomenological perspectives of the model in W-W+→Z Z scattering are studied and it is shown that there is a characteristic oscillatory behavior in azimuthal distribution of scattering cross sections that can be interpreted as a direct signal of the noncommutative standard model. Assuming the integrated luminosity 100 fb-1, the number of W-W+→Z Z subprocesses are estimated for some values of noncommutative scale ΛNC at different center of mass energies and the results are compared with predictions of the standard model.

  7. The coquaternion algebra and complex partial differential equations

    NASA Astrophysics Data System (ADS)

    Dimiev, Stancho; Konstantinov, Mihail; Todorov, Vladimir

    2009-11-01

    In this paper we consider the problem of differentiation of coquaternionic functions. Let us recall that coquaternions are elements of an associative non-commutative real algebra with zero divisor, introduced by James Cockle (1849) under the name of split-quaternions or coquaternions. Developing two type complex representations for Cockle algebra (complex and paracomplex ones) we present the problem in a non-commutative form of the δ¯-type holomorphy. We prove that corresponding differentiable coquaternionic functions, smooth and analytic, satisfy PDE of complex, and respectively of real variables. Applications for coquaternionic polynomials are sketched.

  8. Selective Structural Transformation of Supramolecules to Multinuclear Heterosubstituted Pt Complexes via Ligand Exchange.

    PubMed

    Molev, Gregory; Arif, Atta; Stang, Peter J

    2011-11-16

    Selective triflate to chlorine ligand exchange reaction between ditriflate and dichloride Pt complexes producing pure heterosubstituted complexes is demonstrated. We show that this reaction can be applied for selective chlorination of supramolecules leading to their structural transformation into multinuclear mono-chlorinated Pt(II) complexes. The X-ray structure of complex of 4,4'-bipyridine with two molecules of (Et(3)P)(2)Pt(Cl)OTf is reported.

  9. On the Chern-Gauss-Bonnet theorem for the noncommutative 4-sphere

    NASA Astrophysics Data System (ADS)

    Arnlind, Joakim; Wilson, Mitsuru

    2017-01-01

    We construct a differential calculus over the noncommutative 4-sphere in the framework of pseudo-Riemannian calculi, and show that for every metric in a conformal class of perturbations of the round metric, there exists a unique metric and torsion-free connection. Furthermore, we find a localization of the projective module corresponding to the space of vector fields, which allows us to formulate a Chern-Gauss-Bonnet type theorem for the noncommutative 4-sphere.

  10. Regularization of two-dimensional supersymmetric Yang-Mills theory via non-commutative geometry

    NASA Astrophysics Data System (ADS)

    Valavane, K.

    2000-11-01

    The non-commutative geometry is a possible framework to regularize quantum field theory in a non-perturbative way. This idea is an extension of the lattice approximation by non-commutativity that allows us to preserve symmetries. The supersymmetric version is also studied and more precisely in the case of the Schwinger model on a supersphere. This paper is a generalization of this latter work to more general gauge groups.

  11. Quantization maps, algebra representation, and non-commutative Fourier transform for Lie groups

    SciTech Connect

    Guedes, Carlos; Oriti, Daniele; Raasakka, Matti

    2013-08-15

    The phase space given by the cotangent bundle of a Lie group appears in the context of several models for physical systems. A representation for the quantum system in terms of non-commutative functions on the (dual) Lie algebra, and a generalized notion of (non-commutative) Fourier transform, different from standard harmonic analysis, has been recently developed, and found several applications, especially in the quantum gravity literature. We show that this algebra representation can be defined on the sole basis of a quantization map of the classical Poisson algebra, and identify the conditions for its existence. In particular, the corresponding non-commutative star-product carried by this representation is obtained directly from the quantization map via deformation quantization. We then clarify under which conditions a unitary intertwiner between such algebra representation and the usual group representation can be constructed giving rise to the non-commutative plane waves and consequently, the non-commutative Fourier transform. The compact groups U(1) and SU(2) are considered for different choices of quantization maps, such as the symmetric and the Duflo map, and we exhibit the corresponding star-products, algebra representations, and non-commutative plane waves.

  12. Structural Insight into Anaphase Promoting Complex 3 Structure and Docking with a Natural Inhibitory Compound

    PubMed Central

    Rahimi, Hamzeh; Shokrgozar, Mohammad Ali; Madadkar-Sobhani, Armin; Mahdian, Reza; Foroumadi, Alireza; Karimipoor, Morteza

    2017-01-01

    Background: Anaphase promoting complex (APC) is the biggest Cullin-RING E3 ligase and is very important in cell cycle control; many anti-cancer agents target this. APC controls the onset of chromosome separation and mitotic exit through securin and cyclin B degradation, respectively. Its APC3 subunit identifies the APC activators-Cdh1 and Cdc20. Materials and Methods: The structural model of the APC3 subunit of APC was developed by means of computational techniques; the binding of a natural inhibitory compound to APC3 was also investigated. Results: It was found that APC3 structure consists of numerous helices organized in anti-parallel and the overall model is superhelical of tetratrico-peptide repeat (TPR) domains. Furthermore, binding pocket of the natural inhibitory compound as APC3 inhibitor was shown. Conclusion: The findings are beneficial to understand the mechanism of the APC activation and design inhibitory compounds.

  13. Structural determinants for the formation of sulfhemeprotein complexes

    PubMed Central

    Román-Morales, Elddie; Pietri, Ruth; Ramos-Santana, Brenda; Vinogradov, Serge N.; Lewis-Ballester, Ariel; López-Garriga, Juan

    2010-01-01

    Several hemoglobins were explored by UV-Vis and resonance Raman spectroscopy to define sulfheme complex formation. Evaluation of these proteins upon the reaction with H2O2 or O2 in the presence of H2S suggest: (a) the formation of the sulfheme derivate requires a HisE7 residue in the heme distal site with an adequate orientation to form an active ternary complex; (b) that the ternary complex intermediate involves the HisE7, the peroxo or ferryl species, and the H2S molecule. This moiety precedes and triggers the sulfheme formation. PMID:20732304

  14. The Pyruvate Dehydrogenase Complexes: Structure-based Function and Regulation*

    PubMed Central

    Patel, Mulchand S.; Nemeria, Natalia S.; Furey, William; Jordan, Frank

    2014-01-01

    The pyruvate dehydrogenase complexes (PDCs) from all known living organisms comprise three principal catalytic components for their mission: E1 and E2 generate acetyl-coenzyme A, whereas the FAD/NAD+-dependent E3 performs redox recycling. Here we compare bacterial (Escherichia coli) and human PDCs, as they represent the two major classes of the superfamily of 2-oxo acid dehydrogenase complexes with different assembly of, and interactions among components. The human PDC is subject to inactivation at E1 by serine phosphorylation by four kinases, an inactivation reversed by the action of two phosphatases. Progress in our understanding of these complexes important in metabolism is reviewed. PMID:24798336

  15. A unified perspective of complex band structure: interpretations, formulations, and applications

    NASA Astrophysics Data System (ADS)

    Reuter, Matthew G.

    2017-02-01

    Complex band structure generalizes conventional band structure by also considering wavevectors with complex components. In this way, complex band structure describes both the bulk-propagating states from conventional band structure and the evanescent states that grow or decay from one unit cell to the next. Even though these latter states are excluded by translational symmetry, they become important when translational symmetry is broken via, for example, a surface or impurity. Many studies over the last 80 years have directly or indirectly developed complex band structure for an impressive range of applications, but very few discuss its fundamentals or compare its various results. In this work we build upon these previous efforts to expose the physical foundation of complex band structure, which mathematically implies its existence. We find that a material’s static and dynamic electronic structure are both completely described by complex band structure. Furthermore, we show that complex band structure reflects the minimal, intrinsic information contained in the material’s Hamiltonian. These realizations then provide a context for comparing and unifying the different formulations and applications of complex band structure that have been reported over the years. Ultimately, this discussion introduces the idea of examining the amount of information contained in a material’s Hamiltonian so that we can find and exploit the minimal information necessary for understanding a material’s properties.

  16. A unified perspective of complex band structure: interpretations, formulations, and applications.

    PubMed

    Reuter, Matthew G

    2017-02-08

    Complex band structure generalizes conventional band structure by also considering wavevectors with complex components. In this way, complex band structure describes both the bulk-propagating states from conventional band structure and the evanescent states that grow or decay from one unit cell to the next. Even though these latter states are excluded by translational symmetry, they become important when translational symmetry is broken via, for example, a surface or impurity. Many studies over the last 80 years have directly or indirectly developed complex band structure for an impressive range of applications, but very few discuss its fundamentals or compare its various results. In this work we build upon these previous efforts to expose the physical foundation of complex band structure, which mathematically implies its existence. We find that a material's static and dynamic electronic structure are both completely described by complex band structure. Furthermore, we show that complex band structure reflects the minimal, intrinsic information contained in the material's Hamiltonian. These realizations then provide a context for comparing and unifying the different formulations and applications of complex band structure that have been reported over the years. Ultimately, this discussion introduces the idea of examining the amount of information contained in a material's Hamiltonian so that we can find and exploit the minimal information necessary for understanding a material's properties.

  17. Structural investigation of amylose complexes with small ligands: helical conformation, crystalline structure and thermostability.

    PubMed

    Le Bail, P; Rondeau, C; Buléon, A

    2005-03-01

    Crystalline amylose complexes were prepared with decanal, 1-butanol, menthone and alpha-naphtol. Their crystalline structure and the related helical conformation, determined by wide angle X-ray diffraction (WAXD) and 13C CPMAS solid state NMR, were assigned to V6I, V6II, V6III and V8 types, respectively. It was possible to propose some hypotheses on the possible nature of interactions and especially intra-/inter-helical inclusion. Some shifts in the NMR C1 carbon signals were attributed to the presence of ligand in specific sites inside the structure for a same type of V6 helical conformation. Moreover, the crystallinity and polymorphic changes induced by desorption/rehydration were studied. A general increase of the carbon resonances sharpness upon rehydration has been observed, but also a V6II-V6I transition when decreasing the water content. Differential scanning calorimetry (DSC) experiments were also performed to approach the thermostability of the four types of complex and also the way they form again after melting/cooling sequences.

  18. Interpolymer complexation: comparisons of bulk and interfacial structures.

    PubMed

    Cattoz, Beatrice; de Vos, Wiebe M; Cosgrove, Terence; Crossman, Martin; Espidel, Youssef; Prescott, Stuart W

    2015-04-14

    The interactions between the strong polyelectrolyte sodium poly(styrenesulfonate), NaPSS, and the neutral polymer poly(vinylpyrrolidone), PVP, were investigated in bulk and at the silica/solution interface using a combination of diffusion nuclear magnetic resonance spectroscopy (NMR), small-angle neutron scattering (SANS), solvent relaxation NMR, and ellipsometry. We show for the first time that complex formation occurs between NaPSS and PVP in solution; the complexes formed were shown not to be influenced by pH variation, whereas increasing the ionic strength increases the complexation of NaPSS but does not influence the PVP directly. The complexes formed contained a large proportion of NaPSS. Study of these interactions at the silica interface demonstrated that complexes also form at the nanoparticle interface where PVP is added in the system prior to NaPSS. For a constant PVP concentration and varying NaPSS concentration, the system remains stable until NaPSS is added in excess, which leads to depletion flocculation. Surface complex formation using the layer-by-layer technique was also reported at a planar silica interface.

  19. Phylogeography of the neotropical Anopheles triannulatus complex (Diptera: Culicidae) supports deep structure and complex patterns

    PubMed Central

    2013-01-01

    Background The molecular phylogenetic relationships and population structure of the species of the Anopheles triannulatus complex: Anopheles triannulatus s.s., Anopheles halophylus and the putative species Anopheles triannulatus C were investigated. Methods The mitochondrial COI gene, the nuclear white gene and rDNA ITS2 of samples that include the known geographic distribution of these taxa were analyzed. Phylogenetic analyses were performed using Bayesian inference, Maximum parsimony and Maximum likelihood approaches. Results Each data set analyzed septely yielded a different topology but none provided evidence for the seption of An. halophylus and An. triannulatus C, consistent with the hypothesis that the two are undergoing incipient speciation. The phylogenetic analyses of the white gene found three main clades, whereas the statistical parsimony network detected only a single metapopulation of Anopheles triannulatus s.l. Seven COI lineages were detected by phylogenetic and network analysis. In contrast, the network, but not the phylogenetic analyses, strongly supported three ITS2 groups. Combined data analyses provided the best resolution of the trees, with two major clades, Amazonian (clade I) and trans-Andean + Amazon Delta (clade II). Clade I consists of multiple subclades: An. halophylus + An. triannulatus C; trans-Andean Venezuela; central Amazonia + central Bolivia; Atlantic coastal lowland; and Amazon delta. Clade II includes three subclades: Panama; cis-Andean Colombia; and cis-Venezuela. The Amazon delta specimens are in both clades, likely indicating local sympatry. Spatial and molecular variance analyses detected nine groups, corroborating some of subclades obtained in the combined data analysis. Conclusion Combination of the three molecular markers provided the best resolution for differentiation within An. triannulatus s.s. and An. halophylus and C. The latest two species seem to be very closely related and the analyses performed were

  20. Complexing ability of (-)-cytisine--synthesis, spectroscopy and crystal structures of the new copper and zinc complexes.

    PubMed

    Przybył, Anna K; Kubicki, Maciej; Jastrzab, Renata

    2014-09-01

    For the first time the NMR spectra of quinolizidine alkaloid with Cu(II) are studied. Structures of new complexes of (-)-cytisine with Cu(+2) and Zn(+2) cations are visualized, discussed in detail and characterized by spectroscopic methods: ESI-MS, NMR, UV-vis, EPR and crystallographic methods. In solution metal coordinates through the protonated nitrogen atoms of secondary amino groups (in piperidine ring) of cytisine molecule. While in solid state the most stable structures of the complexes are those in which the coordination of Cu(II) and Zn(II) salts is realized solely through the lactam carbonyl oxygen atom.

  1. Integrability of classical strings dual for noncommutative gauge theories

    NASA Astrophysics Data System (ADS)

    Matsumoto, Takuya; Yoshida, Kentaroh

    2014-06-01

    We derive the gravity duals of noncommutative gauge theories from the Yang-Baxter sigma model description of the AdS5 × S5 superstring with classical r-matrices. The corresponding classical r-matrices are 1) solutions of the classical Yang-Baxter equation (CYBE), 2) skew-symmetric, 3) nilpotent and 4) abelian. Hence these should be called abelian Jordanian deformations. As a result, the gravity duals are shown to be integrable deformations of AdS5 × S5. Then, abelian twists of AdS5 are also investigated. These results provide a support for the gravity/CYBE correspondence proposed in arXiv:1404.1838.

  2. Euler polynomials and identities for non-commutative operators

    NASA Astrophysics Data System (ADS)

    De Angelis, Valerio; Vignat, Christophe

    2015-12-01

    Three kinds of identities involving non-commutating operators and Euler and Bernoulli polynomials are studied. The first identity, as given by Bender and Bettencourt [Phys. Rev. D 54(12), 7710-7723 (1996)], expresses the nested commutator of the Hamiltonian and momentum operators as the commutator of the momentum and the shifted Euler polynomial of the Hamiltonian. The second one, by Pain [J. Phys. A: Math. Theor. 46, 035304 (2013)], links the commutators and anti-commutators of the monomials of the position and momentum operators. The third appears in a work by Figuieira de Morisson and Fring [J. Phys. A: Math. Gen. 39, 9269 (2006)] in the context of non-Hermitian Hamiltonian systems. In each case, we provide several proofs and extensions of these identities that highlight the role of Euler and Bernoulli polynomials.

  3. The noncommutative family Atiyah-Patodi-Singer index theorem

    NASA Astrophysics Data System (ADS)

    Wang, Yong

    2016-12-01

    In this paper, we define the eta cochain form and prove its regularity when the kernel of a family of Dirac operators is a vector bundle. We decompose the eta form as a pairing of the eta cochain form with the Chern character of an idempotent matrix and we also decompose the Chern character of the index bundle for a fibration with boundary as a pairing of the family Chern-Connes character for a manifold with boundary with the Chern character of an idempotent matrix. We define the family b-Chern-Connes character and then we prove that it is entire and give its variation formula. By this variation formula, we prove another noncommutative family Atiyah-Patodi-Singer index theorem. Thus, we extend the results of Getzler and Wu to the family case.

  4. Spacetime-noncommutativity regime of loop quantum gravity

    NASA Astrophysics Data System (ADS)

    Amelino-Camelia, Giovanni; Da Silva, Malú Maira; Ronco, Michele; Cesarini, Lorenzo; Lecian, Orchidea Maria

    2017-01-01

    A recent study by Bojowald and Paily [M. Bojowald and G. M. Paily, Phys. Rev. D 87, 044044 (2013)., 10.1103/PhysRevD.87.044044] provided a path toward the identification of an effective quantum-spacetime picture of loop quantum gravity, applicable in the "Minkowski regime," the regime where the large-scale (coarse-grained) spacetime metric is flat. A pivotal role in the analysis is played by loop-quantum-gravity-based modifications to the hypersurface deformation algebra, which leave a trace in the Minkowski regime. We here show that the symmetry-algebra results reported by Bojowald and Paily are consistent with a description of spacetime in the Minkowski regime given in terms of the κ -Minkowski noncommutative spacetime, whose relevance for the study of the quantum-gravity problem had already been proposed for independent reasons.

  5. Relativistic differential-difference momentum operators and noncommutative differential calculus

    SciTech Connect

    Mir-Kasimov, R. M.

    2013-09-15

    The relativistic kinetic momentum operators are introduced in the framework of the Quantum Mechanics (QM) in the Relativistic Configuration Space (RCS). These operators correspond to the half of the non-Euclidean distance in the Lobachevsky momentum space. In terms of kinetic momentum operators the relativistic kinetic energy is separated as the independent term of the total Hamiltonian. This relativistic kinetic energy term is not distinguishing in form from its nonrelativistic counterpart. The role of the plane wave (wave function of the motion with definite value of momentum and energy) plays the generating function for the matrix elements of the unitary irreps of Lorentz group (generalized Jacobi polynomials). The kinetic momentum operators are the interior derivatives in the framework of the noncommutative differential calculus over the commutative algebra generated by the coordinate functions over the RCS.

  6. Separation of noncommutative differential calculus on quantum Minkowski space

    SciTech Connect

    Bachmaier, Fabian; Blohmann, Christian

    2006-02-15

    Noncommutative differential calculus on quantum Minkowski space is not separated with respect to the standard generators, in the sense that partial derivatives of functions of a single generator can depend on all other generators. It is shown that this problem can be overcome by a separation of variables. We study the action of the universal L-matrix, appearing in the coproduct of partial derivatives, on generators. Powers of the resulting quantum Minkowski algebra valued matrices are calculated. This leads to a nonlinear coordinate transformation which essentially separates the calculus. A compact formula for general derivatives is obtained in form of a chain rule with partial Jackson derivatives. It is applied to the massive quantum Klein-Gordon equation by reducing it to an ordinary q-difference equation. The rest state solution can be expressed in terms of a product of q-exponential functions in the separated variables.

  7. Measurement of noncommuting spin components using spin-orbit interaction

    SciTech Connect

    Sokolovski, D.; Sherman, E. Ya.

    2011-09-15

    We propose a possible experiment aimed at a joint measurement of two noncommuting spin-1/2 components and analyze its physical meaning. We demonstrate that switching of a strong spin-orbit interaction, e.g., in a solid-state or a cold-atom system, for a short time interval simulates a simultaneous von Neumann measurement of the operators {sigma}{sub x} and {sigma}{sub y}. With the spin dynamics mapped onto the quantum coordinate-space motion, such an experiment determines averages of {sigma}{sub x} and {sigma}{sub y} over the duration of the measurement, however short the latter may be. These time averages, unlike the instantaneous values of {sigma}{sub x} and {sigma}{sub y}, may be evaluated simultaneously to an arbitrary accuracy.

  8. Constraining the Noncommutative Spectral Action via Astrophysical Observations

    SciTech Connect

    Nelson, William; Ochoa, Joseph; Sakellariadou, Mairi

    2010-09-03

    The noncommutative spectral action extends our familiar notion of commutative spaces, using the data encoded in a spectral triple on an almost commutative space. Varying a rather simple action, one can derive all of the standard model of particle physics in this setting, in addition to a modified version of Einstein-Hilbert gravity. In this Letter we use observations of pulsar timings, assuming that no deviation from general relativity has been observed, to constrain the gravitational sector of this theory. While the bounds on the coupling constants remain rather weak, they are comparable to existing bounds on deviations from general relativity in other settings and are likely to be further constrained by future observations.

  9. Gravitational waves in the spectral action of noncommutative geometry

    SciTech Connect

    Nelson, William; Ochoa, Joseph; Sakellariadou, Mairi

    2010-10-15

    The spectral triple approach to noncommutative geometry allows one to develop the entire standard model (and supersymmetric extensions) of particle physics from a purely geometry standpoint and thus treats both gravity and particle physics on the same footing. The bosonic sector of the theory contains a modification to Einstein-Hilbert gravity, involving a nonconformal coupling of curvature to the Higgs field and conformal Weyl term (in addition to a nondynamical topological term). In this paper we derive the weak-field limit of this gravitational theory and show that the production and dynamics of gravitational waves are significantly altered. In particular, we show that the graviton contains a massive mode that alters the energy lost to gravitational radiation, in systems with evolving quadrupole moment. We explicitly calculate the general solution and apply it to systems with periodically varying quadrupole moments, focusing, in particular, on the well-known energy loss formula for circular binaries.

  10. Noncommutativity and Non-Anticommutativity Perturbative Quantum Gravity

    NASA Astrophysics Data System (ADS)

    Faizal, Mir

    2012-05-01

    In this paper, we will study perturbative quantum gravity on supermanifolds with both noncommutativity and non-anticommutativity of spacetime coordinates. We shall first analyze the BRST and the anti-BRST symmetries of this theory. Then we will also analyze the effect of shifting all the fields of this theory in background field method. We will construct a Lagrangian density which apart from being invariant under the extended BRST transformations is also invariant under on-shell extended anti-BRST transformations. This will be done by using the Batalin-Vilkovisky (BV) formalism. Finally, we will show that the sum of the gauge-fixing term and the ghost term for this theory can be elegantly written down in superspace with a two Grassmann parameter.

  11. Noncommutative-geometry model for closed bosonic strings

    NASA Technical Reports Server (NTRS)

    Sen, Siddhartha; Holman, R.

    1987-01-01

    It is shown how Witten's (1986) noncommutative geometry may be extended to describe the closed bosonic string. For closed strings, an explicit representation is provided of the integral operator needed to construct an action and of an associative product on string fields. The proper choice of the action of the integral operator and the associative product in order to give rise to a reasonable theory is explained, and the consequences of such a choice are discussed. It is shown that the ghost numbers of the operator and associative product can be chosen arbitrarily for both open and closed strings, and that this construct can be used as an action for interacting closed bosonic strings.

  12. Complex fluid-fluid interfaces: rheology and structure.

    PubMed

    Fuller, Gerald G; Vermant, Jan

    2012-01-01

    Complex fluid-fluid interfaces are common to living systems, foods, personal products, and the environment. They occur wherever surface-active molecules and particles collect at fluid interfaces and render them nonlinear in their response to flow and deformation. When this occurs, the interfaces acquire a complex microstructure that must be interrogated. Interfacial rheological material properties must be measured to appreciate their role in such varied processes as lung function, cell division, and foam and emulsion stability. This review presents the methods that have been devised to determine the microstructure of complex fluid-fluid interfaces. Complex interfacial microstructure leads to rheological complexity. This behavior is often responsible for stabilizing interfacial systems such as foams and emulsions, and it can also have a profound influence on wetting/dewetting dynamics. Interfacial rheological characterization relies on the development of tools with the sensitivity to respond to small surface stresses in a way that isolates them from bulk stresses. This development is relatively recent, and reviews of methods for both shear and dilatational measurements are offered here.

  13. Generalized network structures: The configuration model and the canonical ensemble of simplicial complexes

    NASA Astrophysics Data System (ADS)

    Courtney, Owen T.; Bianconi, Ginestra

    2016-06-01

    Simplicial complexes are generalized network structures able to encode interactions occurring between more than two nodes. Simplicial complexes describe a large variety of complex interacting systems ranging from brain networks to social and collaboration networks. Here we characterize the structure of simplicial complexes using their generalized degrees that capture fundamental properties of one, two, three, or more linked nodes. Moreover, we introduce the configuration model and the canonical ensemble of simplicial complexes, enforcing, respectively, the sequence of generalized degrees of the nodes and the sequence of the expected generalized degrees of the nodes. We evaluate the entropy of these ensembles, finding the asymptotic expression for the number of simplicial complexes in the configuration model. We provide the algorithms for the construction of simplicial complexes belonging to the configuration model and the canonical ensemble of simplicial complexes. We give an expression for the structural cutoff of simplicial complexes that for simplicial complexes of dimension d =1 reduces to the structural cutoff of simple networks. Finally, we provide a numerical analysis of the natural correlations emerging in the configuration model of simplicial complexes without structural cutoff.

  14. The structural linguistic complexity of lawyers' questions and children's responses in Scottish criminal courts.

    PubMed

    Andrews, Samantha J; Lamb, Michael E

    2017-02-08

    In the first study to systematically assess the structural linguistic complexity of lawyers' questions of children in Scotland, we examined 56 trial transcripts of 5- to 17-year-old children testifying as alleged victims of sexual abuse. Complexity was assessed using 8 quantitative measures of each utterance's components (number of questions, phrases, clauses, sentences, false starts, average word count, word length, and sentence length) and a composite measure was used in the analyses. Lawyers did not alter the complexity of questions when prompting children of different ages. Defense lawyers asked more structurally complex questions than prosecutors. Directive questions were the least structurally complex questions, followed by option-posing questions. Suggestive questions, followed by invitations, were the most structurally complex questions. Option-posing and suggestive questions were more complex when asked by defense lawyers than prosecutors. Of suggestive questions, confrontation and tagged questions were more complex than any other question type. Increased structural complexity led to more unresponsiveness, more expressions of uncertainty, and more self-contradictions regardless of which lawyer asked, the question type, or the children's ages. These findings highlight the additional risks associated with asking some types of questions in structurally complex ways and highlight the need for further innovations (e.g., the use of intermediaries) to facilitate the questioning of vulnerable witnesses in Scottish criminal courts.

  15. Epidemic spreading on complex networks with community structures

    PubMed Central

    Stegehuis, Clara; van der Hofstad, Remco; van Leeuwaarden, Johan S. H.

    2016-01-01

    Many real-world networks display a community structure. We study two random graph models that create a network with similar community structure as a given network. One model preserves the exact community structure of the original network, while the other model only preserves the set of communities and the vertex degrees. These models show that community structure is an important determinant of the behavior of percolation processes on networks, such as information diffusion or virus spreading: the community structure can both enforce as well as inhibit diffusion processes. Our models further show that it is the mesoscopic set of communities that matters. The exact internal structures of communities barely influence the behavior of percolation processes across networks. This insensitivity is likely due to the relative denseness of the communities. PMID:27440176

  16. Inherent structure length in metallic glasses: simplicity behind complexity

    PubMed Central

    Wu, Yuan; Wang, Hui; Cheng, Yongqiang; Liu, Xiongjun; Hui, Xidong; Nieh, Taigang; Wang, Yandong; Lu, Zhaoping

    2015-01-01

    One of the central themes in materials science is the structure-property relationship. In conventional crystalline metals, their mechanical behaviour is often dictated by well-defined structural defects such as dislocations, impurities, and twins. However, the structure-property relationship in amorphous alloys is far from being understood, due to great difficulties in characterizing and describing the disordered atomic-level structure. Herein, we report a universal, yet simple, correlation between the macroscopic mechanical properties (i.e., yield strength and shear modulus) and a unique characteristic structural length in metallic glasses (MGs). Our analysis indicates that this characteristic length can incorporate effects of both the inter-atomic distance and valence electron density in MGs, and result in the observed universal correlation. The current findings shed lights on the basic understanding of mechanical properties of MGs from their disordered atomic structures. PMID:26245801

  17. Inherent structure length in metallic glasses: Simplicity behind complexity

    DOE PAGES

    Wu, Yuan; Wang, Hui; Cheng, Yongqiang; ...

    2015-08-06

    One of the central themes in materials science is the structure-property relationship. In conventional crystalline metals, their mechanical behaviour is often dictated by well-defined structural defects such as dislocations, impurities, and twins. However, the structure-property relationship in amorphous alloys is far from being understood, due to great difficulties in characterizing and describing the disordered atomic-level structure. Here, we report a universal, yet simple, correlation between the macroscopic mechanical properties (i.e., yield strength and shear modulus) and a unique characteristic structural length in metallic glasses (MGs). Lastly, our analysis indicates that this characteristic length can incorporate effects of both the inter-atomicmore » distance and valence electron density in MGs, and result in the observed universal correlation. The current findings shed lights on the basic understanding of mechanical properties of MGs from their disordered atomic structures.« less

  18. Inherent structure length in metallic glasses: Simplicity behind complexity

    SciTech Connect

    Wu, Yuan; Wang, Hui; Cheng, Yongqiang; Liu, Xiongjun; Hui, Xidong; Nieh, Taigang; Wang, Yandong; Lu, Zhaoping

    2015-08-06

    One of the central themes in materials science is the structure-property relationship. In conventional crystalline metals, their mechanical behaviour is often dictated by well-defined structural defects such as dislocations, impurities, and twins. However, the structure-property relationship in amorphous alloys is far from being understood, due to great difficulties in characterizing and describing the disordered atomic-level structure. Here, we report a universal, yet simple, correlation between the macroscopic mechanical properties (i.e., yield strength and shear modulus) and a unique characteristic structural length in metallic glasses (MGs). Lastly, our analysis indicates that this characteristic length can incorporate effects of both the inter-atomic distance and valence electron density in MGs, and result in the observed universal correlation. The current findings shed lights on the basic understanding of mechanical properties of MGs from their disordered atomic structures.

  19. Structure of commelinin, a blue complex pigment from the blue flowers of Commelina communis

    PubMed Central

    Shiono, Masaaki; Matsugaki, Naohiro; Takeda, Kosaku

    2008-01-01

    The X-ray crystal structure of natural commelinin is investigated. The results demonstrate that commelinin is a tetranuclear (4 Mg2+) metal complex, in which two Mg2+ ions chelate to six anthocyanin molecules, while the other two Mg2+ ions bind to six flavone molecules, stabilizing the commelinin complex, a new type of supramolecular complex. PMID:19075517

  20. The subcortical maternal complex: multiple functions for one biological structure?

    PubMed

    Bebbere, D; Masala, L; Albertini, D F; Ledda, S

    2016-11-01

    The subcortical maternal complex (SCMC) is a multiprotein complex uniquely expressed in mammalian oocytes and early embryos, essential for zygote progression beyond the first embryonic cell divisions. Similiar to other factors encoded by maternal effect genes, the physiological role of SCMC remains unclear, although recent evidence has provided important molecular insights into different possible functions. Its potential involvement in human fertility is attracting increasing attention; however, the complete story is far from being told. The present mini review provides an overview of recent findings related to the SCMC and discusses its potential physiological role/s with the aim of inspiring new directions for future research.

  1. Social scale and structural complexity in human languages.

    PubMed

    Nettle, Daniel

    2012-07-05

    The complexity of different components of the grammars of human languages can be quantified. For example, languages vary greatly in the size of their phonological inventories, and in the degree to which they make use of inflectional morphology. Recent studies have shown that there are relationships between these types of grammatical complexity and the number of speakers a language has. Languages spoken by large populations have been found to have larger phonological inventories, but simpler morphology, than languages spoken by small populations. The results require further investigation, and, most importantly, the mechanism whereby the social context of learning and use affects the grammatical evolution of a language needs elucidation.

  2. 75 FR 77047 - Statement on Sound Practices Concerning Elevated Risk Complex Structured Finance Activities

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-10

    ... Office of Thrift Supervision Statement on Sound Practices Concerning Elevated Risk Complex Structured.... Title of Proposal: Statement on Sound Practices Concerning Elevated Risk Complex Structured Finance Activities. OMB Number: 1550-0111. Form Number: N/A. Description: Statement on Sound Practices...

  3. Atomic Structure of the Y-Complex of the Nuclear Pore

    PubMed Central

    Kabachinski, Greg; Schwartz, Thomas U.

    2015-01-01

    The nuclear pore complex (NPC) is the principal gateway for transport into and out of the nucleus. Selectivity is achieved through the hydrogel-like core of the NPC. The structural integrity of the NPC depends on ~15 architectural proteins, which are organized in distinct subcomplexes to form the >40 MDa ring-like structure. Here we present the 4.1 Å crystal structure of a heterotetrameric core element (‘hub’) of the Y-complex, the essential NPC building block, from Myceliophthora thermophila. Using the ‘hub’ structure together with known Y-complex fragments we built the entire ~0.5 MDa Y-complex. Our data reveal that the conserved core of the Y-complex has 6, rather than 7 members. Evolutionarily distant Y-complex assemblies share a conserved core that is very similar in shape and dimension, suggesting that there are closely related architectural codes for constructing the NPC in all eukaryotes. PMID:25822992

  4. Finite temperature corrections and embedded strings in noncommutative geometry and the standard model with neutrino mixing

    SciTech Connect

    Martins, R. A.

    2007-08-15

    The recent extension of the standard model to include massive neutrinos in the framework of noncommutative geometry and the spectral action principle involves new scalar fields and their interactions with the usual complex scalar doublet. After ensuring that they bring no unphysical consequences, we address the question of how these fields affect the physics predicted in the Weinberg-Salam theory, particularly in the context of the electroweak phase transition. Applying the Dolan-Jackiw procedure, we calculate the finite temperature corrections, and find that the phase transition is first order. The new scalar interactions significantly improve the stability of the electroweak Z string, through the 'bag' phenomenon described by Vachaspati and Watkins ['Bound states can stabilize electroweak strings', Phys. Lett. B 318, 163-168 (1993)]. (Recently, cosmic strings have climbed back into interest due to a new evidence.) Sourced by static embedded strings, an internal space analogy of Cartan's torsion is drawn, and a possible Higgs-force-like 'gravitational' effect of this nonpropagating torsion on the fermion masses is described. We also check that the field generating the Majorana mass for the {nu}{sub R} is nonzero in the physical vacuum.

  5. Exploiting Explicit and Implicit Structure in Complex Optimization Problems

    DTIC Science & Technology

    2014-09-24

    for minimizing implicitly defined functions resulting from applying decomposition , relaxation and/or dualization techniques to complex real-world...Fariba Fahroo Reporting Period: 16 June 2011 to 15 June 2014 Accomplishments: Decomposition techniques are often the best choice for solving large...publications [11], [13], [14], [3] and [5]. The decomposition type of approach involves minimizing a nonsmooth objective function with special

  6. Improved wax mold technique forms complex passages in solid structures

    NASA Technical Reports Server (NTRS)

    Hellbaum, R. F.; Page, A. D.; Phillips, A. R.

    1971-01-01

    Low-cost fabricating technique produces minute, complex air passages in fluidic devices. Air jet interactions in these function as electronic and electromechanical control systems. Wax cores are fabricated without distortion by two-wax process using nonsoluble pattern-wax and water-soluble wax. Significant steps in fabrication process are discussed.

  7. Epidemic fronts in complex networks with metapopulation structure

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Infection dynamics have been studied extensively on complex networks, yielding insight into the effects of heterogeneity in contact patterns on disease spread. Somewhat separately, metapopulations have provided a paradigm for modeling systems with spatially extended and “patchy” organization. In thi...

  8. Using Plants to Explore the Nature & Structural Complexity of Life

    ERIC Educational Resources Information Center

    Howard, Ava R.

    2014-01-01

    Use of real specimens brings the study of biology to life. This activity brings easily acquired plant specimens into the classroom to tackle common alternative conceptions regarding life, size, complexity, the nature of science, and plants as multicellular organisms. The activity occurs after a discussion of the characteristics of life and engages…

  9. Fluctuation electron microscopy studies of complex structured materials

    NASA Astrophysics Data System (ADS)

    Zhao, Gongpu; Rougée, Annick; Buseck, Peter; Treacy, Michael

    2008-03-01

    Fluctuation electron microscopy (FEM) is a hybrid imaging-diffraction technique. This technique is particularly sensitive to paracrystalline structures of dimension 0.5-2 nm, which are difficult to detect by either imaging or diffraction techniques alone. It has been successfully deployed to study paracrystalline structures in amorphous silicon, germanium thin film. This technique has also been used to study metallic glasses and oxide glasses. Until now, FEM has not been used to study disordered geological materials. In this talk we present our FEM studies of shungite, a naturally occurring disordered carbonaceous material, reveal that trace quantities of tightly curved graphene structures such as C60, or fragments of C60, is present in shungite. We also present results from our study of metamict zircon, whose crystal structure is destroyed by self-radiation during naturally occurring α decay events. Work is in progress to study the structural evolution during the metamictization process.

  10. Electronic structure and driving forces in β-cyclodextrin: Diclofenac inclusion complexes

    NASA Astrophysics Data System (ADS)

    Bogdan, Diana; Morari, C.

    2007-07-01

    We investigate the geometry and electronic structure for complexes of β-cyclodextrin with diclofenac using DFT calculations. The effect of solvent is explicitly taken into account. This investigation allows us to draw meaningful conclusions upon the stability of the complex and the nature of the driving forces leading to the complexation process. In particular we emphasize the role of the water, by pointing out the changes in the solvent's electronic structure for different docking geometries.

  11. Structural load inventory database for the Kansas City federal complex

    SciTech Connect

    Hashimoto, P.S.; Johnson, M.W.; Nakaki, D.K.; Lynch, D.T.; Drury, M.A.

    1995-12-01

    A structural load inventory database (LID) has been developed to support configuration management at the DOE Kansas City Plant (KCP). The objective of the LID is to record loads supported by the plant structures and to provide rapid assessments of the impact of future facility modifications on structural adequacy. Development of the LID was initiated for the KCP`s Main Manufacturing Building. Field walkdowns were performed to determine all significant loads supported by the structure, including the weight of piping, service equipment, etc. These loads were compiled in the LID. Structural analyses for natural phenomena hazards were performed in accordance with UCRL-15910. Software to calculate demands on the structural members due to gravity loads, total demands including both gravity and seismic loads, and structural member demand-to-capacity ratios were also developed and integrated into the LID. Operation of the LID is menu-driven. The LID user has options to review and print existing loads and corresponding demand-to-capacity ratios, and to update the supported loads and demand-to-capacity ratios for any future facility modifications.

  12. Insight into the structure and stability of Tc and Re DMSA complexes: A computational study.

    PubMed

    Hernández-Valdés, Daniel; Blanco-González, Alejandro; García-Fleitas, Ariel; Rodríguez-Riera, Zalua; Meola, Giuseppe; Alberto, Roger; Jáuregui-Haza, Ulises

    2017-01-01

    Meso-2,3-dimercaptosuccinic acid (DMSA) is used in nuclear medicine as ligand for preparation of diagnostic and therapy radiopharmaceuticals. DMSA has been the subject of numerous investigations during the past three decades and new and significant information of the chemistry and pharmacology of DMSA complexes have emerged. In comparison to other ligands, the structure of some DMSA complexes is unclear up today. The structures and applications of DMSA complexes are strictly dependent on the chemical conditions of their preparation, especially pH and components ratio. A computational study of M-DMSA (M=Tc, Re) complexes has been performed using density functional theory. Different isomers for M(V) and M(III) complexes were studied. The pH influence over ligand structures was taken into account and the solvent effect was evaluated using an implicit solvation model. The fully optimized complex syn-endo Re((V))-DMSA shows a geometry similar to the X-ray data and was used to validate the methodology. Moreover, new alternative structures for the renal agent (99m)Tc((III))-DMSA were proposed and computationally studied. For two complex structures, a larger stability respect to that proposed in the literature was obtained. Furthermore, Tc((V))-DMSA complexes are more stable than Tc((III))-DMSA proposed structures. In general, Re complexes are more stable than the corresponding Tc ones.

  13. Time-dependent Aharonov-Bohm effect on the noncommutative space

    NASA Astrophysics Data System (ADS)

    Ma, Kai; Wang, Jian-Hua; Yang, Huan-Xiong

    2016-08-01

    We study the time-dependent Aharonov-Bohm effect on the noncommutative space. Because there is no net Aharonov-Bohm phase shift in the time-dependent case on the commutative space, therefore, a tiny deviation from zero indicates new physics. Based on the Seiberg-Witten map we obtain the gauge invariant and Lorentz covariant Aharonov-Bohm phase shift in general case on noncommutative space. We find there are two kinds of contribution: momentum-dependent and momentum-independent corrections. For the momentum-dependent correction, there is a cancellation between the magnetic and electric phase shifts, just like the case on the commutative space. However, there is a non-trivial contribution in the momentum-independent correction. This is true for both the time-independent and time-dependent Aharonov-Bohm effects on the noncommutative space. However, for the time-dependent Aharonov-Bohm effect, there is no overwhelming background which exists in the time-independent Aharonov-Bohm effect on both commutative and noncommutative space. Therefore, the time-dependent Aharonov-Bohm can be sensitive to the spatial noncommutativity. The net correction is proportional to the product of the magnetic fluxes through the fundamental area represented by the noncommutative parameter θ, and through the surface enclosed by the trajectory of charged particle. More interestingly, there is an anti-collinear relation between the logarithms of the magnetic field B and the averaged flux Φ / N (N is the number of fringes shifted). This nontrivial relation can also provide a way to test the spatial noncommutativity. For BΦ / N ∼ 1, our estimation on the experimental sensitivity shows that it can reach the 10 GeV scale. This sensitivity can be enhanced by using stronger magnetic field strength, larger magnetic flux, as well as higher experimental precision on the phase shift.

  14. Macroscopic analyses of communicability structures in complex networks

    NASA Astrophysics Data System (ADS)

    Min, Seungsik; Chang, Ki-Ho; Na, Sungjoon; Kim, Kyungsik

    2016-11-01

    We study the dynamical property of macroscopic community structures in two scientific societies. The type of data is extracted from author networks in both the Korean Meteorological Society and the Korean Physical Society. We discuss some notable methods for giving evolutionary information as the community structure is investigated using the model of oscillator networks. We simulate and analyze macroscopic community metrics such as the entropy, the natural connectivity, the free energy, the total energy, and the bipartivity in the community structures of the two scientific societies. We particularly compare and analyze the statistical values between the two scientific societies.

  15. Habitat complexity: coral structural loss leads to fisheries declines.

    PubMed

    Graham, Nicholas A J

    2014-05-05

    Direct human impacts and global climate change are altering the composition and structure of coral reef habitats. These changes are simplifying size-abundance relationships of reef fish communities, reducing productivity through the system and ultimately threatening fisheries yields.

  16. Study of the structure and dynamics of complex biological networks

    NASA Astrophysics Data System (ADS)

    Samal, Areejit

    2008-12-01

    In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large scale metabolic networks inside three organisms, Escherichia coli, Saccharomyces cerevisiae and Staphylococcus aureus. We also study the dynamics of the large scale genetic network controlling E. coli metabolism. We have tried to explain the observed system level dynamical properties of these networks in terms of their underlying structure. Our studies of the system level dynamics of these large scale biological networks provide a different perspective on their functioning compared to that obtained from purely structural studies. Our study also leads to some new insights on features such as robustness, fragility and modularity of these large scale biological networks. We also shed light on how different networks inside the cell such as metabolic networks and genetic networks are interrelated to each other.

  17. Bacteriorhodopsin/Amphipol Complexes: Structural and Functional Properties

    PubMed Central

    Gohon, Yann; Dahmane, Tassadite; Ruigrok, Rob W. H.; Schuck, Peter; Charvolin, Delphine; Rappaport, Fabrice; Timmins, Peter; Engelman, Donald M.; Tribet, Christophe; Popot, Jean-Luc; Ebel, Christine

    2008-01-01

    The membrane protein bacteriorhodopsin (BR) can be kept soluble in its native state for months in the absence of detergent by amphipol (APol) A8-35, an amphiphilic polymer. After an actinic flash, A8-35-complexed BR undergoes a complete photocycle, with kinetics intermediate between that in detergent solution and that in its native membrane. BR/APol complexes form well defined, globular particles comprising a monomer of BR, a complete set of purple membrane lipids, and, in a peripheral distribution, ∼2 g APol/g BR, arranged in a compact layer. In the absence of free APol, BR/APol particles can autoassociate into small or large ordered fibrils. PMID:18192360

  18. Structural limits for evolutive capacities in complex molecular systems.

    PubMed

    Bergareche, A M; Ostolaza, J F

    1990-01-01

    The possibilities of evolution for a system with and without a code of translation from nucleic acids into proteins are evaluated. Our interest is mainly centred on the enzymatic RNA case since this molecule has, at the same time, reproductive and functional properties. After scanning the evolutive capacities of the enzymatic RNAs, including the possibility to play the role of "synthetase" which would match nucleic acids with amino acids as a transition step towards a code, we will try to show that due to their own functional limitative factors, the matching system (code) is necessary. This would be the only way to transform the formal complexity--complexity which has not entered into action before the translation process--into functional information to drive the instructive self-reproductive process. Once this stage is reached, the system could evolve without a limit.

  19. Stage structure alters how complexity affects stability of ecological networks

    USGS Publications Warehouse

    Rudolf, V.H.W.; Lafferty, Kevin D.

    2011-01-01

    Resolving how complexity affects stability of natural communities is of key importance for predicting the consequences of biodiversity loss. Central to previous stability analysis has been the assumption that the resources of a consumer are substitutable. However, during their development, most species change diets; for instance, adults often use different resources than larvae or juveniles. Here, we show that such ontogenetic niche shifts are common in real ecological networks and that consideration of these shifts can alter which species are predicted to be at risk of extinction. Furthermore, niche shifts reduce and can even reverse the otherwise stabilizing effect of complexity. This pattern arises because species with several specialized life stages appear to be generalists at the species level but act as sequential specialists that are hypersensitive to resource loss. These results suggest that natural communities are more vulnerable to biodiversity loss than indicated by previous analyses.

  20. Structure and dynamics of small van der Waals complexes

    SciTech Connect

    Loreau, J.

    2014-10-06

    We illustrate computational aspects of the calculation of the potential energy surfaces of small (up to five atoms) van der Waals complexes with high-level quantum chemistry techniques such as the CCSD(T) method with extended basis sets. We discuss the compromise between the required accuracy and the computational time. Further, we show how these potential energy surfaces can be fitted and used in dynamical calculations such as non-reactive inelastic scattering.