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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. 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.

  16. 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.

  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. 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.

  14. 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.

  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. 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.

  2. 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.

  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. 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.

  17. 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.

  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. 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.

  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. 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

  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. 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.

  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. 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.

  9. 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.

  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

    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.

  8. 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.

  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. 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

  16. 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).

  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. 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…

  9. 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.

  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. 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.

  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. 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.

  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. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  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. 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.

  4. 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.

  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. 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

  14. 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).

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  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. 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

  6. 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.

  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. 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.

  1. 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.

  2. 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.

  3. 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.

  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. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  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. 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

  9. 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

  10. 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).