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Sample records for noncommuting complex structures

  1. Noncommutative complex structures on quantum homogeneous spaces

    NASA Astrophysics Data System (ADS)

    Ó Buachalla, Réamonn

    2016-01-01

    A new framework for noncommutative complex geometry on quantum homogeneous spaces is introduced. The main ingredients used are covariant differential calculi and Takeuchi's categorical equivalence for quantum homogeneous spaces. A number of basic results are established, producing a simple set of necessary and sufficient conditions for noncommutative complex structures to exist. Throughout, the framework is applied to the quantum projective spaces endowed with the Heckenberger-Kolb calculus.

  2. Construction of the noncommutative complex ball

    SciTech Connect

    Wang, Zhituo

    2014-09-15

    We describe the construction of the noncommutative complex ball whose commutative analog is the Hermitian symmetric space D = SU(m, 1)/U(m), with the method of coherent state quantization. In the commutative limit, we obtain the standard manifold. We also consider a quantum field theory model on the noncommutative manifold.

  3. 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.

  4. 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

  5. Noncommutative Biology: Sequential Regulation of Complex Networks.

    PubMed

    Letsou, William; Cai, Long

    2016-08-01

    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

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

    NASA Astrophysics Data System (ADS)

    Varshovi, Amir Abbass

    2013-07-01

    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.

  7. The noncommutative S-Matrix

    NASA Astrophysics Data System (ADS)

    Raju, Suvrat

    2009-06-01

    As a simple example of how recently developed on-shell techniques apply to nonlocal theories, we study the S-matrix of noncommutative gauge theories. In the complex plane, this S-matrix has essential singularities that signal the nonlocal behavior of the theory. In spite of this, we show that tree-level amplitudes may be obtained by BCFW type recursion relations. At one loop we find a complete basis of master integrals (this basis is larger than the corresponding basis in the ordinary theory). Any one-loop noncommutative amplitude may be written as a linear combination of these integrals with coefficients that we relate to products of tree amplitudes. We show that the noncommutative Script N = 4 SYM theory has a structurally simple S-matrix, just like the ordinary Script N = 4 SYM theory.

  8. Noncommutative Gravity and Quantum Field Theory on Noncommutative Curved Spacetimes

    NASA Astrophysics Data System (ADS)

    Schenkel, Alexander

    2012-10-01

    The focus of this PhD thesis is on applications, new developments and extensions of the noncommutative gravity theory proposed by Julius Wess and his group. In part one we propose an extension of the usual symmetry reduction procedure to noncommutative gravity. We classify in the case of abelian Drinfel'd twists all consistent deformations of spatially flat Friedmann-Robertson-Walker cosmologies and of the Schwarzschild black hole. The deformed symmetry structure allows us to obtain exact solutions of the noncommutative Einstein equations in many of our models. In part two we develop a new formalism for quantum field theory on noncommutative curved spacetimes by combining methods from the algebraic approach to quantum field theory with noncommutative differential geometry. We also study explicit examples of deformed wave operators and find that there can be noncommutative corrections even on the level of free field theories. The convergent deformation of simple toy models is investigated and it is found that these theories have an improved behaviour at short distances, i.e. in the ultraviolet. In part three we study homomorphisms between and connections on noncommutative vector bundles. We prove that all homomorphisms and connections of the deformed theory can be obtained by applying a quantization isomorphism to undeformed homomorphisms and connections. The extension of homomorphisms and connections to tensor products of bimodules is clarified. As a nontrivial application of the new mathematical formalism we extend our studies of exact noncommutative gravity solutions to more general deformations.

  9. Noncommutative Point Sources

    SciTech Connect

    Stern, A.

    2008-02-15

    We construct a perturbative solution to classical noncommutative gauge theory on R{sup 3} minus the origin using the Groenewald-Moyal star product. The result describes a noncommutative point charge. Applying it to the quantum mechanics of the noncommutative hydrogen atom gives shifts in the 1S hyperfine splitting which are first order in the noncommutativity parameter.

  10. Noncommutativity and the Friedmann Equations

    NASA Astrophysics Data System (ADS)

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

    2010-07-01

    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.

  11. Noncommutative solitonic black hole

    NASA Astrophysics Data System (ADS)

    Chang-Young, Ee; Kimm, Kyoungtae; Lee, Daeho; Lee, Youngone

    2012-05-01

    We investigate solitonic black hole solutions in three-dimensional noncommutative spacetime. We do this in gravity with a negative cosmological constant coupled to a scalar field. Noncommutativity is realized with the Moyal product which is expanded up to first order in the noncommutativity parameter in two spatial directions. With numerical simulation we study the effect of noncommutativity by increasing the value of the noncommutativity parameter starting from commutative solutions. We find that even a regular soliton solution in the commutative case becomes a black hole solution when the noncommutativity parameter reaches a certain value.

  12. Noncommutative corrections to the Robertson-Walker metric

    SciTech Connect

    Fabi, S.; Harms, B.; Stern, A.

    2008-09-15

    Upon applying Chamseddine's noncommutative deformation of gravity, we obtain the leading order noncommutative corrections to the Robertson-Walker metric tensor. We get an isotropic inhomogeneous metric tensor for a certain choice of the noncommutativity parameters. Moreover, the singularity of the commutative metric at t=0 is replaced by a more involved space-time structure in the noncommutative theory. In a toy model we construct a scenario where there is no singularity at t=0 at leading order in the noncommutativity parameter. Although singularities may still be present for nonzero t, they need not be the source of all timelike geodesics and the result resembles a bouncing cosmology.

  13. 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).

  14. 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.

  15. Noncommutativity due to spin

    NASA Astrophysics Data System (ADS)

    Gomes, M.; Kupriyanov, V. G.; da Silva, A. J.

    2010-04-01

    Using the Berezin-Marinov pseudoclassical formulation of the spin particle we propose a classical model of spin noncommutativity. In the nonrelativistic case, the Poisson brackets between the coordinates are proportional to the spin angular momentum. The quantization of the model leads to the noncommutativity with mixed spatial and spin degrees of freedom. A modified Pauli equation, describing a spin half particle in an external electromagnetic field is obtained. We show that nonlocality caused by the spin noncommutativity depends on the spin of the particle; for spin zero, nonlocality does not appear, for spin half, ΔxΔy≥θ2/2, etc. In the relativistic case the noncommutative Dirac equation was derived. For that we introduce a new star product. The advantage of our model is that in spite of the presence of noncommutativity and nonlocality, it is Lorentz invariant. Also, in the quasiclassical approximation it gives noncommutativity with a nilpotent parameter.

  16. Noncommutative Anandan quantum phase

    NASA Astrophysics Data System (ADS)

    Passos, E.; Ribeiro, L. R.; Furtado, C.; Nascimento, J. R.

    2007-07-01

    In this work, we study the noncommutative nonrelativistic quantum dynamics of a neutral particle, which possesses permanent magnetic and electric dipole moments, in the presence of external electric and magnetic fields. We use the Foldy-Wouthuysen transformation of the Dirac spinor with a nonminimal coupling to obtain the nonrelativistic limit. In this limit, we study the noncommutative quantum dynamics and obtain the noncommutative Anandan geometric phase. We analyze the situation where the magnetic dipole moment of the particle is zero, and we obtain the noncommutative version of the He-McKellar-Wilkens effect. We demonstrate that this phase in the noncommutative case is a geometric dispersive phase. We also investigate this geometric phase by considering the noncommutativity in the phase space, and the Anandan phase is obtained.

  17. Noncommutative effects of spacetime on holographic superconductors

    NASA Astrophysics Data System (ADS)

    Ghorai, Debabrata; Gangopadhyay, Sunandan

    2016-07-01

    The Sturm-Liouville eigenvalue method is employed to analytically investigate the properties of holographic superconductors in higher dimensions in the framework of Born-Infeld electrodynamics incorporating the effects of noncommutative spacetime. In the background of pure Einstein gravity in noncommutative spacetime, we obtain the relation between the critical temperature and the charge density. We also obtain the value of the condensation operator and the critical exponent. Our findings suggest that the higher value of noncommutative parameter and Born-Infeld parameter make the condensate harder to form. We also observe that the noncommutative structure of spacetime makes the critical temperature depend on the mass of the black hole and higher value of black hole mass is favourable for the formation of the condensate.

  18. Covariant non-commutative space-time

    NASA Astrophysics Data System (ADS)

    Heckman, Jonathan J.; Verlinde, Herman

    2015-05-01

    We introduce a covariant non-commutative deformation of 3 + 1-dimensional conformal field theory. The deformation introduces a short-distance scale ℓp, and thus breaks scale invariance, but preserves all space-time isometries. The non-commutative algebra is defined on space-times with non-zero constant curvature, i.e. dS4 or AdS4. The construction makes essential use of the representation of CFT tensor operators as polynomials in an auxiliary polarization tensor. The polarization tensor takes active part in the non-commutative algebra, which for dS4 takes the form of so (5, 1), while for AdS4 it assembles into so (4, 2). The structure of the non-commutative correlation functions hints that the deformed theory contains gravitational interactions and a Regge-like trajectory of higher spin excitations.

  19. Noncommutative Singular Black Holes

    NASA Astrophysics Data System (ADS)

    Hamid Mehdipour, S.

    2010-11-01

    In this paper, applying the method of coordinate coherent states to describe a noncommutative model of Vaidya black holes leads to an exact (t — r) dependence of solution in terms of the noncommutative parameter σ. In this setup, there is no black hole remnant at long times.

  20. Homogeneous noncommutative quantum cosmology

    SciTech Connect

    Maceda, Marco; Macias, Alfredo; Pimentel, Luis O.

    2008-09-15

    Using the Groenewold-Moyal product, the noncommutative Bianchi IX model is constructed by imposing commutation relations on the minisuperspace variables ({omega},{beta}{sub +},{beta}{sub -}). A noncommutative 'wormhole' solution to the corresponding Wheeler-DeWitt equation is constructed and its behavior at fixed {omega} is analyzed.

  1. 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.

  2. 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.

  3. Noncommutative black holes

    NASA Astrophysics Data System (ADS)

    Bastos, C.; Bertolami, O.; Dias, N. C.; Prata, J. N.

    2010-04-01

    One considers phase-space noncommutativity in the context of a Kantowski-Sachs cosmological model to study the interior of a Schwarzschild black hole. It is shown that the potential function of the corresponding quantum cosmology problem has a local minimum. One deduces the thermodynamics and show that the Hawking temperature and entropy exhibit an explicit dependence on the momentum noncommutativity parameter, η. Furthermore, the t = r = 0 singularity is analysed in the noncommutative regime and it is shown that the wave function vanishes in this limit.

  4. Inflation on a non-commutative space-time

    NASA Astrophysics Data System (ADS)

    Calmet, Xavier; Fritz, Christopher

    2015-07-01

    We study inflation on a non-commutative space-time within the framework of enveloping algebra approach which allows for a consistent formulation of general relativity and of the standard model of particle physics. We show that within this framework, the effects of the non-commutativity of spacetime are very subtle. The dominant effect comes from contributions to the process of structure formation. We describe the bound relevant to this class of non-commutative theories and derive the tightest bound to date of the value of the non-commutative scale within this framework. Assuming that inflation took place, we get a model independent bound on the scale of space-time non-commutativity of the order of 19 TeV.

  5. Noncommutative Involutive Bases

    NASA Astrophysics Data System (ADS)

    Alun Evans, Gareth

    2006-02-01

    The theory of Groebner Bases originated in the work of Buchberger and is now considered to be one of the most important and useful areas of symbolic computation. A great deal of effort has been put into improving Buchberger's algorithm for computing a Groebner Basis, and indeed in finding alternative methods of computing Groebner Bases. Two of these methods include the Groebner Walk method and the computation of Involutive Bases. By the mid 1980's, Buchberger's work had been generalised for noncommutative polynomial rings by Bergman and Mora. This thesis provides the corresponding generalisation for Involutive Bases and (to a lesser extent) the Groebner Walk, with the main results being as follows. (1) Algorithms for several new noncommutative involutive divisions are given, including strong; weak; global and local divisions. (2) An algorithm for computing a noncommutative Involutive Basis is given. When used with one of the aforementioned involutive divisions, it is shown that this algorithm returns a noncommutative Groebner Basis on termination. (3) An algorithm for a noncommutative Groebner Walk is given, in the case of conversion between two harmonious monomial orderings. It is shown that this algorithm generalises to give an algorithm for performing a noncommutative Involutive Walk, again in the case of conversion between two harmonious monomial orderings. (4) Two new properties of commutative involutive divisions are introduced (stability and extendibility), respectively ensuring the termination of the Involutive Basis algorithm and the applicability (under certain conditions) of homogeneous methods of computing Involutive Bases.

  6. 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.

  7. Towards Noncommutative Supersymmetric Quantum Cosmology

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

    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.

  8. The standard model and beyond in noncommutative geometry

    NASA Astrophysics Data System (ADS)

    Schelp, Richard Charles

    2000-11-01

    Noncommutative geometry and the formulation of the standard model within it is reviewed. The phrasing within noncommutative geometry of a model of particle physics based on S(U(2) × U(3)) is attempted and found to be incompatible with the mathematical structure. Noncommutative geometry versions of unified theories based on SU(15) and SU(16) are found not to yield the necessary spontaneous symmetry breaking. An extension of the standard model which includes right-handed neutrinos (and no additional fermions) is shown to be compatible with Poincaré duality only if the number of right- handed neutrinos is not equal to three.

  9. Morita equivalence and spectral triples on noncommutative orbifolds

    NASA Astrophysics Data System (ADS)

    Harju, Antti J.

    2016-08-01

    Let G be a finite group. Noncommutative geometry of unital G-algebras is studied. A geometric structure is determined by a spectral triple on the crossed product algebra associated with the group action. This structure is to be viewed as a representative of a noncommutative orbifold. Based on a study of classical orbifold groupoids, a Morita equivalence for the crossed product spectral triples is developed. Noncommutative orbifolds are Morita equivalence classes of the crossed product spectral triples. As a special case of this Morita theory one can study freeness of the G-action on the noncommutative level. In the case of a free action, the crossed product formalism reduced to the usual spectral triple formalism on the algebra of G-invariant functions.

  10. Multi-Matrix Models and Noncommutative Frobenius Algebras Obtained from Symmetric Groups and Brauer Algebras

    NASA Astrophysics Data System (ADS)

    Kimura, Yusuke

    2015-07-01

    It has been understood that correlation functions of multi-trace operators in SYM can be neatly computed using the group algebra of symmetric groups or walled Brauer algebras. On the other hand, such algebras have been known to construct 2D topological field theories (TFTs). After reviewing the construction of 2D TFTs based on symmetric groups, we construct 2D TFTs based on walled Brauer algebras. In the construction, the introduction of a dual basis manifests a similarity between the two theories. We next construct a class of 2D field theories whose physical operators have the same symmetry as multi-trace operators constructed from some matrices. Such field theories correspond to non-commutative Frobenius algebras. A matrix structure arises as a consequence of the noncommutativity. Correlation functions of the Gaussian complex multi-matrix models can be translated into correlation functions of the two-dimensional field theories.

  11. Noncommutative Geometry and Physics

    NASA Astrophysics Data System (ADS)

    Connes, Alain

    2006-11-01

    In this very short essay we shall describe a "spectral" point of view on geometry which allows to start taking into account the lessons from both renormalization and of general relativity. We shall first do that for renormalization and explain in rough outline the content of our recent collaborations with Dirk Kreimer and Matilde Marcolli leading to the universal Galois symmetry of renormalizable quantum field theories provided by the renormalization group in its cosmic Galois group incarnation. As far as general relativity is concerned, since the functional integral cannot be treated in the traditional perturbative manner, it relies heavily as a "sum over geometries" on the chosen paradigm of geometric space. This will give us the occasion to discuss, in the light of noncommutative geometry, the issue of "observables" in gravity and our joint work with Ali Chamseddine on the spectral action, with a first attempt to write down a functional integral on the space of noncommutative geometries.

  12. Noncommutative fluid dynamics in the Kähler parametrization

    NASA Astrophysics Data System (ADS)

    Holender, L.; Santos, M. A.; Orlando, M. T. D.; Vancea, I. V.

    2011-11-01

    In this paper, we propose a first-order action functional for a large class of systems that generalize the relativistic perfect fluids in the Kähler parametrization to noncommutative spacetimes. The noncommutative action is parametrized by two arbitrary functions K(z,z¯) and f(-j2) that depend on the fluid potentials and represent the generalization of the Kähler potential of the complex surface parametrized by z and z¯, respectively, and the characteristic function of each model. We calculate the equations of motion for the fluid potentials and the energy-momentum tensor in the first order in the noncommutative parameter. The density current does not receive any noncommutative corrections and it is conserved under the action of the commutative generators Pμ but the energy-momentum tensor is not. Therefore, we determine the set of constraints under which the energy-momentum tensor is divergenceless. Another set of constraints on the fluid potentials is obtained from the requirement of the invariance of the action under the generalization of the volume preserving transformations of the noncommutative spacetime. We show that the proposed action describes noncommutative fluid models by casting the energy-momentum tensor in the familiar fluid form and identifying the corresponding energy and momentum densities. In the commutative limit, they are identical to the corresponding quantities of the relativistic perfect fluids. The energy-momentum tensor contains a dissipative term that is due to the noncommutative spacetime and vanishes in the commutative limit. Finally, we particularize the theory to the case when the complex fluid potentials are characterized by a function K(z,z¯) that is a deformation of the complex plane and show that this model has important common features with the commutative fluid such as infinitely many conserved currents and a conserved axial current that in the commutative case is associated to the topologically conserved linking number.

  13. Noncommutative SO(2,3) gauge theory and noncommutative gravity

    NASA Astrophysics Data System (ADS)

    Dimitrijević, Marija; Radovanović, Voja

    2014-06-01

    In this paper noncommutative gravity is constructed as a gauge theory of the noncommutative SO(2,3)⋆ group, while the noncommutativity is canonical (constant). The Seiberg-Witten 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 with the cosmological constant term and the topological Gauss-Bonnet term. We calculate the second order correction to this model and obtain terms that are of zeroth to fourth power in the curvature tensor and torsion. Trying to relate our results with f(R) and f(T) models, we analyze different limits of our model. In the limit of big cosmological constant and vanishing torsion we obtain an x-dependent correction to the cosmological constant; i.e. noncommutativity leads to an x-dependent cosmological constant. We also discuss the limit of small cosmological constant and vanishing torsion and the teleparallel limit.

  14. 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.

  15. Noncommutative Einstein-Proca spacetime

    NASA Astrophysics Data System (ADS)

    González, Angélica; Linares, Román; Maceda, Marco; Sánchez-Santos, Oscar

    2014-12-01

    In this paper, we present a deformed model of Einstein-Proca spacetime based on the replacement of pointlike sources by noncommutative smeared distributions. We discuss the solutions to the set of noncommutative Einstein-Proca equations thus obtained, with emphasis on the issue of singularities and horizons.

  16. Towards Structural Complexity with Colloids

    NASA Astrophysics Data System (ADS)

    Engel, Michael

    2012-02-01

    Colloids rather easily assemble into simple crystal structures like the face-centered cubic lattice or the body-centered cubic lattice. More complex phases are harder to achieve, but have recently been reported using a number of approaches. Yet, assembling complex structures often results from trial-and-error and is not well understood. In this presentation, we show how novel crystals, quasicrystals, and liquid crystals can be achieved with colloidal building blocks by varying the interactions and the shapes of the building blocks. Using computer simulations, we demonstrate the formation of unusually ordered phases both with isotropic pair potentials, as well as with facetted shapes like polyhedra. We describe new tools we have developed to perform complex structural analysis on simulated systems and show how they may be used to analyze real space images from colloid experiments. We also compare the assembled structures with densest packings of the building blocks and show that good packings can often be distinct from what is observed to assemble from the disordered state. This suggests that dense packings may not be illustrative of what is achievable in colloid experiments.

  17. 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

  18. 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.

  19. Noncommutative quantum mechanics

    NASA Astrophysics Data System (ADS)

    Gamboa, J.; Loewe, M.; Rojas, J. C.

    2001-09-01

    A general noncommutative quantum mechanical system in a central potential V=V(r) in two dimensions is considered. The spectrum is bounded from below and, for large values of the anticommutative parameter θ, we find an explicit expression for the eigenvalues. In fact, any quantum mechanical system with these characteristics is equivalent to a commutative one in such a way that the interaction V(r) is replaced by V=V(HHO,Lz), where HHO is the Hamiltonian of the two-dimensional harmonic oscillator and Lz is the z component of the angular momentum. For other finite values of θ the model can be solved by using perturbation theory.

  20. 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).

  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. Plane waves in noncommutative fluids

    NASA Astrophysics Data System (ADS)

    Abdalla, M. C. B.; Holender, L.; Santos, M. A.; Vancea, I. V.

    2013-08-01

    We study the dynamics of the noncommutative fluid in the Snyder space perturbatively at the first order in powers of the noncommutative parameter. The linearized noncommutative fluid dynamics is described by a system of coupled linear partial differential equations in which the variables are the fluid density and the fluid potentials. We show that these equations admit a set of solutions that are monochromatic plane waves for the fluid density and two of the potentials and a linear function for the third potential. The energy-momentum tensor of the plane waves is calculated.

  3. The complex structured singular value

    NASA Technical Reports Server (NTRS)

    Packard, A.; Doyle, J.

    1993-01-01

    A tutorial introduction to the complex structured singular value (mu) is presented, with an emphasis on the mathematical aspects of mu. The mu-based methods discussed here have been useful for analyzing the performance and robustness properties of linear feedback systems. Several tests for robust stability and performance with computable bounds for transfer functions and their state space realizations are compared, and a simple synthesis problem is studied. Uncertain systems are represented using linear fractional transformations which naturally unify the frequency-domain and state space methods.

  4. Oscillators in a (2+1)-dimensional noncommutative space

    SciTech Connect

    Vega, F.

    2014-03-15

    We study the Harmonic and Dirac Oscillator problem extended to a three-dimensional noncommutative space where the noncommutativity is induced by the shift of the dynamical variables with generators of SL(2,R) in a unitary irreducible representation considered in Falomir et al. [Phys. Rev. D 86, 105035 (2012)]. This redefinition is interpreted in the framework of the Levi's decomposition of the deformed algebra satisfied by the noncommutative variables. The Hilbert space gets the structure of a direct product with the representation space as a factor, where there exist operators which realize the algebra of Lorentz transformations. The spectrum of these models are considered in perturbation theory, both for small and large noncommutativity parameters, finding no constraints between coordinates and momenta noncommutativity parameters. Since the representation space of the unitary irreducible representations SL(2,R) can be realized in terms of spaces of square-integrable functions, we conclude that these models are equivalent to quantum mechanical models of particles living in a space with an additional compact dimension.

  5. K-theory of noncommutative Bieberbach manifolds

    NASA Astrophysics Data System (ADS)

    Olczykowski, P.; Sitarz, A.

    2015-07-01

    We compute the K-theory of noncommutative Bieberbach manifolds, which are fixed point C* subalgebras of a three-dimensional noncommutative torus by a free action of a cyclic group ℤ N , N = 2, 3, 4, 6.

  6. Signatures of Noncommutative Geometry in Muon Decay for Nonsymmetric Gravity

    NASA Astrophysics Data System (ADS)

    Singh, Dinesh; Mobed, Nader; Ouimet, Pierre-Philippe

    2010-12-01

    It is shown how to identify potential signatures of noncommutative geometry within the decay spectrum of a muon in orbit near the event horizon of a microscopic Schwarzschild black hole. This possibility follows from a re-interpretation of Moffat’s nonsymmetric theory of gravity, first published in Phys. Rev. D 19:3554, 1979, where the antisymmetric part of the metric tensor manifests the hypothesized noncommutative geometric structure throughout the manifold. It is further shown that for a given sign convention, the predicted signatures counteract the effects of curvature-induced muon stabilization predicted by Singh and Mobed in Phys. Rev. D 79:024026, 2009. While it is unclear whether evidence for noncommutative geometry may become observable anytime soon, this approach at least provides a useful direction for future quantum gravity research based on the ideas presented here.

  7. Noncommutative Black Holes and the Singularity Problem

    NASA Astrophysics Data System (ADS)

    Bastos, C.; Bertolami, O.; Dias, N. C.; Prata, J. N.

    2011-09-01

    A phase-space noncommutativity in the context of a Kantowski-Sachs cosmological model is considered to study the interior of a Schwarzschild black hole. Due to the divergence of the probability of finding the black hole at the singularity from a canonical noncommutativity, one considers a non-canonical noncommutativity. It is shown that this more involved type of noncommutativity removes the problem of the singularity in a Schwarzschild black hole.

  8. Structure determination of transient transcription complexes.

    PubMed

    Cramer, Patrick

    2016-08-15

    The determination of detailed 3D structures of large and transient multicomponent complexes remains challenging. Here I describe the approaches that were used and developed by our laboratory to achieve structure solution of eukaryotic transcription complexes. I hope this collection serves as a resource for structural biologists seeking solutions for difficult structure determination projects. PMID:27528766

  9. Lifshitz field theories, Snyder noncommutative spacetime and momentum-dependent metric

    NASA Astrophysics Data System (ADS)

    Romero, Juan M.; Vergara, J. David

    2015-08-01

    In this paper, we propose three different modified relativistic particles. In the first case, we propose a particle with metrics depending on the momenta and we show that the quantum version of these systems includes different field theories, as Lifshitz field theories. As a second case, we propose a particle that implies a modified symplectic structure and we show that the quantum version of this system gives different noncommutative spacetimes, for example the Snyder spacetime. In the third case, we combine both structures before mentioned, namely noncommutative spacetimes and momentum-dependent metrics. In this last case, we show that anisotropic field theories can be seen as a limit of noncommutative field theory.

  10. Quanta of Geometry: Noncommutative Aspects

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    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 M2(H ) and M4(C ) are obtained, which are the exact constituents of the standard model. Using the two maps from M4 to S4 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.

  11. Quanta of geometry: noncommutative aspects.

    PubMed

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

    2015-03-01

    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. PMID:25793795

  12. BTZ black holes inspired by noncommutative geometry

    NASA Astrophysics Data System (ADS)

    Rahaman, Farook; Kuhfittig, P. K. F.; Bhui, B. C.; Rahaman, Mosiur; Ray, Saibal; Mondal, U. F.

    2013-04-01

    In this paper, a Bañados-Teitelboim-Zanelli (BTZ) black hole [Phys. Rev. Lett. 69, 1849 (1992)] is constructed from an exact solution of the Einstein field equations in a (2+1)—dimensional anti—de Sitter spacetime in the context of noncommutative geometry. The BTZ black hole turns out to have either two horizons, no horizon, or a single horizon corresponding to a minimal mass. Certain thermodynamical properties are investigated, including Hawking temperature, entropy, and heat capacity. Also discussed is the geodesic structure of BTZ black holes for both massless and massive particles. In particular, it is shown that bound orbits for test particles are possible.

  13. Noncommutative Btz Black Hole in Different Coordinates

    NASA Astrophysics Data System (ADS)

    Ee, Chang-Young

    We consider noncommutative BTZ black hole solutions in two different coordinate systems, the polar and rectangular coordinates. The analysis is carried out by obtaining noncommutative solutions of U(1, 1) × U(1, 1) Chern-Simons theory on AdS3 in the two coordinate systems via the Seiberg-Witten map. This is based on the noncommutative extension of the equivalence between the classical BTZ solution and the solution of ordinary SU(1, 1) × SU(1, 1) Chern-Simons theory on AdS3. The obtained solutions in these noncommutative coordinate systems become different in the first order of the noncommutativity parameter θ.

  14. Chiral symmetry restoration in holographic noncommutative QCD

    NASA Astrophysics Data System (ADS)

    Nakajima, Tadahito; Ohtake, Yukiko; Suzuki, Kenji

    2011-09-01

    We consider the noncommutative deformation of the Sakai-Sugimoto model at finite temperature and finite baryon chemical potential. The space noncommutativity is possible to have an influence on the flavor dynamics of the QCD. The critical temperature and critical value of the chemical potential are modified by the space noncommutativity. The influence of the space noncommutativity on the flavor dynamics of the QCD is caused by the Wess-Zumino term in the effective action of the D8-branes. The intermediate temperature phase, in which the gluons deconfine but the chiral symmetry remains broken, is easy to be realized in some region of the noncommutativity parameter.

  15. Landau problem in noncommutative quantum mechanics

    NASA Astrophysics Data System (ADS)

    Sayipjamal, Dulat; Li, Kang

    2008-02-01

    The Landau problem in non-commutative quantum mechanics (NCQM) is studied. First by solving the Schrödinger equations on noncommutative (NC) space we obtain the Landau energy levels and the energy correction that is caused by space-space noncommutativity. Then we discuss the noncommutative phase space case, namely, space-space and momentum-momentum non-commutative case, and we get the explicit expression of the Hamiltonian as well as the corresponding eigenfunctions and eigenvalues. Supported by National Natural Science Foundation of China (10465004, 10665001, 10575026) and Abdus Salam ICTP, Trieste, Italy

  16. 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.

  17. 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.

  18. 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.

  19. Closed star product on noncommutative ℝ 3 and scalar field dynamics

    NASA Astrophysics Data System (ADS)

    Jurić, Tajron; Poulain, Timothé; Wallet, Jean-Christophe

    2016-05-01

    We consider the noncommutative space ℝ θ 3 , a deformation of ℝ 3 for which the star product is closed for the trace functional. We study one-loop IR and UV properties of the 2-point function for real and complex noncommutative scalar field theories with quartic interactions and Laplacian on ℝ 3 as kinetic operator. We find that the 2-point functions for these noncommutative scalar field theories have no IR singularities in the external momenta, indicating the absence of UV/IR mixing. We also find that the 2-point functions are UV finite with the deformation parameter θ playing the role of a natural UV cut-off. The possible origin of the absence of UV/IR mixing in noncommutative scalar field theories on ℝ θ 3 as well as on ℝ λ 3 , another deformation of ℝ 3, is discussed.

  20. 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. PMID:26441052

  1. 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.

  2. 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.

  3. 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.

  4. Noncommutative geometry inspired entropic inflation

    NASA Astrophysics Data System (ADS)

    Nozari, Kourosh; Akhshabi, Siamak

    2011-06-01

    Recently Verlinde proposed that gravity can be described as an emergent phenomena arising from changes in the information associated with the positions of material bodies. By using noncommutative geometry as a way to describe the microscopic microstructure of quantum spacetime, we derive modified Friedmann equation in this setup and study the entropic force modifications to the inflationary dynamics of early universe.

  5. Exploring the thermodynamics of noncommutative scalar fields

    NASA Astrophysics Data System (ADS)

    Brito, Francisco A.; Lima, Elisama E. M.

    2016-04-01

    We study the thermodynamic properties of the Bose-Einstein condensate (BEC) in the context of the quantum field theory with noncommutative target space. Our main goal is to investigate in which temperature and/or energy regimes the noncommutativity can characterize some influence on the BEC properties described by a relativistic massive noncommutative boson gas. The noncommutativity parameters play a key role in the modified dispersion relations of the noncommutative fields, leading to a new phenomenology. We have obtained the condensate fraction, internal energy, pressure and specific heat of the system and taken ultrarelativistic (UR) and nonrelativistic (NR) limits. The noncommutative effects on the thermodynamic properties of the system are discussed. We found that there appear interesting signatures around the critical temperature.

  6. Supersonic velocities in noncommutative acoustic black holes

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

    In this paper we derive Schwarzschild and Kerr-like noncommutative acoustic black hole metrics in the (3+1)-dimensional noncommutative Abelian Higgs model. We have found that the changing ΔTH in the Hawking temperature TH due to spacetime noncommutativity accounts for supersonic velocities vg, whose deviation with respect to the sound speed cs is given in the form (vg-cs)/cs=ΔTH/8TH.

  7. 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.

  8. Initiation complex structure and promoter proofreading.

    PubMed

    Liu, Xin; Bushnell, David A; Silva, Daniel-Adriano; Huang, Xuhui; Kornberg, Roger D

    2011-07-29

    The initiation of transcription by RNA polymerase II is a multistage process. X-ray crystal structures of transcription complexes containing short RNAs reveal three structural states: one with 2- and 3-nucleotide RNAs, in which only the 3'-end of the RNA is detectable; a second state with 4- and 5-nucleotide RNAs, with an RNA-DNA hybrid in a grossly distorted conformation; and a third state with RNAs of 6 nucleotides and longer, essentially the same as a stable elongating complex. The transition from the first to the second state correlates with a markedly reduced frequency of abortive initiation. The transition from the second to the third state correlates with partial "bubble collapse" and promoter escape. Polymerase structure is permissive for abortive initiation, thereby setting a lower limit on polymerase-promoter complex lifetime and allowing the dissociation of nonspecific complexes. Abortive initiation may be viewed as promoter proofreading, and the structural transitions as checkpoints for promoter control. PMID:21798951

  9. 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.

  10. Structure of Mutualistic Complex Networks

    NASA Astrophysics Data System (ADS)

    Hwang, Jun Kyung; Maeng, Seong Eun; Cha, Moon Yong; Lee, Jae Woo

    We consider the structures of six plant-pollinator mutualistic networks. The plants and pollinators are linked by the plant-pollinating relation. We assigned the visiting frequency of pollinators to a plant as a weight of each link. We calculated the cumulative distribution functions of the degree and strength for the networks. We observed a power-law, linear, and stretched exponential dependence of the cumulative distribution function. We also calculated the disparity and the strength of the nodes s(k) with degree k. We observed that the plant-pollinator networks exhibit an disassortative behaviors and nonlinear dependence of the strength on the nodes. In mutualistic networks links with large weight are connected to the neighbors with small degrees.

  11. Structure of mammalian respiratory complex I.

    PubMed

    Zhu, Jiapeng; Vinothkumar, Kutti R; Hirst, Judy

    2016-08-18

    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 mitochondrial membrane. Mammalian complex I (ref. 1) 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 subunits. Knowledge of the structures and functions of the supernumerary subunits is fragmentary. Here we describe a 4.2-Å resolution single-particle electron cryomicroscopy structure of complex I from Bos taurus. We have located and modelled all 45 subunits, including the 31 supernumerary subunits, to provide the entire structure of the mammalian complex. 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-de-active' enzyme transition that occurs during hypoxia. Our structures therefore provide a foundation for understanding complex I assembly and the effects of mutations that cause clinically relevant complex I dysfunctions, give insights into the structural and functional roles of the supernumerary subunits and reveal new information on the mechanism and regulation of catalysis. PMID:27509854

  12. Structure and function of mitochondrial complex I.

    PubMed

    Wirth, Christophe; Brandt, Ulrich; Hunte, Carola; Zickermann, Volker

    2016-07-01

    Proton-pumping NADH:ubiquinone oxidoreductase (complex I) is the largest and most complicated enzyme of the respiratory chain. Fourteen central subunits represent the minimal form of complex I and can be assigned to functional modules for NADH oxidation, ubiquinone reduction, and proton pumping. In addition, the mitochondrial enzyme comprises some 30 accessory subunits surrounding the central subunits that are not directly associated with energy conservation. Complex I is known to release deleterious oxygen radicals (ROS) and its dysfunction has been linked to a number of hereditary and degenerative diseases. We here review recent progress in structure determination, and in understanding the role of accessory subunits and functional analysis of mitochondrial complex I. For the central subunits, structures provide insight into the arrangement of functional modules including the substrate binding sites, redox-centers and putative proton channels and pump sites. Only for two of the accessory subunits, detailed structures are available. Nevertheless, many of them could be localized in the overall structure of complex I, but most of these assignments have to be considered tentative. Strikingly, redox reactions and proton pumping machinery are spatially completely separated and the site of reduction for the hydrophobic substrate ubiquinone is found deeply buried in the hydrophilic domain of the complex. The X-ray structure of complex I from Yarrowia lipolytica provides clues supporting the previously proposed two-state stabilization change mechanism, in which ubiquinone redox chemistry induces conformational states and thereby drives proton pumping. The same structural rearrangements may explain the active/deactive transition of complex I implying an integrated mechanistic model for energy conversion and regulation. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt. PMID:26921811

  13. Complex structures – smart solutions

    PubMed Central

    2011-01-01

    The siliceous skeletal elements of the sponges, the spicules, represent one of the very few examples from where the molecule toolkit required for the formation of an extracellular mineral-based skeleton, has been elucidated. The distinguished feature of the inorganic matrix, the bio-silica, is its enzymatic synthesis mediated by silicatein. Ortho-silicate undergoes in the presence of silicatein a polycondensation reaction and forms bio-silica under release of reaction water. The protein silicatein aggregates non-covalently to larger filaments, a process that is stabilized by the silicatein-associated protein, silintaphin-1. These structured clusters form the axial filament that is located in the center of the spicules, the axial canal. Surprisingly it has now been found that the initial axial orientation, in which the spicules grow, is guided by cell processes through evagination. The approximately two µm wide cell extensions release silicatein that forms the first organic axial filament, which then synthesizes the inner core of the siliceous spicule rods. In parallel, the radial growth of the spicules is controlled by a telescopic arrangement of organic layers, into which bio-silica and ortho-silicate are deposited. Hence, the formation of a mature siliceous spicule is completed by a centrifugal accretion of bio-silica mediated by the silicatein in the axial filament, and a centripetal bio-silica deposition catalyzed by the extra-spicular silicatein. Finally this contribution highlights that for the ultimate determination of the spicule shapes, their species-specific morphologies, bio-silica hardens during a process which removes reaction water. The data presented can also provide new blueprints for the fabrication of novel biomaterials for biomedical applications.  PMID:22446527

  14. Properties of noncommutative axionic electrodynamics

    NASA Astrophysics Data System (ADS)

    Gaete, Patricio; Schmidt, Iván

    2007-07-01

    Using the gauge-invariant but path-dependent variables formalism, we compute the static quantum potential for noncommutative axionic electrodynamics, and find a radically different result than the corresponding commutative case. We explicitly show that the static potential profile is analogous to that encountered in both non-Abelian axionic electrodynamics and in Yang-Mills theory with spontaneous symmetry breaking of scale symmetry.

  15. Structural complexity and configurational entropy of crystals.

    PubMed

    Krivovichev, Sergey V

    2016-04-01

    Using a statistical approach, it is demonstrated that the complexity of a crystal structure measured as the Shannon information per atom [Krivovichev (2012). Acta Cryst. A68, 393-398] represents a negative contribution to the configurational entropy of a crystalline solid. This conclusion is in full accordance with the general agreement that information and entropy are reciprocal variables. It also agrees well with the understanding that complex structures possess lower entropies relative to their simpler counterparts. The obtained equation is consistent with the Landauer principle and points out that the information encoded in a crystal structure has a physical nature. PMID:27048729

  16. 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.

  17. Fock modules and noncommutative line bundles

    NASA Astrophysics Data System (ADS)

    Landi, Giovanni

    2016-09-01

    To a line bundle over a noncommutative space there is naturally associated a Fock module. The algebra of corresponding creation and annihilation operators is the total space algebra of a principal U(1) -bundle over the noncommutative space. We describe the general construction and illustrate it with examples.

  18. 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.

  19. Analyzing Static Loading of Complex Structures

    NASA Technical Reports Server (NTRS)

    Gallear, D. C.

    1986-01-01

    Critical loading conditions determined from analysis of each structural element. Automated Thrust Structures Loads and Stresses (ATLAS) system is series of programs developed to analyze elements of complex structure under static-loading conditions. ATLAS calculates internal loads, beam-bending loads, column- and web-buckling loads, beam and panel stresses, and beam-corner stresses. Programs written in FORTRAN IV and Assembler for batch execution.

  20. 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.

  1. Variable Complexity Optimization of Composite Structures

    NASA Technical Reports Server (NTRS)

    Haftka, Raphael T.

    1999-01-01

    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 plates with discontinuities subject to uncertainty in material properties and geometry, design of stiffened composite plates for improved damage tolerance, and the use of response surfaces for fitting weights obtained by structural optimization.

  2. Structural biology of presenilin 1 complexes.

    PubMed

    Li, Yi; Bohm, Christopher; Dodd, Roger; Chen, Fusheng; Qamar, Seema; Schmitt-Ulms, Gerold; Fraser, Paul E; St George-Hyslop, Peter H

    2014-01-01

    The presenilin genes were first identified as the site of missense mutations causing early onset autosomal dominant familial Alzheimer's disease. Subsequent work has shown that the presenilin proteins are the catalytic subunits of a hetero-tetrameric complex containing APH1, nicastrin and PEN-2. This complex (variously termed presenilin complex or gamma-secretase complex) performs an unusual type of proteolysis in which the transmembrane domains of Type I proteins are cleaved within the hydrophobic compartment of the membrane. This review describes some of the molecular and structural biology of this unusual enzyme complex. The presenilin complex is a bilobed structure. The head domain contains the ectodomain of nicastrin. The base domain contains a central cavity with a lateral cleft that likely provides the route for access of the substrate to the catalytic cavity within the centre of the base domain. There are reciprocal allosteric interactions between various sites in the complex that affect its function. For instance, binding of Compound E, a peptidomimetic inhibitor to the PS1 N-terminus, induces significant conformational changes that reduces substrate binding at the initial substrate docking site, and thus inhibits substrate cleavage. However, there is a reciprocal allosteric interaction between these sites such that prior binding of the substrate to the initial docking site paradoxically increases the binding of the Compound E peptidomimetic inhibitor. Such reciprocal interactions are likely to form the basis of a gating mechanism that underlies access of substrate to the catalytic site. An increasingly detailed understanding of the structural biology of the presenilin complex is an essential step towards rational design of substrate- and/or cleavage site-specific modulators of presenilin complex function. PMID:25523933

  3. Intraflagellar transport complex structure and cargo interactions

    PubMed Central

    2013-01-01

    Intraflagellar transport (IFT) is required for the assembly and maintenance of cilia, as well as the proper function of ciliary motility and signaling. IFT is powered by molecular motors that move along the axonemal microtubules, carrying large complexes of IFT proteins that travel together as so-called trains. IFT complexes likely function as adaptors that mediate interactions between anterograde/retrograde motors and ciliary cargoes, facilitating cargo transport between the base and tip of the cilium. Here, we provide an up-to-date review of IFT complex structure and architecture, and discuss how interactions with cargoes and motors may be achieved. PMID:23945166

  4. 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.

  5. 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

  6. On the structure of valiant's complexity classes

    NASA Astrophysics Data System (ADS)

    Bürgisser, Peter

    In [25,27] Valiant developed an algebraic analogue of the theory of NP-completeness for computations with polynomials over a field. We further develop this theory in the spirit of structural complexity and obtain analogues of well-known results by Baker, Gill, and Solovay [1], Ladner [18], and Schöning [23,24].

  7. Imprecise probability for non-commuting observables

    NASA Astrophysics Data System (ADS)

    Allahverdyan, Armen E.

    2015-08-01

    It is known that non-commuting observables in quantum mechanics do not have joint probability. This statement refers to the precise (additive) probability model. I show that the joint distribution of any non-commuting pair of variables can be quantified via upper and lower probabilities, i.e. the joint probability is described by an interval instead of a number (imprecise probability). I propose transparent axioms from which the upper and lower probability operators follow. The imprecise probability depend on the non-commuting observables, is linear over the state (density matrix) and reverts to the usual expression for commuting observables.

  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. Electric-magnetic dualities in non-abelian and non-commutative gauge theories

    NASA Astrophysics Data System (ADS)

    Ho, Jun-Kai; Ma, Chen-Te

    2016-08-01

    Electric-magnetic dualities are equivalence between strong and weak coupling constants. A standard example is the exchange of electric and magnetic fields in an abelian gauge theory. We show three methods to perform electric-magnetic dualities in the case of the non-commutative U (1) gauge theory. The first method is to use covariant field strengths to be the electric and magnetic fields. We find an invariant form of an equation of motion after performing the electric-magnetic duality. The second method is to use the Seiberg-Witten map to rewrite the non-commutative U (1) gauge theory in terms of abelian field strength. The third method is to use the large Neveu Schwarz-Neveu Schwarz (NS-NS) background limit (non-commutativity parameter only has one degree of freedom) to consider the non-commutative U (1) gauge theory or D3-brane. In this limit, we introduce or dualize a new one-form gauge potential to get a D3-brane in a large Ramond-Ramond (R-R) background via field redefinition. We also use perturbation to study the equivalence between two D3-brane theories. Comparison of these methods in the non-commutative U (1) gauge theory gives different physical implications. The comparison reflects the differences between the non-abelian and non-commutative gauge theories in the electric-magnetic dualities. For a complete study, we also extend our studies to the simplest abelian and non-abelian p-form gauge theories, and a non-commutative theory with the non-abelian structure.

  10. 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. PMID:26807915

  11. 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.

  12. 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.

  13. 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.

  14. Entropic force, noncommutative gravity, and ungravity

    NASA Astrophysics Data System (ADS)

    Nicolini, Piero

    2010-08-01

    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. 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.

  16. Non-commutativity measure of quantum discord.

    PubMed

    Guo, Yu

    2016-01-01

    Quantum discord is a manifestation of quantum correlations due to non-commutativity rather than entanglement. Two measures of quantum discord by the amount of non-commutativity via the trace norm and the Hilbert-Schmidt norm respectively are proposed in this paper. These two measures can be calculated easily for any state with arbitrary dimension. It is shown by several examples that these measures can reflect the amount of the original quantum discord. PMID:27122226

  17. The noncommutative sine-Gordon breather

    SciTech Connect

    Fischer, Andre; Lechtenfeld, Olaf

    2009-09-15

    As shown by Lechtenfeld et al. [Nucl. Phys. B 705, 447 (2005)], there exists a noncommutative deformation of the sine-Gordon model which remains (classically) integrable but features a second scalar field. We employ the dressing method (adapted to the Moyal-deformed situation) for constructing the deformed kink-antikink and breather configurations. Explicit results and plots are presented for the leading noncommutativity correction to the breather. Its temporal periodicity is unchanged.

  18. Non-commutativity measure of quantum discord

    PubMed Central

    Guo, Yu

    2016-01-01

    Quantum discord is a manifestation of quantum correlations due to non-commutativity rather than entanglement. Two measures of quantum discord by the amount of non-commutativity via the trace norm and the Hilbert-Schmidt norm respectively are proposed in this paper. These two measures can be calculated easily for any state with arbitrary dimension. It is shown by several examples that these measures can reflect the amount of the original quantum discord. PMID:27122226

  19. 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.

  20. Structure of tetracarbonylethyleneosmium: ethylene structure changes upon complex formation.

    PubMed

    Karunatilaka, Chandana; Tackett, Brandon S; Washington, John; Kukolich, Stephen G

    2007-08-29

    Rotational spectra of seven isotopomers of tetracarbonylethyleneosmium, Os(CO)4(eta2-C2H4), were measured in the 4-12 GHz range using a Flygare-Balle-type pulsed-beam Fourier transform microwave spectrometer system. Olefin-transition metal complexes of this type occur extensively in recent organic syntheses and serve as important models for transition states in the metal-mediated transformations of alkenes. Three osmium ((192)Os, (190)Os, and (188)Os) and three unique 13C isotopomers (13C in ethylene, axial, and equatorial positions) were observed in natural abundance. Additional spectra were measured for a perdeuterated sample, Os(CO)4(eta2-C2D4). The measured rotational constants for the main osmium isotopomer ((192)Os) are A = 929.3256(6), B = 755.1707(3), and C = 752.7446(3) MHz, indicating a near-prolate asymmetric top molecule. The approximately 140 assigned b-type transitions were fit using a Watson S-reduced Hamiltonian including A, B, C, and five centrifugal distortion constants. A near-complete r0 gas-phase structure has been determined from a least-squares structural fit using eight adjustable structural parameters to fit the 21 measured rotational constants. Changes in the structure of ethylene on coordination to Os(CO)4 are large and well-determined. For the complex, the experimental ethylene C-C bond length is 1.432(5) A, which falls between the free ethylene value of 1.3391(13) A and the ethane value of 1.534(2) A. The angle between the plane of the CH2 group and the extended ethylene C-C bond ( angleout-of-plane) is 26.0(3) degrees , indicating that this complex is better described as a metallacyclopropane than as a pi-bonded olefin-metal complex. The Os-C-C-H dihedral angle is 106.7(2) degrees , indicating that the ethylene carbon atoms have near sp3 character in the complex. Kraitchman analysis of the available rotational constants gave principal axis coordinates for the carbon and hydrogen atoms in excellent agreement with the least-squares fit

  1. Quantum mechanics with coordinate dependent noncommutativity

    SciTech Connect

    Kupriyanov, V. G.

    2013-11-15

    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.

  2. 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

  3. Minimum structural controllability problems of complex networks

    NASA Astrophysics Data System (ADS)

    Yin, Hongli; Zhang, Siying

    2016-02-01

    Controllability of complex networks has been one of the attractive research areas for both network and control community, and has yielded many promising and significant results in minimum inputs and minimum driver vertices. However, few studies have been devoted to studying the minimum controlled vertex set through which control over the network with arbitrary structure can be achieved. In this paper, we prove that the minimum driver vertices driven by different inputs are not sufficient to ensure the full control of the network when the associated graph contains the inaccessible strongly connected component which has perfect matching and propose an algorithm to identify a minimum controlled vertex set for network with arbitrary structure using convenient graph and mathematical tools. And the simulation results show that the controllability of network is correlated to the number of inaccessible strongly connected components which have perfect matching and these results promote us to better understand the relationship between the network's structural characteristics and its control.

  4. Structural Alignment of RNA with Complex Pseudoknot Structure

    NASA Astrophysics Data System (ADS)

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

    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 paper, 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 cover all known ncRNAs in both Rfam and PseudoBase databases. A preliminary evaluation on our algorithms show that it is useful to identify ncRNA molecules in other species which are in the same family of a known ncRNA.

  5. 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

  6. 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.

  7. Structurally robust control of complex networks.

    PubMed

    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. PMID:25679675

  8. Physical systems in a space with noncommutativity of coordinates

    NASA Astrophysics Data System (ADS)

    Gnatenko, Kh. P.

    2016-01-01

    We consider a space with canonical noncommutativity of coordinates. The problem of rotational symmetry breaking is studied in this space. To preserve the rotational symmetry we consider the generalization of constant matrix of noncommutativity to a tensor defined with the help of additional coordinates governed by a rotationally symmetric system. The properties of physical systems are examined in the rotationally invariant space with noncommutativity of coordinates. Namely, we consider an effect of coordinate noncommutativity on the energy levels of the hydrogen atom in the rotationally invariant noncommutative space. The motion of a particle in the uniform field is also studied in the noncommutative space with preserved rotational symmetry. On the basis of exact calculations we show that there is an effect of coordinate noncommutativity on the mass of a particle and conclude that noncommutativity causes the anisotropy of mass.

  9. Calabi-Yau manifolds from noncommutative Hermitian U (1 ) instantons

    NASA Astrophysics Data System (ADS)

    Yang, Hyun Seok

    2015-05-01

    We show that Calabi-Yau manifolds are emergent from the commutative limit of six-dimensional noncommutative Hermitian U (1 ) instantons. Therefore, we argue that the noncommutative Hermitian U (1 ) instantons correspond to quantized Calabi-Yau manifolds.

  10. 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.

  11. Hawking radiation as tunneling from a Vaidya black hole in noncommutative gravity

    NASA Astrophysics Data System (ADS)

    Mehdipour, S. Hamid

    2010-06-01

    In the context of a noncommutative model of coordinate coherent states, we present a Schwarzschild-like metric for a Vaidya solution instead of the standard Eddington-Finkelstein metric. This leads to the appearance of an exact (t-r) dependent case of the metric. We analyze the resulting metric in three possible causal structures. In this setup, we find a zero remnant mass in the long-time limit, i.e. an instable black hole remnant. We also study the tunneling process across the quantum horizon of such a Vaidya black hole. The tunneling probability including the time-dependent part is obtained by using the tunneling method proposed by Parikh and Wilczek in terms of the noncommutative parameter σ. After that, we calculate the entropy associated to this noncommutative black hole solution. However, the corrections are fundamentally trifling; one could respect this as a consequence of quantum inspection at the level of semiclassical quantum gravity.

  12. Hawking radiation as tunneling from a Vaidya black hole in noncommutative gravity

    SciTech Connect

    Mehdipour, S. Hamid

    2010-06-15

    In the context of a noncommutative model of coordinate coherent states, we present a Schwarzschild-like metric for a Vaidya solution instead of the standard Eddington-Finkelstein metric. This leads to the appearance of an exact (t-r) dependent case of the metric. We analyze the resulting metric in three possible causal structures. In this setup, we find a zero remnant mass in the long-time limit, i.e. an instable black hole remnant. We also study the tunneling process across the quantum horizon of such a Vaidya black hole. The tunneling probability including the time-dependent part is obtained by using the tunneling method proposed by Parikh and Wilczek in terms of the noncommutative parameter {sigma}. After that, we calculate the entropy associated to this noncommutative black hole solution. However, the corrections are fundamentally trifling; one could respect this as a consequence of quantum inspection at the level of semiclassical quantum gravity.

  13. Noncommutative information is revealed from Hawking radiation as tunneling

    NASA Astrophysics Data System (ADS)

    Zhang, Baocheng; Cai, Qing-yu; Zhan, Ming-sheng; You, Li

    2011-04-01

    We revisit the tunneling process from a Schwarzschild black hole in the noncommutative spacetime and obtain the nonthermal tunneling probability. In such nonthermal spectrum, the correlations are discovered, which can carry the information about the noncommutativity. Thus this enlightens a way to find the noncommutative information in the Hawking radiation. The entropy is also shown to be conserved in the whole radiation process, which implies that the unitarity is held even for the Hawking radiation from noncommutative black holes.

  14. Noncommutative fluid dynamics in the Snyder space-time

    NASA Astrophysics Data System (ADS)

    Abdalla, M. C. B.; Holender, L.; Santos, M. A.; Vancea, I. V.

    2012-08-01

    In this paper, we construct for the first time the noncommutative fluid with the deformed Poincaré invariance. To this end, the realization formalism of the noncommutative spaces is employed and the results are particularized to the Snyder space. The noncommutative fluid generalizes the fluid model in the action functional formulation to the noncommutative space. The fluid equations of motion and the conserved energy-momentum tensor are obtained.

  15. Chiral fermions in noncommutative electrodynamics: Renormalizability and dispersion

    SciTech Connect

    Buric, Maja; Latas, Dusko; Radovanovic, Voja; Trampetic, Josip

    2011-02-15

    We analyze quantization of noncommutative chiral electrodynamics in the enveloping algebra formalism in linear order in noncommutativity parameter {theta}. Calculations show that divergences exist and cannot be removed by ordinary renormalization; however, they can be removed by the Seiberg-Witten redefinition of fields. Performing redefinitions explicitly, we obtain renormalizable Lagrangian and discuss the influence of noncommutativity on field propagation. Noncommutativity affects the propagation of chiral fermions only: half of the fermionic modes become massive and birefringent.

  16. 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.

  17. Non-commutative relativistic equation with a Coulomb potential

    SciTech Connect

    Zaim, Slimane; Khodja, Lamine; Delenda, Yazid

    2012-06-27

    We improve the previous study of the Klein-Gordon equation in a non-commutative space-time as applied to the Hydrogen atom to extract the energy levels, by considering the secondorder corrections in the non-commutativity parameter. Phenomenologically we show that noncommutativity plays the role of spin.

  18. 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.

  19. Perception of interstellar structure - Facing complexity

    NASA Technical Reports Server (NTRS)

    Scalo, John

    1990-01-01

    Some orthodox notions concerning the structure and evolution of star-forming regions are challenged; it is proposed that they arise largely by a dual process in which conceptual models are fashioned after categories which are in great part reflections of observational limitations, and the models are projected onto interpretations of data. Several examples are discussed. The need for internal support of molecular clouds is questioned. It is suggested that the inverse density-size relation often claimed for clouds and accounted for by several theoretical models is an artifact caused by limited dynamic range column density detectability, selection bias, distance uncertainties, and internal density gradients, and is contradicted by several unbiased surveys. Column density structures mapped with a large spatial and column density dynamic range are found to be dominated by irregular, connected, and nested forms on all sides. These features and a technique for the quantification of the complex structure are illustrated with a densely-sampled column density image of the Taurus region constructed from IRAS data.

  20. 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.

  1. 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 U{sub q}(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 Fun{sub q} (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.

  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. 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.

  4. Transcription initiation complex structures elucidate DNA opening.

    PubMed

    Plaschka, C; Hantsche, M; Dienemann, C; Burzinski, C; Plitzko, J; Cramer, P

    2016-05-19

    Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 Å and 3.6 Å, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH. Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE 'E-ribbon' domain. The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein-protein and protein-DNA contacts. PMID:27193681

  5. Shadow of noncommutative geometry inspired black hole

    NASA Astrophysics Data System (ADS)

    Wei, Shao-Wen; Cheng, Peng; Zhong, Yi; Zhou, Xiang-Nan

    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/M0 with M0 black hole mass and inclination angle i, the dimensionless noncommutative parameter √vartheta/M0 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 √vartheta/M0, while the distortion increases with it. Compared to the Kerr black hole, the parameter √vartheta/M0 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.

  6. 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.

  7. 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.

  8. 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.

  9. ∗-compatible connections in noncommutative Riemannian geometry

    NASA Astrophysics Data System (ADS)

    Beggs, E. J.; Majid, S.

    2011-01-01

    We develop the formalism for noncommutative differential geometry and Riemmannian geometry to take full account of the ∗-algebra structure on the (possibly noncommutative) coordinate ring and the bimodule structure on the differential forms. We show that ∗-compatible bimodule connections lead to braid operators σ in some generality (going beyond the quantum group case) and we develop their role in the exterior algebra. We study metrics in the form of Hermitian structures on Hilbert ∗-modules and metric compatibility in both the usual form and a cotorsion form. We show that the theory works well for the quantum group Cq[SU2] with its three-dimensional calculus, finding for each point of a three-parameter space of covariant metrics a unique 'Levi-Civita' connection deforming the classical one and characterised by zero torsion, metric preservation and ∗-compatibility. Allowing torsion, we find a unique connection with a classical limit that is metric preserving and ∗-compatible and for which σ obeys the braid relations. It projects to a unique 'Levi-Civita' connection on the quantum sphere. The theory also works for finite groups, and in particular for the permutation group S3, where we find somewhat similar results.

  10. Dilaton cosmology, noncommutativity, and generalized uncertainty principle

    SciTech Connect

    Vakili, Babak

    2008-02-15

    The effects of noncommutativity and of the existence of a minimal length on the phase space of a dilatonic cosmological model are investigated. The existence of a minimum length results in the generalized uncertainty principle (GUP), which is a deformed Heisenberg algebra between the minisuperspace variables and their momenta operators. I extend these deformed commutating relations to the corresponding deformed Poisson algebra. For an exponential dilaton potential, the exact classical and quantum solutions in the commutative and noncommutative cases, and some approximate analytical solutions in the case of GUP, are presented and compared.

  11. Sequential measurements of non-commuting observables with quantum controlled interactions

    NASA Astrophysics Data System (ADS)

    Hofmann, Holger F.

    2014-06-01

    The origin of non-classical correlations is difficult to identify since the uncertainty principle requires that information obtained about one observable invariably results in the disturbance of any other non-commuting observable. Here, this problem is addressed by investigating the uncertainty trade-off between measurement errors and disturbance for measurement interactions controlled by the state of a single qubit, where the measurement is described by a quantum coherent superposition of a fully projective measurement and the identity operation. It is shown that the measurement statistics obtained from a quantum controlled measurement of \\hat{A} followed by a projective measurement of \\hat{B} can be explained in terms of a simple combination of resolution and back-action errors acting on an intrinsic joint probability of the non-commuting observables defined by the input state of the system. These intrinsic joint probabilities are consistent with the complex-valued joint probabilities recently observed in weak measurements of quantum systems and provide direct evidence of non-commutativity in the form of imaginary correlations between the non-commuting operators. In quantum controlled measurements, these imaginary correlations can be converted into well-defined contributions to the real measurement statistics, allowing a direct experimental observation of the less intuitive aspects of quantum theory.

  12. Yang-Baxter deformations, AdS/CFT, and twist-noncommutative gauge theory

    NASA Astrophysics Data System (ADS)

    van Tongeren, Stijn J.

    2016-03-01

    We give an AdS/CFT interpretation to homogeneous Yang-Baxter deformations of the AdS5 ×S5 superstring as noncommutative deformations of the dual gauge theory, going well beyond the canonical noncommutative case. These homogeneous Yang-Baxter deformations can be of so-called abelian or jordanian type. While abelian deformations have a clear interpretation in string theory and many already had well understood gauge theory duals, jordanian deformations appear novel on both counts. We discuss the symmetry structure of the deformed string from the uniformizing perspective of Drinfeld twists and indicate that this structure can be realized on the gauge theory side by considering theories on various noncommutative spaces. We then conjecture that these are the gauge theory duals of our strings, modulo subtleties involving singularities. We support this conjecture by a brane construction for two jordanian examples, corresponding to noncommutative spaces with [x- , ⋆xi ] ∼xi (i = 1 , 2). We also discuss κ-Minkowski type deformations of AdS5 ×S5, one of which may be the gravity dual of gauge theory on spacelike κ-Minkowski space.

  13. Structure of polyacetylene-iodine complexes

    NASA Astrophysics Data System (ADS)

    Murthy, N. S.; Miller, G. G.; Baughman, R. H.

    1988-08-01

    We confirm the existence of a 15 Å period in iodine-doped polyacetylene and provide a new interpretation for this key feature as part of a general model for structural changes during iodine doping. The observed diffraction intensities for different samples suggest the existence of structures with two different types of dopant-containing layers: layers obtained by complete replacement of polyacetylene chains by iodine columns (F layers) and layers obtained by replacement of every other polyacetylene chain by an iodine column (P layers). The F layers in the heavily doped complex alternate with dopant-free layers of polyacetylene chains (U layers), corresponding to a (UF)n stacking sequence. The phase obtained at a lower dopant concentration, which provides the 15 Å spacing, is attributed to a (UPUF)n stacking sequence. At still lower dopant concentrations, one obtains a (UP)n stacking sequence. This model, along with published Raman, Mössbauer, and photoelectron spectroscopy data, suggests that the ratio of I-5 to I-3 increases in going from P layers to F layers. Intense and monotonically decreasing, diffuse x-ray scattering suggests that vacancies of size ˜3 Å are present, probably in iodine columns. A diffuse reflection at 3.1 Å, observed in all iodine-doped samples, is due to an average iodine-iodine distance in disordered columnar arrays. On the other hand, ordered arrays of iodine columns in oriented samples give rise to sharp meridional reflections. All ten observed reflections (down to 1.17 Å) in one sample could be indexed based on a 33.8 Å repeat corresponding to (-I-3-I-5-I-3-)n arrays. The observed diffraction pattern was calculated from this model without using any freely adjustable parameters.

  14. Renyi complexities and information planes: Atomic structure in conjugated spaces

    NASA Astrophysics Data System (ADS)

    Antolín, J.; López-Rosa, S.; Angulo, J. C.

    2009-05-01

    Generalized Renyi complexity measures are defined and numerically analyzed for atomic one-particle densities in both conjugated spaces. These complexities provide, as particular cases, the previously known statistical and Fisher-Shannon complexities. The generalized complexities provide information on the atomic shell structure and shell-filling patterns, allowing to appropriately weight different regions of the electronic cloud.

  15. Nonseparability and noncommutativity in quantum systems

    NASA Astrophysics Data System (ADS)

    de La Torre, A. C.; Catuogno, P.; Ferrando, S.

    1991-02-01

    The quantum covariance function is calculated in some EPR-like systems for commuting observables in order to illustrate the nonseparability contribution to the incompatibility between commuting operators. It is shown that an attempt to eliminate the noncommutativity contribution to incompatibility fails in finite-dimensional cases and would require a nonseparable Hilbert space (nonseparable in the mathematical sense).

  16. Non-commutativity in the brain.

    PubMed

    Tweed, D B; Haslwanter, T P; Happe, V; Fetter, M

    1999-05-20

    In non-commutative algebra, order makes a difference to multiplication, so that a x b not equal to b x a. This feature is necessary for computing rotary motion, because order makes a difference to the combined effect of two rotations. It has therefore been proposed that there are non-commutative operators in the brain circuits that deal with rotations, including motor circuits that steer the eyes, head and limbs, and sensory circuits that handle spatial information. This idea is controversial: studies of eye and head control have revealed behaviours that are consistent with non-commutativity in the brain, but none that clearly rules out all commutative models. Here we demonstrate non-commutative computation in the vestibulo-ocular reflex. We show that subjects rotated in darkness can hold their gaze points stable in space, correctly computing different final eye-position commands when put through the same two rotations in different orders, in a way that is unattainable by any commutative system. PMID:10353248

  17. An extended Dirac equation in noncommutative spacetime

    NASA Astrophysics Data System (ADS)

    Mendes, R. Vilela

    2016-05-01

    Stabilizing, by deformation, the algebra of relativistic quantum mechanics a noncommutative spacetime geometry is obtained. The exterior algebra of this geometry leads to an extended massless Dirac equation which has both a massless and a large mass solution. The nature of the solutions is discussed as well as the effects of coupling the two solutions.

  18. 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

  19. 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

  20. 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

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

    NASA Astrophysics Data System (ADS)

    Ding, Chikun; Kang, Shuai; Chen, Chang-Yong; Chen, Songbai; Jing, Jiliang

    2011-04-01

    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-Norström 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-Norström black hole, and may permit us to probe the spacetime noncommutative constant ϑ by the astronomical instruments in the future.

  2. Commuting flows and conservation laws for noncommutative Lax hierarchies

    SciTech Connect

    Hamanaka, Masashi

    2005-05-01

    We discuss commuting flows and conservation laws for Lax hierarchies on noncommutative spaces in the framework of the Sato theory. On commutative spaces, the Sato theory has revealed essential aspects of the integrability for wide class of soliton equations which are derived from the Lax hierarchies in terms of pseudodifferential operators. Noncommutative extension of the Sato theory has been already studied by the author and Toda, and the existence of various noncommutative Lax hierarchies are guaranteed. In this paper, we present conservation laws for the noncommutative Lax hierarchies with both space-space and space-time noncommutativities and prove the existence of infinite number of conserved densities. We also give the explicit representations of them in terms of Lax operators. Our results include noncommutative versions of KP, KdV, Boussinesq, coupled KdV, Sawada-Kotera, modified KdV equation and so on.

  3. Voros product, noncommutative Schwarzschild black hole and corrected area law

    NASA Astrophysics Data System (ADS)

    Banerjee, Rabin; Gangopadhyay, Sunandan; Modak, Sujoy Kumar

    2010-03-01

    We show the importance of the Voros product in defining a noncommutative Schwarzschild black hole. The corrected entropy/area law is then computed in the tunneling formalism. Two types of corrections are considered; one, due to the effects of noncommutativity and the other, due to the effects of going beyond the semiclassical approximation. The leading correction to the semiclassical entropy/area-law is logarithmic and its coefficient involves the noncommutative parameter.

  4. Particles and Scalar Waves in Noncommutative Charged Black Hole Spacetime

    NASA Astrophysics Data System (ADS)

    Piyali, Bhar; Farook, Rahaman; Ritabrata, Biswas; U. F., Mondal

    2015-07-01

    In this paper we have discussed geodesics and the motion of test particle in the gravitational field of non-commutative charged black hole spacetime. The motion of massive and massless particle have been discussed seperately. A comparative study of noncommutative charged black hole and usual Reissner-Nordström black hole has been done. The study of effective potential has also been included. Finally, we have examined the scattering of scalar waves in noncommutative charged black hole spacetime.

  5. Tunneling of massive particles from noncommutative inspired Schwarzschild black hole

    NASA Astrophysics Data System (ADS)

    Miao, Yan-Gang; Xue, Zhao; Zhang, Shao-Jun

    2012-02-01

    We apply the generalization of the Parikh-Wilczek method to the tunneling of massive particles from noncommutative inspired Schwarzschild black holes. By deriving the equation of radial motion of the tunneling particle directly, we calculate the emission rate which is shown to be dependent on the noncommutative parameter besides the energy and mass of the tunneling particle. After equating the emission rate to the Boltzmann factor, we obtain the modified Hawking temperature which relates to the noncommutativity and recovers the standard Hawking temperature in the commutative limit. We also discuss the entropy of the noncommutative inspired Schwarzschild black hole and its difference after and before a massive particle's emission.

  6. An overview of the structures of protein-DNA complexes

    PubMed Central

    Luscombe, Nicholas M; Austin, Susan E; Berman , Helen M; Thornton, Janet M

    2000-01-01

    On the basis of a structural analysis of 240 protein-DNA complexes contained in the Protein Data Bank (PDB), we have classified the DNA-binding proteins involved into eight different structural/functional groups, which are further classified into 54 structural families. Here we present this classification and review the functions, structures and binding interactions of these protein-DNA complexes. PMID:11104519

  7. Complexity and white-dwarf structure

    NASA Astrophysics Data System (ADS)

    Sañudo, J.; Pacheco, A. F.

    2009-02-01

    From the low-mass non-relativistic case to the extreme relativistic limit, the density profile of a white dwarf is used to evaluate the C complexity measure [R. López-Ruiz, H.L. Mancini, X. Calbet, Phys. Lett. A 209 (1995) 321]. Similarly to the recently reported atomic case where, by averaging shell effects, complexity grows with the atomic number [C.P. Panos, K.Ch. Chatzisavvas, Ch.C. Moustakidis, E.G. Kyrkou, Phys. Lett. A 363 (2007) 78; A. Borgoo, F. De Proft, P. Geerlings, K.D. Sen, Chem. Phys. Lett. 444 (2007) 186; J. Sañudo, R. López-Ruiz, Int. Rev. Phys. 2 (2008) 223], here complexity grows as a function of the star mass reaching a maximum finite value in the Chandrasekhar limit.

  8. 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.

  9. 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…

  10. LEADERSHIP IN NEGOTIATIONS AND THE COMPLEXITY OF CONCEPTUAL STRUCTURE.

    ERIC Educational Resources Information Center

    STREUFERT, SIEGFRIED; AND OTHERS

    TO DETERMINE THE THEORETICAL IMPORT OF TWO KINDS OF LEADERS, SIMPLE AND COMPLEX, A GAME EXPERIMENT SIMULATING INTERNATIONAL NEGOTIATIONS WAS CONDUCTED WITH 20 DYAD NEGOTIATION TEAMS (10 HAVING MEMBERS WITH SIMPLE CONCEPTUAL STRUCTURE AND 10 HAVING MEMBERS WITH COMPLEX CONCEPTUAL STRUCTURE) SELECTED FROM 350 MALE UNDERGRADUATE STUDENTS IN AN…

  11. Crystallization and Structure Determination of Superantigens and Immune Receptor Complexes.

    PubMed

    Rödström, Karin E J; Lindkvist-Petersson, Karin

    2016-01-01

    Structure determination of superantigens and the complexes they form with immune receptors have over the years provided insight in their modes of action. This technique requires growing large and highly ordered crystals of the superantigen or receptor-superantigen complex, followed by exposure to X-ray radiation and data collection. Here, we describe methods for crystallizing superantigens and superantigen-receptor complexes using the vapor diffusion technique, how the crystals may be optimized, and lastly data collection and structure determination. PMID:26676036

  12. Voros Product and Noncommutative Inspired Black Holes

    NASA Astrophysics Data System (ADS)

    Gangopadhyay, Sunandan

    2013-03-01

    We emphasize the importance of the Voros product in defining the noncommutative (NC) inspired black holes. The computation of entropy for both the noncommutative inspired Schwarzschild and Reissner-Nordström (RN) black holes show that the area law holds up to order (1)/(√ {θ )}e-M2/θ . The leading correction to the entropy (computed in the tunneling formalism) is shown to be logarithmic. The Komar energy E for these black holes is then obtained and a deviation from the standard identity E = 2STH is found at the order √ {θ }e-M2/θ . This deviation leads to a nonvanishing Komar energy at the extremal point TH = 0 of these black holes. The Smarr formula is finally worked out for the NC Schwarzschild black hole. Similar features also exist for a de Sitter-Schwarzschild geometry.

  13. Noncommutative ordered spaces: examples and counterexamples

    NASA Astrophysics Data System (ADS)

    Besnard, Fabien

    2015-07-01

    In order to introduce the notion of causality in noncommutative geometry, it is necessary to extend Gelfand theory to the context of ordered spaces. In a previous work we have already given an algebraic characterization of the set of non-decreasing continuous functions on a certain class of topological ordered spaces. Such a set is called an isocone, and there exist at least two versions of them (strong and weak) which coincide in the commutative case. In this paper, we introduce yet another breed of isocones, ultraweak isocones, which has a simpler definition with a clear physical meaning. We show that ultraweak and weak isocones are in fact the same, and completely classify those that live in a finite-dimensional {C}*-algebra, hence corresponding to finite noncommutative ordered spaces. We also give some examples in infinite dimension.

  14. 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.

  15. 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.

  16. Noncanonical phase-space noncommutative black holes

    NASA Astrophysics Data System (ADS)

    Bastos, Catarina; Bertolami, Orfeu; Dias, Nuno Costa; Prata, Joa~o. Nuno

    2012-07-01

    In this contribution we present a noncanonical phase-space noncommutative (NC) extension of a Kantowski Sachs (KS) cosmological model to describe the interior of a Schwarzschild black hole (BH). We evaluate the thermodynamical quantities inside this NC Schwarzschild BH and compare with the well known quantities. We find that for a NCBH the temperature and entropy have the same mass dependence as the Hawking quantities for a Schwarzschild BH.

  17. From Noncommutative Sphere to Nonrelativistic Spin

    NASA Astrophysics Data System (ADS)

    Deriglazov, Alexei A.

    2010-02-01

    Reparametrization invariant dynamics on a sphere, being parameterized by angular momentum coordinates, represents an example of noncommutative theory. It can be quantized according to Berezin-Marinov prescription, replacing the coordinates by Pauli matrices. Following the scheme, we present two semiclassical models for description of spin without use of Grassman variables. The first model implies Pauli equation upon the canonical quantization. The second model produces nonrelativistic limit of the Dirac equation implying correct value for the electron spin magnetic moment.

  18. 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.

  19. Exact BPS bound for noncommutative baby Skyrmions

    NASA Astrophysics Data System (ADS)

    Domrin, Andrei; Lechtenfeld, Olaf; Linares, Román; Maceda, Marco

    2013-11-01

    The noncommutative baby Skyrme model is a Moyal deformation of the two-dimensional sigma model plus a Skyrme term, with a group-valued or Grassmannian target. Exact abelian solitonic solutions have been identified analytically in this model, with a singular commutative limit. Inside any given Grassmannian, we establish a BPS bound for the energy functional, which is saturated by these baby Skyrmions. This asserts their stability for unit charge, as we also test in second-order perturbation theory.

  20. Group field theory with noncommutative metric variables.

    PubMed

    Baratin, Aristide; Oriti, Daniele

    2010-11-26

    We introduce a dual formulation of group field theories as a type of noncommutative field theories, making their simplicial geometry manifest. For Ooguri-type models, the Feynman amplitudes are simplicial path integrals for BF theories. We give a new definition of the Barrett-Crane model for gravity by imposing the simplicity constraints directly at the level of the group field theory action. PMID:21231377

  1. 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)

  2. Imaging complex structures with diffuse light

    PubMed Central

    Konecky, Soren D.; Panasyuk, George Y.; Lee, Kijoon; Markel, Vadim; Yodh, Arjun G.; Schotland, John C.

    2008-01-01

    We use diffuse optical tomography to quantitatively reconstruct images of complex phantoms with millimeter sized features located centimeters deep within a highly-scattering medium. A non-contact instrument was employed to collect large data sets consisting of greater than 107 source-detector pairs. Images were reconstructed using a fast image reconstruction algorithm based on an analytic solution to the inverse scattering problem for diffuse light. PMID:18542605

  3. Cosmological production of noncommutative black holes

    NASA Astrophysics Data System (ADS)

    Mann, Robert B.; Nicolini, Piero

    2011-09-01

    We investigate the pair creation of noncommutative black holes in a background with a positive cosmological constant. As a first step we derive the noncommutative geometry inspired Schwarzschild-de Sitter solution. By varying the mass and the cosmological constant parameters, we find several spacetimes compatible with the new solution: positive-mass spacetimes admit one cosmological horizon and two, one, or no black hole horizons, while negative-mass spacetimes have just a cosmological horizon. These new black holes share the properties of the corresponding asymptotically flat solutions, including the nonsingular core and thermodynamic stability in the final phase of the evaporation. As a second step we determine the action which generates the matter sector of gravitational field equations and we construct instantons describing the pair production of black holes and the other admissible topologies. As a result we find that for current values of the cosmological constant the de Sitter background is quantum mechanically stable according to experience. However, positive-mass noncommutative black holes and solitons would have plentifully been produced during inflationary times for Planckian values of the cosmological constant. As a special result we find that, in these early epochs of the Universe, Planck size black holes production would have been largely disfavored. We also find a potential instability for production of negative-mass solitons.

  4. Gravitons, inflatons, twisted bits: A noncommutative bestiary

    NASA Astrophysics Data System (ADS)

    Pearson, John

    In this work, we examine ideas connected with the noncommutativity of spacetime and its realizations in string theory. Motivated by Matrix Theory and the AdS-CFT correspondence, we propose a survey of selected noncommutative objects, assessing their implications for inflation, gauge theory duals, and solvable backgrounds. Our initial pair of examples, related to the Myers effect, incorporate elements of so-called "giant graviton" behavior. In the first, the formation of an extended, supersymmetry-restoring domain wall from point-brane sources in a flux background is related to a nonperturbative process of brane-flux annihilation. In the second, we reexamine these phenomena from a cosmological vantage, investigating the prospect of slow-roll inflation in the noncommutative configuration space of multiple d-branes. For our third and final example, we turn to the solvable pp-wave background, outlining a combinatorial, permutation-based approach to string physics which interpolates between gauge theory and worldsheet methods. This "string bit" language will allow us to find exact agreement between Yang-Mills theory in the large R-charge sector and string field theory on the light cone, resolving some previous discrepancies in the literature.

  5. Noncommutativity of the zero chemical potential limit and the thermodynamic limit in finite density systems

    NASA Astrophysics Data System (ADS)

    Ambjørn, J.; Anagnostopoulos, K. N.; Nishimura, J.; Verbaarschot, J. J.

    2004-08-01

    Monte Carlo simulations of finite density systems are often plagued by the complex action problem. We point out that there exists certain noncommutativity in the zero chemical potential limit and the thermodynamic limit when one tries to study such systems by reweighting techniques. This is demonstrated by explicit calculations in a Random Matrix Theory, which is thought to be a simple qualitative model for finite density QCD. The factorization method allows us to understand how the noncommutativity, which appears at the intermediate steps, cancels in the end results for physical observables. In the recent reweighting type of approaches to QCD in the small μ regime, we expect a transition when the volume reaches Vtr≃const./μ2, which however may not be in the range of current lattice calculations.

  6. 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. PMID:26416747

  7. Parabosonic string and space-time non-commutativity

    SciTech Connect

    Seridi, M. A.; Belaloui, N.

    2012-06-27

    We investigate the para-quantum extension of the bosonic strings in a non-commutative space-time. We calculate the trilinear relations between the mass-center variables and the modes and we derive the Virasoro algebra where a new anomaly term due to the non-commutativity is obtained.

  8. 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.

  9. Conformal invariance in noncommutative geometry and mutually interacting Snyder particles

    NASA Astrophysics Data System (ADS)

    Pramanik, Souvik; Ghosh, Subir; Pal, Probir

    2014-11-01

    A system of relativistic Snyder particles with mutual two-body interaction that lives in a noncommutative Snyder geometry is studied. The underlying novel symplectic structure is a coupled and extended version of (single-particle) Snyder algebra. In a recent work by Casalbuoni and Gomis [Phys. Rev. D 90, 026001 (2014)], a system of interacting conventional particles (in commutative spacetime) was studied with special emphasis on its conformal invariance. Proceeding along the same lines, we have shown that our interacting Snyder particle model is also conformally invariant. Moreover, the conformal Killing vectors have been constructed. Our main emphasis is on the Hamiltonian analysis of the conformal symmetry generators. We demonstrate that the Lorentz algebra remains undeformed, but validity of the full conformal algebra requires further restrictions.

  10. 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.

  11. 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

  12. 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.

  13. On matrix model formulations of noncommutative Yang-Mills theories

    SciTech Connect

    Azeyanagi, Tatsuo; Hirata, Tomoyoshi; Hanada, Masanori

    2008-11-15

    We study the stability of noncommutative spaces in matrix models and discuss the continuum limit which leads to the noncommutative Yang-Mills theories. It turns out that most noncommutative spaces in bosonic models are unstable. This indicates perturbative instability of fuzzy R{sup D} pointed out by Van Raamsdonk and Armoni et al. persists to nonperturbative level in these cases. In this sense, these bosonic noncommutative Yang-Mills theories are not well-defined, or at least their matrix model formulations studied in this paper do not work. We also show that noncommutative backgrounds are stable in a supersymmetric matrix model deformed by a cubic Myers term, though the deformation itself breaks supersymmetry.

  14. Noncommutative Extension of \\bar{\\partial}-Dressing Method

    NASA Astrophysics Data System (ADS)

    Wang, Ning; Wadati, Miki

    2003-06-01

    The \\bar{\\partial}-dressing method is extended to noncommutative space-time. It is shown that a noncommutative soliton equation and its Lax operators can be represented in the forms of Moyal product, the operator (functional of creation-annihilation operators) and the kernel function of the operator in coherent state representation (CSR). Noncommutative KP (ncKP) equation is taken as an example to illustrate how to solve a noncommutative soliton equation. It is found that the induced soliton equation in the CSR is different from the matrix KP equation usually considered in articles, but is a new soliton equation of integral operator. It is shown that the solutions of a noncommutative soliton equation (both multi-lump and multi-line solitons) can be reduced to solving a set of c-number linear differential equations.

  15. 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.

  16. 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).

  17. 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.

  18. 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. PMID:26356911

  19. 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.

  20. 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

  1. Complex banded structures in directional solidification processes.

    PubMed

    Korzhenevskii, A L; Rozas, R E; Horbach, J

    2016-01-27

    A combination of theory and numerical simulation is used to investigate impurity superstructures that form in rapid directional solidification (RDS) processes in the presence of a temperature gradient and a pulling velocity with an oscillatory component. Based on a capillary wave model, we show that the RDS processes are associated with a rich morphology of banded structures, including frequency locking and the transition to chaos. PMID:26704726

  2. Synthesis and structures of cuprous triptycylthiolate complexes.

    PubMed

    Ferrara, Skylar J; Mague, Joel T; Donahue, James P

    2012-06-18

    A synthesis of 1-(thioacetyl)triptycene (5), a convenient protected form of 1-(thiolato)triptycene [STrip](-), is described, a key transformation being the high yield conversion of tert-butyl 1-triptycenyl sulfide (8) to 5 by a protocol employing BBr(3)/AcCl. Syntheses of the two-coordinate copper(I) compounds [Bu(4)N][Cu(STrip)(2)], [Bu(4)N]10, and [(Cu(IMes)(STrip)] (13) proceed readily by chloride displacement from CuCl and [Cu(IMes)Cl], respectively. Reaction of 10 with Ph(3)SiSH or Me(3)SiI produces the heteroleptic species [Cu(STrip)(SSiPh(3))](-) (11) and [Cu(STrip)I](-) (12), detected by mass spectrometry, in mixture with the homoleptic bis(thiolate) anions. Structural identification by X-ray crystallography of the ligand precursor molecules 9-(thioacetyl)anthracene (4, triclinic and orthorhombic polymorphs), tert-butyl 9-anthracenyl sulfide (7), 5, and tert-butyl 1-triptycenyl sulfide (8) are presented. Crystallographic characterization of bis(9-anthracenyl)sulfide (3), which features a C-S-C angle of 104.0° and twist angle of 54.8° between anthracenyl planes, is also given. A crystal structure of [Bu(4)N][(STrip)], [Bu(4)N]9, provides an experimental measure of 144.6° for the ligand cone angle. The crystal structures of [Bu(4)N]10 and 13 are reported, the former of which reveals an unexpectedly small C-S···S-C torsion angle of ∼41° (average of two values), which confers a near "cis" disposition of the triptycenyl groups with respect the S-Cu-S axis. This conformation is governed by interligand π···π and CH···π interactions. A crystal structure of an adventitious product, [Bu(4)N][(Cu-STrip)(6)(μ(6)-Br)]·[Bu(4)N][PF(6)], [Bu(4)N]14·[Bu(4)N][PF(6)] is described, which reveals a cyclic hexameric structure previously unobserved in cuprous thiolate chemistry. The Cu(6)S(6) ring displays a centrosymmetric cyclohexane chair type conformation with a Br(-) ion residing at the inversion center and held in place by apparent soft

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

    PubMed Central

    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

    2016-01-01

    Summary Nuclear pore complexes (NPCs) are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Elucidating their 110 MDa structure imposes a formidable challenge and requires in situ structural biology approaches. Fifteen out of about thirty nucleoporins (Nups) 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 1. The scaffold is decorated with transport channel Nups that often contain phenylalanine (FG)-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 combined cryo electron tomography with mass spectrometry, biochemical analysis, perturbation experiments and structural modeling to generate the most comprehensive architectural model of the NPC to date. Our data suggest previously unknown protein interfaces across Y-complexes and to inner ring complex members. We demonstrate that the higher eukaryotic transport channel Nup358 (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, similarly to coated vesicles, multiple copies of the same structural building block - although compositionally identical - engage in different local sets of interactions and conformations. PMID:26416747

  4. 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

  5. MATERIALS WITH COMPLEX ELECTRONIC/ATOMIC STRUCTURES

    SciTech Connect

    D. M. PARKIN; L. CHEN; ET AL

    2000-09-01

    We explored both experimentally and theoretically the behavior of materials at stresses close to their theoretical strength. This involves the preparation of ultra fine scale structures by a variety of fabrication methods. In the past year work has concentrated on wire drawing of in situ composites such as Cu-Ag and Cu-Nb. Materials were also fabricated by melting alloys in glass and drawing them into filaments at high temperatures by a method known as Taylor wire technique. Cu-Ag microwires have been drawn by this technique to produce wires 10 {micro}m in diameter that consist of nanoscale grains of supersaturated solid solution. Organogels formed from novel organic gelators containing cholesterol tethered to squaraine dyes or trans-stilbene derivatives have been studied from several different perspectives. The two types of molecules are active toward several organic liquids, gelling in some cases at w/w percentages as low as 0.1. While relatively robust, acroscopically dry gels are formed in several cases, studies with a variety of probes indicate that much of the solvent may exist in domains that are essentially liquid-like in terms of their microenvironment. The gels have been imaged by atomic force microscopy and conventional and fluorescence microscopy, monitoring both the gelator fluorescence in the case of the stilbene-cholesterol gels and, the fluorescence of solutes dissolved in the solvent. Remarkably, our findings show that several of the gels are composed of similarly appearing fibrous structures visible at the nano-, micro-, and macroscale.

  6. 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

  7. 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.

  8. Complexation of Actinides in Solution: Thermodynamic Measurementsand Structural Characterization

    SciTech Connect

    Rao, L.

    2007-02-01

    This paper presents a brief introduction of the studies of actinide complexation in solution at Lawrence Berkeley National Laboratory. An integrated approach of thermodynamic measurements and structural characterization is taken to obtain fundamental understanding of actinide complexation in solution that is of importance in predicting the behavior of actinides in separation processes and environmental transport.

  9. [Problems of formal organizational structure of industrial health care complexes].

    PubMed

    Włodarczyk, C

    1978-01-01

    The author formulates the thesis that the description of organizational structure of industrial health care complex calls for isolation of the following aspects:--structure of territorial links--systemof organizational units and divisions--organization of basic functions--structure of management--structure of supervision of middle and lowe-level personnel--composition of health care complex council--system of accessibility ranges. Each of the above aspects has been considered on the basis of operative rules of law, using organizational analysis methods. PMID:745544

  10. 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.

  11. A Dream of Yukawa — Non-Local Fields out of Non-Commutative Spacetime —

    NASA Astrophysics Data System (ADS)

    Naka, Shigefumi; Toyoda, Haruki; Takanashi, Takahiro; Umezawa, Eizo

    The coordinates of κ-Minkowski spacetime form Lie algebraic elements, in which time and space coordinates do not commute in spite of that space coordinates commute each other. The non-commutativity is realized by a Planck-length-scale constant κ - 1( ne 0), which is a universal constant other than the light velocity under the κ-Poincare transformation. Such a non-commutative structure can be realized by SO(1,4) generators in dS4 spacetime. In this work, we try to construct a κ-Minkowski like spacetime with commutative 4-dimensional spacetime based on Adsn+1 spacetime. Another aim of this work is to study invariant wave equations in this spacetime from the viewpoint of non-local field theory by H. Yukawa, who expected to realize elementary particle theories without divergence according to this viewpoint.

  12. 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.

  13. Dynamics of a complex streamer structure

    NASA Astrophysics Data System (ADS)

    Lehtinen, N. G.; Ostgaard, N.; Inan, U.

    2014-12-01

    Streamer corona formation and propagation is an important process in the development of lightning. In order to understand its dynamics, the streamer front velocity is calculated in a 1D model with curvature. We show that streamers may only propagate only the presence of mechanisms such as electron drift, electron diffusion and photoionization. The results indicate, in particular, that: (1) the effect of photoionization on the streamer velocity for both positive and negative streamers is mostly determined by the photoionization length, with a weaker dependence on the amount of photoionization; (2) the electron drift may increase the velocity of the negative streamers but has an opposite effect on the positive streamers; (3) the contributions of photoionization and electron diffusion to the velocity are decreased for positive curvature, i.e., convex fronts, while the contribution of electron drift is independent of curvature. These results are used in a fractal model in which the front propagation velocity is simulated as the cluster growth probability [Niemeyer et al, 1984, doi:10.1103/PhysRevLett.52.1033]. In the case when the photoionization is the main mechanism which determines the streamer propagation, the emerging transverse size of the streamers is of the order of the photoionization length, and at the larger scale the streamer structure is a fractal similar to the one obtained in a diffusion-limited aggregation system.

  14. 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. PMID:27016207

  15. 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.

  16. The evolution of cerebellum structure correlates with nest complexity.

    PubMed

    Hall, Zachary J; Street, Sally E; Healy, Susan D

    2013-01-01

    Across the brains of different bird species, the cerebellum varies greatly in the amount of surface folding (foliation). The degree of cerebellar foliation is thought to correlate positively with the processing capacity of the cerebellum, supporting complex motor abilities, particularly manipulative skills. Here, we tested this hypothesis by investigating the relationship between cerebellar foliation and species-typical nest structure in birds. Increasing complexity of nest structure is a measure of a bird's ability to manipulate nesting material into the required shape. Consistent with our hypothesis, avian cerebellar foliation increases as the complexity of the nest built increases, setting the scene for the exploration of nest building at the neural level. PMID:24307527

  17. Modeling of protein binary complexes using structural mass spectrometry data

    PubMed Central

    Kamal, J.K. Amisha; Chance, Mark R.

    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. PMID:18042684

  18. Formation, structure, and reactivity of palladium superoxo complexes

    SciTech Connect

    Talsi, E.P.; Babenko, V.P.; Shubin, A.A.; Chinakov, V.D.; Nekipelov, V.M.; Zamaraev, K.I.

    1987-11-18

    The mechanism of formation of palladium superoxo complexes, their structure, and their reactivity are discussed. The formation of the palladium superoxo complexes in the reaction of palladium(II) acetate, propionate, trifluororacetate, and bis(acetylacetonate) and palladium(0) tetrakis(triphenylphosphine) with hydrogen peroxide and potassium superoxide has been detected in solution by electron proton resonance. The oxidation of olefins and carbon monoxide by these complexes is considered. Reaction mechanisms and reaction kinetics for these oxidations are reported using the palladium superoxo complexes. 44 references, 8 figures, 2 tables.

  19. LINC complex proteins in cardiac structure, function, and disease

    PubMed Central

    Stroud, Matthew J; Banerjee, Indroneal; Lowe, Jennifer; Chen, Ju

    2014-01-01

    The LINC (LInker of Nucleoskeleton and Cytoskeleton) complex, composed of proteins within the inner and the outer nuclear membranes, connects the nuclear lamina to the cytoskeleton. The importance of this complex has been highlighted by the discovery of mutations in genes encoding LINC complex proteins, which are causative for skeletal or cardiac myopathies. Herein, this review summarizes structure, function, and interactions of major components of the LINC complex, highlights how mutations in these proteins may lead to cardiac disease, and outlines future challenges in the field. PMID:24481844

  20. Quantum statistics and noncommutative black holes

    NASA Astrophysics Data System (ADS)

    Gupta, Kumar S.; Meljanac, S.; Samsarov, A.

    2012-02-01

    We study the behavior of a scalar field coupled to a noncommutative black hole which is described by a κ-cylinder Hopf algebra. We introduce a new class of realizations of this algebra which has a smooth limit as the deformation parameter vanishes. The twisted flip operator is independent of the choice of realization within this class. We demonstrate that the R-matrix is quasi-triangular up to the first order in the deformation parameter. Our results indicate how a scalar field might behave in the vicinity of a black hole at the Planck scale.

  1. Noncommutative approach to the cosmological constant problem

    SciTech Connect

    Garattini, Remo; Nicolini, Piero

    2011-03-15

    In this paper, we study the cosmological constant emerging from the Wheeler-DeWitt equation as an eigenvalue of the related Sturm-Liouville problem. We employ Gaussian trial functionals and we perform a mode decomposition to extract the transverse-traceless component, namely, the graviton contribution, at one loop. We implement a noncommutative-geometry-induced minimal length to calculate the number of graviton modes. As a result, we find regular graviton fluctuation energies for the Schwarzschild, de Sitter, and anti-de Sitter backgrounds. No renormalization scheme is necessary to remove infinities, in contrast to what happens in conventional approaches.

  2. Dixmier traces and non-commutative analysis

    NASA Astrophysics Data System (ADS)

    Sukochev, Fedor; Usachev, Alexandr

    2016-07-01

    In the present paper we review recent advances in the theory of Dixmier traces and aspects of their application to noncommutative analysis and geometry. We describe J. Dixmier's original construction of singular traces together with recent revisions of his ideas. We pay particular attention to subclasses of Dixmier traces related to exponentiation invariant extended limits and notions of measurability due to A. Connes. We discuss in detail the applications of Dixmier traces to the study of spectral properties of pseudo-differential operators and a very recent application of Dixmier traces in the study the Fréchet differentiability of Haagerup's Lp norm.

  3. Non-commutative tools for topological insulators

    NASA Astrophysics Data System (ADS)

    Prodan, Emil

    2010-06-01

    This paper reviews several analytic tools for the field of topological insulators, developed with the aid of non-commutative calculus and geometry. The set of tools includes bulk topological invariants defined directly in the thermodynamic limit and in the presence of disorder, whose robustness is shown to have nontrivial physical consequences for the bulk states. The set of tools also includes a general relation between the current of an observable and its edge index, a relation that can be used to investigate the robustness of the edge states against disorder. The paper focuses on the motivations behind creating such tools and on how to use them.

  4. 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.

  5. 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.

  6. Integrating Mass Spectrometry of Intact Protein Complexes into Structural Proteomics

    PubMed Central

    Hyung, Suk-Joon; Ruotolo, Brandon T.

    2013-01-01

    Summary Mass spectrometry analysis of intact protein complexes has emerged as an established technology for assessing the composition and connectivity within dynamic, heterogeneous multiprotein complexes at low concentrations and in the context of mixtures. As this technology continues to move forward, one of the main challenges is to integrate the information content of such intact protein complex measurements with other mass spectrometry approaches in structural biology. Methods such as H/D exchange, oxidative foot-printing, chemical cross-linking, affinity purification, and ion mobility separation add complementary information that allows access to every level of protein structure and organization. Here, we survey the structural information that can be retrieved by such experiments, demonstrate the applicability of integrative mass spectrometry approaches in structural proteomics, and look to the future to explore upcoming innovations in this rapidly-advancing area. PMID:22611037

  7. Spacetime Noncommutative Effect on Black Hole as Particle Accelerators

    NASA Astrophysics Data System (ADS)

    Ding, Chikun; Liu, Changqing; Quo, Qian

    2013-03-01

    We study the spacetime noncommutative effect on black hole as particle accelerators and, find that the particles falling from infinity with zero velocity cannot collide with unbound energy, either near the horizon or on the prograde ISCO when the noncommutative Kerr black hole is exactly extremal. Our results also show that the bigger of the spinning black hole's mass is the higher of center of mass energy that the particles obtain. For small and medium noncommutative Schwarzschild black hole, the collision energy depends on the black hole's mass.

  8. Location and direction dependent effects in collider physics from noncommutativity

    SciTech Connect

    Haghighat, Mansour; Okada, Nobuchika; Stern, Allen

    2010-07-01

    We examine the leading order noncommutative corrections to the differential and total cross sections for e{sup +}e{sup -{yields}}qq. After averaging over the Earth's rotation, the results depend on the latitude for the collider, as well as the direction of the incoming beam. They also depend on the scale and direction of the noncommutativity. Using data from LEP, we exclude regions in the parameter space spanned by the noncommutative scale and angle relative to the Earth's axis. We also investigate possible implications for phenomenology at the future International Linear Collider.

  9. 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.

  10. Capturing splicing complexes to study structure and mechanism.

    PubMed

    Jurica, Melissa S; Moore, Melissa J

    2002-11-01

    At its most basic level, pre-mRNA splicing can be described as two coordinated nuclease reactions that cleave an intron at either end and result in ligation of the flanking exons. The fact that these reactions are catalyzed by a approximately 3-MDa behemoth of protein and RNA (the spliceosome) challenges most biochemical and structural approaches currently used to characterize lesser-sized enzymes. In addition to this molecular complexity, the highly dynamic nature of splicing complexes provides additional hurdles for mechanistic studies or three-dimensional structure determination. Thus, the methods used to study the spliceosome often probe individual properties of the machine, but no complete, high-resolution picture of splicing catalysis has yet emerged. To facilitate biochemical and structural studies of native splicing complexes, we recently described purification of the catalytic form of the spliceosome (known as C complex). This native complex is suitable for electron microscopic structure determination by single-particle methods. In this paper, we describe the purification in detail and discuss additional methods for trapping and analyzing other splicing complexes. PMID:12431437

  11. 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.

  12. Entanglement entropy renormalization for the noncommutative scalar field coupled to classical BTZ geometry

    NASA Astrophysics Data System (ADS)

    Jurić, Tajron; Samsarov, Andjelo

    2016-05-01

    In this work, we consider a noncommutative (NC) massless scalar field coupled to the classical nonrotational BTZ geometry. In a manner of the theories where the gravity emerges from the underlying scalar field theory, we study the effective action and the entropy derived from this noncommutative model. In particular, the entropy is calculated by making use of the two different approaches, the brick-wall method and the heat kernel method designed for spaces with conical singularity. We show that the UV divergent structures of the entropy obtained through these two different methods agree with each other. It is also shown that the same renormalization condition that removes the infinities from the effective action can also be used to renormalize the entanglement entropy for the same system. Besides, the interesting feature of the NC model considered here is that it allows an interpretation in terms of an equivalent system comprising a commutative massive scalar field but in a modified geometry: that of the rotational BTZ black hole, the result that hints at a duality between the commutative and noncommutative systems in the background of a BTZ black hole.

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

    PubMed Central

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

    2013-01-01

    SUMMARY Recently, the structure, function, stability, and dynamics of subcellular structures, organelles, and multi-protein 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. PMID:23212797

  14. 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.

  15. 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.

  16. Surprise maximization reveals the community structure of complex networks

    NASA Astrophysics Data System (ADS)

    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.

  17. Surprise maximization reveals the community structure of complex networks.

    PubMed

    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

  18. Eocene Structural Development of the Valhalla Complex, Southeastern British Columbia

    NASA Astrophysics Data System (ADS)

    Carr, Sharon D.; Parrish, Randall R.; Brown, Richard L.

    1987-04-01

    The Valhalla complex, a Cordilleran metamorphic core complex, is a 100 km by 30 km structural culmination within the Omineca belt of southeastern British Columbia. It comprises sheets of granitic orthogneiss ranging in age from 100 to 59 Ma with intervening paragneiss of uncertain age and stratigraphic correlation. The complex is roofed by the ductile Valkyr shear zone and the ductile/brittle Slocan Lake fault zone; the upper plate comprises lower grade metasedimentary rocks intruded by middle Jurassic plutons. The Valkyr shear zone and the Slocan Lake fault zone deform 62 and 59 Ma granitic sheets in their footwalls. The easterly directed Valkyr shear zone is a 2 to 3 km thick zone of distributed ductile strain which is arched over the complex and is exposed around the periphery on the northern, western, and southern margins. The shear zone was active between 59 and 54 Ma under amphibolite facies conditions. The juxtaposition of upper and lower plates with different structural and metamorphic histories indicates that the Valkyr shear zone is a significant structure with large displacement. There is evidence to support an easterly rooting direction consistent with an extensional origin; its surface breakaway is suggested to be west of the Valhalla complex. The Slocan Lake fault zone on the eastern side of the complex is a gently (30°), easterly dipping ductile/brittle normal fault which roots to the east. It was active between 54 and approximately 45 Ma and truncates the Valkyr shear zone. Timing and structural relationships indicate that the Valkyr shear zone and the Slocan Lake fault zone are genetically related. Movement on the ductile Valkyr shear zone, arching of the complex, and displacement on the Slocan Lake fault zone occurred as a continuum in Early to Middle Eocene time. This paper documents the presence of significant Eocene ductile strain in the Valhalla complex and suggests that the role of extension in this region is more profound than had been

  19. Structural Assembly of Molecular Complexes Based on Residual Dipolar Couplings

    PubMed Central

    Berlin, Konstantin; O’Leary, Dianne P.; Fushman, David

    2010-01-01

    We present and evaluate a rigid-body molecular docking method, called PATIDOCK, that relies solely on the three-dimensional structure of the individual components and the experimentally derived residual dipolar couplings (RDC) for the complex. We show that, given an accurate ab initio predictor of the alignment tensor from a protein structure, it is possible to accurately assemble a protein-protein complex by utilizing the RDC’s sensitivity to molecular shape to guide the docking. The proposed docking method is robust against experimental errors in the RDCs and computationally efficient. We analyze the accuracy and efficiency of this method using experimental or synthetic RDC data for several proteins, as well as synthetic data for a large variety of protein-protein complexes. We also test our method on two protein systems for which the structure of the complex and steric-alignment data are available (Lys48-linked diubiquitin and a complex of ubiquitin and a ubiquitin-associated domain) and analyze the effect of flexible unstructured tails on the outcome of docking. The results demonstrate that it is fundamentally possible to assemble a protein-protein complex based solely on experimental RDC data and the prediction of the alignment tensor from three-dimensional structures. Thus, despite the purely angular nature of residual dipolar couplings, they can be converted into intermolecular distance/translational constraints. Additionally we show a method for combining RDCs with other experimental data, such as ambiguous constraints from interface mapping, to further improve structure characterization of the protein complexes. PMID:20550109

  20. Design of layered structure for thermal cloak with complex shape

    NASA Astrophysics Data System (ADS)

    Yuan, Xuebo; Lin, Guochang; Wang, Youshan

    2016-07-01

    Thermal cloaks have potential applications in thermal protection and sensing, and those cloaks with complex shapes are much more efficient in application. Layered discretization is a valid way to realize thermal cloaks designed through spatial transformation which are usually nonhomogeneous and anisotropic. However, previous studies are limited to two-dimensional cylindrical ones. Based on the theories of spatial transformation and effective medium, a four-step design method for layered structure of thermal cloak with complex shape is proposed. It is expected to realize the designed layered structure by utilizing the existing regular materials. According to the numerical simulations, the thermal cloaking performances of layered structures are good and close to that of the perfect thermal cloaks. This study has provided an effective way for realizing thermal cloak with complex shape.

  1. Structure and optoelectrical properties of photopolymerized PAn/DNA complex

    NASA Astrophysics Data System (ADS)

    Kobayashi, Norihisa; Morimoto, Taro; Ushikubo, Takahiro

    2007-09-01

    A Polyaniline (PAn)/ DNA complex has been successfully prepared by the photopolymerization of dimeric aniline via photocatalytic reaction of Ru(bpy) 3 2+ in the presence of DNA. The reaction occurs even in the solution at pH 3.0 - 6.0, due to the specific local "lower-pH" environment provided by DNA. The PAn in the complex has ordered structure associated with double-helical DNA. The complex contains photocatalyst, Ru(bpy) 3 2+, even after purification and the Ru(bpy) 3 2+ also works as emitting material. A Ru(bpy) 3 2+ complex-based red-emitting diode with a fast turn-on response was successfully fabricated by employing this novel, processable and water-soluble PAn/DNA complex.

  2. Visual Analysis of Complex Networks and Community Structure

    NASA Astrophysics Data System (ADS)

    Wu, Bin; Ye, Qi; Wang, Yi; Bi, Ran; Suo, Lijun; Hu, Deyong; Yang, Shengqi

    Many real-world domains can be represented as complex networks.A good visualization of a large and complex network is worth more than millions of words. Visual depictions of networks, which exploit human visual processing, are more prone to cognition of the structure of such complex networks than the computational representation. We star by briefly introducing some key technologies of network visualization, such as graph drawing algorithm and community discovery methods. The typical tools for network visualization are also reviewed. A newly developed software framework JSNVA for network visual analysis is introduced. Finally,the applications of JSNVA in bibliometric analysis and mobile call graph analysis are presented.

  3. Effect of Lanthanide Complex Structure on Cell Viability and Association

    PubMed Central

    2015-01-01

    A systematic study of the effect of hydrophobicity and charge on the cell viability and cell association of lanthanide metal complexes is presented. The terbium luminescent probes feature a macrocyclic polyaminocarboxylate ligand (DOTA) in which the hydrophobicity of the antenna and that of the carboxyamide pendant arms are independently varied. Three sensitizing antennas were investigated in terms of their function in vitro: 2-methoxyisophthalamide (IAM(OMe)), 2-hydroxyisophthalamide (IAM), and 6-methylphenanthridine (Phen). Of these complexes, Tb-DOTA-IAM exhibited the highest quantum yield, although the higher cell viability and more facile synthesis of the structurally related Tb-DOTA-IAM(OMe) platform renders it more attractive. Further modification of this latter core structure with carboxyamide arms featuring hydrophobic benzyl, hexyl, and trifluoro groups as well as hydrophilic amino acid based moieties generated a family of complexes that exhibit high cell viability (ED50 > 300 μM) regardless of the lipophilicity or the overall complex charge. Only the hexyl-substituted complex reduced cell viability to 60% in the presence of 100 μM complex. Additionally, cellular association was investigated by ICP-MS and fluorescence microscopy. Surprisingly, the hydrophobic moieties did not increase cell association in comparison to the hydrophilic amino acid derivatives. It is thus postulated that the hydrophilic nature of the 2-methoxyisophthalamide antenna (IAM(OMe)) disfavors the cellular association of these complexes. As such, responsive luminescent probes based on this scaffold would be appropriate for the detection of extracellular species. PMID:24901440

  4. 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.

  5. 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.

  6. Quantum Tunneling and Spectroscopy of Noncommutative Inspired Kerr Black Hole

    NASA Astrophysics Data System (ADS)

    Miao, Yan-Gang; Xue, Zhao; Zhang, Shao-Jun

    We discuss the thermodynamics of the noncommutative inspired Kerr black hole by means of a reformulated Hamilton-Jacobi method and a dimensional reduction technique. In order to investigate the effect of the angular momentum of the tunneling particle, we calculate the wave function to the first order of the WKB ansatz. Then, using a density matrix technique we derive the radiation spectrum from which the radiation temperature can be read out. Our results show that the radiation of this noncommutative inspired black hole corresponds to a modified temperature which involves the effect of noncommutativity. However, the angular momentum of the tunneling particle has no influence on the radiation temperature. Moreover, we analyze the entropy spectrum and verify that its quantization is modified neither by the noncommutativity of spacetime nor by the quantum correction of wave functions.

  7. Vortex scattering and intercommuting cosmic strings on a noncommutative spacetime

    SciTech Connect

    Joseph, Anosh; Trodden, Mark

    2010-02-15

    We study the scattering of noncommutative vortices, based on the noncommutative field theory developed in [A. P. Balachandran, T. R. Govindarajan, G. Mangano, A. Pinzul, B. A. Qureshi, and ?>S. Vaidya, Phys. Rev. D 75, 045009 (2007).], as a way to understand the interaction of cosmic strings. In the center-of-mass frame, the effects of noncommutativity vanish, and therefore the reconnection of cosmic strings occurs in an identical manner to the commutative case. However, when scattering occurs in a frame other than the center-of-mass frame, strings still reconnect but the well-known 90 deg. scattering no longer need correspond to the head-on collision of the strings, due to the breakdown of Lorentz invariance in the underlying noncommutative field theory.

  8. 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.

  9. 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.

  10. Net-Shape Tailored Fabrics For Complex Composite Structures

    NASA Technical Reports Server (NTRS)

    Farley, Gary L.

    1995-01-01

    Proposed novel looms used to make fabric preforms for complex structural elements, both stiffening elements and skin, from continuous fiber-reinforced composite material. Components of looms include custom reed and differential fabric takeup system. Structural parts made best explained by reference to curved "I" cross-section frame. Technology not limited to these fiber orientations or geometry; fiber angles, frame radius of curvature, frame height, and flange width changed along length of structure. Weaving technology equally applicable to structural skins, such as wing of fuselage skins.

  11. 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

  12. 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.

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

    PubMed

    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

  14. 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.

  15. Gravitational energy of a noncommutative Vaidya black hole

    NASA Astrophysics Data System (ADS)

    Mehdipour, S. Hamid

    2013-03-01

    In this paper we evaluate the components of the energy-momentum pseudotensors of Landau and Lifshitz for the noncommutative Vaidya spacetime. The effective gravitational mass experienced by a neutral test particle present at any finite distance in the gravitational field of the noncommutative Vaidya black hole is derived. Using the effective mass parameter one finds that the naked singularity is massless and this supports Seifert's conjecture.

  16. Aharonov-Bohm effect in a class of noncommutative theories

    NASA Astrophysics Data System (ADS)

    Das, Ashok; Falomir, H.; Nieto, M.; Gamboa, J.; Méndez, F.

    2011-08-01

    The Aharonov-Bohm effect including spin-noncommutative effects is considered. At linear order in θ, the magnetic field is gauge invariant although spatially strongly anisotropic. Despite this anisotropy, the Schrödinger-Pauli equation is separable through successive unitary transformations and the exact solution is found. The scattering amplitude is calculated and compared with the usual case. In the noncommutative Aharonov-Bohm case the differential cross section is independent of θ.

  17. Topics in Noncommutative Gauge Theories and Deformed Relativistic Theories

    NASA Astrophysics Data System (ADS)

    Chandra, Nitin

    2013-01-01

    This is my PhD thesis. In this thesis we study the gauge theories on noncommutative Moyal space. We find new static solitons and instantons in terms of the so called generalized Bose operators. Generalized Bose operators are constructed to describe reducible representation of the oscillator algebra. They create/annihilate k-quanta, k being a positive integer. We start with giving an alternative description to the already found static magnetic flux tube solutions of the noncommutative gauge theories in terms of generalized Bose operators. The Nielsen-Olesen vortex solutions found in terms of these operators reduce to the already found ones. On the contrary we find a class of new instaton solutions which are unitarily inequivalant to the the ones found from ADHM construction on noncommutative space. The charge of the instaton has a description in terms of the index representing the reducibility of the Fock space, i.e., k. After studying the static solitonic solutions in noncommutative Minkowski space and the instaton solutions in noncommutative Euclidean space we go on to study the implications of the time-space noncommutativity in Minkowski space. To understand it properly we study the time-dependent transitions of a forced harmonic oscillator in noncommutative 1+1 dimensional spacetime. We also try to understand the implications of the found results in the context of quantum optics. We then shift to the so called DSR theories which are related to a different kind of noncommutative (kappa-Minkowski) space. DSR (Doubly/Deformed Special Relativity) aims to search for an alternate relativistic theory which keeps a length/energy scale (the Planck scale) and a velocity scale (the speed of light scale) invariant. We study thermodynamics of an ideal gas in such a scenario.

  18. Non-commutativity, teleology and GRB time delay

    NASA Astrophysics Data System (ADS)

    Li, Miao; Pang, Yi; Wang, Yi

    2010-01-01

    We propose a model in which an energy-dependent time delay of a photon originates from space-time non-commutativity, the time delay is due to a non-commutative coupling between dilaton and photon. We predict that in our model, high energy photons with different momentum can either be delayed or superluminal, this may be related to a possible time delay reported by the Fermi LAT and Fermi GBM Collaborations.

  19. Coulomb's Law Modification in Nonlinear and in Noncommutative Electrodynamics

    NASA Astrophysics Data System (ADS)

    Gaete, Patricio; Schmidt, Iván

    We study the lowest-order modifications of the static potential for Born-Infeld electrodynamics and for the θ-expanded version of the noncommutative U(1) gauge theory, within the framework of the gauge-invariant but path-dependent variables formalism. The calculation shows a long-range correction (1/r5-type) to the Coulomb potential in Born-Infeld electrodynamics. However, the Coulomb nature of the potential (to order e2) is preserved in noncommutative electrodynamics.

  20. Generalized Uncertainty Relations in the Non-commutative Plane

    NASA Astrophysics Data System (ADS)

    Chung, Won Sang

    2015-09-01

    In this paper we study two-dimensional noncommutative quantum mechanics (NCQM) with the generalized uncertainty relations . We find the new NCQM algebra from the generalized uncertainty relations. We construct a operator commuting with and discuss two possibilities; One is the case that also commutes with and another is the case that does not commute with . For both case we consider a motion of a charged particle in a magnetic field with a harmonic oscillator potential in the noncommutative plane.

  1. Analyzing Large Protein Complexes by Structural Mass Spectrometry

    PubMed Central

    Kirshenbaum, Noam; Michaelevski, Izhak; Sharon, Michal

    2010-01-01

    Living cells control and regulate their biological processes through the coordinated action of a large number of proteins that assemble themselves into an array of dynamic, multi-protein complexes1. To gain a mechanistic understanding of the various cellular processes, it is crucial to determine the structure of such protein complexes, and reveal how their structural organization dictates their function. Many aspects of multi-protein complexes are, however, difficult to characterize, due to their heterogeneous nature, asymmetric structure, and dynamics. Therefore, new approaches are required for the study of the tertiary levels of protein organization. One of the emerging structural biology tools for analyzing macromolecular complexes is mass spectrometry (MS)2-5. This method yields information on the complex protein composition, subunit stoichiometry, and structural topology. The power of MS derives from its high sensitivity and, as a consequence, low sample requirement, which enables examination of protein complexes expressed at endogenous levels. Another advantage is the speed of analysis, which allows monitoring of reactions in real time. Moreover, the technique can simultaneously measure the characteristics of separate populations co-existing in a mixture. Here, we describe a detailed protocol for the application of structural MS to the analysis of large protein assemblies. The procedure begins with the preparation of gold-coated capillaries for nanoflow electrospray ionization (nESI). It then continues with sample preparation, emphasizing the buffer conditions which should be compatible with nESI on the one hand, and enable to maintain complexes intact on the other. We then explain, step-by-step, how to optimize the experimental conditions for high mass measurements and acquire MS and tandem MS spectra. Finally, we chart the data processing and analyses that follow. Rather than attempting to characterize every aspect of protein assemblies, this protocol

  2. Probing spacetime noncommutative constant via charged astrophysical black hole lensing

    NASA Astrophysics Data System (ADS)

    Ding, Chikun; Jing, Jiliang

    2011-10-01

    We study the influence of the spacetime noncommutative parameter on the strong field gravitational lensing in the noncommutative Reissner-Nordström black-hole spacetime. Supposing that the gravitational field of the supermassive central object of the Galaxy is described by this metric, we estimate the numerical values of the coefficients and observables for strong gravitational lensing. Our results show that with the increase of the parameter sqrt {\\vartheta } , the observables θ ∞ and r m decrease, while s increases. Our results also show that i) if sqrt {\\vartheta } is strong, the observables are close to those of the noncommutative Schwarzschild black hole lensing; ii) if sqrt {\\vartheta } is weak, the observables are close to those of the commutative Reissner-Nordström black hole lensing; iii) the detectable scope of ϑ in a noncommutative Reissner-Nordström black hole lensing is 0.12 ≤ sqrt {\\vartheta } ≤ 0.26 , which is wider than that in a noncommutative Schwarzschild black hole lensing, 0.18 ≤ sqrt {\\vartheta } ≤ 0.26 . This may offer a way to probe the spacetime noncommutative constant ϑ by the astronomical instruments in the future.

  3. 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.

  4. From structure to function via complex supramolecular dendrimer systems.

    PubMed

    Sun, Hao-Jan; Zhang, Shaodong; Percec, Virgil

    2015-06-21

    This tutorial review summarizes strategies elaborated for the discovery and prediction of programmed primary structures derived from quasi-equivalent constitutional isomeric libraries of self-assembling dendrons, dendrimers and dendronized polymers. These libraries demonstrate an 82% predictability, defined as the percentage of similar primary structures resulting in at least one conserved supramolecular shape with internal order. A combination of structural and retrostructural analysis that employs methodologies transplanted from structural biology, adapted to giant supramolecular assemblies was used for this process. A periodic table database of programmed primary structures was elaborated and used to facilitate the emergence of a diversity of functions in complex dendrimer systems via first principles. Assemblies generated by supramolecular and covalent polymer backbones were critically compared. Although by definition complex functional systems cannot be designed, this tutorial hints to a methodology based on database analysis principles to facilitate design principles that may help to mediate an accelerated emergence of chemical, physical and most probably also societal, political and economic complex systems on a shorter time scale and lower cost than by the current methods. This tutorial review is limited to the simplest, synthetically most accessible self-assembling minidendrons, minidendrimers and polymers dendronized with minidendrons that are best analyzed and elucidated at molecular, supramolecular and theoretical levels, and most used in other laboratories. These structures are all interrelated, and their principles expand in a simple way to their higher generations. PMID:25325787

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    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.

  7. Analyzing Complex and Structured Data via Unsupervised Learning Techniques

    NASA Astrophysics Data System (ADS)

    Polsterer, Kai Lars; Gieseke, Fabian; Gianniotis, Nikos; Kügler, Dennis

    2015-08-01

    In the last decades more and more dedicated all-sky-surveys created an enormous amount of data which is publicly available on the internet. The resulting datasets contain spatial, spectral, and temporal information which exhibit complex structures in the respective domain. The capability to deal with morphological features, spectral signatures, and complex time series data has become very important but is still a challenging task. A common approach when processing this kind of structured data is to extract representative features and use those for a further analysis. We present unsupervised learning approaches that help to visualize / cluster these complex data sets by e.g. deriving rotation / translation invariant prototypes or capturing the latent dynamics of time series without employing features and using echo-state-networks instead.

  8. 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. PMID:27563967

  9. Calculation of complex band structure for low symmetry lattices

    NASA Astrophysics Data System (ADS)

    Srivastava, Manoj; Zhang, Xiaoguang; Cheng, Hai-Ping

    2009-03-01

    Complex band structure calculation is an integral part of a first-principles plane-wave based quantum transport method. [1] The direction of decay for the complex wave vectors is also the transport direction. The existing algorithm [1] has the limitation that it only allows the transport direction along a lattice vector perpendicular to the basal plane formed by two other lattice vectors, e.g., the c-axis of a tetragonal lattice. We generalize this algorithm to nonorthogonal lattices with transport direction not aligned with any lattice vector. We show that this generalization leads to changes in the boundary conditions and the Schrodinger's equation projected to the transport direction. We present, as an example, the calculation of the complex band structure of fcc Cu along a direction perpendicular to the (111) basal plane. [1] Hyoung Joon Choi and Jisoon Ihm, Phys. Rev. B 59, 2267 (1999).

  10. Crystal structure of the human mitochondrial chaperonin symmetrical football complex.

    PubMed

    Nisemblat, Shahar; Yaniv, Oren; Parnas, Avital; Frolow, Felix; Azem, Abdussalam

    2015-05-12

    Human mitochondria harbor a single type I chaperonin system that is generally thought to function via a unique single-ring intermediate. To date, no crystal structure has been published for any mammalian type I chaperonin complex. In this study, we describe the crystal structure of a football-shaped, double-ring human mitochondrial chaperonin complex at 3.15 Å, which is a novel intermediate, likely representing the complex in an early stage of dissociation. Interestingly, the mitochondrial chaperonin was captured in a state that exhibits subunit asymmetry within the rings and nucleotide symmetry between the rings. Moreover, the chaperonin tetradecamers show a different interring subunit arrangement when compared to GroEL. Our findings suggest that the mitochondrial chaperonins use a mechanism that is distinct from the mechanism of the well-studied Escherichia coli system. PMID:25918392

  11. Crystal structure of the human mitochondrial chaperonin symmetrical football complex

    PubMed Central

    Nisemblat, Shahar; Yaniv, Oren; Parnas, Avital; Frolow, Felix; Azem, Abdussalam

    2015-01-01

    Human mitochondria harbor a single type I chaperonin system that is generally thought to function via a unique single-ring intermediate. To date, no crystal structure has been published for any mammalian type I chaperonin complex. In this study, we describe the crystal structure of a football-shaped, double-ring human mitochondrial chaperonin complex at 3.15 Å, which is a novel intermediate, likely representing the complex in an early stage of dissociation. Interestingly, the mitochondrial chaperonin was captured in a state that exhibits subunit asymmetry within the rings and nucleotide symmetry between the rings. Moreover, the chaperonin tetradecamers show a different interring subunit arrangement when compared to GroEL. Our findings suggest that the mitochondrial chaperonins use a mechanism that is distinct from the mechanism of the well-studied Escherichia coli system. PMID:25918392

  12. Modeling complex diffusion mechanisms in L1 2 -structured compounds

    NASA Astrophysics Data System (ADS)

    Zacate, M. O.; Lape, M.; Stufflebeam, M.; Evenson, W. E.

    2010-04-01

    We report on a procedure developed to create stochastic models of hyperfine interactions for complex diffusion mechanisms and demonstrate its application to simulate perturbed angular correlation spectra for the divacancy and 6-jump cycle diffusion mechanisms in L12-structured compounds.

  13. Structural properties of poly C-scleroglucan complexes.

    PubMed

    Sletmoen, Marit; Stokke, Bjørn T

    2005-10-15

    Successive changes of solvent conditions can be used to dissociate and reassociate the triple-helical structure of (1,3)-beta-D-glucans. Ultramicroscopic techniques have revealed a blend of circular and other structures following renaturation. When this solvent exchange process is carried out in the presence of certain polynucleotides, the process creates a novel macromolecular complex. Here, we use size exclusion chromatography (SEC) to study such (1,3)-beta-D-glucan-polynucleotide complexes. Online multi-angle laser-light scattering (MALLS) and refractive index (RI) detectors allowed determination of molecular weight and radius of gyration of the molecules. An ultraviolet (UV) detector allowed specific detection of the polynucleotide. The poly-cytidylic acid (poly C) shifted to coelution with the linear fraction of the scleroglucan following the renaturation of poly C-scleroglucan blends, indicating that poly C is incorporated in linear, but not in circular, structures of scleroglucan. This conclusion was consistent with AFM topographs that revealed a decreased fraction of circular structures upon addition of poly C during the renaturation process. The combined information about radius of gyration (R(g)) and molecular weight (M(w)) allowed us to conclude that the poly C-scleroglucan complexes are more dense and have a higher persistence length than linear scleroglucan triple helixes. The experimentally determined mass per unit length was used as a basis for elucidating possible molecular arrangements within the poly C-scleroglucan complex. PMID:16013056

  14. 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…

  15. 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.

  16. 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…

  17. Effects of Structural Complexity on Administrative Role Demands.

    ERIC Educational Resources Information Center

    Carr, John C.

    This report of a 1986 survey conducted in Maine addresses the relationship between stated time use demands on principals and superintendents and the structural complexity of the organizations in which they work. Researchers, comparing single with multiple schools and districts of supervisory responsibility, mailed the Maine Administrative…

  18. Hybrid structural model of the complete human ESCRT-0 complex.

    PubMed

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

    2009-03-11

    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 RH = 7.9 nm and is a 1:1 heterodimer. The 2.3 Angstroms 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 RH values for ESCRT-0 reveal a dynamic ensemble of conformations well suited for diverse functions. PMID:19278655

  19. Spontaneous PT-Symmetry Breaking for Systems of Noncommutative Euclidean Lie Algebraic Type

    NASA Astrophysics Data System (ADS)

    Dey, Sanjib; Fring, Andreas; Mathanaranjan, Thilagarajah

    2015-11-01

    We propose a noncommutative version of the Euclidean Lie algebra E 2. Several types of non-Hermitian Hamiltonian systems expressed in terms of generic combinations of the generators of this algebra are investigated. Using the breakdown of the explicitly constructed Dyson maps as a criterium, we identify the domains in the parameter space in which the Hamiltonians have real energy spectra and determine the exceptional points signifying the crossover into the different types of spontaneously broken PT-symmetric regions with pairs of complex conjugate eigenvalues. We find exceptional points which remain invariant under the deformation as well as exceptional points becoming dependent on the deformation parameter of the algebra.

  20. Structure and Abundance of Nitrous Oxide Complexes in Earth's Atmosphere.

    PubMed

    Salmon, Steven R; de Lange, Katrina M; Lane, Joseph R

    2016-04-01

    We have investigated the lowest energy structures and binding energies of a series of atmospherically relevant nitrous oxide (N2O) complexes using explicitly correlated coupled cluster theory. Specifically, we have considered complexes with nitrogen (N2-N2O), oxygen (O2-N2O), argon (Ar-N2O), and water (H2O-N2O). We have calculated rotational constants and harmonic vibrational frequencies for the complexes and the constituent monomers. Statistical mechanics was used to determine the thermodynamic parameters for complex formation as a function of temperature and pressure. These results, in combination with relevant atmospheric data, were used to estimate the abundance of N2O complexes in Earth's atmosphere as a function of altitude. We find that the abundance of N2O complexes in Earth's atmosphere is small but non-negligible, and we suggest that N2O complexes may contribute to absorption of terrestrial radiation and be relevant for understanding the atmospheric fate of N2O. PMID:26983553

  1. On complexity of trellis structure of linear block codes

    NASA Technical Reports Server (NTRS)

    Lin, Shu

    1990-01-01

    The trellis structure of linear block codes (LBCs) is discussed. The state and branch complexities of a trellis diagram (TD) for a LBC is investigated. The TD with the minimum number of states is said to be minimal. The branch complexity of a minimal TD for a LBC is expressed in terms of the dimensions of specific subcodes of the given code. Then upper and lower bounds are derived on the number of states of a minimal TD for a LBC, and it is shown that a cyclic (or shortened cyclic) code is the worst in terms of the state complexity among the LBCs of the same length and dimension. Furthermore, it is shown that the structural complexity of a minimal TD for a LBC depends on the order of its bit positions. This fact suggests that an appropriate permutation of the bit positions of a code may result in an equivalent code with a much simpler minimal TD. Boolean polynomial representation of codewords of a LBC is also considered. This representation helps in study of the trellis structure of the code. Boolean polynomial representation of a code is applied to construct its minimal TD. Particularly, the construction of minimal trellises for Reed-Muller codes and the extended and permuted binary primitive BCH codes which contain Reed-Muller as subcodes is emphasized. Finally, the structural complexity of minimal trellises for the extended and permuted, and double-error-correcting BCH codes is analyzed and presented. It is shown that these codes have relatively simple trellis structure and hence can be decoded with the Viterbi decoding algorithm.

  2. 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

  3. 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.

  4. 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.

  5. Structure of the membrane domain of respiratory complex I.

    PubMed

    Efremov, Rouslan G; Sazanov, Leonid A

    2011-08-25

    Complex I is the first and largest enzyme of the respiratory chain, coupling electron transfer between NADH and ubiquinone to the translocation of four protons across the membrane. It has a central role in cellular energy production and has been implicated in many human neurodegenerative diseases. The L-shaped enzyme consists of hydrophilic and membrane domains. Previously, we determined the structure of the hydrophilic domain. Here we report the crystal structure of the Esherichia coli complex I membrane domain at 3.0 Å resolution. It includes six subunits, NuoL, NuoM, NuoN, NuoA, NuoJ and NuoK, with 55 transmembrane helices. The fold of the homologous antiporter-like subunits L, M and N is novel, with two inverted structural repeats of five transmembrane helices arranged, unusually, face-to-back. Each repeat includes a discontinuous transmembrane helix and forms half of a channel across the membrane. A network of conserved polar residues connects the two half-channels, completing the proton translocation pathway. Unexpectedly, lysines rather than carboxylate residues act as the main elements of the proton pump in these subunits. The fourth probable proton-translocation channel is at the interface of subunits N, K, J and A. The structure indicates that proton translocation in complex I, uniquely, involves coordinated conformational changes in six symmetrical structural elements. PMID:21822288

  6. 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

  7. 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

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

    NASA Astrophysics Data System (ADS)

    Li, Tsung-Lung; Lu, Wen-Cai

    2015-06-01

    The geometric and electronic structures of potassium-adsorbed rubrene complexes are studied in this article. It is found that the potassium-rubrene (K1RUB) complexes inherit the main symmetry characteristics from their pristine counterparts and are thus classified into D2- and C2h-like complexes according to the relative orientations of the four phenyl side groups. The geometric structures of K1RUB 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 D2- and C2h-like K1RUB, however, exhibit their respective peculiarities. These peculiarities can be illustrated by their energy profiles of equilibrium structures. For the potassium adsorption-sites, the D2-like complexes show minimum-energy basins, whereas the C2h-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 D2-like complexes is most likely along the backbone in contrast to the C2h-like ones. Although the electronic structures of the minimum-energy structures of D2- and C2h-like K1RUB 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 than the other two on the opposite side, which leads to the largely enhanced

  9. 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.

  10. 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.

  11. Structural Preferences in Phosphanylthiolato Platinum(II) Complexes

    PubMed Central

    Duran, Josep; Real, Julio; Benet‐Buchholz, Jordi; Solà, Miquel

    2015-01-01

    Abstract The transition‐metal complexes of heterotopic phosphanylthiolato ligands are useful in various reactions which depend on the stereochemistry of the complexes. Bis‐chelate complex [Pt(SCH2CH2PPh2‐κ2 P,S)2] (1) was obtained in good yields by direct base‐free substitution reaction of the corresponding phosphanylthiol (HSCH2CH2PPh2) with K2PtCl4 or by oxidative addition of the same phosphanylthiol to Pt(PPh3)4. In agreement with the antisymbiosis rule, complex 1 shows a cis‐P,P arrangement in solid state crystallizing in the monoclinic system (C2/c). Density functional theory (DFT) calculations on 1 reveal the right characteristics for the preferred cis‐P,P arrangement, rationalizing its formation. Direct base‐free reaction of [PtCl2(1,5‐cyclooctadiene)] with one equivalent of the same phosphanylthiol produce the trinuclear complex [PtCl(μ‐SCH2CH2PPh2‐κ2 P,S)]3 (2) instead of the binuclear structure common in palladium and nickel derivatives. Crystals of 2 are triclinic (P 1‾ ) showing a sulfur‐bridging edge‐sharing cyclic trinuclear complex with square‐planar coordination geometry around the platinum atoms and a Pt3S3 cycle in skew‐boat conformation. This preference for the trinuclear structure was rationalized mechanistically and through conceptual DFT. PMID:27308212

  12. 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.

  13. A uranium (VI) complex: Synthesis, structural and thermal kinetic analysis

    NASA Astrophysics Data System (ADS)

    Goel, Nidhi

    2016-08-01

    A new complex [UO2(2,6-DNP)2phen] (1) (2,6-DNP = 2,6-dinitrophenol, phen = 1,10-phenanthroline) was synthesized, and identified by elemental analysis, IR, Powder XRD and single crystal X-ray crystallography. Crystal structure provides the abundant information's about the bonding and geometry around the U(VI) metal center. The thermal decomposition was studied by TG-DSC, and the kinetics of thermolysis was investigated by applying model fitting as well as isoconversional methods. Explosion delay measurement (De) was also evaluated to determine the response of this complex under the condition of rapid heating.

  14. Molecular structure, photophysical and thermal properties of samarium (III) complexes

    NASA Astrophysics Data System (ADS)

    Kumar, Rajeev; Singh, Udai P.

    2008-03-01

    Some 8-coordinated samarium (III) complexes ( 1- 4) having bipy (2,2'-bipyridine), terpy (2,2':6',2″-terpyridine), phen (1,10-phenanthroline) and tp [hydrotris (pyrazol-1-yl) borate] as supporting ligands have been synthesized and structurally characterized by different techniques including X-ray crystallography. The X-ray studies demonstrated that the complexes 1, 2 and 4 crystallized in triclinic space group P1¯ with cell dimensions a = 8.5640(2) Å, b = 8.8696(2) Å, c = 15.8608(4) Å for 1; a = 7.2113(9) Å, b = 11.0737(14) Å, c = 13.6289(18) Å for 2; a = 12.440(3) Å, b = 12.874(3) Å, c = 17.822(4) Å for 4, whereas the complex 3 crystallized in the monoclinic space group P2 1/ c with cell dimensions a = 9.472(3) Å, b = 17.092(5) Å, c = 14.516(5) Å. The IR study suggested that the azide is coordinated in 1, 3-bridging mode in complex 4. The photophysical properties of above complexes have been studied with ultraviolet absorption and emission spectral studies. Thermogravimetric analyses suggested that all these complexes undergo the complete decomposition to form the thermally stable samarium oxide (Sm 2O 3).

  15. Structural rearrangement through lanthanide contraction in dinuclear complexes.

    PubMed

    Hutchings, Amy-Jayne; Habib, Fatemah; Holmberg, Rebecca J; Korobkov, Ilia; Murugesu, Muralee

    2014-02-17

    A new series of lanthanide complexes was synthesized, and the geometry and preliminary magnetic measurements of the complexes were explored. The specific ligand used (N'-(2-hydroxy-3-methoxybenzylidene)benzhydrazide) (H2hmb) was synthesized using a Schiff-base approach and was employed due to the presence of a coordination pocket that is able to accommodate magnetically selective lanthanide ions. The series can be divided into two groups that are categorized by a drastic structural rearrangement. The first group, Type I, contains six analogous complexes with the formula [M(III)2(Hhmb)3(NCS)3]·2MeOH·py (M = Y 1, Eu 2, Gd 3, Tb 4, Dy 5, Ho 6), while the second group, Type II, contains two dinuclear complexes with formula [M(III)2(Hhmb)2(NCS)4(MeOH)2] (M = Er 7, and Yb 8). Single-crystal X-ray analysis revealed that all M(III) ions in Type I exhibit monocapped distorted square antiprismatic geometries, while those of Type II exhibit distorted dodecahedron geometry. The direct current and alternating current magnetic measurements were carried out on all complexes, with 5, 7, and 8 exhibiting slow relaxation of the magnetization under an applied optimum dc field. Furthermore, complex 8 is the first example of a dinuclear Yb-based single-molecule magnet showing field-dependent multiple relaxation processes. PMID:24499030

  16. Noncommutative Chern-Simons gauge and gravity theories and their geometric Seiberg-Witten map

    NASA Astrophysics Data System (ADS)

    Aschieri, Paolo; Castellani, Leonardo

    2014-11-01

    We use a geometric generalization of the Seiberg-Witten map between noncommutative and commutative gauge theories to find the expansion of noncommutative Chern-Simons (CS) theory in any odd dimension D and at first order in the noncommutativity parameter θ. This expansion extends the classical CS theory with higher powers of the curvatures and their derivatives.

  17. Semi-Classical Localisation Properties of Quantum Oscillators on a Noncommutative Configuration Space

    NASA Astrophysics Data System (ADS)

    Benatti, Fabio; Gouba, Laure

    2015-11-01

    When dealing with the classical limit of two quantum mechanical oscillators on a noncommutative configuration space, the limits corresponding to the removal of configuration-space noncommutativity and position-momentum noncommutativity do not commute. We address this behaviour from the point of view of the phase-space localisation properties of the Wigner functions of coherent states under the two limits.

  18. CryoEM structure of yeast cytoplasmic exosome complex.

    PubMed

    Liu, Jun-Jie; Niu, Chu-Ya; Wu, Yao; Tan, Dan; Wang, Yang; Ye, Ming-Da; Liu, Yang; Zhao, Wenwei; Zhou, Ke; Liu, Quan-Sheng; Dai, Junbiao; Yang, Xuerui; Dong, Meng-Qiu; Huang, Niu; Wang, Hong-Wei

    2016-07-01

    The eukaryotic multi-subunit RNA exosome complex plays crucial roles in 3'-to-5' RNA processing and decay. Rrp6 and Ski7 are the major cofactors for the nuclear and cytoplasmic exosomes, respectively. In the cytoplasm, Ski7 helps the exosome to target mRNAs for degradation and turnover via a through-core pathway. However, the interaction between Ski7 and the exosome complex has remained unclear. The transaction of RNA substrates within the exosome is also elusive. In this work, we used single-particle cryo-electron microscopy to solve the structures of the Ski7-exosome complex in RNA-free and RNA-bound forms at resolutions of 4.2 Å and 5.8 Å, respectively. These structures reveal that the N-terminal domain of Ski7 adopts a structural arrangement and interacts with the exosome in a similar fashion to the C-terminal domain of nuclear Rrp6. Further structural analysis of exosomes with RNA substrates harboring 3' overhangs of different length suggests a switch mechanism of RNA-induced exosome activation in the through-core pathway of RNA processing. PMID:27174052

  19. A zeolite family with expanding structural complexity and embedded isoreticular structures

    NASA Astrophysics Data System (ADS)

    Guo, Peng; Shin, Jiho; Greenaway, Alex G.; Min, Jung Gi; Su, Jie; Choi, Hyun June; Liu, Leifeng; Cox, Paul A.; Hong, Suk Bong; Wright, Paul A.; Zou, Xiaodong

    2015-08-01

    The prediction and synthesis of new crystal structures enable the targeted preparation of materials with desired properties. Among porous solids, this has been achieved for metal-organic frameworks, but not for the more widely applicable zeolites, where new materials are usually discovered using exploratory synthesis. Although millions of hypothetical zeolite structures have been proposed, not enough is known about their synthesis mechanism to allow any given structure to be prepared. Here we present an approach that combines structure solution with structure prediction, and inspires the targeted synthesis of new super-complex zeolites. We used electron diffraction to identify a family of related structures and to discover the structural `coding' within them. This allowed us to determine the complex, and previously unknown, structure of zeolite ZSM-25 (ref. 8), which has the largest unit-cell volume of all known zeolites (91,554 cubic ångströms) and demonstrates selective CO2 adsorption. By extending our method, we were able to predict other members of a family of increasingly complex, but structurally related, zeolites and to synthesize two more-complex zeolites in the family, PST-20 and PST-25, with much larger cell volumes (166,988 and 275,178 cubic ångströms, respectively) and similar selective adsorption properties. Members of this family have the same symmetry, but an expanding unit cell, and are related by hitherto unrecognized structural principles; we call these family members embedded isoreticular zeolite structures.

  20. Polymer complexes. LX. Supramolecular coordination and structures of N(4-(acrylamido)-2-hydroxybenzoic acid) polymer complexes

    NASA Astrophysics Data System (ADS)

    Ghoneim, M. M.; El-Sonbati, A. Z.; El-Bindary, A. A.; Diab, M. A.; Serag, L. S.

    2015-04-01

    A number of novel polymer complexes of various anions of copper(II), cobalt(II), nickel(II) and uranyl(II) with N(4-(acrylamido)-2-hydroxy benzoic acid) (ABH) have been synthesized and characterized by elemental analysis, IR, 1H NMR, magnetic susceptibility measurements, electronic spin resonance, vibrational spectra and thermal analysis. The molecular structures of the ligand are optimized theoretically and the quantum chemical parameters are calculated. Tentative structures for the polymeric metal complexes due to their potential application are also suggested. The IR data exhibit the coordination of ONO2/OAc/SO4 with the metal ions in the polymeric metal complex. Vibrational spectra indicate coordination of carboxylate oxygen and phenolic OH of the ligand giving a MO4 square planar chromophore. Ligand field ESR spectra support square planar geometry around Cu(II). The thermal decomposition of the polymer complexes were discussed in relation to structure, and the thermodynamic parameters of the decomposition stages were evaluated applying Coast-Redfern and Horowitz-Metzger methods.

  1. STRIPAK Complexes: structure, biological function, and involvement in human diseases

    PubMed Central

    Hwang, Juyeon; Pallas, David C.

    2014-01-01

    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–like complexes in cellular processes of multiple organisms. These studies have identified novel STRIPAK or 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 will explore possible roles of striatin family complexes in disease, especially cerebral cavernous malformation. PMID:24333164

  2. Heterodimeric structure of superoxide dismutase in complex with its metallochaperone

    SciTech Connect

    Lamb, A.L.; Torres, A.S.; O'Halloran, T.V.; Rosenzweig, A.C.

    2010-03-08

    The copper chaperone for superoxide dismutase (CCS) activates the eukaryotic antioxidant enzyme copper, zinc superoxide dismutase (SOD1). The 2.9 {angstrom} resolution structure of yeast SOD1 complexed with yeast CCS (yCCS) reveals that SOD1 interacts with its metallochaperone to form a complex comprising one monomer of each protein. The heterodimer interface is remarkably similar to the SOD1 and yCCS homodimer interfaces. Striking conformational rearrangements are observed in both the chaperone and target enzyme upon complex formation, and the functionally essential C-terminal domain of yCCS is well positioned to play a key role in the metal ion transfer mechanism. This domain is linked to SOD1 by an intermolecular disulfide bond that may facilitate or regulate copper delivery.

  3. 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. PMID:26478316

  4. 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

    2015-05-01

    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

  5. Parallel Structural Evolution of Mitochondrial Ribosomes and OXPHOS Complexes

    PubMed Central

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

    2015-01-01

    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

  6. Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes.

    PubMed

    Martin, Juliette; Regad, Leslie; Etchebest, Catherine; Camproux, Anne-Claude

    2008-11-15

    Interresidue protein contacts in proteins structures and at protein-protein interface are classically described by the amino acid types of interacting residues and the local structural context of the contact, if any, is described using secondary structures. In this study, we present an alternate analysis of interresidue contact using local structures defined by the structural alphabet introduced by Camproux et al. This structural alphabet allows to describe a 3D structure as a sequence of prototype fragments called structural letters, of 27 different types. Each residue can then be assigned to a particular local structure, even in loop regions. The analysis of interresidue contacts within protein structures defined using Voronoï tessellations reveals that pairwise contact specificity is greater in terms of structural letters than amino acids. Using a simple heuristic based on specificity score comparison, we find that 74% of the long-range contacts within protein structures are better described using structural letters than amino acid types. The investigation is extended to a set of protein-protein complexes, showing that the similar global rules apply as for intraprotein contacts, with 64% of the interprotein contacts best described by local structures. We then present an evaluation of pairing functions integrating structural letters to decoy scoring and show that some complexes could benefit from the use of structural letter-based pairing functions. PMID:18491388

  7. Lithium, sodium and potassium picolyl complexes: syntheses, structures and bonding.

    PubMed

    Kennedy, Alan R; Mulvey, Robert E; Urquhart, Robert I; Robertson, Stuart D

    2014-10-14

    Synthetically important for introducing a picolyl scaffold into a molecular construction, alkali metallated picoline (methylpyridine) complexes are also interesting in their own right for the diversity of their ligand-metal bonding possibilities. Here the syntheses of seven new such complexes are reported: namely three 4-picoline derivatives 4-picLi·Me6TREN, 1, 4-picNa·Me6TREN, 2, and [4-picK·2(4-picH)]∞, 3; and four 2-picoline derivatives, 2-picLi·Me6TREN, 4, 2-picLi·PMDETA, 4', 2-picNa·Me6TREN, 5, and [2-picK·PMDETA]2, 6' [where pic = NC5H4(CH2); Me6TREN = tris(N,N-dimethyl-2-aminoethyl)amine, (Me2NCH2CH2)3N; PMDETA = N,N,N',N'',N''-pentamethyldiethylenetriamine, (Me2NCH2CH2)2NMe]. X-ray crystallographic studies establish that the lighter alkali metal complexes 1, 2, 4' and 5 adopt monomeric structures in contrast to the polymeric and dimeric arrangements adopted by potassium complexes 3 and 6' respectively. All complexes have also been characterized by solution NMR spectroscopy ((1)H, (13)C, and where relevant (7)Li). This study represents the first example of sodium and potassium picolyl complexes to be isolated and characterized. DOSY (Diffusion-Ordered Spectroscopy) experiments performed on 4 and 4' suggest both compounds retain their monomeric constitutions in C6D6 solution. Discussion focuses on the influence of the metal and neutral donor molecule on the structures and the nature of the ligand-metal (enamido versus aza-allylic) interactions. PMID:24770550

  8. Chelation-Induced Polymer Structural Hierarchy/Complexity in Water.

    PubMed

    Han, Jie; Zhou, Kaiyi; Zhu, Xuechao; Yu, Qiuping; Ding, Yi; Lu, Xinhua; Cai, Yuanli

    2016-08-01

    Understanding nanoscale structural hierarchy/complexity of hydrophilic flexible polymers is imperative because it can be viewed as an analogue to protein-alike superstructures. However, current understanding is still in infancy. Herein the first demonstration of nanoscale structural hierarchy/complexity via copper chelation-induced self-assembly (CCISA) is presented. Hierarchically-ordered colloidal networks and disks can be achieved by deliberate control of spacer length and solution pH. Dynamic light scattering, transmission electron microscopy, and atomic force microscopy demonstrate that CCISA underwent supramolecular-to-supracolloidal stepwise-growth mechanism, and underline amazing prospects to the hierarchically-ordered superstructures of hydrophilic flexible polymers in water. PMID:27219860

  9. Community structure from spectral properties in complex networks

    NASA Astrophysics Data System (ADS)

    Servedio, V. D. P.; Colaiori, F.; Capocci, A.; Caldarelli, G.

    2005-06-01

    We analyze the spectral properties of complex networks focusing on their relation to the community structure, and develop an algorithm based on correlations among components of different eigenvectors. The algorithm applies to general weighted networks, and, in a suitably modified version, to the case of directed networks. Our method allows to correctly detect communities in sharply partitioned graphs, however it is useful to the analysis of more complex networks, without a well defined cluster structure, as social and information networks. As an example, we test the algorithm on a large scale data-set from a psychological experiment of free word association, where it proves to be successful both in clustering words, and in uncovering mental association patterns.

  10. Functionalised Clathrochelate Complexes--New Building Blocks for Supramolecular Structures.

    PubMed

    Wise, Matthew D; Severin, Kay

    2015-01-01

    Tris(dioxime) iron(II) clathrochelate complexes functionalised with 3- and 4-pyridyl groups have been employed as building blocks in the preparation of supramolecular structures by coordination-driven self-assembly. These complexes possess a number of desirable characteristics, being straightforward to synthesise and offering ample opportunity for steric and functional modification. Clathrochelate-based 4,4'-bipyridyl metalloligands from 1.5 nm to 5.4 nm in length were prepared in up to two steps and their potential as building blocks for supramolecular architectures demonstrated through the preparation of a discrete molecular square and a three dimensional (3D) coordination polymer. Furthermore, the structure-directing capability of clathrochelate building blocks was illustrated through the synthesis of octahedral cage compounds, which are capable of encapsulating the large, hydrophobic BPh4- anion in aqueous solvent mixtures. PMID:26668936

  11. The Analysis of Complex Structure for China Education Network

    NASA Astrophysics Data System (ADS)

    Deng, Zhu-Jun; Zhang, Ning

    We collected the data of the documents and their links of China Education and Research Network’s which construct the complex directed network China Education Network (CEN) with large amount of documents with their edges (URLs). This paper analyzes some statistical properties, including degree distributions, average path length, clustering coefficient, and the community structure of China Education Network basing on the practical data. By analyzing the practical data, we found that the in-degree and out-degree distribution of the CEN has power-law tail and the network displays both properties of small world and scale free. The CEN has a considerably small average path length and its clustering coefficient is in the mediate. As a large scale complex network, China Education Network clearly present its community structure in which the colleges in a school constitute communities generally with a large modularity.

  12. Structure and dynamics of complex liquid water: Molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    S, Indrajith V.; Natesan, Baskaran

    2015-06-01

    We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.

  13. Linking structural features of protein complexes and biological function.

    PubMed

    Sowmya, Gopichandran; Breen, Edmond J; Ranganathan, Shoba

    2015-09-01

    Protein-protein interaction (PPI) establishes the central basis for complex cellular networks in a biological cell. Association of proteins with other proteins occurs at varying affinities, yet with a high degree of specificity. PPIs lead to diverse functionality such as catalysis, regulation, signaling, immunity, and inhibition, playing a crucial role in functional genomics. The molecular principle of such interactions is often elusive in nature. Therefore, a comprehensive analysis of known protein complexes from the Protein Data Bank (PDB) is essential for the characterization of structural interface features to determine structure-function relationship. Thus, we analyzed a nonredundant dataset of 278 heterodimer protein complexes, categorized into major functional classes, for distinguishing features. Interestingly, our analysis has identified five key features (interface area, interface polar residue abundance, hydrogen bonds, solvation free energy gain from interface formation, and binding energy) that are discriminatory among the functional classes using Kruskal-Wallis rank sum test. Significant correlations between these PPI interface features amongst functional categories are also documented. Salt bridges correlate with interface area in regulator-inhibitors (r = 0.75). These representative features have implications for the prediction of potential function of novel protein complexes. The results provide molecular insights for better understanding of PPIs and their relation to biological functions. PMID:26131659

  14. 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.

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

    DOE PAGESBeta

    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 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

  16. Structure and Interactions in Polypeptide Cationic Lipid Complexes

    NASA Astrophysics Data System (ADS)

    Subramanian, G.; Hjelm, R. P.; Smith, G. S.; Safinya, C. R.

    1998-03-01

    Complexes of polypeptides and cationic lipids have elicited much interest recently because of their potential in developing novel biomolecular materials. We have investigated the solution structure of complexes made from the anionic polypeptide poly-L-glutamic acid (PGA), the cationic lipid DDAB, and the neutral lipid DLPC. X-ray scattering and SANS revealed the structure of the complexes to be multilamellar in nature with the PGA molecules sandwiched in between the lipid bilayers and that the PGA molecules are in the disordered state on the plane of the bilayers. Lipid dilution experiments at charge neutrality indicated that the "d" spacing of the complexes monotonically increases from 39Åupto 60Åat very high dilutions. While lipid chain stretching alone does not account for the increase in "d" spacing, we propose a "pinching" mechanism where the PGA and DDAB molecules are localized to form a tightly packed layer. Away from these "pinches" the system behaves as a pure DLPC membrane with an equilibrium spacing of 60ÅSupported by NSF-DMR-9624091, PRF-31352-AC7, and Los Alamos-STB/UC:96-108.

  17. 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.

  18. 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. PMID:21987109

  19. 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

  20. Structural models for alkali-metal complexes of polyacetylene

    NASA Astrophysics Data System (ADS)

    Murthy, N. S.; Shacklette, L. W.; Baughman, R. H.

    1990-02-01

    Structural models for a stage-2 complex are proposed for polyacetylene doped with less than about 0.1 potassium or rubidium atoms per carbon. These structures utilize as a basic motif an alkali-metal column surrounded by four planar-zig-zag polyacetylene chains, a structure found at the highest dopant levels. In the new stage-2 structures, each polyacetylene chain neighbors only one alkali-metal column, so the phase contains four polymer chains per alkali-metal column. Basic structural aspects for stage-1 and stage-2 structures are now established for both potassium- and rubidium-doped polyacetylene. X-ray-diffraction and electrochemical data show that undoped and doped phases coexist at low dopant concentrations (<0.06 K atom per C). X-ray-diffraction data, down to a Bragg spacing of 1.3 Å, for polyacetylene heavily doped with potassium (0.125-0.167 K atom per C) is fully consistent with our previously proposed stage-1 tetragonal unit cell containing two polyacetylene chains per alkali-metal column. There is no evidence for our samples requiring a distortion to a monoclinic unit cell as reported by others for heavily doped samples. The nature of structural transformations and the relationship between structure and electronic properties are discussed for potassium-doped polyacetylene.

  1. Control of complex networks requires both structure and dynamics.

    PubMed

    Gates, Alexander J; Rocha, Luis M

    2016-01-01

    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. PMID:27087469

  2. Control of complex networks requires both structure and dynamics

    PubMed Central

    Gates, Alexander J.; Rocha, Luis M.

    2016-01-01

    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. PMID:27087469

  3. Generating a 2D Representation of a Complex Data Structure

    NASA Technical Reports Server (NTRS)

    James, Mark

    2006-01-01

    A computer program, designed to assist in the development and debugging of other software, generates a two-dimensional (2D) representation of a possibly complex n-dimensional (where n is an integer >2) data structure or abstract rank-n object in that other software. The nature of the 2D representation is such that it can be displayed on a non-graphical output device and distributed by non-graphical means.

  4. 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.

  5. Capacitance extraction from complex 3D interconnect structures

    SciTech Connect

    Cartwright, D.; Csanak, G.; George, D.; Walker, R.; Kuprat, A.; Dengi, A.; Grobman, W.

    1999-06-01

    A new tool has been developed for calculating the capacitance matrix for complex 3D interconnect structures involving multiple layers of irregularly shaped interconnect, imbedded in different dielectric materials. This method utilizes a new 3D adaptive unstructured grid capability, and a linear finite element algorithm. The capacitance is determined from the minimum in the total system energy as the nodes are varied to minimize the error in the electric field in the dielectric(s).

  6. Artificial Market Simulation with Embedded Complex Network Structures

    NASA Astrophysics Data System (ADS)

    Uchida, Makoto; Shirayama, Susumu

    We investigate a factor of the `network effect' that affects on communication service markets by a multi-agent based simulation approach. The network effect is one of a market characteristic, whereby the benefit of a service or a product increase with use. So far, the network effect has been studied in terms of macroscopic metrics, and interaction patterns of consumers in the market were often ignored. To investigate an infulence of structures of the interaction patterns, we propose a multi-agent based model for a communication serivce market, in which embedded complex network structures are considered as an interaction pattern of agents. Using several complex network models as the interaction patterns, we study the dynamics of a market in which two providers are competing. By a series of simulations, we show that the structural properties of the complex networks, such as the clustering coefficient and degree correlations, are the major factors of the network effect. We also discuss an adequate model of the interaction pattern for reproducing the market dynamics in the real world by performing simulations exploiting with a real data of social network.

  7. The structure of the β-barrel assembly machinery complex

    PubMed Central

    Bakelar, Jeremy; Buchanan, Susan K.; Noinaj, Nicholas

    2016-01-01

    β-barrel outer membrane proteins (OMPs) are found within the outer membranes (OM) of Gram-negative bacteria and are essential for nutrient import, signaling, and adhesion. While the exact mechanism is unknown, a 200 kDa five component complex called the β-barrel assembly machinery (BAM) complex has been implicated in the biogenesis of OMPs. Here, we report the structure of the BAM complex from E. coli, revealing that binding of the accessory proteins BamCDE modulates the conformation of BamA, the central component of the complex, which may regulate the function of the BAM complex. The periplasmic domain of BamA was found in a closed state that prevents access to the barrel lumen from the periplasm, indicating substrate OMPs likely do not enter the barrel during biogenesis. Further, the first eight strands of the β-barrel domain undergo an unprecedented conformational shift leading to opening of the exit pore and rearrangement at the lateral gate. PMID:26744406

  8. Structure and function of the Mitochondrial Calcium Uniporter complex

    PubMed Central

    De Stefani, Diego; Patron, Maria; Rizzuto, Rosario

    2015-01-01

    The Mitochondrial Calcium Uniporter (MCU) is the critical protein of the inner mitochondrial membrane mediating the electrophoretic Ca2+ uptake into the matrix. It plays a fundamental role in the shaping of global calcium signaling and in the control of aerobic metabolism as well as apoptosis. Two features of mitochondrial calcium signaling have been known for a long time: i) mitochondrial Ca2+ uptake widely varies among cells and tissues, and ii) channel opening strongly relies on the extramitochondrial Ca2+ concentration, with low activity at resting [Ca2+] and high capacity as soon as calcium signaling is activated. Such complexity requires a specialized molecular machinery, with several primary components can be variably gathered together in order to match energy demands and protect from toxic stimuli. In line with this, MCU is now recognized to be part of a macromolecular complex known as the MCU complex. Our understanding of the structure and function of the MCU complex is now growing promptly, revealing an unexpected complexity that highlights the pleiotropic role of mitochondrial Ca2+ signals. PMID:25896525

  9. Structure and function of the mitochondrial calcium uniporter complex.

    PubMed

    De Stefani, Diego; Patron, Maria; Rizzuto, Rosario

    2015-09-01

    The mitochondrial calcium uniporter (MCU) is the critical protein of the inner mitochondrial membrane mediating the electrophoretic Ca²⁺ uptake into the matrix. It plays a fundamental role in the shaping of global calcium signaling and in the control of aerobic metabolism as well as apoptosis. Two features of mitochondrial calcium signaling have been known for a long time: i) mitochondrial Ca²⁺ uptake widely varies among cells and tissues, and ii) channel opening strongly relies on the extramitochondrial Ca²⁺ concentration, with low activity at resting [Ca²⁺] and high capacity as soon as calcium signaling is activated. Such complexity requires a specialized molecular machinery, with several primary components can be variably gathered together in order to match energy demands and protect from toxic stimuli. In line with this, MCU is now recognized to be part of a macromolecular complex known as the MCU complex. Our understanding of the structure and function of the MCU complex is now growing promptly, revealing an unexpected complexity that highlights the pleiotropic role of mitochondrial Ca²⁺ signals. This article is part of a Special Issue entitled: 13th European Symposium on Calcium. PMID:25896525

  10. Colored Extensions of GLq(2) Quantum Group and Related Noncommutative Planes

    NASA Astrophysics Data System (ADS)

    Basu-Mallick, B.

    An infinite-dimensional quantum group, containing the standard GLq(2) and GLp,q(2) cases as different subalgebras, is constructed by using a colored braid group representation. It turns out that all algebraic relations occurring in this “colored” quantum group can be expressed in the Heisenberg-Weyl form, for a nontrivial choice of corresponding basis elements. Moreover a novel quadratic algebra, defined through Kac-Moody-like generators, is obtained by making some power series expansion of related monodromy matrix elements. The structure of invariant noncommutative planes associated with this “colored” quantum group has also been investigated.

  11. Noncommutative Inverse Scattering Method for the Kontsevich System

    NASA Astrophysics Data System (ADS)

    Arthamonov, Semeon

    2015-09-01

    We formulate an analog of Inverse Scattering Method for integrable systems on noncommutative associative algebras. In particular, we define Hamilton flows, Casimir elements and noncommutative analog of the Lax matrix. The noncommutative Lax element generates infinite family of commuting Hamilton flows on an associative algebra. The proposed approach to integrable systems on associative algebras satisfies certain universal property, in particular, it incorporates both classical and quantum integrable systems as well as provides a basis for further generalization. We motivate our definition by explicit construction of noncommutative analog of Lax matrix for a system of differential equations on associative algebra recently proposed by Kontsevich. First, we present these equations in the Hamilton form by defining a bracket of Loday type on the group algebra of the free group with two generators. To make the definition more constructive, we utilize (with certain generalizations) the Van den Bergh approach to Loday brackets via double Poisson brackets. We show that there exists an infinite family of commuting flows generated by the noncommutative Lax element.

  12. 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.

  13. Non-commutativity from the double sigma model

    NASA Astrophysics Data System (ADS)

    Polyakov, Dimitri; Wang, Peng; Wu, Houwen; Yang, Haitang

    2015-03-01

    We show how non-commutativity arises from commutativity in the double sigma model. We demonstrate that this model is intrinsically non-commutative by calculating the propagators. In the simplest phase configuration, there are two dual copies of commutative theories. In general rotated frames, one gets a non-commutative theory and a commutative partner. Thus a non-vanishing B also leads to a commutative theory. Our results imply that O( D, D) symmetry unifies not only the big and small torus physics, but also the commutative and non-commutative theories. The physical interpretations of the metric and other parameters in the double sigma model are completely dictated by the boundary conditions. The open-closed relation is also an O( D, D) rotation and naturally leads to the Seiberg-Witten map. Moreover, after applying a second dual rotation, we identify the description parameter in the Seiberg-Witten map as an O( D, D) group parameter and all theories are non-commutative under this composite rotation. As a bonus, the propagators of general frames in double sigma model for open string are also presented.

  14. 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

  15. 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

  16. 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. PMID:26369172

  17. GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking

    PubMed Central

    Heo, Lim; Lee, Hasup; Seok, Chaok

    2016-01-01

    Protein-protein docking methods have been widely used to gain an atomic-level understanding of protein interactions. However, docking methods that employ low-resolution energy functions are popular because of computational efficiency. Low-resolution docking tends to generate protein complex structures that are not fully optimized. GalaxyRefineComplex takes such low-resolution docking structures and refines them to improve model accuracy in terms of both interface contact and inter-protein orientation. This refinement method allows flexibility at the protein interface and in the overall docking structure to capture conformational changes that occur upon binding. Symmetric refinement is also provided for symmetric homo-complexes. This method was validated by refining models produced by available docking programs, including ZDOCK and M-ZDOCK, and was successfully applied to CAPRI targets in a blind fashion. An example of using the refinement method with an existing docking method for ligand binding mode prediction of a drug target is also presented. A web server that implements the method is freely available at http://galaxy.seoklab.org/refinecomplex. PMID:27535582

  18. GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking.

    PubMed

    Heo, Lim; Lee, Hasup; Seok, Chaok

    2016-01-01

    Protein-protein docking methods have been widely used to gain an atomic-level understanding of protein interactions. However, docking methods that employ low-resolution energy functions are popular because of computational efficiency. Low-resolution docking tends to generate protein complex structures that are not fully optimized. GalaxyRefineComplex takes such low-resolution docking structures and refines them to improve model accuracy in terms of both interface contact and inter-protein orientation. This refinement method allows flexibility at the protein interface and in the overall docking structure to capture conformational changes that occur upon binding. Symmetric refinement is also provided for symmetric homo-complexes. This method was validated by refining models produced by available docking programs, including ZDOCK and M-ZDOCK, and was successfully applied to CAPRI targets in a blind fashion. An example of using the refinement method with an existing docking method for ligand binding mode prediction of a drug target is also presented. A web server that implements the method is freely available at http://galaxy.seoklab.org/refinecomplex. PMID:27535582

  19. The minimal and the new minimal supersymmetric Grand Unified Theories on noncommutative space-time

    NASA Astrophysics Data System (ADS)

    Martín, C. P.

    2013-08-01

    We construct noncommutative versions of both the minimal and the new minimal supersymmetric Grand Unified Theories (GUTs). The enveloping-algebra formalism is used to carry out such constructions. The beautiful formulation of the Higgs sector of these noncommutative theories is a consequence of the fact that, in the GUTs at hand, the ordinary Higgs fields can be realized as elements of the Clifford algebra {C}{l}_{10}( {C}). In the noncommutative supersymmetric GUTs we formulate, supersymmetry is linearly realized by the noncommutative fields; but it is not realized by the ordinary fields that define those noncommutative fields via the Seiberg-Witten map.

  20. Quantum phase for an electric quadrupole moment in noncommutative quantum mechanics

    NASA Astrophysics Data System (ADS)

    Nizamidin, Halqem; Anwar, Abduwali; Dulat, Sayipjamal; Li, Kang

    2014-08-01

    We study the noncommutative nonrelativistic quantum dynamics of a neutral particle, which possesses an electric qaudrupole moment, in the presence of an external magnetic field. First, by introducing a shift for the magnetic field, we give the Schrödinger equations in the presence of an external magnetic field both on a noncommutative space and a noncommutative phase space, respectively. Then by solving the Schrödinger equations both on a noncommutative space and a noncommutative phase space, we obtain quantum phases of the electric quadrupole moment, respectively. We demonstrate that these phases are geometric and dispersive.

  1. Quantum Phase for an Electric Multipole Moment in Noncommutative Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Hekim, Mamatabdulla; Anwar, Abduwali; Wang, Jianhua

    2016-02-01

    We study the noncommutative nonrelativistic quantum dynamics of a neutral particle, which possesses an electric multipole moment, in the presence of an external magnetic field. First, by introducing a shift for the magnetic field we give the Schrödinger equations in the presence of an external magnetic field both on a noncommutative space and a noncommutative phase space, respectively. Then by solving the Schrödinger equations, we obtain quantum phases of the electric multipole moment both on a noncommutative space and a noncommutative phase space. We demonstrate that these phase are geometric and dispersive.

  2. Quantum Phase for an Electric Multipole Moment in Noncommutative Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Hekim, Mamatabdulla; Anwar, Abduwali; Wang, Jianhua

    2016-07-01

    We study the noncommutative nonrelativistic quantum dynamics of a neutral particle, which possesses an electric multipole moment, in the presence of an external magnetic field. First, by introducing a shift for the magnetic field we give the Schrödinger equations in the presence of an external magnetic field both on a noncommutative space and a noncommutative phase space, respectively. Then by solving the Schrödinger equations, we obtain quantum phases of the electric multipole moment both on a noncommutative space and a noncommutative phase space. We demonstrate that these phase are geometric and dispersive.

  3. 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. PMID:26686054

  4. The structure of metallic complexes of polyacetylene with alkali metals

    NASA Astrophysics Data System (ADS)

    Baughman, R. H.; Murthy, N. S.; Miller, G. G.

    1983-07-01

    The crystal structures of sodium, potassium, rubidium, and cesium doped polyacetylene have been determined using crystal packing and x-ray diffraction analyses. Each of these metallic complexes is tetragonal, with the polyacetylene chains forming a host lattice in which the alkali metal ions are present in channels. Lithium appears to be too small to stabilize the channel structure and an amorphous structure is observed. Predicted unit cell parameters and x-ray diffraction intensities are in agreement with observed values. Similarities with the alkali metal doped graphite suggest that hybridization between carbon pz orbitals and metal s orbitals occurs. Such hybridization is expected to result in a high conductivity component normal to the chain direction. On the other hand, direct overlap between polymer chains appears small, since alkali metal columns separate polymer chains. Compositions calculated for the channel structures (from meridional diffraction spacings, the intensity of equatorial diffraction lines, measured volume expansion, and distances in model complexes) all range from y=0.12 to 0.18 for (CHMy)x, where M is sodium, potassium, rubidium, or cesium.

  5. Crystal structure of a nuclear actin ternary complex.

    PubMed

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

    2016-08-01

    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

  6. Crystal Structure of a Lipoxygenase in Complex with Substrate

    PubMed Central

    Neau, David B.; Bender, Gunes; Boeglin, William E.; Bartlett, Sue G.; Brash, Alan R.; Newcomer, Marcia E.

    2014-01-01

    Lipoxygenases (LOX) play critical roles in mammalian biology in the generation of potent lipid mediators of the inflammatory response; consequently, they are targets for the development of isoform-specific inhibitors. The regio- and stereo-specificity of the oxygenation of polyunsaturated fatty acids by the enzymes is understood in terms of the chemistry, but structural observation of the enzyme-substrate interactions is lacking. Although several LOX crystal structures are available, heretofore the rapid oxygenation of bound substrate has precluded capture of the enzyme-substrate complex, leaving a gap between chemical and structural insights. In this report, we describe the 2.0 Å resolution structure of 8R-LOX in complex with arachidonic acid obtained under anaerobic conditions. Subtle rearrangements, primarily in the side chains of three amino acids, allow binding of arachidonic acid in a catalytically competent conformation. Accompanying experimental work supports a model in which both substrate tethering and cavity depth contribute to positioning the appropriate carbon at the catalytic machinery. PMID:25231982

  7. CMB statistical anisotropy from noncommutative gravitational waves

    SciTech Connect

    Shiraishi, Maresuke; Ricciardone, Angelo; Mota, David F.; Arroja, Frederico E-mail: d.f.mota@astro.uio.no E-mail: arroja@pd.infn.it

    2014-07-01

    Primordial statistical anisotropy is a key indicator to investigate early Universe models and has been probed by the cosmic microwave background (CMB) anisotropies. In this paper, we examine tensor-mode CMB fluctuations generated from anisotropic gravitational waves, parametrised by P{sub h}(k) = P{sub h}{sup (0)}(k) [ 1 + ∑{sub LM} f{sub L}(k) g{sub LM} Y{sub LM} ( k-circumflex )], where P{sub h}{sup (0)}(k) is the usual scale-invariant power spectrum. Such anisotropic tensor fluctuations may arise from an inflationary model with noncommutativity of fields. It is verified that in this model, an isotropic component and a quadrupole asymmetry with f{sub 0}(k) = f{sub 2}(k) ∝ k{sup -2} are created and hence highly red-tilted off-diagonal components arise in the CMB power spectra, namely ℓ{sub 2} = ℓ{sub 1} ± 2 in TT, TE, EE and BB, and ℓ{sub 2} = ℓ{sub 1} ± 1 in TB and EB. We find that B-mode polarisation is more sensitive to such signals than temperature and E-mode polarisation due to the smallness of large-scale cosmic variance and we can potentially measure g{sub 00} = 30 and g{sub 2M} = 58 at 68% CL in a cosmic-variance-limited experiment. Such a level of signal may be measured in a PRISM like experiment, while the instrumental noise contaminates it in the Planck experiment. These results imply that it is impossible to measure the noncommutative parameter if it is small enough for the perturbative treatment to be valid. Our formalism and methodology for dealing with the CMB tensor statistical anisotropy are general and straightforwardly applicable to other early Universe models.

  8. Structure of an RNA polymerase II preinitiation complex

    PubMed Central

    Murakami, Kenji; Tsai, Kuang-Lei; Kalisman, Nir; Bushnell, David A.; Asturias, Francisco J.; Kornberg, Roger D.

    2015-01-01

    The structure of a 33-protein, 1.5-MDa RNA polymerase II preinitiation complex (PIC) was determined by cryo-EM and image processing at a resolution of 6–11 Å. Atomic structures of over 50% of the mass were fitted into the electron density map in a manner consistent with protein–protein cross-links previously identified by mass spectrometry. The resulting model of the PIC confirmed the main conclusions from previous cryo-EM at lower resolution, including the association of promoter DNA only with general transcription factors and not with the polymerase. Electron density due to DNA was identifiable by the grooves of the double helix and exhibited sharp bends at points downstream of the TATA box, with an important consequence: The DNA at the downstream end coincides with the DNA in a transcribing polymerase. The structure of the PIC is therefore conducive to promoter melting, start-site scanning, and the initiation of transcription. PMID:26483468

  9. Structure of an RNA polymerase II preinitiation complex.

    PubMed

    Murakami, Kenji; Tsai, Kuang-Lei; Kalisman, Nir; Bushnell, David A; Asturias, Francisco J; Kornberg, Roger D

    2015-11-01

    The structure of a 33-protein, 1.5-MDa RNA polymerase II preinitiation complex (PIC) was determined by cryo-EM and image processing at a resolution of 6-11 Å. Atomic structures of over 50% of the mass were fitted into the electron density map in a manner consistent with protein-protein cross-links previously identified by mass spectrometry. The resulting model of the PIC confirmed the main conclusions from previous cryo-EM at lower resolution, including the association of promoter DNA only with general transcription factors and not with the polymerase. Electron density due to DNA was identifiable by the grooves of the double helix and exhibited sharp bends at points downstream of the TATA box, with an important consequence: The DNA at the downstream end coincides with the DNA in a transcribing polymerase. The structure of the PIC is therefore conducive to promoter melting, start-site scanning, and the initiation of transcription. PMID:26483468

  10. Structure and staging in polyacetylene charge-transfer complexes

    NASA Astrophysics Data System (ADS)

    Murthy, N. S.; Shacklette, L. W.; Baughman, R. H.

    1989-10-01

    A structure is proposed for a stage-2 complex of polyacetylene which contains potassium as the dopant ion. This structure utilizes as a basic motif an alkali-metal column surrounded by four polyacetylene chains; this motif is also found in the tetragonal phase that appears at higher dopant concentrations. In the new structure, each polyacetylene is adjacent to one alkali-metal column, so the phase contains four polymer chains per alkali-metal column as compared with two chains per column for the tetragonal phase. X-ray diffraction and electrochemical data show that a mixture of undoped and doped phases are present at low dopant concentrations. In light of these results, general aspects of staging in n-doped and p-doped polyacetylene are discussed.

  11. 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.

  12. Structure determination of picolinato copper(II)-amine complexes

    NASA Astrophysics Data System (ADS)

    Mautner, Franz A.; Massoud, Salah S.

    2007-12-01

    Two series of Cu(II)-picolinato complexes of 1:1 and 3:2 Cu(II)-amine/picolinate namely [Cu(L 1)(pic)]ClO 4 and [Cu 3(L 2) 3(pic) 2(H 2O)](ClO 4) 4· xH 2O or [Cu 3(dpt) 3(pic) 2](ClO 4) 4, where pic = picolinate anion, L 1 = dien (diethylenetriamine), Et 2dien ( N, N-diethyldiethylenetriamine), Medpt (3,3'-diamino- N-methyldipropylamine), L 2 = pmedien ( N, N, N', N″, N″-pentamethyl-diethylenetriamine), TPA (tris(2-pyridylmethyl)amine), and dpt = dipropylenetriamine were synthesized and structurally characterized by electronic and IR spectroscopy. Single crystal X-ray diffraction analysis of the complex [Cu(dien)(pic)]ClO 4 ( 1) reveals its monomeric nature whereas for [Cu 3(pmedien) 3(pic) 2(H 2O)](ClO 4) 4·2H 2O ( 4), it was shown that the complex consists of two subunits of the mononuclear [Cu(pmedien)(pic)] + and the dinuclear [Cu 2(pmedien) 2(pic)(H 2O)] 3+ cations with the perchlorate as counter ions and lattice water molecules. In the mononuclear complexes of 1 and 4 the picolinato anions act as N, O-chelating ligands, whereas N, O, O'-picolinato bridges are observed in the dinuclear [Cu 2(pmedien) 2(pic)(H 2O)] 3+ cations of 4. The aqueous visible spectra of the complexes 1- 6 are consistent with five-coordinate Cu(II) species where distorted square pyramidal geometry (SP) was assigned for complexes 2- 5, trigonal bipyramidal geometry (TBP) for 6 and an intermediate geometry between SP and TBP for 1.

  13. 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.

  14. Complex band structure of topological insulator Bi2Se3.

    PubMed

    Betancourt, J; Li, S; Dang, X; Burton, J D; Tsymbal, E Y; Velev, J P

    2016-10-01

    Topological insulators are very interesting from a fundamental point of view, and their unique properties may be useful for electronic and spintronic device applications. From the point of view of applications it is important to understand the decay behavior of carriers injected in the band gap of the topological insulator, which is determined by its complex band structure (CBS). Using first-principles calculations, we investigate the dispersion and symmetry of the complex bands of Bi2Se3 family of three-dimensional topological insulators. We compare the CBS of a band insulator and a topological insulator and follow the CBS evolution in both when the spin-orbit interaction is turned on. We find significant differences in the CBS linked to the topological band structure. In particular, our results demonstrate that the evanescent states in Bi2Se3 are non-trivially complex, i.e. contain both the real and imaginary contributions. This explains quantitatively the oscillatory behavior of the band gap obtained from Bi2Se3 (0 0 0 1) slab calculations. PMID:27485021

  15. Structural and Biochemical Insights into MLL1 Core Complex Assembly

    SciTech Connect

    Avdic, Vanja; Zhang, Pamela; Lanouette, Sylvain; Groulx, Adam; Tremblay, Véronique; Brunzelle, Joseph; Couture, Jean-François

    2012-05-02

    Histone H3 Lys-4 methylation is predominantly catalyzed by a family of methyltransferases whose enzymatic activity depends on their interaction with a three-subunit complex composed of WDR5, RbBP5, and Ash2L. Here, we report that a segment of 50 residues of RbBP5 bridges the Ash2L C-terminal domain to WDR5. The crystal structure of WDR5 in ternary complex with RbBP5 and MLL1 reveals that both proteins binds peptide-binding clefts located on opposite sides of WDR5s {beta}-propeller domain. RbBP5 engages in several hydrogen bonds and van der Waals contacts within a V-shaped cleft formed by the junction of two blades on WDR5. Mutational analyses of both the WDR5 V-shaped cleft and RbBP5 residues reveal that the interactions between RbBP5 and WDR5 are important for the stimulation of MLL1 methyltransferase activity. Overall, this study provides the structural basis underlying the formation of the WDR5-RbBP5 subcomplex and further highlight the crucial role of WDR5 in scaffolding the MLL1 core complex.

  16. Landscape structure controls on biogeochemical fluxes in complex terrain (Invited)

    NASA Astrophysics Data System (ADS)

    McGlynn, B. L.; Riveros-Iregui, D.; Emanuel, R. E.; Pacific, V. J.; Epstein, H. E.; Welsch, D. L.

    2010-12-01

    Complex topography, topology, and strong environmental gradients in mountainous terrain impart fundamental controls on the distribution and redistribution of water, energy, and nutrients across the landscape. Many of these variables exhibit spatial patterns influenced by landscape structure and hydrologically mediated redistribution processes. Landscape structure therefore can lead to organized heterogeneity of ecosystem dynamics because of the interplay between abiotic and biotic processes. Mountainous terrain can also experience large diel, seasonal and interannual fluctuations in hydrometeorology. These temporal fluctuations will manifest differently across the landscape due to strong biophysical gradients and redistribution processes less influential in more homogenous terrain. Investigation in complex terrain therefore can provide insight into processes and feedbacks among nutrients, water, and climate. Here we examine space-time variability in ecosystem processes at the catchment scale with focus on carbon cycle science. We highlight controls on soil respiration and stream DOC export from plots to watershed scales based on high spatial and temporal resolution observation, empirical and numerical modeling, and eddy covariance approaches. We suggest complex terrain imparts organization on observed heterogeneity that can be used to gain new understanding of fundamental controls on ecosystem processes.

  17. Integrated structure investigation in complex networks by label propagation

    NASA Astrophysics Data System (ADS)

    Wu, Tao; Guo, Yuxiao; Chen, Leiting; Liu, Yanbing

    2016-04-01

    The investigation of network structure has important significance to understand the functions of various complex networks. The communities with hierarchical and overlapping structures and the special nodes like hubs and outliers are all common structure features to the networks. Network structure investigation has attracted considerable research effort recently. However, existing studies have only partially explored the structure features. In this paper, a label propagation based integrated network structure investigation algorithm (LINSIA) is proposed. The main novelty here is that LINSIA can uncover hierarchical and overlapping communities, as well as hubs and outliers. Moreover, LINSIA can provide insight into the label propagation mechanism and propose a parameter-free solution that requires no prior knowledge. In addition, LINSIA can give out a soft-partitioning result and depict the degree of overlapping nodes belonging to each relevant community. The proposed algorithm is validated on various synthetic and real-world networks. Experimental results demonstrate that the algorithm outperforms several state-of-the-art methods.

  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. Black hole evaporation in a noncommutative charged Vaidya model

    NASA Astrophysics Data System (ADS)

    Sharif, M.; Javed, W.

    2012-06-01

    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-Nordström-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.

  20. Thermodynamics of a Bardeen black hole in noncommutative space

    NASA Astrophysics Data System (ADS)

    Sharif, M.; Javed, Wajiha

    2011-10-01

    In this paper, we examine the effects of space noncommutativity on the thermodynamics of a Bardeen charged regular black hole. For a suitable choice of sets of parameters, the behavior of the singularity, horizon, mass function, black hole mass, temperature, entropy and its differential, area and energy distribution of the Bardeen solution have been discussed graphically for both noncommutative and commutative spaces. Graphs show that the commutative coordinates extrapolate all such quantities (except temperature) for a given set of parameters. It is interesting to mention here that these sets of parameters provide the singularity (essential for $r_h>0$) and horizon ($f(r_h)=0$ for $r_h>0$) for the black hole solution in noncommutative space, while for commutative space no such quantity exists.

  1. Instability of the noncommutative geometry inspired black hole

    NASA Astrophysics Data System (ADS)

    Brown, Eric; Mann, Robert

    2011-01-01

    Noncommutative geometries have been proposed as an approach to quantum gravity and have led to the construction of noncommutative black holes, whose interior singularities are purportedly eliminated due to quantum effects. Here we find evidence that these black holes are in fact unstable, with infalling matter near the Cauchy (inner) horizon being subject to an infinite blueshift of the type that has been repeatedly demonstrated for the Reissner-Nordström black hole. This instability is present even when an ultraviolet cutoff (induced by anticipated noncommutative geometric effects) to a field propagating in that spacetime is included. We demonstrate this by following an analogous argument made for Reissner-Nordström black holes, and conclude that stability is dependent on the surface gravities κ- and κ+ of the inner and outer horizons respectively. In general if κ- >κ+, as we show to be the case here, then the stability of the Cauchy horizon becomes highly questionable, contrary to recent claims.

  2. 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.

  3. 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

  4. 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.

  5. Noncommutative (supersymmetric) electrodynamics in the Yang-Feldman formalism

    SciTech Connect

    Zahn, Jochen

    2010-11-15

    We study quantum electrodynamics on the noncommutative Minkowski space (NCQED) in the Yang-Feldman formalism. Local observables are defined by using covariant coordinates. We compute the two-point function of the interacting field strength to second order and find the infrared divergent terms already known from computations using the so-called modified Feynman rules. It is shown that these lead to nonlocal renormalization ambiguities. Also new nonlocal divergences stemming from the covariant coordinates are found. Furthermore, we study the supersymmetric extension of the model. For this, the supersymmetric generalization of the covariant coordinates is introduced. We find that the nonlocal divergences cancel. At the one-loop level, the only effect of noncommutativity is then a momentum-dependent field strength normalization. We interpret it as an acausal effect and show that its range is independent of the noncommutativity scale.

  6. The Structure of DNA within Cationic Lipid/DNA Complexes

    PubMed Central

    Braun, Chad S.; Jas, Gouri S.; Choosakoonkriang, Sirirat; Koe, Gary S.; Smith, Janet G.; Middaugh, C. Russell

    2003-01-01

    The structure of DNA within CLDCs used for gene delivery is controversial. Previous studies using CD have been interpreted to indicate that the DNA is converted from normal B to C form in complexes. This investigation reexamines this interpretation using CD of model complexes, FTIR as well as Raman spectroscopy and molecular dynamics simulations to address this issue. CD spectra of supercoiled plasmid DNA undergo a significant loss of rotational strength in the signal near 275 nm upon interaction with either the cationic lipid dimethyldioctadecylammonium bromide or 1,2-dioleoyltrimethylammonium propane. This loss of rotational strength is shown, however, by both FTIR and Raman spectroscopy to occur within the parameters of the B-type conformation. Contributions of absorption flattening and differential scattering to the CD spectra of complexes are unable to account for the observed spectra. Model studies of the CD of complexes prepared from synthetic oligonucleotides of varying length suggest that significant reductions in rotational strength can occur within short stretches of DNA. Furthermore, some alteration in the hydrogen bonding of bases within CLDCs is indicated in the FTIR and Raman spectroscopy results. In addition, alterations in base stacking interactions as well as hydrogen bonding are suggested by molecular dynamics simulations. A global interpretation of all of the data suggests the DNA component of CLDCs remains in a variant B form in which base/base interactions are perturbed. PMID:12547792

  7. Structure of a Cytoplasmic 11-Subunit RNA Exosome Complex.

    PubMed

    Kowalinski, Eva; Kögel, Alexander; Ebert, Judith; Reichelt, Peter; Stegmann, Elisabeth; Habermann, Bianca; Conti, Elena

    2016-07-01

    The RNA exosome complex associates with nuclear and cytoplasmic cofactors to mediate the decay, surveillance, or processing of a wide variety of transcripts. In the cytoplasm, the conserved core of the exosome (Exo10) functions together with the conserved Ski complex. The interaction of S. cerevisiae Exo10 and Ski is not direct but requires a bridging cofactor, Ski7. Here, we report the 2.65 Å resolution structure of S. cerevisiae Exo10 bound to the interacting domain of Ski7. Extensive hydrophobic interactions rationalize the high affinity and stability of this complex, pointing to Ski7 as a constitutive component of the cytosolic exosome. Despite the absence of sequence homology, cytoplasmic Ski7 and nuclear Rrp6 bind Exo10 using similar surfaces and recognition motifs. Knowledge of the interacting residues in the yeast complexes allowed us to identify a splice variant of human HBS1-Like as a Ski7-like exosome-binding protein, revealing the evolutionary conservation of this cytoplasmic cofactor. PMID:27345150

  8. Crystal Structure of the Eukaryotic Origin Recognition Complex

    PubMed Central

    Bleichert, Franziska; Botchan, Michael R.; Berger, James M.

    2015-01-01

    Initiation of cellular DNA replication is tightly controlled to sustain genomic integrity. In eukaryotes, the heterohexameric origin recognition complex (ORC) is essential for coordinating replication onset. The 3.5 Å resolution crystal structure of Drosophila ORC reveals that the 270 kDa initiator core complex comprises a two-layered notched ring in which a collar of winged-helix domains from the Orc1-5 subunits sits atop a layer of AAA+ ATPase folds. Although canonical inter-AAA+ domain interactions exist between four of the six ORC subunits, unanticipated features are also evident, including highly interdigitated domain-swapping interactions between the winged-helix folds and AAA+ modules of neighboring protomers, and a quasi-spiral arrangement of DNA binding elements that circumnavigate a ~20 Å wide channel in the center of the complex. Comparative analyses indicate that ORC encircles DNA, using its winged-helix domain face to engage the MCM2-7 complex during replicative helicase loading; however, an observed >90° out-of-plane rotation for the Orc1 AAA+ domain disrupts interactions with catalytic amino acids in Orc4, narrowing and sealing off entry into the central channel. Prima facie, our data indicate that Drosophila ORC can switch between active and autoinhibited conformations, suggesting a novel means for cell cycle and/or developmental control of ORC functions. PMID:25762138

  9. Morphological and genetic structuring in the Utah Lake sucker complex.

    PubMed

    Cole, D D; Mock, K E; Cardall, B L; Crowl, T A

    2008-12-01

    Population decline in the federally endangered June sucker (Chasmistes liorus), a lakesucker unique to Utah Lake, Utah, has been attributed in part to hybridization with the more widespread Utah sucker (Catostomus ardens). As a group, suckers in Utah Lake exhibit considerable external morphological variation. Meristic and morphological ambiguities, presumably the result of hybridization, create a continuum of intermediate forms between Chasmistes and Catostomus extremes and prevent definitive identification to species. Here we describe and evaluate the morphological and genetic variation in suckers in Utah Lake by comparing a morphological analysis with amplified fragment length polymorphism and microsatellite analyses. Suckers were morphologically differentiated using mouth characters associated with different feeding strategies: planktivory (June sucker) and benthivory (Utah sucker). Although we found no genetic evidence for a deep divergence between June and Utah morphs, significant, but slight population structuring accompanied the substantial morphological variation. Bayesian model-based genetic clustering analyses detected two sucker populations in Utah Lake; however, these clusters were not strongly concordant with morphological groupings or between marker systems. The suckers in Utah Lake present an interesting dilemma regarding conservation: should one conserve (breed and stock) a subset of the morphotypic variation in the Utah Lake sucker complex, focusing on the endangered June sucker morphotype, or should one conserve both June sucker and Utah sucker morphotypes in this complex, possibly maximizing evolutionary potential? We explore this question in the context of current genetic and morphological variation in the Utah Lake sucker complex as well as historical information on this complex and other lakesuckers. PMID:19067800

  10. Computational structure analysis of biomacromolecule complexes by interface geometry.

    PubMed

    Mahdavi, Sedigheh; Salehzadeh-Yazdi, Ali; Mohades, Ali; Masoudi-Nejad, Ali

    2013-12-01

    The ability to analyze and compare protein-nucleic acid and protein-protein interaction interface has critical importance in understanding the biological function and essential processes occurring in the cells. Since high-resolution three-dimensional (3D) structures of biomacromolecule complexes are available, computational characterizing of the interface geometry become an important research topic in the field of molecular biology. In this study, the interfaces of a set of 180 protein-nucleic acid and protein-protein complexes are computed to understand the principles of their interactions. The weighted Voronoi diagram of the atoms and the Alpha complex has provided an accurate description of the interface atoms. Our method is implemented in the presence and absence of water molecules. A comparison among the three types of interaction interfaces show that RNA-protein complexes have the largest size of an interface. The results show a high correlation coefficient between our method and the PISA server in the presence and absence of water molecules in the Voronoi model and the traditional model based on solvent accessibility and the high validation parameters in comparison to the classical model. PMID:23850846

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. Curvature and geometric modules of noncommutative spheres and tori

    NASA Astrophysics Data System (ADS)

    Arnlind, Joakim

    2014-04-01

    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.

  17. On the Landau system in noncommutative phase-space

    NASA Astrophysics Data System (ADS)

    Gangopadhyay, Sunandan; Saha, Anirban; Halder, Aslam

    2015-12-01

    We consider the Landau system in a canonically noncommutative phase-space. A set of generalized transformations containing scaling parameters is derived which maps the NC problem to an equivalent commutative problem. The energy spectrum admits NC corrections which are computed using the explicit NC variables as well as the commutative-equivalent variables. Their exact matching solidifies the evidence of the equivalence of the two approaches. We also obtain the magnetic length and level degeneracy, which admit NC corrections. We further study the Aharonov-Bohm effect where the phase-shift is found to alter due to noncommutativity and also depends on the scaling parameters.

  18. Generalized Uncertainty Relation in the Non-commutative Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Chung, Won Sang

    2016-06-01

    In this paper the non-commutative quantum mechanics (NCQM) with the generalized uncertainty relations {Δ } x1 {Δ } x2 ≥ {θ}/{2}, {Δ} p1 {Δ } p2 ≥ {bar{θ}}/{2}, {Δ } xi {Δ } pi ≥ {hbar _{eff}}/{2} is discussed. Four each uncertainty relation, wave functions saturating each uncertainty relation are explicitly constructed. The unitary operators relating the non-commutative position and momentum operators to the commutative position and momentum operators are also investigated. We also discuss the uncertainty relation related to the harmonic oscillator.

  19. Quantum-corrected finite entropy of noncommutative acoustic black holes

    NASA Astrophysics Data System (ADS)

    Anacleto, M. A.; Brito, F. A.; Luna, G. C.; Passos, E.; Spinelly, J.

    2015-11-01

    In this paper we consider the generalized uncertainty principle in the tunneling formalism via Hamilton-Jacobi method to determine the quantum-corrected Hawking temperature and entropy for 2 + 1-dimensional noncommutative acoustic black holes. In our results we obtain an area entropy, a correction logarithmic in leading order, a correction term in subleading order proportional to the radiation temperature associated with the noncommutative acoustic black holes and an extra term that depends on a conserved charge. Thus, as in the gravitational case, there is no need to introduce the ultraviolet cut-off and divergences are eliminated.

  20. 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.

  1. 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.

  2. Structure of the BoNT/A1--receptor complex.

    PubMed

    Benoit, Roger M; Frey, Daniel; Wieser, Mara M; Thieltges, Katherine M; Jaussi, Rolf; Capitani, Guido; Kammerer, Richard A

    2015-12-01

    Botulinum neurotoxin A causes botulism but is also used for medical and cosmetic applications. A detailed molecular understanding of BoNT/A--host receptor interactions is therefore fundamental for improving current clinical applications and for developing new medical strategies targeting human disorders. Towards this end, we recently solved an X-ray crystal structure of BoNT/A1 in complex with its neuronal protein receptor SV2C. Based on our findings, we discuss the potential implications for BoNT/A function. PMID:26260692

  3. Structure and luminescence properties of tellurium(IV) complex compounds

    NASA Astrophysics Data System (ADS)

    Sedakova, T. V.; Mirochnik, A. G.; Karasev, V. E.

    2011-05-01

    Using the tellurium(IV) complex compounds as an example, we study the interrelation between the geometric structure and spectral luminescence properties. We find that, in the series of compounds of Te(IV), which are characterized by the island octahedral coordination of Te(IV) ions, the luminescence intensity depends on the degree of distortion of the Te(IV) coordination polyhedron, the Stokes shift, and the energy of the luminescence transition. We revealed that the considered series of Te(IV) compounds possess reversible thermochromic properties.

  4. 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. PMID:24042456

  5. Order parameter in complex dipolar structures: Microscopic modeling

    NASA Astrophysics Data System (ADS)

    Prosandeev, S.; Bellaiche, L.

    2008-02-01

    Microscopic models have been used to reveal the existence of an order parameter that is associated with many complex dipolar structures in magnets and ferroelectrics. This order parameter involves a double cross product of the local dipoles with their positions. It provides a measure of subtle microscopic features, such as the helicity of the two domains inherent to onion states, curvature of the dipolar pattern in flower states, or characteristics of sets of vortices with opposite chirality (e.g., distance between the vortex centers and/or the magnitude of their local dipoles).

  6. Complex band structure in neutron-deficient {sup 178}Hg

    SciTech Connect

    Kondev, F. G.; Carpenter, M. P.; Janssens, R. V. F.; Wiedenhoever, I.; Alcorta, M.; Bhattacharyya, P.; Brown, L. T.; Davids, C. N.; Fischer, S. M.; Khoo, T. L.

    2000-01-01

    Using the GAMMASPHERE array in conjunction with the Fragment Mass Analyzer, the level structure of the near drip-line nucleus {sup 178}Hg has been considerably expanded with the recoil-decay tagging technique. Of particular interest is a new rotational band which exhibits a complex decay towards the low spin states arising from both the prolate-deformed and the nearly spherical coexisting minima. It is proposed that this band is associated at low spin with an octupole vibration which is crossed at moderate frequency by a shape driving, two quasiproton excitation. (c) 1999 The American Physical Society.

  7. 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.

  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. Structural biology. Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine.

    PubMed

    Qin, Ling; Kufareva, Irina; Holden, Lauren G; Wang, Chong; Zheng, Yi; Zhao, Chunxia; Fenalti, Gustavo; Wu, Huixian; Han, Gye Won; Cherezov, Vadim; Abagyan, Ruben; Stevens, Raymond C; Handel, Tracy M

    2015-03-01

    Chemokines and their receptors control cell migration during development, immune system responses, and in numerous diseases, including inflammation and cancer. The structural basis of receptor:chemokine recognition has been a long-standing unanswered question due to the challenges of structure determination for membrane protein complexes. Here, we report the crystal structure of the chemokine receptor CXCR4 in complex with the viral chemokine antagonist vMIP-II at 3.1 angstrom resolution. The structure revealed a 1:1 stoichiometry and a more extensive binding interface than anticipated from the paradigmatic two-site model. The structure helped rationalize a large body of mutagenesis data and together with modeling provided insights into CXCR4 interactions with its endogenous ligand CXCL12, its ability to recognize diverse ligands, and the specificity of CC and CXC receptors for their respective chemokines. PMID:25612609

  10. From metallaborane to borylene complexes: syntheses and structures of triply bridged ruthenium and tantalum borylene complexes.

    PubMed

    Geetharani, K; Bose, Shubhankar Kumar; Varghese, Babu; Ghosh, Sundargopal

    2010-10-01

    Reaction of [1,2-(Cp*RuH)(2)B(3)H(7)] (1; Cp*=η(5)-C(5)Me(5)) with [Mo(CO)(3)(CH(3)CN)(3)] yielded arachno-[(Cp*RuCO)(2)B(2)H(6)] (2), which exhibits a butterfly structure, reminiscent of 7 sep B(4)H(10). Compound 2 was found to be a very good precursor for the generation of bridged borylene species. Mild pyrolysis of 2 with [Fe(2)(CO)(9)] yielded a triply bridged heterotrinuclear borylene complex [(μ(3)-BH)(Cp*RuCO)(2)(μ-CO){Fe(CO)(3)}] (3) and bis-borylene complexes [{(μ(3)-BH)(Cp*Ru)(μ-CO)}(2)Fe(2)(CO)(5)] (4) and [{(μ(3)-BH)(Cp*Ru)Fe(CO)(3)}(2)(μ-CO)] (5). In a similar fashion, pyrolysis of 2 with [Mn(2)(CO)(10)] permits the isolation of μ(3)-borylene complex [(μ(3)-BH)(Cp*RuCO)(2)(μ-H)(μ-CO){Mn(CO)(3)}] (6). Both compounds 3 and 6 have a trigonal-pyramidal geometry with the μ(3)-BH ligand occupying the apical vertex, whereas 4 and 5 can be viewed as bicapped tetrahedra, with two μ(3)-borylene ligands occupying the capping position. The synthesis of tantalum borylene complex [(μ(3)-BH)(Cp*TaCO)(2)(μ-CO){Fe(CO)(3)}] (7) was achieved by the reaction of [(Cp*Ta)(2)B(4)H(9)(μ-BH(4))] [corrected] at ambient temperature with [Fe(2)(CO)(9)]. Compounds 2-7 have been isolated in modest yield as yellow to red crystalline solids. All the new compounds have been characterized in solution by mass spectrometry; IR spectroscopy; and (1)H, (11)B, and (13)C NMR spectroscopy and the structural types were unequivocally established by crystallographic analysis of 2-6. PMID:20730749

  11. Comprehensive spectral approach for community structure analysis on complex networks

    NASA Astrophysics Data System (ADS)

    Danila, Bogdan

    2016-02-01

    A simple but efficient spectral approach for analyzing the community structure of complex networks is introduced. It works the same way for all types of networks, by spectrally splitting the adjacency matrix into a "unipartite" and a "multipartite" component. These two matrices reveal the structure of the network from different perspectives and can be analyzed at different levels of detail. Their entries, or the entries of their lower-rank approximations, provide measures of the affinity or antagonism between the nodes that highlight the communities and the "gateway" links that connect them together. An algorithm is then proposed to achieve the automatic assignment of the nodes to communities based on the information provided by either matrix. This algorithm naturally generates overlapping communities but can also be tuned to eliminate the overlaps.

  12. Structure and gating of the nuclear pore complex

    PubMed Central

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

    2015-01-01

    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. PMID:26112706

  13. Reduction method for thermal analysis of complex aerospace structures

    NASA Technical Reports Server (NTRS)

    Shore, C. P.

    1985-01-01

    A reduction method which combines classical Rayleigh-Ritz modal superposition techniques with contemporary finite-element methods is applied to transient nonlinear thermal analysis of aerospace structures. The essence of the method is the use of a few thermal modes from eigenvalue analyses as basis vectors to represent the temperature response in the structure. The method is used to obtain approximate temperature histories for a portion of the Shuttle orbiter wing subject to reentry heating and for a large space antenna reflector subject to heating associated with a low Earth orbit. The reduction method has excellent potential for significant size reduction for radiation-dominated problems such as the antenna reflector. However, for conduction-dominated problems such as the Shuttle wing, especially those with complex spatial and temporal variations in the applied heating, additional work appears necessary to find alternate sources of basis vectors which will permit significant problem size reductions.

  14. Structural permeability of complex networks to control signals

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    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.

  15. 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

  16. 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.

  17. A tool for the prediction of structures of complex sugars.

    PubMed

    Xia, Junchao; Margulis, Claudio

    2008-12-01

    In two recent back to back articles(Xia et al., J Chem Theory Comput 3:1620-1628 and 1629-1643, 2007a, b) we have started to address the problem of complex oligosaccharide conformation and folding. The scheme previously presented was based on exhaustive searches in configuration space in conjunction with Nuclear Overhauser Effect (NOE) calculations and the use of a complex rotameric library that takes branching into account. NOEs are extremely useful for structural determination but only provide information about short range interactions and ordering. Instead, the measurement of residual dipolar couplings (RDC), yields information about molecular ordering or folding that is long range in nature. In this article we show the results obtained by incorporation RDC calculations into our prediction scheme. Using this new approach we are able to accurately predict the structure of six human milk sugars: LNF-1, LND-1, LNF-2, LNF-3, LNnT and LNT. Our exhaustive search in dihedral configuration space combined with RDC and NOE calculations allows for highly accurate structural predictions that, because of the non-ergodic nature of these molecules on a time scale compatible with molecular dynamics simulations, are extremely hard to obtain otherwise (Almond et al., Biochemistry 43:5853-5863, 2004). Molecular dynamics simulations in explicit solvent using as initial configurations the structures predicted by our algorithm show that the histo-blood group epitopes in these sugars are relatively rigid and that the whole family of oligosaccharides derives its conformational variability almost exclusively from their common linkage (beta-D: -GlcNAc-(1-->3)-beta-D: -Gal) which can exist in two distinct conformational states. A population analysis based on the conformational variability of this flexible glycosidic link indicates that the relative population of the two distinct states varies for different human milk oligosaccharides. PMID:18953494

  18. The structure and function of Alzheimer's gamma secretase enzyme complex.

    PubMed

    Krishnaswamy, Sudarsan; Verdile, Giuseppe; Groth, David; Kanyenda, Limbikani; Martins, Ralph N

    2009-01-01

    The production and accumulation of the beta amyloid protein (Abeta) is a key event in the cascade of oxidative and inflammatory processes that characterizes Alzheimer's disease (AD). A multi-subunit enzyme complex, referred to as gamma (gamma) secretase, plays a pivotal role in the generation of Abeta from its parent molecule, the amyloid precursor protein (APP). Four core components (presenilin, nicastrin, aph-1, and pen-2) interact in a high-molecular-weight complex to perform intramembrane proteolysis on a number of membrane-bound proteins, including APP and Notch. Inhibitors and modulators of this enzyme have been assessed for their therapeutic benefit in AD. However, although these agents reduce Abeta levels, the majority have been shown to have severe side effects in pre-clinical animal studies, most likely due to the enzymes role in processing other proteins involved in normal cellular function. Current research is directed at understanding this enzyme and, in particular, at elucidating the roles that each of the core proteins plays in its function. In addition, a number of interacting proteins that are not components of gamma-secretase also appear to play important roles in modulating enzyme activity. This review will discuss the structural and functional complexity of the gamma-secretase enzyme and the effects of inhibiting its activity. PMID:19958215

  19. Correlations between Community Structure and Link Formation in Complex Networks

    PubMed Central

    Liu, Zhen; He, Jia-Lin; Kapoor, Komal; Srivastava, Jaideep

    2013-01-01

    Background Links in complex networks commonly represent specific ties between pairs of nodes, such as protein-protein interactions in biological networks or friendships in social networks. However, understanding the mechanism of link formation in complex networks is a long standing challenge for network analysis and data mining. Methodology/Principal Findings Links in complex networks have a tendency to cluster locally and form so-called communities. This widely existed phenomenon reflects some underlying mechanism of link formation. To study the correlations between community structure and link formation, we present a general computational framework including a theory for network partitioning and link probability estimation. Our approach enables us to accurately identify missing links in partially observed networks in an efficient way. The links having high connection likelihoods in the communities reveal that links are formed preferentially to create cliques and accordingly promote the clustering level of the communities. The experimental results verify that such a mechanism can be well captured by our approach. Conclusions/Significance Our findings provide a new insight into understanding how links are created in the communities. The computational framework opens a wide range of possibilities to develop new approaches and applications, such as community detection and missing link prediction. PMID:24039818

  20. 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.

  1. 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.

  2. Structural Basis of Clostridium perfringens Toxin Complex Formation

    SciTech Connect

    Adams,J.; Gregg, K.; Bayer, E.; Boraston, A.; Smith, S.

    2008-01-01

    The virulent properties of the common human and livestock pathogen Clostridium perfringens are attributable to a formidable battery of toxins. Among these are a number of large and highly modular carbohydrate-active enzymes, including the {mu}-toxin and sialidases, whose catalytic properties are consistent with degradation of the mucosal layer of the human gut, glycosaminoglycans, and other cellular glycans found throughout the body. The conservation of noncatalytic ancillary modules among these enzymes suggests they make significant contributions to the overall functionality of the toxins. Here, we describe the structural basis of an ultra-tight interaction (Ka = 1.44 x 1011 M-1) between the X82 and dockerin modules, which are found throughout numerous C. perfringens carbohydrate-active enzymes. Extensive hydrogen-bonding and van der Waals contacts between the X82 and dockerin modules give rise to the observed high affinity. The {mu}-toxin dockerin module in this complex is positioned {approx}180 relative to the orientation of the dockerin modules on the cohesin module surface within cellulolytic complexes. These observations represent a unique property of these clostridial toxins whereby they can associate into large, noncovalent multitoxin complexes that allow potentiation of the activities of the individual toxins by combining complementary toxin specificities.

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

    SciTech Connect

    Schupp, P

    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.

  4. 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.

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

    DOE PAGESBeta

    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 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

  6. 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

  7. Parameter estimation for distributed parameter models of complex, flexible structures

    NASA Technical Reports Server (NTRS)

    Taylor, Lawrence W., Jr.

    1991-01-01

    Distributed parameter modeling of structural dynamics has been limited to simple spacecraft configurations because of the difficulty of handling several distributed parameter systems linked at their boundaries. Although there is other computer software able to generate such models or complex, flexible spacecraft, unfortunately, neither is suitable for parameter estimation. Because of this limitation the computer software PDEMOD is being developed for the express purposes of modeling, control system analysis, parameter estimation and structure optimization. PDEMOD is capable of modeling complex, flexible spacecraft which consist of a three-dimensional network of flexible beams and rigid bodies. Each beam has bending (Bernoulli-Euler or Timoshenko) in two directions, torsion, and elongation degrees of freedom. The rigid bodies can be attached to the beam ends at any angle or body location. PDEMOD is also capable of performing parameter estimation based on matching experimental modal frequencies and static deflection test data. The underlying formulation and the results of using this approach for test data of the Mini-MAST truss will be discussed. The resulting accuracy of the parameter estimates when using such limited data can impact significantly the instrumentation requirements for on-orbit tests.

  8. 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.

  9. Increased complexity of gene structure and base composition in vertebrates.

    PubMed

    Wu, Ying; Yuan, Huizhong; Tan, Shengjun; Chen, Jian-Qun; Tian, Dacheng; Yang, Haiwang

    2011-07-20

    How the structure and base composition of genes changed with the evolution of vertebrates remains a puzzling question. Here we analyzed 895 orthologous protein-coding genes in six multicellular animals: human, chicken, zebrafish, sea squirt, fruit fly, and worm. Our analyses reveal that many gene regions, particularly intron and 3' UTR, gradually expanded throughout the evolution of vertebrates from their invertebrate ancestors, and that the number of exons per gene increased. Studies based on all protein-coding genes in each genome provide consistent results. We also find that GC-content increased in many gene regions (especially 5' UTR) in the evolution of endotherms, except in coding-exons. Analysis of individual genomes shows that 3' UTR demonstrated stronger length and GC-content correlation with intron than 5' UTR, and gene with large intron in all six species demonstrated relatively similar GC-content. Our data indicates a great increase in complexity in vertebrate genes and we propose that the requirement for morphological and functional changes is probably the driving force behind the evolution of structure and base composition complexity in multicellular animal genes. PMID:21777854

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

    PubMed Central

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

    2015-01-01

    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. Addition of an 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. DOI: http://dx.doi.org/10.7554/eLife.08504.001 PMID:26349032

  11. 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.

  12. 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.

  13. 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

  14. Crystal structure of the eukaryotic origin recognition complex.

    PubMed

    Bleichert, Franziska; Botchan, Michael R; Berger, James M

    2015-03-19

    Initiation of cellular DNA replication is tightly controlled to sustain genomic integrity. In eukaryotes, the heterohexameric origin recognition complex (ORC) is essential for coordinating replication onset. Here we describe the crystal structure of Drosophila ORC at 3.5 Å resolution, showing that the 270 kilodalton initiator core complex comprises a two-layered notched ring in which a collar of winged-helix domains from the Orc1-5 subunits sits atop a layer of AAA+ (ATPases associated with a variety of cellular activities) folds. Although canonical inter-AAA+ domain interactions exist between four of the six ORC subunits, unanticipated features are also evident. These include highly interdigitated domain-swapping interactions between the winged-helix folds and AAA+ modules of neighbouring protomers, and a quasi-spiral arrangement of DNA binding elements that circumnavigate an approximately 20 Å wide channel in the centre of the complex. Comparative analyses indicate that ORC encircles DNA, using its winged-helix domain face to engage the mini-chromosome maintenance 2-7 (MCM2-7) complex during replicative helicase loading; however, an observed out-of-plane rotation of more than 90° for the Orc1 AAA+ domain disrupts interactions with catalytic amino acids in Orc4, narrowing and sealing off entry into the central channel. Prima facie, our data indicate that Drosophila ORC can switch between active and autoinhibited conformations, suggesting a novel means for cell cycle and/or developmental control of ORC functions. PMID:25762138

  15. Unprecedented Alkene Complex of Zinc(II): Structures and Bonding of Divinylzinc Complexes

    PubMed Central

    Wooten, Alfred; Carroll, Patrick J.; Maestri, Aaron G.

    2008-01-01

    This report describes the solid state structures of a series of divinylzinc complexes, one of which represents the only structurally characterized zinc(II) π-complex. Vinylzinc reagents, Zn[C(Me)=CH2]2 (1) and Zn[C(H)=CMe2]2 (2), have been synthesized and isolated as white crystalline solids in 66% and 72% yield, respectively. Each compound exhibits an infinite polymeric architecture in the solid state via a series of zinc-π (1) and zinc-σ-bonded (2) bridging interactions. Addition of chelating ligands to these divinylzinc compounds allowed isolation of the monomeric adducts (bipy)Zn[C(Me)=CH2]2 (1·bipy), (tmeda)Zn[C(Me)=CH2]2 (1·tmeda), (bipy)Zn[C(H)=CMe2]2 (2·bipy), and (tmeda)Zn[C(H)=CMe2]2 (2·tmeda), of which (1·bipy), (2·bipy), and (2·tmeda) have been characterized crystallography. PMID:16594699

  16. Thermodynamic and structural insights into CSL-DNA complexes

    SciTech Connect

    Friedmann, David R.; Kovall, Rhett A.

    2010-10-28

    The Notch pathway is an intercellular signaling mechanism that plays important roles in cell fates decisions throughout the developing and adult organism. Extracellular complexation of Notch receptors with ligands ultimately results in changes in gene expression, which is regulated by the nuclear effector of the pathway, CSL (C-promoter binding factor 1 (CBF-1), suppressor of hairless (Su(H)), lin-12 and glp-1 (Lag-1)). CSL is a DNA binding protein that is involved in both repression and activation of transcription from genes that are responsive to Notch signaling. One well-characterized Notch target gene is hairy and enhancer of split-1 (HES-1), which is regulated by a promoter element consisting of two CSL binding sites oriented in a head-to-head arrangement. Although previous studies have identified in vivo and consensus binding sites for CSL, and crystal structures of these complexes have been determined, to date, a quantitative description of the energetics that underlie CSL-DNA binding is unknown. Here, we provide a thermodynamic and structural analysis of the interaction between CSL and the two individual sites that comprise the HES-1 promoter element. Our comprehensive studies that analyze binding as a function of temperature, salt, and pH reveal moderate, but distinct, differences in the affinities of CSL for the two HES-1 binding sites. Similarly, our structural results indicate that overall CSL binds both DNA sites in a similar manner; however, minor changes are observed in both the conformation of CSL and DNA. Taken together, our results provide a quantitative and biophysical basis for understanding how CSL interacts with DNA sites in vivo.

  17. From structure of the complex to understanding of the biology

    SciTech Connect

    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.; 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 single-particle reconstructions. This paper concerns itself with the study of the macromolecular complexes that constitute viruses, using structural hybrid techniques. 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.

  18. 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

  19. 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.

  20. Noncommutative geometry-inspired rotating black hole in three dimensions

    NASA Astrophysics Data System (ADS)

    Tejeiro, Juan Manuel; Larrañaga, Alexis

    2012-01-01

    We find a new rotating black hole in three-dimensional anti-de Sitter space using an anisotropic perfect fluid inspired by the noncommutative black hole. We deduce the thermodynamical quantities of this black hole and compare them with those of a rotating BTZ solution.

  1. On supermatrix models, Poisson geometry, and noncommutative supersymmetric gauge theories

    SciTech Connect

    Klimčík, Ctirad

    2015-12-15

    We construct a new supermatrix model which represents a manifestly supersymmetric noncommutative regularisation of the UOSp(2|1) supersymmetric Schwinger model on the supersphere. Our construction is much simpler than those already existing in the literature and it was found by using Poisson geometry in a substantial way.

  2. Curved noncommutative tori as Leibniz quantum compact metric spaces

    NASA Astrophysics Data System (ADS)

    Latrémolière, Frédéric

    2015-12-01

    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.

  3. 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.

  4. 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.

  5. A comparison of remnants in noncommutative Bardeen black holes

    NASA Astrophysics Data System (ADS)

    Mehdipour, S. Hamid; Ahmadi, M. H.

    2016-09-01

    We derive the mass term of the Bardeen metric in the presence of a noncommutative geometry induced minimal length. In this setup, the proposal of a stable black hole remnant as a candidate to store information is confirmed. We consider the possibility of having an extremal configuration with one degenerate event horizon and compare different sizes of black hole remnants. As a result, once the magnetic charge g of the noncommutative Bardeen solution becomes larger, both the minimal nonzero mass M0 and the minimal nonzero horizon radius r0 get larger. This means, subsequently, under the condition of an adequate amount of g, the three parameters g, M0, and r0 are in a connection with each other linearly. According to our results, a noncommutative Bardeen black hole is colder than the noncommutative Schwarzschild black hole and its remnant is bigger, so the minimum required energy for the formation of such a black hole at particle colliders will be larger. We also find a closely similar result for the Hayward solution.

  6. 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.

  7. A comparative review of four formulations of noncommutative quantum mechanics

    NASA Astrophysics Data System (ADS)

    Gouba, Laure

    2016-07-01

    Four formulations of quantum mechanics on noncommutative Moyal phase spaces are reviewed. These are the canonical, path-integral, Weyl-Wigner and systematic formulations. Although all these formulations represent quantum mechanics on a phase space with the same deformed Heisenberg algebra, there are mathematical and conceptual differences which we discuss.

  8. 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

  9. A phased approach to enable hybrid simulation of complex structures

    NASA Astrophysics Data System (ADS)

    Spencer, Billie F.; Chang, Chia-Ming; Frankie, Thomas M.; Kuchma, Daniel A.; Silva, Pedro F.; Abdelnaby, Adel E.

    2014-08-01

    Hybrid simulation has been shown to be a cost-effective approach for assessing the seismic performance of structures. In hybrid simulation, critical parts of a structure are physically tested, while the remaining portions of the system are concurrently simulated computationally, typically using a finite element model. This combination is realized through a numerical time-integration scheme, which allows for investigation of full system-level responses of a structure in a cost-effective manner. However, conducting hybrid simulation of complex structures within large-scale testing facilities presents significant challenges. For example, the chosen modeling scheme may create numerical inaccuracies or even result in unstable simulations; the displacement and force capacity of the experimental system can be exceeded; and a hybrid test may be terminated due to poor communication between modules (e.g., loading controllers, data acquisition systems, simulation coordinator). These problems can cause the simulation to stop suddenly, and in some cases can even result in damage to the experimental specimens; the end result can be failure of the entire experiment. This study proposes a phased approach to hybrid simulation that can validate all of the hybrid simulation components and ensure the integrity large-scale hybrid simulation. In this approach, a series of hybrid simulations employing numerical components and small-scale experimental components are examined to establish this preparedness for the large-scale experiment. This validation program is incorporated into an existing, mature hybrid simulation framework, which is currently utilized in the Multi-Axial Full-Scale Sub-Structuring Testing and Simulation (MUST-SIM) facility of the George E. Brown Network for Earthquake Engineering Simulation (NEES) equipment site at the University of Illinois at Urbana-Champaign. A hybrid simulation of a four-span curved bridge is presented as an example, in which three piers are

  10. 75 FR 77047 - Statement on Sound Practices Concerning Elevated Risk Complex Structured Finance Activities

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-10

    ... Finance Activities AGENCY: Office of Thrift Supervision (OTS), Treasury. ACTION: Notice and request for.... Title of Proposal: Statement on Sound Practices Concerning Elevated Risk Complex Structured Finance... Elevated Risk Complex Structured Finance Activities describes the types of internal controls and...

  11. Structural basis of complement membrane attack complex formation.

    PubMed

    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

  12. Crystal structures of human transthyretin complexed with glabridin.

    PubMed

    Yokoyama, Takeshi; Kosaka, Yuto; Mizuguchi, Mineyuki

    2014-02-13

    Transthyretin (TTR) is a plasma protein implicated in human amyloid diseases. Several small molecules that bind to the thyroxine-binding site of TTR have been shown to stabilize the TTR tetramer and to inhibit amyloid fibril formation of TTR. Herein, we demonstrated that glabridin (Glab), a prenylated isoflavan isolated from Glycyrrhiza glabra L., inhibited aggregation of TTR in a thioflavin assay. The TTR-Glab complex structure revealed a novel binding mode including a CH-π interaction with A108 and a hydrogen bond with K15. A structural comparison with the wild type-apo structure revealed that the CH-π interaction with A108 was strengthened by the induced-fit conformational change upon Glab binding. Furthermore, the binding of Glab induced a rotation of the T119 side chain, and the inclusion of a water molecule, leading to stabilization of the dimer-dimer interface. These results demonstrate that Glab is a novel inhibitor of TTR fibrillization and suggest the molecular mechanism by which Glab binding stabilizes the tetramer. PMID:24422526

  13. Cryo-Electron Tomography for Structural Characterization of Macromolecular Complexes

    PubMed Central

    Cope, Julia; Heumann, John; Hoenger, Andreas

    2011-01-01

    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 material 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 the 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. PMID:21842467

  14. Altered Structural Brain Networks in Tuberous Sclerosis Complex.

    PubMed

    Im, Kiho; Ahtam, Banu; Haehn, Daniel; Peters, Jurriaan M; Warfield, Simon K; Sahin, Mustafa; Ellen Grant, P

    2016-05-01

    Tuberous sclerosis complex (TSC) is characterized by benign hamartomas in multiple organs including the brain and its clinical phenotypes may be associated with abnormal neural connections. We aimed to provide the first detailed findings on disrupted structural brain networks in TSC patients. Structural whole-brain connectivity maps were constructed using structural and diffusion MRI in 20 TSC (age range: 3-24 years) and 20 typically developing (TD; 3-23 years) subjects. We assessed global (short- and long-association and interhemispheric fibers) and regional white matter connectivity, and performed graph theoretical analysis using gyral pattern- and atlas-based node parcellations. Significantly higher mean diffusivity (MD) was shown in TSC patients than in TD controls throughout the whole brain and positively correlated with tuber load severity. A significant increase in MD was mainly influenced by an increase in radial diffusivity. Furthermore, interhemispheric connectivity was particularly reduced in TSC, which leads to increased network segregation within hemispheres. TSC patients with developmental delay (DD) showed significantly higher MD than those without DD primarily in intrahemispheric connections. Our analysis allows non-biased determination of differential white matter involvement, which may provide better measures of "lesion load" and lead to a better understanding of disease mechanisms. PMID:25750257

  15. Predicting electrical measurements by applying scatterometry to complex spacer structures

    NASA Astrophysics Data System (ADS)

    Sendelbach, Matthew; Ayala, Javier; Herrera, Pedro

    2007-03-01

    The comparison of scatterometry measurements of complex spacer structures to electrical test measurements is discussed. Details of the NFET and PFET structures are presented, along with a summary of the scatterometry models used to represent the structures. Before comparison data are shown, a methodology and set of metrics are presented that assist in the analysis and interpretation of comparison data. The methodology, called Prediction Analysis, has its roots in TMU analysis, where both measurements are subject to error. But in Prediction Analysis, an "apples-to-apples" comparison of the measurements is not the goal, and the measurements may be reported in different units. The goal of Prediction Analysis is to analyze the components of error in a correlation and use this analysis to predict a measurement based on the knowledge of another measurement, such that the predicted measurement is bounded. This method is used in this work to determine how well scatterometry measurements of certain parameters correlate to electrical measurements of gate resistance, gate Lpoly, and transistor current Ion. Clear correlations are demonstrated, and physical explanations that explain these correlations are presented. Due to the correlations, the scatterometry measurements can be used as a predictor of electrical performance significantly before the electrical test occurs. Because of this, scatterometry can be a reliable measurement technique for improving spacer controls and reducing the mean time to detect (MTTD) some profile abnormalities.

  16. Numerical Simulation of Flow-Induced Structure in Complex Fluids

    NASA Astrophysics Data System (ADS)

    Yamamoto, Takehiro

    2007-04-01

    It is important to investigate the flow-induced structure for the analysis of the mechanism of flow behavior of complex fluids. The present paper includes two topics in which the flow-induced structure is numerically investigated. The first topic treats the suspensions of disc-like particles under simple shear flows. Disc-like particles were modeled by oblate spheroid particles, and the Brownian dynamics simulation was performed for suspensions of the particles interacting via the Gay-Berne potential. This simulation confirmed that this model system was applicable to the analysis of flow of suspension of disc-like particles. The second one is the numerical simulation of the deformation behavior of a droplet in shear flows. The present simulation is the first step for the numerical simulation of the flow-induced structure in emulsions. This simulation can demonstrate the deformation behavior of droplet observed in experiments and predict effects of non-Newtonian property of fluids on the droplet deformation.

  17. Structural basis of complement membrane attack complex formation

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

    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.

  18. 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

  19. Statistical characterization of complex object structure by dynamic tomography

    NASA Astrophysics Data System (ADS)

    Tillack, Gerd-Rüdiger; Goebbels, Jürgen; Illerhaus, Bernhard; Artemiev, Valentin; Naumov, Alexander

    2002-05-01

    Considering modern materials like reinforced plastics or metal foams the mechanical properties of the component are not determined by every single structural element like a single fiber in a composite. Moreover the ensemble mean and correlation properties of all structural elements form the mechanical properties of the component. Accordingly a statistical description of material properties on a macroscopic scale allow to characterize its mechanical behavior or aging. State of the art tomographic techniques assign a measure of material properties to a volume element. The discretization, i.e., the volume or size of a single element, is limited mainly by the physical mechanisms and the equipment used for the data acquisition. In any case the result of reconstruction yields a statistical average within the considered volume element. To evaluate the integrity of the component the determined measures have to be correlated with the mechanical properties of the component. Special reconstruction algorithms are investigated that allow the statistical description of complex object structures including its dynamics. The algorithm is based on the Kalman filter using statistical prior. The prior includes knowledge about the covariance matrix as well as a prior assumption about the probability density distribution function. The resulting algorithm is recursive yielding a quasi-optimal solution at every reconstruction step. The applicability of the developed algorithm is discussed for the investigation of a specimen made from aluminum foam.

  20. Solution structure of the chromomycin-DNA complex

    SciTech Connect

    Gao, X.; Patel, D.J. )

    1989-01-24

    The structure of the chromomycin-DNA complex at the deoxyoctanucleotide duplex level has been determined from one- and two-dimensional proton NMR studies in Mg-containing aqueous solution. The NMR results demonstrate that the antitumor agent binds as a symmetrical dimer to the self-complementary d(T-T-G-G-C-C-A-A) duplex with retention of the 2-fold symmetry in the complex. A set of intermolecular nuclear Overhauser enhancements (NOEs) established that two chromomycin molecules in the dimer share the minor groove at the G-G-C-C{center dot}G-G-C-C segment in such a way that each hydrophilic edge of the chromophore is located next to the G-G{center dot}C-C half-site and each C-D-E trisaccharide chain extends toward the 3{prime}-direction of the octanucleotide duplex. In addition, the A-B disaccharide segment and the hydrophilic side chain of the antitumor agent are directed toward the phosphate backbone. The observed changes in nucleic acid NOEs and coupling patterns on complex formation establish a transition to a wider and shallower minor groove at the central G-G-C-C{center dot}G-G-C-C segment required for accommodating the chromomycin dimer. The present demonstration that chromomycin binds as a dimer and switches the conformation of the DNA at its G{center dot}C-rich minor groove binding site provides new insights into antitumor agent design and the sequence specificity of antitumor agent-DNA recognition.

  1. Biological pattern formation: from basic mechanisms to complex structures

    SciTech Connect

    Koch, A.J.; Meinhardt, H. )

    1994-10-01

    The reliable development of highly complex organisms is an intriguing and fascinating problem. The genetic material is, as a rule, the same in each cell of an organism. How then do cells, under the influence of their common genes, produce spatial patterns Simple models are discussed that describe the generation of patterns out of an initially nearly homogeneous state. They are based on nonlinear interactions of at least two chemicals and on their diffusion. The concepts of local autocatalysis and of long-range inhibition play a fundamental role. Numerical simulations show that the models account for many basic biological observations such as the regeneration of a pattern after excision of tissue or the production of regular (or nearly regular) arrays of organs during (or after) completion of growth. Very complex patterns can be generated in a reproducible way by hierarchical coupling of several such elementary reactions. Applications to animal coats and to the generation of polygonally shaped patterns are provided. It is further shown how to generate a strictly periodic pattern of units that themselves exhibit a complex and polar fine structure. This is illustrated by two examples: the assembly of photoreceptor cells in the eye of [ital Drosophila] and the positioning of leaves and axillary buds in a growing shoot. In both cases, the substructures have to achieve an internal polarity under the influence of some primary pattern-forming system existing in the fly's eye or in the plant. The fact that similar models can describe essential steps in organisms as distantly related as animals and plants suggests that they reveal some universal mechanisms.

  2. Cryo electron microscopy to determine the structure of macromolecular complexes.

    PubMed

    Carroni, Marta; Saibil, Helen R

    2016-02-15

    Cryo-electron microscopy (cryo-EM) is a structural molecular and cellular biology technique that has experienced major advances in recent years. Technological developments in image recording as well as in processing software make it possible to obtain three-dimensional reconstructions of macromolecular assemblies at near-atomic resolution that were formerly obtained only by X-ray crystallography or NMR spectroscopy. In parallel, cryo-electron tomography has also benefitted from these technological advances, so that visualization of irregular complexes, organelles or whole cells with their molecular machines in situ has reached subnanometre resolution. Cryo-EM can therefore address a broad range of biological questions. The aim of this review is to provide a brief overview of the principles and current state of the cryo-EM field. PMID:26638773

  3. The γ-secretase complex: from structure to function

    PubMed Central

    Zhang, Xian; Li, Yanfang; Xu, Huaxi; Zhang, Yun-wu

    2014-01-01

    One of the most critical pathological features of Alzheimer’s disease (AD) is the accumulation of β-amyloid (Aβ) peptides that form extracellular senile plaques in the brain. Aβ is derived from β-amyloid precursor protein (APP) through sequential cleavage by β- and γ-secretases. γ-secretase is a high molecular weight complex minimally composed of four components: presenilins (PS), nicastrin, anterior pharynx defective 1 (APH-1), and presenilin enhancer 2 (PEN-2). In addition to APP, γ-secretase also cleaves many other type I transmembrane (TM) protein substrates. As a crucial enzyme for Aβ production, γ-secretase is an appealing therapeutic target for AD. Here, we summarize current knowledge on the structure and function of γ-secretase, as well as recent progress in developing γ-secretase targeting drugs for AD treatment. PMID:25565961

  4. Iterated tabu search for identifying community structure in complex networks

    NASA Astrophysics Data System (ADS)

    Lü, Zhipeng; Huang, Wenqi

    2009-08-01

    This paper presents an iterated tabu search (denoted by ITS) algorithm for optimizing the modularity of community structure in complex networks. The proposed algorithm follows a general framework composed of two phases: basic optimization and postrefinement. When the basic optimization cannot improve the modularity any more, a postrefinement procedure is employed to further optimize the objective function with a global view. For both these two phases, iterated tabu search algorithm is employed to optimize the objective function. Computational results show the high effectiveness of the proposed ITS algorithm compared with six state-of-the-art algorithms in the literature. In particular, our ITS algorithm improves the previous best known modularity for several small and medium size networks.

  5. Iterated tabu search for identifying community structure in complex networks.

    PubMed

    Lü, Zhipeng; Huang, Wenqi

    2009-08-01

    This paper presents an iterated tabu search (denoted by ITS) algorithm for optimizing the modularity of community structure in complex networks. The proposed algorithm follows a general framework composed of two phases: basic optimization and postrefinement. When the basic optimization cannot improve the modularity any more, a postrefinement procedure is employed to further optimize the objective function with a global view. For both these two phases, iterated tabu search algorithm is employed to optimize the objective function. Computational results show the high effectiveness of the proposed ITS algorithm compared with six state-of-the-art algorithms in the literature. In particular, our ITS algorithm improves the previous best known modularity for several small and medium size networks. PMID:19792223

  6. A new order parameter in complex dipolar structures

    NASA Astrophysics Data System (ADS)

    Prosandeev, Sergey; Bellaiche, Laurent

    2008-03-01

    Microscopic models have been used to reveal the existence of a new order parameter that is associated with many complex dipolar structures in magnets and ferroelectrics. This overlooked order parameter involves a double cross product of the local dipoles with their positions. It provides a measure of subtle microscopic features, such as the helicity of the two domains inherent to onion states, curvature of the dipolar pattern in flower states or characteristics of set of vortices with opposite chirality (e.g., distance between vortices' centers and/or magnitude of their local dipoles). This work is mostly supported by DOE grant DE-FG02-05ER46188. We also acknowledge support from ONR grant N00014-04-1-0413 and NSF grants DMR-0701558, DMR-0404335 and DMR-0080054 (C-SPIN). Some computations were made possible thanks to the MRI Grants 0421099 and 0722625 from NSF.

  7. Complex dental structure and wear biomechanics in hadrosaurid dinosaurs.

    PubMed

    Erickson, Gregory M; Krick, Brandon A; Hamilton, Matthew; Bourne, Gerald R; Norell, Mark A; Lilleodden, Erica; Sawyer, W Gregory

    2012-10-01

    Mammalian grinding dentitions are composed of four major tissues that wear differentially, creating coarse surfaces for pulverizing tough plants and liberating nutrients. Although such dentition evolved repeatedly in mammals (such as horses, bison, and elephants), a similar innovation occurred much earlier (~85 million years ago) within the duck-billed dinosaur group Hadrosauridae, fueling their 35-million-year occupation of Laurasian megaherbivorous niches. How this complexity was achieved is unknown, as reptilian teeth are generally two-tissue structures presumably lacking biomechanical attributes for grinding. Here we show that hadrosaurids broke from the primitive reptilian archetype and evolved a six-tissue dental composition that is among the most sophisticated known. Three-dimensional wear models incorporating fossilized wear properties reveal how these tissues interacted for grinding and ecological specialization. PMID:23042891

  8. Structuring temporal sequences: comparison of models and factors of complexity.

    PubMed

    Essens, P

    1995-05-01

    Two stages for structuring tone sequences have been distinguished by Povel and Essens (1985). In the first, a mental clock segments a sequence into equal time units (clock model); in the second, intervals are specified in terms of subdivisions of these units. The present findings support the clock model in that it predicts human performance better than three other algorithmic models. Two further experiments in which clock and subdivision characteristics were varied did not support the hypothesized effect of the nature of the subdivisions on complexity. A model focusing on the variations in the beat-anchored envelopes of the tone clusters was proposed. Errors in reproduction suggest a dual-code representation comprising temporal and figural characteristics. The temporal part of the representation is based on the clock model but specifies, in addition, the metric of the level below the clock. The beat-tone-cluster envelope concept was proposed to specify the figural part. PMID:7596749

  9. 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.

  10. Atomic structure of the actin: DNase I complex

    NASA Astrophysics Data System (ADS)

    Kabsch, Wolfgang; Mannherz, Hans Georg; Suck, Dietrich; Pai, Emil F.; Holmes, Kenneth C.

    1990-09-01

    The atomic models of the complex between rabbit skeletal muscle actin and bovine pancreatic deoxyribonuclease I both in the ATP and ADP forms have been determined byo X-ray analysis at an effective resolution of 2.8 Å and 3 Å, respectively. The two structures are very similar. The actin molecule consists of two domains which can be further subdivided into two subdomains. ADP or ATP is located in the cleft between the domains with a calcium ion bound to the β- or β- and γ-phosphates, respectively. The motif of a five-stranded (3 sheet consisting of a (3 meander and a right handed βαβ unit appears in each domain suggesting that gene duplication might have occurred. These sheets have the same topology as that found in hexokinase.

  11. 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.

  12. 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

  13. Structures of Large RNAs and RNA-Protein Complexes: Toward Structure Determination of Riboswitches.

    PubMed

    Grigg, Jason C; Ke, Ailong

    2015-01-01

    Riboswitches are widespread and important regulatory elements. They are typically present in the mRNA of the gene under their regulation, where they form complex three-dimensional structures that can bind an effector and regulate either transcription or translation of the mRNA. Structural biology has been essential to our understanding of their ligand recognition and conformational switching mechanisms, but riboswitch determination presents several important complications. Overcoming these challenges requires a synergistic approach using rational design of the constructs and supporting methods to biochemically validate the designs and resulting structures. PMID:26068743

  14. Complex wet-environments in electronic-structure calculations

    NASA Astrophysics Data System (ADS)

    Fisicaro, Giuseppe; Genovese, Luigi; Andreussi, Oliviero; Marzari, Nicola; Goedecker, Stefan

    The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of an applied electrochemical potentials, including complex electrostatic screening coming from the solvent. In the present work we present a solver to handle both the Generalized Poisson and the Poisson-Boltzmann equation. A preconditioned conjugate gradient (PCG) method has been implemented for the Generalized Poisson and the linear regime of the Poisson-Boltzmann, allowing to solve iteratively the minimization problem with some ten iterations. On the other hand, a self-consistent procedure enables us to solve the Poisson-Boltzmann problem. The algorithms take advantage of a preconditioning procedure based on the BigDFT Poisson solver for the standard Poisson equation. They exhibit very high accuracy and parallel efficiency, and allow different boundary conditions, including surfaces. The solver has been integrated into the BigDFT and Quantum-ESPRESSO electronic-structure packages and it will be released as a independent program, suitable for integration in other codes. We present test calculations for large proteins to demonstrate efficiency and performances. This work was done within the PASC and NCCR MARVEL projects. Computer resources were provided by the Swiss National Supercomputing Centre (CSCS) under Project ID s499. LG acknowledges also support from the EXTMOS EU project.

  15. 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.

  16. 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.

  17. Complexity of coherent structures computed from braids of passive particles

    NASA Astrophysics Data System (ADS)

    Budisic, Marko; Thiffeault, Jean-Luc

    2015-11-01

    Transport in fluids can be characterized by tracking passive particles advected by the fluid flow. When particles are distributed densely, as can be achieved in laboratory, the fluid velocity field can be reconstructed through Particle Tracking Velocimetry, enabling computation of Lyapunov exponents or other numerical analyses. When particles are sparse, as in drifter measurements of oceans, the velocity field cannot be reliably reconstructed. Nevertheless, the amount of entanglement of particle paths over time can be used to estimate the dynamical complexity of the flow by computing the Finite-Time Braiding Exponent (FTBE). The technique is based on braid dynamics and measures the rate at which particle motion stretches topological loops, i.e., the ``rubber bands'' enclosing subsets of particles. Allshouse and Thiffeault showed that minimally-stretching loops correspond to the structures coherent under material transport in flows. We extend their work and couple it to the FTBE calculations in order to characterize the spatial distribution of flow complexity. Analysis is demonstrated on the Hackborn rotor-oscillator model, which exhibits regions of chaotic and regular dynamics, and can be realized both numerically and experimentally. Funded by NSF CMMI-1233935.

  18. 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

  19. Nonconservativity and noncommutativity in locomotion. Geometric mechanics in minimum-perturbation coordinates

    NASA Astrophysics Data System (ADS)

    Hatton, R. L.; Choset, H.

    2015-12-01

    Geometric mechanics techniques based on Lie brackets provide high-level characterizations of the motion capabilities of locomoting systems. In particular, they relate the net displacement they experience over cyclic gaits to area integrals of their constraints; plotting these constraints thus provides a visual "landscape" that intuitively captures all available solutions of the system's dynamic equations. Recently, we have found that choices of system coordinates heavily influence the effectiveness of these approaches. This property appears at first to run counter to the principle that differential geometric structures should be coordinate-invariant. In this paper, we provide a tutorial overview of the Lie bracket techniques, then examine how the coordinate-independent nonholonomy of these systems has a coordinate-dependent separation into nonconservative and noncommutative components that respectively capture how the system constraints vary over the shape and position components of the configuration space. Nonconservative constraint variations can be integrated geometrically via Stokes' theorem, but noncommutative effects can only be approximated by similar means; therefore choices of coordinates in which the nonholonomy is primarily nonconservative improve the accuracy of the geometric techniques.

  20. High throughput parametric studies of the structure of complex nanomaterials

    NASA Astrophysics Data System (ADS)

    Tian, Peng

    The structure of nanoscale materials is difficult to study because crystallography, the gold-standard for structure studies, no longer works at the nanoscale. New tools are needed to study nanostructure. Furthermore, it is important to study the evolution of nanostructure of complex nanostructured materials as a function of various parameters such as temperature or other environmental variables. These are called parametric studies because an environmental parameter is being varied. This means that the new tools for studying nanostructure also need to be extended to work quickly and on large numbers of datasets. This thesis describes the development of new tools for high throughput studies of complex and nanostructured materials, and their application to study the structural evolution of bulk, and nanoparticles of, MnAs as a function of temperature. The tool for high throughput analysis of the bulk material was developed as part of this PhD thesis work and is called SrRietveld. A large part of making a new tool is to validate it and we did this for SrRietveld by carrying out a high-throughput study of uncertainties coming from the program using different ways of estimating the uncertainty. This tool was applied to study structural changes in MnAs as a function of temperature. We were also interested in studying different MnAs nanoparticles fabricated through different methods because of their applications in information storage. PDFgui, an existing tool for analyzing nanoparticles using Pair distribution function (PDF) refinement, was used in these cases. Comparing the results from the analysis by SrRietveld and PDFgui, we got more comprehensive structure information about MnAs. The layout of the thesis is as follows. First, the background knowledge about material structures is given. The conventional crystallographic analysis is introduced in both theoretical and practical ways. For high throughput study, the next-generation Rietveld analysis program: Sr

  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. Ray Tracing for Complex Astrophysical High-opacity Structures

    NASA Astrophysics Data System (ADS)

    Steinacker, J.; Bacmann, A.; Henning, T.

    2006-07-01

    We present a ray-tracing technique for radiative transfer modeling of complex three-dimensional (3D) structures that include dense regions of high optical depth, such as that in dense molecular clouds, circumstellar disks, envelopes of evolved stars, and dust tori around active galactic nuclei. The corresponding continuum radiative transfer problem is described, and the numerical requirements for inverse 3D density and temperature modeling are defined. We introduce a relative intensity and transform the radiative transfer equation along the rays to solve machine precision problems and to relax strong gradients in the source term. For the optically thick regions where common ray tracers are forced to perform small trace steps, we give two criteria for making use of a simple approximative solver crossing the optically thick region quickly. Using an example of a density structure with optical depth changes of 6 orders of magnitude and sharp temperature variations, we demonstrate the accuracy of the proposed scheme using a common fifth-order Runge-Kutta ray tracer with adaptive step-size control. In our test case, the gain in computational speed is about a factor of 870. The method is applied in order to calculate the temperature distribution within a massive molecular cloud core for different boundary conditions for the radiation field.

  3. Evolution of complex dynamics in spatially structured populations

    PubMed Central

    Johst, K.; Doebeli, M.; Brandl, R.

    1999-01-01

    Dynamics of populations depend on demographic parameters which may change during evolution. In simple ecological models given by one-dimensional difference equations, the evolution of demographic parameters generally leads to equilibrium population dynamics. Here we show that this is not true in spatially structured ecological models. Using a multi-patch metapopulation model, we study the evolutionary dynamics of phenotypes that differ both in their response to local crowding, i.e. in their competitive behaviour within a habitat, and in their rate of dispersal between habitats. Our simulation results show that evolution can favour phenotypes that have the intrinsic potential for very complex dynamics provided that the environment is spatially structured and temporally variable. These phenotypes owe their evolutionary persistence to their large dispersal rates. They typically coexist with phenotypes that have low dispersal rates and that exhibit equilibrium dynamics when alone. This coexistence is brought about through the phenomenon of evolutionary branching, during which an initially uniform population splits into the two phenotypic classes.

  4. Structural insights into Paf1 complex assembly and histone binding.

    PubMed

    Chu, Xinlei; Qin, Xiaohong; Xu, Huisha; Li, Lei; Wang, Zheng; Li, Fengzhi; Xie, Xingqiao; Zhou, Hao; Shen, Yuequan; Long, Jiafu

    2013-12-01

    The highly conserved Paf1 complex (PAF1C) plays critical roles in RNA polymerase II transcription elongation and in the regulation of histone modifications. It has also been implicated in other diverse cellular activities, including posttranscriptional events, embryonic development and cell survival and maintenance of embryonic stem cell identity. Here, we report the structure of the human Paf1/Leo1 subcomplex within PAF1C. The overall structure reveals that the Paf1 and Leo1 subunits form a tightly associated heterodimer through antiparallel beta-sheet interactions. Detailed biochemical experiments indicate that Leo1 binds to PAF1C through Paf1 and that the Ctr9 subunit is the key scaffold protein in assembling PAF1C. Furthermore, we show that the Paf1/Leo1 heterodimer is necessary for its binding to histone H3, the histone octamer, and nucleosome in vitro. Our results shed light on the PAF1C assembly process and substrate recognition during various PAF1C-coordinated histone modifications. PMID:24038468

  5. 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.

  6. Thermal properties of composite materials with a complex fractal structure

    NASA Astrophysics Data System (ADS)

    Cervantes-Álvarez, F.; Reyes-Salgado, J. J.; Dossetti, V.; Carrillo, J. L.

    2014-06-01

    In this work, we report the thermal characterization of platelike composite samples made of polyester resin and magnetite inclusions. By means of photoacoustic spectroscopy and thermal relaxation, the thermal diffusivity, conductivity and volumetric heat capacity of the samples were experimentally measured. The volume fraction of the inclusions was systematically varied in order to study the changes in the effective thermal conductivity of the composites. For some samples, a static magnetic field was applied during the polymerization process, resulting in anisotropic inclusion distributions. Our results show a decrease in the thermal conductivity of some of the anisotropic samples, compared to the isotropic randomly distributed ones. Our analysis indicates that the development of elongated inclusion structures leads to the formation of magnetite and resin domains, causing this effect. We correlate the complexity of the inclusion structure with the observed thermal response through a multifractal and lacunarity analysis. All the experimental data are contrasted with the well known Maxwell-Garnett effective media approximation for composite materials.

  7. Motif structure and cooperation in real-world complex networks

    NASA Astrophysics Data System (ADS)

    Salehi, Mostafa; Rabiee, Hamid R.; Jalili, Mahdi

    2010-12-01

    Networks of dynamical nodes serve as generic models for real-world systems in many branches of science ranging from mathematics to physics, technology, sociology and biology. Collective behavior of agents interacting over complex networks is important in many applications. The cooperation between selfish individuals is one of the most interesting collective phenomena. In this paper we address the interplay between the motifs’ cooperation properties and their abundance in a number of real-world networks including yeast protein-protein interaction, human brain, protein structure, email communication, dolphins’ social interaction, Zachary karate club and Net-science coauthorship networks. First, the amount of cooperativity for all possible undirected subgraphs with three to six nodes is calculated. To this end, the evolutionary dynamics of the Prisoner’s Dilemma game is considered and the cooperativity of each subgraph is calculated as the percentage of cooperating agents at the end of the simulation time. Then, the three- to six-node motifs are extracted for each network. The significance of the abundance of a motif, represented by a Z-value, is obtained by comparing them with some properly randomized versions of the original network. We found that there is always a group of motifs showing a significant inverse correlation between their cooperativity amount and Z-value, i.e. the more the Z-value the less the amount of cooperativity. This suggests that networks composed of well-structured units do not have good cooperativity properties.

  8. Structure of the heterodimeric ecdysone receptor DNA-binding complex

    PubMed Central

    Devarakonda, Srikripa; Harp, Joel M.; Kim, Youngchang; Ożyhar, Andrzej; Rastinejad, Fraydoon

    2003-01-01

    Ecdysteroids initiate molting and metamorphosis in insects via a heterodimeric receptor consisting of the ecdysone receptor (EcR) and ultraspiracle (USP). The EcR–USP heterodimer preferentially mediates transcription through highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5′-AGGTCA-3′ separated by 1 bp (IR-1). The requirement for a heterodimeric arrangement of EcR–USP subunits to bind to a symmetric DNA is unusual within the nuclear receptor superfamily. We describe the 2.24 Å structure of the EcR–USP DNA-binding domain (DBD) heterodimer bound to an idealized IR-1 element. EcR and USP use similar surfaces, and rely on the deformed minor groove of the DNA to establish protein–protein contacts. As retinoid X receptor (RXR) is the mammalian homolog of USP, we also solved the 2.60 Å crystal structure of the EcR–RXR DBD heterodimer on IR-1 and found the dimerization and DNA-binding interfaces to be the same as in the EcR–USP complex. Sequence alignments indicate that the EcR–RXR heterodimer is an important model for understanding how the FXR–RXR heterodimer binds to IR-1 sites. PMID:14592980

  9. 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.

  10. Crystal structure of human dehydroepiandrosterone sulphotransferase in complex with substrate.

    PubMed Central

    Rehse, Peter H; Zhou, Ming; Lin, Sheng-Xiang

    2002-01-01

    Dehydroepiandrosterone sulphotransferase (DHEA-ST) is an enzyme that converts dehydroepiandrosterone (DHEA), and some other steroids, into their sulphonated forms. The enzyme catalyses the sulphonation of DHEA on the 3alpha-oxygen, with 3'-phosphoadenosine-5'-phosphosulphate contributing the sulphate. The structure of human DHEA-ST in complex with its preferred substrate DHEA has been solved here to 1.99 A using molecular replacement with oestradiol sulphotransferase (37% sequence identity) as a model. Two alternative substrate-binding orientations have been identified. The primary, catalytic, orientation has the DHEA 3alpha-oxygen and the highly conserved catalytic histidine in nearly identical positions as are seen for the related oestradiol sulphotransferase. The substrate, however, shows rotations of up to 30 degrees, and there is a corresponding rearrangement of the protein loops contributing to the active site. This may also reflect the low identity between the two enzymes. The second orientation penetrates further into the active site and can form a potential hydrogen bond with the desulphonated cofactor 3',5'-phosphoadenosine (PAP). This second site contains more van der Waal interactions with hydrophobic residues than the catalytic site and may also reflect the substrate-inhibition site. The PAP position was obtained from the previously solved structure of DHEA-ST co-crystallized with PAP. This latter structure, due to the arrangement of loops within the active site and monomer interactions, cannot bind substrate. The results presented here describe details of substrate binding to DHEA-ST and the potential relationship to substrate inhibition. PMID:11988089

  11. Structure of the F-actin-tropomyosin complex.

    PubMed

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

    2015-03-01

    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 loss, familial thoracic aortic aneurysms and dissections, and multiple variations of myopathies. In striated muscle fibres, the binding of myosin motors to actin filaments is mainly regulated by tropomyosin and troponin. 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 troponin. Although crystal structures for monomeric actin (G-actin) are available, 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 Å in complex with tropomyosin at a resolution of 6.5 Å, 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 map density corresponding to ADP and Mg(2+) 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 F-actin-tropomyosin-myosin structure 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 foundation for the targeted

  12. 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

  13. Gravitational collapse of the shells with the smeared gravitational source in noncommutative geometry

    NASA Astrophysics Data System (ADS)

    Oh, John J.; Park, Chanyong

    2010-03-01

    We study the formation of the (noncommutative) Schwarzschild black hole from collapsing shell of the generalized matters containing polytropic and Chaplygin gas. We show that this collapsing shell depending on various parameters forms either a black hole or a naked singular shell with the help of the pressure. Furthermore, by considering the smeared gravitational sources, we investigate the noncommutative black holes formation. Though this mild noncommutative correction of matters cannot ultimately resolve the emergence of the naked singularity, we show that in some parameter region the collapsing shell evolves to a noncommutative black hole before becoming a naked singular shell.

  14. 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. PMID:19113767

  15. Structure and photoluminescence of silver(i) trinuclear halopyrazolato complexes.

    PubMed

    Morishima, Yui; Young, David James; Fujisawa, Kiyoshi

    2014-11-14

    Five halogen substituted pyrazolates, 4-chloro-3,5-diisopropylpyrazole (4-Cl-3,5-iPr2pzH), 4-bromo-3,5-diisopropylpyrazole (4-Br-3,5-iPr2pzH), 4-iodo-3,5-diisopropylpyrazole (4-I-3,5-iPr2pzH), 4-chloro-3,5-diphenylpyrazole (4-Cl-3,5-Ph2pzH), and 4-bromo-3,5-diphenylpyrazole (4-Br-3,5-Ph2pzH), were conveniently prepared by halogenation of the appropriate pyrazoles with N-halosuccinimides (NXS) (X = Cl, Br, and I) followed by complexation of the pyrazolate anions with silver(i) nitrate. Single crystal X-ray analysis revealed either dimeric trinuclear {[Ag(μ-4-X-3,5-R2pz)]3}2 (R = iPr, X = Cl, Br, and I) or trinuclear [Ag(μ-4-X 3,5-R2pz)]3 (R = iPr, X = I; R = Ph, X = Cl, R = Ph, X = Br) structures, the latter held together with argentophilic interactions (AgAg interactions) that could also be observed in the Raman spectra. The electronegativity of the halogen substituent could be correlated with the strength of the AgAg interaction and the wavelength of solid-state photoluminescence. All complexes were emissive on UV irradiation at low temperatures, with the colour of emission from the diisopropyl substituted analogues red shifted by the halogens in the order Cl (red) > Br (orange) > I (yellow). Emission from the diphenyl substituted analogues was dominated by the extended aromatic system and was largely invariant to the halogens. PMID:25230795

  16. 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.

  17. 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.

  18. The Complex Velocity Structure of the Chromosphere of VV Cephei

    NASA Astrophysics Data System (ADS)

    Bauer, Wendy Hagen; Bennett, Philip D.

    2014-06-01

    The eclipsing binary system VV Cephei consists of an M2 Iab supergiant primary and a hotter, probably B-type main-sequence companion. The last eclipse was observed with the HST-STIS spectrograph at 21 epochs ranging from mid-totality through first quadrature. These observations sampled seven lines of sight through the entire, extended chromosphere of the M supergiant star, beginning shortly after the hot companion emerged from total eclipse. At all seven of these egress epochs, the observed chromospheric absorption line profiles had a typical FWHM of 25-30 km/s. These profiles contained multiple (usually two) components that persisted throughout the chromosphere. The relative strengths of the two components were observed to depend on the ionization level and excitation potential, with the longer-wavelength (red) component tending to be stronger than the shorter-wavelength (blue) component in the higher-ionization and higher-excitation lines, while the strengths of the two components were more similar in lower-excitation features. This behavior suggests the red components form in hotter gas than the blue components. The great width of these chromospheric lines has been attributed both to intrinsic chromospheric turbulence and absorption due to the accelerating stellar wind. Here we present evidence that the complex absorption line profiles observed in the extended chromosphere of VV Cep reflect an intrinsic, coherent, multi-temperature component, azimuthal velocity structure present over the entire height of the M supergiant chromosphere, which is about a stellar radius in extent. This velocity model is inferred from the behavior of weak ultraviolet lines of species including Al I, Ti I, Fe I, Co I, Ni I, and Zr II. We present observations, analysis of the line profile velocity structure, and discuss the implications for driving the stellar wind and associated mass loss.

  19. 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

  20. Cloud structure and feedback effects in the Carina Nebula Complex

    NASA Astrophysics Data System (ADS)

    Roccatagliata, Veronica; Preibisch, Thomas; Gaczkowski, Benjamin; Ratzka, Thorsten

    2013-07-01

    The star formation process in large clusters/associations can be strongly influenced by the feedback from high mass stars. Whether the resulting net effect of the feedback is predominantly negative (cloud dispersal) or positive (triggering of star formation due to cloud compression) is still an open question. The Carina Nebula complex (CNC) represents one of the most massive star-forming regions in our Galaxy. We use our Herschel far-infrared observations to study the properties of the clouds over the entire CNC and LABOCA/APEX telescope on the central part of the CNC.Our Herschel maps resolve, for the first time, the small-scale structure of the dense clouds over the entire spatial extent of the CNC. Several particularly interesting regions, including the prominent pillars south of eta Car, are analyzed in detail. Our maps also reveal a peculiar 'wave'-like pattern in the northern part of the Carina Nebula. The total mass of the clouds seen by Herschel in the central region is about 656 000 Msun. We derive the global spectral energy distribution in the mid-infrared to mm wavelength range and derive a total mass of < 890 000 Msun. We find that the density and temperature structure of the clouds in most parts of the CNC is dominated by the strong feedback from the numerous massive stars, rather than random turbulence. Comparing the cloud mass and the star formation rate derived for the CNC to other Galactic star forming regions suggests that the CNC is forming stars very efficiently. We suggest this to be a consequence of triggered star formation by radiative cloud compression.In our LABOCA sub-mm map, we identify about 600 individual clumps. We analyze and interpret the clump initial mass function (CIMF) as signature of turbulent pre-stellar clouds or star-forming clouds.

  1. Quantum geometry and quantization on U(u(2)) background. Noncommutative Dirac monopole

    NASA Astrophysics Data System (ADS)

    Gurevich, Dimitri; Saponov, Pavel

    2016-08-01

    In our previous publications we introduced differential calculus on the enveloping algebras U(gl(m)) similar to the usual calculus on the commutative algebra Sym (gl(m)) . The main ingredients of our calculus are quantum partial derivatives which turn into the usual partial derivatives in the classical limit. In the particular case m = 2 we prolonged this calculus on a central extension A of the algebra U(gl(2)) . In the present paper we consider the problem of a further extension of the quantum partial derivatives on the skew-field of the algebra A and define the corresponding de Rham complex. As an application of the differential calculus we suggest a method of transferring dynamical models defined on an extended Sym (u(2)) to an extended algebra U(u(2)) . We call this procedure the quantization with noncommutative configuration space. In this sense we quantize the Dirac monopole and find a solution of this model.

  2. Unsaturated platinum-rhenium cluster complexes. Synthesis, structures and reactivity.

    PubMed

    Adams, Richard D; Captain, Burjor; Smith, Mark D; Beddie, Chad; Hall, Michael B

    2007-05-01

    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

  3. Structural controllability of complex networks based on preferential matching.

    PubMed

    Zhang, Xizhe; Lv, Tianyang; Yang, XueYing; Zhang, Bin

    2014-01-01

    Minimum driver node sets (MDSs) play an important role in studying the structural controllability of complex networks. Recent research has shown that MDSs tend to avoid high-degree nodes. However, this observation is based on the analysis of a small number of MDSs, because enumerating all of the MDSs of a network is a #P problem. Therefore, past research has not been sufficient to arrive at a convincing conclusion. In this paper, first, we propose a preferential matching algorithm to find MDSs that have a specific degree property. Then, we show that the MDSs obtained by preferential matching can be composed of high- and medium-degree nodes. Moreover, the experimental results also show that the average degree of the MDSs of some networks tends to be greater than that of the overall network, even when the MDSs are obtained using previous research method. Further analysis shows that whether the driver nodes tend to be high-degree nodes or not is closely related to the edge direction of the network. PMID:25375628

  4. Structural basis underlying viral hijacking of a histone chaperone complex.

    PubMed

    Huang, Hongda; Deng, Zhong; Vladimirova, Olga; Wiedmer, Andreas; Lu, Fang; Lieberman, Paul M; Patel, Dinshaw J

    2016-01-01

    The histone H3.3 chaperone DAXX is implicated in formation of heterochromatin and transcription silencing, especially for newly infecting DNA virus genomes entering the nucleus. Epstein-Barr virus (EBV) can efficiently establish stable latent infection as a chromatinized episome in the nucleus of infected cells. The EBV tegument BNRF1 is a DAXX-interacting protein required for the establishment of selective viral gene expression during latency. Here we report the structure of BNRF1 DAXX-interaction domain (DID) in complex with DAXX histone-binding domain (HBD) and histones H3.3-H4. BNRF1 DID contacts DAXX HBD and histones through non-conserved loops. The BNRF1-DAXX interface is responsible for BNRF1 localization to PML-nuclear bodies typically associated with host-antiviral resistance and transcriptional repression. Paradoxically, the interface is also required for selective transcription activation of viral latent cycle genes required for driving B-cell proliferation. These findings reveal molecular details of virus reprogramming of an antiviral histone chaperone to promote viral latency and cellular immortalization. PMID:27581705

  5. Structural Controllability of Complex Networks Based on Preferential Matching

    PubMed Central

    Zhang, Xizhe; Lv, Tianyang; Yang, XueYing; Zhang, Bin

    2014-01-01

    Minimum driver node sets (MDSs) play an important role in studying the structural controllability of complex networks. Recent research has shown that MDSs tend to avoid high-degree nodes. However, this observation is based on the analysis of a small number of MDSs, because enumerating all of the MDSs of a network is a #P problem. Therefore, past research has not been sufficient to arrive at a convincing conclusion. In this paper, first, we propose a preferential matching algorithm to find MDSs that have a specific degree property. Then, we show that the MDSs obtained by preferential matching can be composed of high- and medium-degree nodes. Moreover, the experimental results also show that the average degree of the MDSs of some networks tends to be greater than that of the overall network, even when the MDSs are obtained using previous research method. Further analysis shows that whether the driver nodes tend to be high-degree nodes or not is closely related to the edge direction of the network. PMID:25375628

  6. 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.

  7. Structural Preferences in Phosphanylthiolato Platinum(II) Complexes

    PubMed Central

    Duran, Josep; Real, Julio; Benet‐Buchholz, Jordi; Solà, Miquel

    2016-01-01

    Abstract Invited for this month's cover picture are the groups of Prof. Alfonso Polo and Dr. Albert Poater at the Universitat de Girona, as well as their collaborators from the Universitat Autònoma de Barcelona and the Institute of Chemical Research of Catalonia. The cover picture shows phosphanylthiolate ligand coordination on a platinum(II) center to give only the bischelate cis ‐P,P isomer when the ligand/Pt ratio is 2, whereas a trinuclear unexpected complex is achieved with a ligand/Pt ratio of 1. Here, the synthesis and structural determination is combined with density functional theory (DFT) calculations to rationalize the reaction mechanistically and through conceptual DFT. The exciting point of this study is that it opens the door to test new experimental pathways to monitor the preferred cis or trans arrangement of bidentate ligands to platinum. (Legend: H‐white, C‐black, P‐purple, S‐yellow, Cl‐green, Pt‐blue.) For more details, see the Full Paper on p. 51 ff. PMID:27308218

  8. Complex structure and regulation of the ABP/SHBG gene.

    PubMed

    Joseph, D R; Sullivan, P M; Wang, Y M; Millhorn, D E; Bayliss, D M

    1991-01-01

    Extracellular androgen-binding proteins (ABPs) are thought to modulate the regulatory functions of androgens and the trans-acting nuclear androgen receptor. Testicular ABP and plasma sex hormone-binding globulin (SHBG), which is produced in the liver, are encoded by the same gene. We report here that the ABP/SHBG gene is also expressed in fetal rat liver and adult brain. Immunoreactive ABP was localized in the brain and fetal liver and mRNAs were identified in both tissues by northern blot hybridization. Analysis of brain and fetal liver cDNA clones revealed alternatively processed RNAs with sequence characteristics suggesting the encoded proteins could act as competitors of ABP/SHBG binding to cell surface receptors. One cDNA represented a fused transcript of the ABP/SHBG gene and the histidine decarboxylase gene that was apparently formed by a trans-splicing process. Gene sequencing experiments indicate that tissue-specific ABP/SHBG gene promoter-enhancer elements are utilized in testis, brain and fetal liver. These data demonstrate that the structure, RNA transcript processing and likely regulation of the ABP/SHBG gene are very complex. PMID:1958575

  9. 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

  10. Microstructure-based modelling of multiphase materials and complex structures

    NASA Astrophysics Data System (ADS)

    Werner, Ewald; Wesenjak, Robert; Fillafer, Alexander; Meier, Felix; Krempaszky, Christian

    2015-10-01

    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.

  11. 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. PMID:26820353

  12. The synthesis, structure and reactivity of 4-nonafluorobiphenyl complexes.

    PubMed

    Martin, Eddy; Hughes, David L; Hursthouse, Michael B; Male, Louise; Lancaster, Simon J

    2009-03-01

    The Grignard reagent Ar(F)'MgBr (Ar(F)' = 4-(C(6)F(5))C(6)F(4)) reacts with Me(3)SiCl, Me(2)SiCl(2) and Me(3)SnCl to give the 4-nonafluorobiphenyl group 14 complexes Ar(F)'Me(3)Si, (Ar(F)')(2)Me(2)Si and Ar(F)'Me(3)Sn respectively. Ar(F)'Me(3)Sn undergoes only methyl group exchange when treated with BBr(3), yielding Ar(F)'Me(2)SnBr. The solid state structures of Ar(F)'Me(3)Sn and Ar(F)'Me(2)SnBr have been determined and exhibit the expected distorted tetrahedral geometries at tin. The reaction between three equivalents of Ar(F)'MgBr and BF(3) was not selective, while one equivalent of Ar(F)'MgBr and (Ar(F))(2)BF (Ar(F) = C(6)F(5)) reacted cleanly to give (Ar(F))(2)Ar(F)'B. Treatment of BCl(3) with three equivalents of Ar(F)'Li, prepared at low temperature from the reaction between Ar(F)'Br and n-BuLi, yielded (Ar(F)')(3)B. The molecular structures of the acetonitrile adducts of (Ar(F))(2)Ar(F)'B and (Ar(F)')(3)B closely resemble that of (Ar(F))(3)B.NCMe. During the course of the boron investigations, reaction with adventitious water led to the structural characterization of (Ar(F)')(2)BOH.OH(2) as a hydrogen-bonded dimer. The Grignard reagent reacts selectively with ZnCl(2) in diethyl ether giving first [(Ar(F)')Zn(micro-Cl)(OEt(2))](2) then (Ar(F)')(2)Zn(OEt(2))(2), both of which have been characterised by X-ray diffraction. The corresponding reaction with HgCl(2) requires the use of tetrahydrofuran as the solvent and yields (Ar(F)')(2)Hg(THF)(2). PMID:19421603

  13. On evaluation of nonplanar diagrams in noncommutative field theory

    NASA Astrophysics Data System (ADS)

    Liao, Yi

    2005-05-01

    This is a technical work about how to evaluate loop integrals appearing in one loop nonplanar (NP) diagrams in noncommutative (NC) field theory. The conventional wisdom says that, barring the ultraviolet/infrared (UV/IR) mixing problem, NP diagrams whose planar counterparts are UV divergent are rendered finite by NC phases that couple the loop momentum to the external ones p through an NC momentum ρ=θp. We show that this is generally not the case. We find that subtleties arise already in the simpler case of Euclidean spacetime. The situation is even worse in Minkowski spacetime due to its indefinite metric. We compare different prescriptions that may be used to evaluate loop integrals in ordinary theory. They are equivalent in the sense that they always yield identical results. However, in NC theory there is no a priori reason that these prescriptions, except for the defining one that is built in the Feynman propagator, are physically justified even when they seem mathematically meaningful. Employing them can lead to ambiguous results, which are also different from those obtained according to the defining prescription. For ρ>0, the NC phase can worsen the UV property of loop integrals instead of always improving it in high dimensions. We explain how this surprising phenomenon comes about from the indefinite metric. This lends a strong support to the point of view that the naive approach is not well-founded when time does not commute with space. For ρ<0, the NC phase improves the UV property and softens the quadratic UV divergence in ordinary theory to a bounded but indefinite UV oscillation. We employ a cut-off method to quantify the new UV nonregular terms. For ρ>0, these terms are generally complex and thus also harm unitarity in addition to those found previously. As the new terms for both cases are not available in the Lagrangian and in addition can be non-Hermitian when time does not commute with space, our result casts doubts on previous demonstrations

  14. Quantum Groups, Non-Commutative Differential Geometry and Applications

    NASA Astrophysics Data System (ADS)

    Schupp, Peter

    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 {cal A} of functions and {cal 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({cal U}). It provides invariant maps {cal A} to{cal 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. We attempt a classification of various types of quantum Lie algebras and present a fairly general example for their construction

  15. Generally covariant quantum mechanics on noncommutative configuration spaces

    SciTech Connect

    Kopf, Tomas; Paschke, Mario

    2007-11-15

    We generalize the previously given algebraic version of 'Feynman's proof of Maxwell's equations' to noncommutative configuration spaces. By doing so, we also obtain an axiomatic formulation of nonrelativistic quantum mechanics over such spaces, which, in contrast to most examples discussed in the literature, does not rely on a distinguished set of coordinates. We give a detailed account of several examples, e.g., C{sup {infinity}}(Q)xM{sub n}(C) which leads to non-Abelian Yang-Mills theories, and of noncommutative tori T{sub {theta}}{sup d}. Moreover, we examine models over the Moyal-deformed plane R{sub {theta}}{sup 2}. Assuming the conservation of electrical charges, we show that in this case the canonical uncertainty relation [x{sub k},x{sub l}]=ig{sub kl} with metric g{sub kl} is only consistent if g{sub kl} is constant.

  16. D-branes, gauge/string duality and noncommutative theories

    NASA Astrophysics Data System (ADS)

    Mateos, Toni

    2004-09-01

    In this thesis we elaborate on the three subjects of the title. We first show that supertubes exist and still preserve some supersymmetry in a large variety of curved backgrounds. Within the AdS/CFT correspondence we study the supersymmetry of rotating strings with 3 angular momenta, and we consider the possibility of adding matter in a stable but non-supersymmetric way. We contribute to the extension of the duality to more realistic YM theories by constructing the sugra dual of an N=2 pure SYM in 3d, given in terms of a Calabi-Yau four-fold in M-theory. We study the unitarity of noncommutative nonrelativistic field theories, we construct the sugra dual of noncommutative pure SYM theories with N=1 in 4d and N=2 in 3d, and we study holographically properties like UV/IR mixing, confinement, chiral symmetry breaking and moduli spaces.

  17. Two Dimensional Non-commutative Space and Rydberg Atom Model

    NASA Astrophysics Data System (ADS)

    Chung, Won Sang

    2015-06-01

    In this paper we consider the case of only space-space non-commutativity in two dimension. We also discuss the Rydberg atom model in this space and use the linear realization of the coordinate and momentum operators to solve the Schrödinger equation for the Rydberg atom through the standard perturbation method. Finally, the thermodynamics for the Rydberg atom model is discussed.

  18. TOPICAL REVIEW: Noncommutative torus from Fibonacci chains via foliation

    NASA Astrophysics Data System (ADS)

    Jeong, Hyeong-Chai; Kim, Eunsang; Lee, Chang-Yeong

    2001-08-01

    We classify the Fibonacci chains (F-chains) by their index sequences and construct an approximately finite-dimensional (AF) C*-algebra on the space of F-chains as Connes did on the space of Penrose tiling. The K-theory on this AF algebra suggests a connection between the noncommutative torus and the space of F-chains. A noncommutative torus, which can be regarded as the C*-algebra of a foliation on the torus, is explicitly embedded into the AF algebra on the space of F-chains. As a counterpart of that, we obtain a relation between the space of F-chains and the leaf space of Kronecker foliation on the torus using the cut-procedure of constructing F-chains. Our embedding of the C*-algebra of the foliation is consistent with the recent result of Landi, Lizzi, and Szabo that the C*-algebra of noncommutative torus can be embedded into an AF algebra.

  19. Noncommutativity in weakly curved background by canonical methods

    SciTech Connect

    Davidovic, Lj.; Sazdovic, B.

    2011-03-15

    Using the canonical method, we investigate the Dp-brane world-volume noncommutativity in a weakly curved background. The term 'weakly curved' means that, in the leading order, the source of nonflatness is an infinitesimally small Kalb-Ramond field B{sub {mu}{nu}}, linear in coordinate, while the Ricci tensor does not contribute, being an infinitesimal of the second order. On the solution of boundary conditions, we find a simple expression for the space-time coordinates in terms of the effective coordinates and momenta. This basic relation helped us to prove that noncommutativity appears only on the world sheet boundary. The noncommutativity parameter has a standard form, but with the infinitesimally small and coordinate-dependent antisymmetric tensor B{sub {mu}{nu}}. This result coincides with that obtained on the group manifolds in the limit of the large level n of the current algebra. After quantization, the algebra of the functions on the Dp-brane world volume is represented with the Kontsevich star product instead of the Moyal one in the flat background.

  20. On second quantization on noncommutative spaces with twisted symmetries

    NASA Astrophysics Data System (ADS)

    Fiore, Gaetano

    2010-04-01

    By the application of the general twist-induced sstarf-deformation procedure we translate second quantization of a system of bosons/fermions on a symmetric spacetime into a noncommutative language. The procedure deforms, in a coordinated way, the spacetime algebra and its symmetries, the wave-mechanical description of a system of n bosons/fermions, the algebra of creation and annihilation operators and also the commutation relations of the latter with functions of spacetime; our key requirement is the mode-decomposition independence of the quantum field. In a minimalistic view, the use of noncommutative coordinates can be seen just as a way to better express non-local interactions of a special kind. In a non-conservative one, we obtain a closed, covariant framework for quantum field theory (QFT) on the corresponding noncommutative spacetime consistent with quantum mechanical axioms and Bose-Fermi statistics. One distinguishing feature is that the field commutation relations remain of the type 'field (anti)commutator=a distribution'. We illustrate the results by choosing as examples interacting non-relativistic and free relativistic QFT on Moyal space(time)s.

  1. 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.

  2. Model-based flaw localization from perturbations in the dynamic response of complex mechanical structures

    SciTech Connect

    Chambers, D H

    2009-02-24

    A new method of locating structural damage using measured differences in vibrational response and a numerical model of the undamaged structure has been presented. This method is particularly suited for complex structures with little or no symmetry. In a prior study the method successively located simulated damage from measurements of the vibrational response on two simple structures. Here we demonstrate that it can locate simulated damage in a complex structure. A numerical model of a complex structure was used to calculate the structural response before and after the introduction of a void. The method can now be considered for application to structures of programmatic interest. It could be used to monitor the structural integrity of complex mechanical structures and assemblies over their lifetimes. This would allow early detection of damage, when repair is relatively easy and inexpensive. It would also allow one to schedule maintenance based on actual damage instead of a time schedule.

  3. Population Structure of the North American Cranberry Fruit Rot Complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cranberry fruit rot is caused by a complex of pathogenic fungi. Variation in the populations within this complex from region to region could delay identification of the causal agents(s) and complicate management strategies. Our objective was to assess genetic variation within the four major fruit ro...

  4. Gravitational Aharonov-Bohm effect due to noncommutative BTZ black hole

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    In this paper we consider the scattering of massless planar scalar waves by a noncommutative BTZ black hole. We compute the differential cross section via the partial wave approach, and we mainly show that the scattering of planar waves leads to a modified Aharonov-Bohm effect due to spacetime noncommutativity.

  5. Thermodynamics of noncommutative geometry inspired BTZ black hole based on Lorentzian smeared mass distribution

    NASA Astrophysics Data System (ADS)

    Liang, Jun; Liu, Bo

    2012-11-01

    A noncommutative BTZ black hole is constructed in three-dimensional anti-de Sitter space. In this black-hole model, the noncommutative smearing is obtained by replacing the point-like source term with a Lorentzian distribution. We mainly investigate the thermodynamical properties of this black hole, including Hawking temperature, entropy, heat capacity and free energy.

  6. 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.

  7. A New Program for Detecting the Geometrical Core of a Set of Structures of Macromolecular Complexes.

    PubMed

    Vakulenko, Yu A; Nagaev, B E; Alexeevski, A V; Karyagina, A S; Spirin, S A

    2016-04-01

    Comparison of structures of homological proteins often helps to understand functionally significant features of these structures. This concerns not only structures of separate protein chains, but also structures of macromolecular complexes. In particular, a comparison of complexes of homologous proteins with DNA is significant for analysis of the recognition of DNA by proteins. We present program LCore for detecting geometrical cores of a family of structures; a geometrical core is a set of amino acid residues and nucleotides that disposed similarly in all structures of the family. We describe the algorithm of the program, its web interface, and an example of its application to analysis of complexes of homeodomains with DNA. PMID:27293101

  8. 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.

  9. Finsler black holes induced by noncommutative anholonomic distributions in Einstein gravity

    NASA Astrophysics Data System (ADS)

    Vacaru, Sergiu I.

    2010-05-01

    We study Finsler black holes induced from Einstein gravity as possible effects of quantum spacetime noncommutativity. Such Finsler models are defined by nonholonomic frames not on tangent bundles but on (pseudo)Riemannian manifolds being compatible with standard theories of physics. We focus on noncommutative deformations of Schwarzschild metrics into locally anisotropic stationary ones with spherical/rotoid symmetry. The conditions are derived when black hole configurations can be extracted from two classes of exact solutions depending on noncommutative parameters. The first class of metrics is defined by nonholonomic deformations of the gravitational vacuum by noncommutative geometry. The second class of such solutions is induced by noncommutative matter fields and/or effective polarizations of cosmological constants.

  10. Probing phase-space noncommutativity through quantum beating, missing information, and the thermodynamic limit

    NASA Astrophysics Data System (ADS)

    Bernardini, A. E.; Bertolami, O.

    2013-07-01

    In this work we examine the effect of phase-space noncommutativity on some typically quantum properties such as quantum beating, quantum information, and decoherence. To exemplify these issues we consider the two-dimensional noncommutative quantum harmonic oscillator whose component behavior we monitor in time. This procedure allows us to determine how the noncommutative parameters are related to the missing information quantified by the linear quantum entropy and by the mutual information between the relevant Hilbert space coordinates. Particular questions concerning the thermodynamic limit of some relevant properties are also discussed in order to evidence the effects of noncommutativity. Finally, through an analogy with the Zeeman effect, we identify how some aspects of the axial symmetry of the problem suggest the possibility of decoupling the noncommutative quantum perturbations from unperturbed commutative well-known solutions.

  11. An extended anyon Fock space and noncommutative Meixner-type orthogonal polynomials in infinite dimensions

    NASA Astrophysics Data System (ADS)

    Bożejko, M.; Lytvynov, E. W.; Rodionova, I. V.

    2015-10-01

    Let ν be a finite measure on R whose Laplace transform is analytic in a neighbourhood of zero. An anyon Lévy white noise on ( R^d,dx) is a certain family of noncommuting operators <ω,\\varphi> on the anyon Fock space over L^2( R^d× R,dx\\otimesν), where \\varphi=\\varphi(x) runs over a space of test functions on R^d, while ω=ω(x) is interpreted as an operator-valued distribution on R^d. Let L^2(τ) be the noncommutative L^2-space generated by the algebra of polynomials in the variables <ω,\\varphi>, where τ is the vacuum expectation state. Noncommutative orthogonal polynomials in L^2(τ) of the form < P_n(ω),f(n)> are constructed, where f(n) is a test function on ( R^d)^n, and are then used to derive a unitary isomorphism U between L^2(τ) and an extended anyon Fock space \\mathbf F(L^2( R^d,dx)) over L^2( R^d,dx). The usual anyon Fock space \\mathscr F(L^2( R^d,dx)) over L^2( R^d,dx) is a subspace of \\mathbf F(L^2( R^d,dx)). Furthermore, the equality \\mathbf F(L^2( R^d,dx))=\\mathscr F(L^2( R^d,dx)) holds if and only if the measure ν is concentrated at a single point, that is, in the Gaussian or Poisson case. With use of the unitary isomorphism U, the operators <ω,\\varphi> are realized as a Jacobi (that is, tridiagonal) field in \\mathbf F(L^2( R^d,dx)). A Meixner-type class of anyon Lévy white noise is derived for which the corresponding Jacobi field in \\mathbf F(L^2( R^d,dx)) has a relatively simple structure. Each anyon Lévy white noise of Meixner type is characterized by two parameters, λ\\in R and η≥slant0. In conclusion, the representation ω(x)=\\partial_x^\\dag +λ \\partial_x^\\dag\\partialx +η\\partial_x^\\dag\\partial_x\\partial_x+\\partial_x is obtained, where \\partial_x and \\partial_x^\\dag are the annihilation and creation operators at the point x. Bibliography: 57 titles.

  12. Nano structure zinc (II) Schiff base complexes of a N3-tridentate ligand as new biological active agents: Spectral, thermal behaviors and crystal structure of zinc azide complex

    NASA Astrophysics Data System (ADS)

    Montazerozohori, M.; Mojahedi Jahromi, S.; Masoudiasl, A.; McArdle, P.

    2015-03-01

    In this work, synthesis of some new five coordinated zinc halide/pseudo-halide complexes of a N3-tridentate ligand is presented. All complexes were subjected to spectroscopic and physical methods such as FT-IR, UV-visible, 1H and 13C NMR spectra, thermal analyses and conductivity measurements for identification. Based on spectral data, the general formula of ZnLX2 (X = Cl-, Br-, I-, SCN- and N3-) was proposed for the zinc complexes. Zinc complexes have been also prepared in nano-structure sizes under ultrasonic irradiation. X-ray powder diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were applied for confirmation of nano-structure character for the complexes. Among the complexes, zinc azide complex structure was analyzed by X-ray crystallography. This complex crystallizes as a triplet in trigonal system with space group of P31. The coordination sphere around the zinc center is well shown as a distorted trigonal bipyramidal with three nitrogen atoms from Schiff base ligand and two terminal azide nitrogen atoms attached to zinc ion. Various intermolecular interactions such as Nsbnd H⋯N, Csbnd H⋯N and Csbnd H⋯π hydrogen bonding interactions stabilize crystalline lattice so that they causes a three dimensional supramolecular structure for the complex. In vitro screening of the compounds for their antimicrobial activities showed that ZnLI2, ZnL(N3)2, ZnLCl2 and ZnL(NCS)2 were found as the most effective compound against bacteria of Bacillus subtilis, Staphylococcus aureus, Pseudomonas aeruginosa and Escherichia coli respectively. Also ZnLI2 and ZnLCl2 complexes were found more effective against two selected fungi than others. Finally, thermal behaviors of the zinc complexes showed that they are decomposed via 2-4 thermal steps from room temperature up to 1000 °C.

  13. Magnetoelectric coupling effects in multiferroic complex oxide composite structures.

    PubMed

    Vaz, Carlos A F; Hoffman, Jason; Ahn, Charles H; Ramesh, Ramamoorthy

    2010-07-20

    The study of magnetoelectric materials has recently received renewed interest, in large part stimulated by breakthroughs in the controlled growth of complex materials and by the search for novel materials with functionalities suitable for next generation electronic devices. In this Progress Report, we present an overview of recent developments in the field, with emphasis on magnetoelectric coupling effects in complex oxide multiferroic composite materials. PMID:20414887

  14. 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

  15. Geometric Effects on Complex Network Structure in the Cortex

    NASA Astrophysics Data System (ADS)

    Henderson, J. A.; Robinson, P. A.

    2011-07-01

    It is shown that homogeneous, short-range, two-dimensional (2D) cortical connectivity, without modularity, hierarchy, or other specialized structure, reproduces key observed properties of cortical networks, including low path length, high clustering and modularity index, and apparent hierarchical block-diagonal structure in connection matrices. Geometry strongly influences connection matrices, implying that simple interpretations of connectivity measures as reflecting specialized structure can be misleading: Such apparent structure is seen in strictly uniform, locally connected architectures in 2D. Geometry is thus a proxy for function, modularity, and hierarchy and must be accounted for when structural inferences are made.

  16. Structure of Csm2 elucidates the relationship between small subunits of CRISPR-Cas effector complexes.

    PubMed

    Venclovas, Česlovas

    2016-05-01

    Type I and type III CRISPR-Cas effector complexes share similar architecture and have homologous key subunits. However, the relationship between the so-called small subunits of these complexes remains a contentious issue. Here, it is shown that the recently solved structure of Thermotoga maritima Csm2 represents a dimer with the extensive structure swapping between monomers. Unswapping the structure generates a compact globular monomer which shares similar structure and surface properties with Cmr5, the small subunit of a related Cmr complex. Detailed analysis of available structures of small subunits reveals that they all have a common fold suggesting their common origin. PMID:27091242

  17. Structural and functional characterization of a cell cycle associated HDAC1/2 complex reveals the structural basis for complex assembly and nucleosome targeting

    PubMed Central

    Itoh, Toshimasa; Fairall, Louise; Muskett, Frederick W.; Milano, Charles P.; Watson, Peter J.; Arnaudo, Nadia; Saleh, Almutasem; Millard, Christopher J.; El-Mezgueldi, Mohammed; Martino, Fabrizio; Schwabe, John W.R.

    2015-01-01

    Recent proteomic studies have identified a novel histone deacetylase complex that is upregulated during mitosis and is associated with cyclin A. This complex is conserved from nematodes to man and contains histone deacetylases 1 and 2, the MIDEAS corepressor protein and a protein called DNTTIP1 whose function was hitherto poorly understood. Here, we report the structures of two domains from DNTTIP1. The amino-terminal region forms a tight dimerization domain with a novel structural fold that interacts with and mediates assembly of the HDAC1:MIDEAS complex. The carboxy-terminal domain of DNTTIP1 has a structure related to the SKI/SNO/DAC domain, despite lacking obvious sequence homology. We show that this domain in DNTTIP1 mediates interaction with both DNA and nucleosomes. Thus, DNTTIP1 acts as a dimeric chromatin binding module in the HDAC1:MIDEAS corepressor complex. PMID:25653165

  18. Structural diversity in dinickel(II) complexes of thiosemicarbazones

    NASA Astrophysics Data System (ADS)

    Naik, Anil D.; Annigeri, Satish M.; Gangadharmath, Umesh B.; Revankar, Vidyanand K.; Mahale, Vinayak B.

    2002-10-01

    2,6-Diformyl- p-cresol serves as a starting point for the generation of multidentate N/O/S chelating agents. Condensation with 4-(X-phenyl) thiosemicarbazide yields the pentadentate ligand having SNONS donor sequences, capable of holding two metal ions in close proximity. The ligands behave as mono/di/tri basic depending on the pH of the medium. Stereochemical diversity in the reaction product of such ligands with nickel(II) chloride at different pH is observed. Sterically demanding substituted ligands in association with various exogenous bridges dictate the geometry and coordination number of such complexes. The compounds were investigated by elemental analysis, molar conductivities, electronic spectra, IR, NMR, FAB mass spectra, TG-DTG, magnetic susceptibility measurements. Varieties of geometries such as square planar, square pyramidal, octahedral and square planar-square pyramidal are observed. Cryomagnetic data for the complexes (79-296 K) can be reproduced by an equation based on the Heisenberg model ( H=-2 JS1S2, S1= S2=1). The singlet-triplet splitting, J varies systematically with the coordination geometry about the Ni 2(SNONS) core, with the hydroxo bridged complex exhibiting the greatest degree of antiferromagnetic coupling. The coupling is somewhat weaker for the chloro-bridged complexes. None of the complexes have shown any appreciable antimicrobial activity.

  19. 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.

  20. 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