Noncommutative Complex Scalar Field and Casimir Effect
NASA Astrophysics Data System (ADS)
Khelili, Farid
2012-06-01
Using the noncommutative deformed canonical commutation relations proposed by Carmona et al. [J. M. Carmona, J. L. Cortés, J. Gamboa, and F. Mendez, J. High Energy Phys.JHEPFG1029-8479 03 (2003) 058.10.1088/1126-6708/2003/03/058][J. Gamboa, J. Lopéz-Sarrion, and A. P. Polychronakos, Phys. Lett. B 634, 471 (2006).PYLBAJ0370-269310.1016/j.physletb.2006.02.014][J. M. Carmona, J. L. Cortés, Ashok Das, J. Gamboa, and F. Mendez, Mod. Phys. Lett. A 21, 883 (2006).MPLAEQ0217-732310.1142/S0217732306020111], a model describing the dynamics of the noncommutative complex scalar field is proposed. The noncommutative field equations are solved, and the vacuum energy is calculated to the second order in the parameter of noncommutativity. As an application to this model, the Casimir effect, due to the zero-point fluctuations of the noncommutative complex scalar field, is considered. It turns out that in spite of its smallness, the noncommutativity gives rise to a repulsive force at the microscopic level, leading to a modified Casimir potential with a minimum at the point amin=(5)/(84)πθ.
Noncommutative complex Grosse-Wulkenhaar model
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.
Lie algebraic noncommuting structures from reparametrization symmetry
Gangopadhyay, Sunandan
2007-05-15
We extend our earlier work of revealing both space-space and space-time noncommuting structures in various models in particle mechanics exhibiting reparametrization symmetry. We show explicitly (in contrast to the earlier results in our paper [R. Banerjee et al. J. Phys. A 38, 957 (2005), e-print hep-th/0405178]) that for some special choices of the reparametrization parameter {epsilon}, one can obtain space-space noncommuting structures which are Lie algebraic in form even in the case of the relativistic free particle. The connection of these structures with the existing models in the literature is also briefly discussed. Further, there exists some values of {epsilon} for which the noncommutativity in the space-space sector can be made to vanish. As a matter of internal consistency of our approach, we also study the angular momentum algebra in details.
Noncommutative Biology: Sequential Regulation of Complex Networks
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
Complexity and non-commutativity of learning operations on graphs.
Atmanspacher, Harald; Filk, Thomas
2006-07-01
We present results from numerical studies of supervised learning operations in small recurrent networks considered as graphs, leading from a given set of input conditions to predetermined outputs. Graphs that have optimized their output for particular inputs with respect to predetermined outputs are asymptotically stable and can be characterized by attractors, which form a representation space for an associative multiplicative structure of input operations. As the mapping from a series of inputs onto a series of such attractors generally depends on the sequence of inputs, this structure is generally non-commutative. Moreover, the size of the set of attractors, indicating the complexity of learning, is found to behave non-monotonically as learning proceeds. A tentative relation between this complexity and the notion of pragmatic information is indicated.
Complex analysis methods in noncommutative probability
NASA Astrophysics Data System (ADS)
Teodor Belinschi, Serban
2006-02-01
In this thesis we study convolutions that arise from noncommutative probability theory. We prove several regularity results for free convolutions, and for measures in partially defined one-parameter free convolution semigroups. We discuss connections between Boolean and free convolutions and, in the last chapter, we prove that any infinitely divisible probability measure with respect to monotonic additive or multiplicative convolution belongs to a one-parameter semigroup with respect to the corresponding convolution. Earlier versions of some of the results in this thesis have already been published, while some others have been submitted for publication. We have preserved almost entirely the specific format for PhD theses required by Indiana University. This adds several unnecessary pages to the document, but we wanted to preserve the specificity of the document as a PhD thesis at Indiana University.
Varshovi, Amir Abbass
2013-07-15
The theory of α*-cohomology is studied thoroughly and it is shown that in each cohomology class there exists a unique 2-cocycle, the harmonic form, which generates a particular Groenewold-Moyal star product. This leads to an algebraic classification of translation-invariant non-commutative structures and shows that any general translation-invariant non-commutative quantum field theory is physically equivalent to a Groenewold-Moyal non-commutative quantum field theory.
Exact solutions with noncommutative symmetries in Einstein and gauge gravity
NASA Astrophysics Data System (ADS)
Vacaru, Sergiu I.
2005-04-01
We present new classes of exact solutions with noncommutative symmetries constructed in vacuum Einstein gravity (in general, with nonzero cosmological constant), five-dimensional (5D) gravity and (anti) de Sitter gauge gravity. Such solutions are generated by anholonomic frame transforms and parametrized by generic off-diagonal metrics. For certain particular cases, the new classes of metrics have explicit limits with Killing symmetries but, in general, they may be characterized by certain anholonomic noncommutative matrix geometries. We argue that different classes of noncommutative symmetries can be induced by exact solutions of the field equations in commutative gravity modeled by a corresponding moving real and complex frame geometry. We analyze two classes of black ellipsoid solutions (in the vacuum case and with cosmological constant) in four-dimensional gravity and construct the analytic extensions of metrics for certain classes of associated frames with complex valued coefficients. The third class of solutions describes 5D wormholes which can be extended to complex metrics in complex gravity models defined by noncommutative geometric structures. The anholonomic noncommutative symmetries of such objects are analyzed. We also present a descriptive account how the Einstein gravity can be related to gauge models of gravity and their noncommutative extensions and discuss such constructions in relation to the Seiberg-Witten map for the gauge gravity. Finally, we consider a formalism of vielbeins deformations subjected to noncommutative symmetries in order to generate solutions for noncommutative gravity models with Moyal (star) product.
Branes as Stable Holomorphic Line Bundles On the Non-Commutative Torus
NASA Astrophysics Data System (ADS)
Grange, Pascal
2004-10-01
It was suggested by A. Kapustin that turning on a B-field, and allowing some discrepancy between the left and and right-moving complex structures, must induce an identification of B-branes with holomorphic line bundles on a non-commutative complex torus. The stability condition for the branes is written as a topological identity of non-commutative gauge theory. This identifies stable B-branes with previously proposed non-commutative instanton equations. Consistency of the non-commutative description with complex geometry is examined, using the non-linearities of the Seiberg-Witten map.
Møller's Energy-Momentum Complex for a Spacetime Geometry on a Noncommutative Curved D3-Brane
NASA Astrophysics Data System (ADS)
Radinschi, I.; Grammenos, T.
2008-05-01
Møller’s energy-momentum complex is employed in order to determine the energy and momentum distributions for a spacetime described by a “generalized Schwarzschild” geometry in (3+1)-dimensions on a noncommutative curved D3-brane in an effective, open bosonic string theory. The geometry considered is obtained by an effective theory of gravity coupled with a nonlinear electromagnetic field and depends only on the generalized (effective) mass and charge which incorporate corrections of first order in the noncommutativity parameter.
NASA Astrophysics Data System (ADS)
Saha, Anirban; Gangopadhyay, Sunandan
2016-10-01
We report the plausibility of using quantum mechanical transitions, induced by the combined effect of gravitational waves (GWs) and noncommutative (NC) structure of space, among the states of a 2-dimensional harmonic oscillator, to probe the spatial NC geometry. The phonon modes excited by the passing GW within the resonant bar-detector or spherical detectors are formally identical to forced harmonic oscillator and they represent a length variation of roughly the same order of magnitude as the characteristic length-scale of spatial noncommutativity estimated from the phenomenological upper bound of the NC parameter. This motivates our present work. We employ various GW wave-forms that are typically expected from possible astronomical sources. We find that the transition probablities are quite sensitive to the nature of polarization of the GW. We also elaborate on the particular type of sources of GW, radiation from which one can induce such transitions. We speculate that this can be used as an effective probe of the spatial noncommutative structure when the quantum limit of sensitivity is achieved/surpassed in resonant bar/spherical detectors of GWs in the near future.
Noncommutative Brownian motion
NASA Astrophysics Data System (ADS)
Santos, Willien O.; Almeida, Guilherme M. A.; Souza, Andre M. C.
2017-08-01
We investigate the classical Brownian motion of a particle in a two-dimensional noncommutative (NC) space. Using the standard NC algebra embodied by the symplectic Weyl-Moyal formalism we find that noncommutativity induces a nonvanishing correlation between both coordinates at different times. The effect stands out as a signature of spatial noncommutativity and thus could offer a way to experimentally detect the phenomena. We further discuss some limiting scenarios and the trade-off between the scale imposed by the NC structure and the parameters of the Brownian motion itself.
Noncommutative topological theories of gravity
NASA Astrophysics Data System (ADS)
García-Compeán, H.; Obregón, O.; Ramírez, C.; Sabido, M.
2003-08-01
The possibility of noncommutative topological gravity arising in the same manner as Yang-Mills theory is explored. We use the Seiberg-Witten map to construct such a theory based on a SL(2,C) complex connection, from which the Euler characteristic and the signature invariant are obtained. Finally, we speculate on the description of noncommutative gravitational instantons, as well as noncommutative local gravitational anomalies.
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.
NASA Astrophysics Data System (ADS)
Saha, Anirban
2014-01-01
We construct the quantum mechanical model of the Colella-Overhauser-Werner (COW) experiment assuming that the underlying space time has a granular structure, described by a canonical noncommutative algebra of coordinates xμ. The time-space sector of the algebra is shown to add a mass-dependent contribution to the gravitational acceleration felt by neutron de Brogli waves measured in a COW experiment. This makes time-space noncommutativity a potential candidate for an apparent violation of the weak equivalence principle even if the ratio of the inertial mass mi and gravitational mass mg is a universal constant. The latest experimental result based on the COW principle is shown to place an upper bound several orders of magnitude stronger than the existing one on the time-space noncommutative parameter. We argue that the evidence of noncommutative structure of space-time may be found if the COW-type experiment can be repeated with several particle species.
Instantons and vortices on noncommutative toric varieties
NASA Astrophysics Data System (ADS)
Cirio, Lucio S.; Landi, Giovanni; Szabo, Richard J.
2014-09-01
We elaborate on the quantization of toric varieties by combining techniques from toric geometry, isospectral deformations and noncommutative geometry in braided monoidal categories, and the construction of instantons thereon by combining methods from noncommutative algebraic geometry and a quantized twistor theory. We classify the real structures on a toric noncommutative deformation of the Klein quadric and use this to derive a new noncommutative four-sphere which is the unique deformation compatible with the noncommutative twistor correspondence. We extend the computation of equivariant instanton partition functions to noncommutative gauge theories with both adjoint and fundamental matter fields, finding agreement with the classical results in all instances. We construct moduli spaces of noncommutative vortices from the moduli of invariant instantons, and derive corresponding equivariant partition functions which also agree with those of the classical limit.
Physics on noncommutative spacetimes
NASA Astrophysics Data System (ADS)
Padmanabhan, Pramod
The structure of spacetime at the Planck scale remains a mystery to this date with a lot of insightful attempts to unravel this puzzle. One such attempt is the proposition of a 'pointless' structure for spacetime at this scale. This is done by studying the geometry of the spacetime through a noncommutative algebra of functions defined on it. We call such spacetimes 'noncommutative spacetimes'. This dissertation probes physics on several such spacetimes. These include compact noncommutative spaces called fuzzy spaces and noncompact spacetimes. The compact examples we look at are the fuzzy sphere and the fuzzy Higg's manifold. The noncompact spacetimes we study are the Groenewold-Moyal plane and the Bcn⃗ plane. A broad range of physical effects are studied on these exotic spacetimes. We study spin systems on the fuzzy sphere. The construction of Dirac and chirality operators for an arbitrary spin j is studied on both S2F and S2 in detail. We compute the spectrums of the spin 1 and spin 32 Dirac operators on S2F . These systems have novel thermodynamical properties which have no higher dimensional analogs, making them interesting models. The fuzzy Higg's manifold is found to exhibit topology change, an important property for any theory attempting to quantize gravity. We study how this change occurs in the classical setting and how quantizing this manifold smoothens the classical conical singularity. We also show the construction of the star product on this manifold using coherent states on the noncommutative algebra describing this noncommutative space. On the Moyal plane we develop the LSZ formulation of scalar quantum field theory. We compute scattering amplitudes and remark on renormalization of this theory. We show that the LSZ formalism is equivalent to the interaction representation formalism for computing scattering amplitudes on the Moyal plane. This result is true for on-shell Green's functions and fails to hold for off-shell Green's functions. With the
Morita equivalence of noncommutative supertori
NASA Astrophysics Data System (ADS)
Chang-Young, Ee; Kim, Hoil; Nakajima, Hiroaki
2010-06-01
In this paper we study the extension of Morita equivalence of noncommutative tori to the supersymmetric case. The structure of the symmetry group yielding Morita equivalence appears to be intact but its parameter field becomes supersymmetrized having both body and soul parts. Our result is mainly in the two dimensional case in which noncommutative supertori have been constructed recently: The group SO(2,2,VZ0), where VZ0 denotes Grassmann even number whose body part belongs to Z, yields Morita equivalent noncommutative supertori in two dimensions.
Morita equivalence of noncommutative supertori
Chang-Young, Ee; Kim, Hoil; Nakajima, Hiroaki
2010-06-15
In this paper we study the extension of Morita equivalence of noncommutative tori to the supersymmetric case. The structure of the symmetry group yielding Morita equivalence appears to be intact but its parameter field becomes supersymmetrized having both body and soul parts. Our result is mainly in the two dimensional case in which noncommutative supertori have been constructed recently: The group SO(2,2,V{sub Z}{sup 0}), where V{sub Z}{sup 0} denotes Grassmann even number whose body part belongs to Z, yields Morita equivalent noncommutative supertori in two dimensions.
The Geometry of Noncommutative Space-Time
NASA Astrophysics Data System (ADS)
Mendes, R. Vilela
2016-10-01
Stabilization, by deformation, of the Poincaré-Heisenberg algebra requires both the introduction of a fundamental lentgh and the noncommutativity of translations which is associated to the gravitational field. The noncommutative geometry structure that follows from the deformed algebra is studied both for the non-commutative tangent space and the full space with gravity. The contact points of this approach with the work of David Finkelstein are emphasized.
Baryon number current in holographic noncommutative QCD
NASA Astrophysics Data System (ADS)
Nakajima, Tadahito; Ohtake, Yukiko; Suzuki, Kenji
2017-08-01
We consider the noncommutative deformation of the finite-temperature holographic QCD (Sakai-Sugimoto) model in external electric and magnetic field and evaluate the effect of the noncommutativity on the properties of the conductor-insulator phase transition associated with a baryon number current. Although the noncommutative deformation of the gauge theory does not change the phase structure with respect to the baryon number current, the transition temperature Tc, the transition electric field ec, and magnetic field bc in the conductor-insulator phase transition depend on the noncommutativity parameter θ . Namely, the noncommutativity of space coordinates have an influence on the shape of the phase diagram for the conductor-insulator phase transition. On the other hand, the allowed range of the noncommutativity parameter can be restricted by the reality condition of the constants of motion.
Lechtenfeld, Olaf
2008-03-06
Solitonic objects play a central role in gauge and string theory (as, e.g., monopoles, black holes, D-branes, etc.). Certain string backgrounds produce a noncommutative deformation of the low-energy effective field theory, which allows for new types of solitonic solutions. I present the construction, moduli spaces and dynamics of Moyal-deformed solitons, exemplified in the 2+1 dimensional Yang-Mills-Higgs theory and its Bogomolny system, which is gauge-fixed to an integrable chiral sigma model (the Ward model). Noncommutative solitons for various 1+1 dimensional integrable systems (such as sine-Gordon) easily follow by dimensional and algebraic reduction. Supersymmetric extensions exist as well and are related to twistor string theory.
Non-commutative fields and the short-scale structure of spacetime
NASA Astrophysics Data System (ADS)
Arzano, Michele; Kowalski-Glikman, Jerzy
2017-08-01
There is a growing evidence that due to quantum gravity effects the effective spacetime dimensionality might change in the UV. In this letter we investigate this hypothesis by using quantum fields to derive the UV behaviour of the static, two point sources potential. We mimic quantum gravity effects by using non-commutative fields associated to a Lie group momentum space with a Planck mass curvature scale. We find that the static potential becomes finite in the short-distance limit. This indicates that quantum gravity effects lead to a dimensional reduction in the UV or, alternatively, that point-like sources are effectively smoothed out by the Planck scale features of the non-commutative quantum fields.
Mexican contributions to Noncommutative Theories
Vergara, J. David; Garcia-Compean, H.
2006-09-25
In this paper we summarize the Mexican contributions to the subject of Noncommutative theories. These contributions span several areas: Quantum Groups, Noncommutative Field Theories, Hopf algebra of renormalization, Deformation Quantization, Noncommutative Gravity, and Noncommutative Quantum Mechanics.
Noncommutativity and the Friedmann Equations
Sabido, M.; Socorro, J.; Guzman, W.
2010-07-12
In this paper we study noncommutative scalar field cosmology, we find the noncommutative Friedmann equations as well as the noncommutative Klein-Gordon equation, interestingly the noncommutative contributions are only present up to second order in the noncommutitive parameter.
NASA Astrophysics Data System (ADS)
Fakhri, H.; Sayyah-Fard, M.
The normalized even and odd q-cat states corresponding to Arik-Coon q-oscillator on the noncommutative complex plane ℂq-1 are constructed as the eigenstates of the lowering operator of a q-deformed su(1, 1) algebra with the left eigenvalues. We present the appropriate noncommutative measures in order to realize the resolution of the identity condition by the even and odd q-cat states. Then, we obtain the q-Bargmann-Fock realizations of the Fock representation of the q-deformed su(1, 1) algebra as well as the inner products of standard states in the q-Bargmann representations of the even and odd subspaces. Also, the Euler’s formula of the q-factorial and the Gaussian integrals based on the noncommutative q-integration are obtained. Violation of the uncertainty relation, photon antibunching effect and sub-Poissonian photon statistics by the even and odd q-cat states are considered in the cases 0 < q < 1 and q > 1.
Dirac equation on coordinate dependent noncommutative space-time
NASA Astrophysics Data System (ADS)
Kupriyanov, V. G.
2014-05-01
In this paper we discuss classical aspects of spinor field theory on the coordinate dependent noncommutative space-time. The noncommutative Dirac equation describing spinning particle in an external vector field and the corresponding action principle are proposed. The specific choice of a star product allows us to derive a conserved noncommutative probability current and to obtain the energy-momentum tensor for free noncommutative spinor field. Finally, we consider a free noncommutative Dirac fermion and show that if the Poisson structure is Lorentz-covariant, the standard energy-momentum dispersion relation remains valid.
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).
Noncommutative scalar fields from symplectic deformation
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.
Noncommutative Valuation of Options
NASA Astrophysics Data System (ADS)
Herscovich, Estanislao
2016-12-01
The aim of this note is to show that the classical results in finance theory for pricing of derivatives, given by making use of the replication principle, can be extended to the noncommutative world. We believe that this could be of interest in quantum probability. The main result called the First fundamental theorem of asset pricing, states that a noncommutative stock market admits no-arbitrage if and only if it admits a noncommutative equivalent martingale probability.
Chiral bosonization for non-commutative fields
NASA Astrophysics Data System (ADS)
Das, Ashok; Gamboa, J.; Méndez, Fernando; López-Sarrión, Justo
2004-05-01
A model of chiral bosons on a non-commutative field space is constructed and new generalized bosonization (fermionization) rules for these fields are given. The conformal structure of the theory is characterized by a level of the Kac-Moody algebra equal to (1+theta2) where theta is the non-commutativity parameter and chiral bosons living in a non-commutative fields space are described by a rational conformal field theory with the central charge of the Virasoro algebra equal to 1. The non-commutative chiral bosons are shown to correspond to a free fermion moving with a speed equal to c' = c(1+theta2)1/2 where c is the speed of light. Lorentz invariance remains intact if c is rescaled by crightarrowc'. The dispersion relation for bosons and fermions, in this case, is given by omega = c'|k|.
Homogeneous noncommutative quantum cosmology
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.
Noncommutative geometry of Zitterbewegung
NASA Astrophysics Data System (ADS)
Eckstein, Michał; Franco, Nicolas; Miller, Tomasz
2017-03-01
Drawing from the advanced mathematics of noncommutative geometry, we model a "classical" Dirac fermion propagating in a curved spacetime. We demonstrate that the inherent causal structure of the model encodes the possibility of Zitterbewegung—the "trembling motion" of the fermion. We recover the well-known frequency of Zitterbewegung as the highest possible speed of change in the fermion's "internal space." Furthermore, we show that the bound does not change in the presence of an external electromagnetic field and derive its explicit analogue when the mass parameter is promoted to a Yukawa field. We explain the universal character of the model and discuss a table-top experiment in the domain of quantum simulation to test its predictions.
Noncommutative integrable systems and quasideterminants
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.
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.
Noncommutative black hole thermodynamics
Banerjee, Rabin; Majhi, Bibhas Ranjan; Samanta, Saurav
2008-06-15
We give a general derivation, for any static spherically symmetric metric, of the relation T{sub h}=(K/2{pi}) connecting the black hole temperature (T{sub h}) with the surface gravity (K), following the tunneling interpretation of Hawking radiation. This derivation is valid even beyond the semi-classical regime, i.e. when quantum effects are not negligible. The formalism is then applied to a spherically symmetric, stationary noncommutative Schwarzschild space-time. The effects of backreaction are also included. For such a black hole the Hawking temperature is computed in a closed form. A graphical analysis reveals interesting features regarding the variation of the Hawking temperature (including corrections due to noncommutativity and backreaction) with the small radius of the black hole. The entropy and tunneling rate valid for the leading order in the noncommutative parameter are calculated. We also show that the noncommutative Bekenstein-Hawking area law has the same functional form as the usual one.
Covariant Noncommutative Field Theory
Estrada-Jimenez, S.; Garcia-Compean, H.; Obregon, O.; Ramirez, C.
2008-07-02
The covariant approach to noncommutative field and gauge theories is revisited. In the process the formalism is applied to field theories invariant under diffeomorphisms. Local differentiable forms are defined in this context. The lagrangian and hamiltonian formalism is consistently introduced.
Noncommutativity in near horizon symmetries in gravity
NASA Astrophysics Data System (ADS)
Majhi, Bibhas Ranjan
2017-02-01
We have a new observation that near horizon symmetry generators, corresponding to diffeomorphisms which leave the horizon structure invariant, satisfy noncommutative Heisenberg algebra. The results are valid for any null surfaces (which have Rindler structure in the near null surface limit) and in any spacetime dimensions. Using the Sugawara construction technique the central charge is identified. It is shown that the horizon entropy is consistent with the standard form of the Cardy formula. Therefore we feel that the noncommutative algebra might lead to quantum mechanics of horizon and also can probe into the microscopic description of entropy.
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.
Towards Noncommutative Supersymmetric Quantum Cosmology
Sabido, M.; Socorro, J.; Guzman, W.
2010-12-07
In this work a construction of supersymmetric noncommutative cosmology is presented. We start with a ''noncommutative'' deformation of the minisuperspace variables, and by using the time reparametrization invariance of the noncommutative bosonic model we proceed to construct a super field description of the model.
Noncommuting spherical coordinates
Bander, Myron
2004-10-15
Restricting the states of a charged particle to the lowest Landau level introduces a noncommutativity between Cartesian coordinate operators. This idea is extended to the motion of a charged particle on a sphere in the presence of a magnetic monopole. Restricting the dynamics to the lowest energy level results in noncommutativity for angular variables and to a definition of a noncommuting spherical product. The values of the commutators of various angular variables are not arbitrary but are restricted by the discrete magnitude of the magnetic monopole charge. An algebra, isomorphic to angular momentum, appears. This algebra is used to define a spherical star product. Solutions are obtained for dynamics in the presence of additional angular dependent potentials.
NASA Astrophysics Data System (ADS)
Naka, S.; Toyoda, H.; Takanashi, T.; Umezawa, E.
2014-04-01
In kappa -Minkowski spacetime, the coordinates are Lie algebraic elements such that time and space coordinates do not commute, whereas space coordinates commute with each other. The noncommutativity is proportional to a Planck-length-scale constant kappa ^{-1}, which is a universal constant other than the velocity of light, under the kappa -Poincaré transformation. In this sense, the spacetime has a structure called "doubly special relativity." Such a noncommutative structure is known to be realized by SO(1,4) generators in 4-dimensional de Sitter space. In this paper, we try to construct a noncommutative spacetime having a commutative n-dimensional Minkowski spacetime based on AdS_{n+1} space with SO(2,n) symmetry. We also study an invariant wave equation corresponding to the first Casimir invariant of this symmetry as a nonlocal field equation expected to yield finite loop amplitudes.
Noncommutative geometry and arithmetics
NASA Astrophysics Data System (ADS)
Almeida, P.
2009-09-01
We intend to illustrate how the methods of noncommutative geometry are currently used to tackle problems in class field theory. Noncommutative geometry enables one to think geometrically in situations in which the classical notion of space formed of points is no longer adequate, and thus a “noncommutative space” is needed; a full account of this approach is given in [3] by its main contributor, Alain Connes. The class field theory, i.e., number theory within the realm of Galois theory, is undoubtedly one of the main achievements in arithmetics, leading to an important algebraic machinery; for a modern overview, see [23]. The relationship between noncommutative geometry and number theory is one of the many themes treated in [22, 7-9, 11], a small part of which we will try to put in a more down-to-earth perspective, illustrating through an example what should be called an “application of physics to mathematics,” and our only purpose is to introduce nonspecialists to this beautiful area.
An Asymmetric Noncommutative Torus
NASA Astrophysics Data System (ADS)
Dąbrowski, Ludwik; Sitarz, Andrzej
2015-09-01
We introduce a family of spectral triples that describe the curved noncommutative two-torus. The relevant family of new Dirac operators is given by rescaling one of two terms in the flat Dirac operator. We compute the dressed scalar curvature and show that the Gauss-Bonnet theorem holds (which is not covered by the general result of Connes and Moscovici).
Noncommutative Riemannian geometry on graphs
NASA Astrophysics Data System (ADS)
Majid, Shahn
2013-07-01
We show that arising out of noncommutative geometry is a natural family of edge Laplacians on the edges of a graph. The family includes a canonical edge Laplacian associated to the graph, extending the usual graph Laplacian on vertices, and we find its spectrum. We show that for a connected graph its eigenvalues are strictly positive aside from one mandatory zero mode, and include all the vertex degrees. Our edge Laplacian is not the graph Laplacian on the line graph but rather it arises as the noncommutative Laplace-Beltrami operator on differential 1-forms, where we use the language of differential algebras to functorially interpret a graph as providing a 'finite manifold structure' on the set of vertices. We equip any graph with a canonical 'Euclidean metric' and a canonical bimodule connection, and in the case of a Cayley graph we construct a metric compatible connection for the Euclidean metric. We make use of results on bimodule connections on inner calculi on algebras, which we prove, including a general relation between zero curvature and the braid relations.
Noncommutativity and scalar field cosmology
Guzman, W.; Sabido, M.; Socorro, J.
2007-10-15
In this work we extend and apply a previous proposal to study noncommutative cosmology to the Friedmann-Robertson-Walker cosmological background coupled to a scalar field. This is done in classical and quantum scenarios. In both cases noncommutativity is introduced in the gravitational field as well as in the scalar field through a deformation of minisuperspace, and we are able to find exact solutions. Finally, the effects of noncommutativity on the classical evolution are analyzed.
Towards noncommutative quantum black holes
Lopez-Dominguez, J. C.; Obregon, O.; Sabido, M.; Ramirez, C.
2006-10-15
In this paper we study noncommutative black holes. We use a diffeomorphism between the Schwarzschild black hole and the Kantowski-Sachs cosmological model, which is generalized to noncommutative minisuperspace. Through the use of the Feynman-Hibbs procedure we are able to study the thermodynamics of the black hole, in particular, we calculate the Hawking's temperature and entropy for the noncommutative Schwarzschild black hole.
Solving the Noncommutative Batalin-Vilkovisky Equation
NASA Astrophysics Data System (ADS)
Barannikov, Serguei
2013-06-01
Given an odd symmetry acting on an associative algebra, I show that the summation over arbitrary ribbon graphs gives the construction of the solutions to the noncommutative Batalin-Vilkovisky equation, introduced in (Barannikov in IMRN, rnm075, 2007), and to the equivariant version of this equation. This generalizes the known construction of A ∞-algebra via summation over ribbon trees. I give also the generalizations to other types of algebras and graph complexes, including the stable ribbon graph complex. These solutions to the noncommutative Batalin-Vilkovisky equation and to its equivariant counterpart, provide naturally the supersymmetric matrix action functionals, which are the gl( N)-equivariantly closed differential forms on the matrix spaces, as in (Barannikov in Comptes Rendus Mathematique vol 348, pp. 359-362.
On non-commutative geodesic motion
NASA Astrophysics Data System (ADS)
Ulhoa, S. C.; Amorim, R. G. G.; Santos, A. F.
2014-07-01
In this work we study the geodesic motion on a noncommutative space-time. As a result we find a non-commutative geodesic equation and then we derive corrections of the deviation angle per revolution in terms of the non-commutative parameter when we specify the problem of Mercury's perihelion. In this way, we estimate the noncommutative parameter based in experimental data.
The Gribov problem in noncommutative QED
NASA Astrophysics Data System (ADS)
Canfora, Fabrizio; Kurkov, Maxim A.; Rosa, Luigi; Vitale, Patrizia
2016-01-01
It is shown that in the noncommutative version of QED (NCQED) Gribov copies induced by the noncommutativity of space-time appear in the Landau gauge. This is a genuine effect of noncommutative geometry which disappears when the noncommutative parameter vanishes.
Noncommutative Quantum Scalar Field Cosmology
Diaz Barron, L. R.; Lopez-Dominguez, J. C.; Sabido, M.; Yee, C.
2010-07-12
In this work we study noncommutative Friedmann-Robertson-Walker (FRW) cosmology coupled to a scalar field endowed with an exponential potential. The quantum scenario is analyzed in the Bohmian formalism of quantum trajectories to investigate the effects of noncommutativity in the evolution of the universe.
Structural complexity of quantum networks
Siomau, Michael
2016-06-10
Quantum network is a set of nodes connected with channels, through which the nodes communicate photons and classical information. Classical structural complexity of a quantum network may be defined through its physical structure, i.e. mutual position of nodes and channels connecting them. We show here that the classical structural complexity of a quantum network does not restrict the structural complexity of entanglement graphs, which may be created in the quantum network with local operations and classical communication. We show, in particular, that 1D quantum network can simulate both simple entanglement graphs such as lattices and random graphs and complex small-world graphs.
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.
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.
Principal Fibrations from Noncommutative Spheres
NASA Astrophysics Data System (ADS)
Landi, Giovanni; Suijlekom, Walter Van
2005-11-01
We construct noncommutative principal fibrations Sθ7→Sθ4 which are deformations of the classical SU(2) Hopf fibration over the four sphere. We realize the noncommutative vector bundles associated to the irreducible representations of SU(2) as modules of coequivariant maps and construct corresponding projections. The index of Dirac operators with coefficients in the associated bundles is computed with the Connes-Moscovici local index formula. "The algebra inclusion is an example of a not-trivial quantum principal bundle."
Non-Commutative Martingale Inequalities
NASA Astrophysics Data System (ADS)
Pisier, Gilles; Xu, Quanhua
We prove the analogue of the classical Burkholder-Gundy inequalites for non-commutative martingales. As applications we give a characterization for an Ito-Clifford integral to be an Lp-martingale via its integrand, and then extend the Ito-Clifford integral theory in L2, developed by Barnett, Streater and Wilde, to Lp for all 1
non-commutative analogue of the classical Fefferman duality between $H1 and BMO.
Two roads to noncommutative causality
NASA Astrophysics Data System (ADS)
Besnard, Fabien
2015-08-01
We review the physical motivations and the mathematical results obtained so far in the isocone-based approach to noncommutative causality. We also give a briefer account of the alternative framework of Franco and Eckstein which is based on Lorentzian spectral triples. We compare the two theories on the simple example of the product geometry of the Minkowski plane by the finite noncommutative space with algebra M2(C).
Phase space quantization, noncommutativity, and the gravitational field
NASA Astrophysics Data System (ADS)
Chatzistavrakidis, Athanasios
2014-07-01
In this paper we study the structure of the phase space in noncommutative geometry in the presence of a nontrivial frame. Our basic assumptions are that the underlying space is a symplectic and parallelizable manifold. Furthermore, we assume the validity of the Leibniz rule and the Jacobi identities. We consider noncommutative spaces due to the quantization of the symplectic structure and determine the momentum operators that guarantee a set of canonical commutation relations, appropriately extended to include the nontrivial frame. We stress the important role of left vs right acting operators and of symplectic duality. This enables us to write down the form of the full phase space algebra on these noncommutative spaces, both in the noncompact and in the compact case. We test our results against the class of four-dimensional and six-dimensional symplectic nilmanifolds, thus presenting a large set of nontrivial examples that realizes the general formalism.
Twisted Fock representations of noncommutative Kähler manifolds
NASA Astrophysics Data System (ADS)
Sako, Akifumi; Umetsu, Hiroshi
2016-09-01
We introduce twisted Fock representations of noncommutative Kähler manifolds and give their explicit expressions. The twisted Fock representation is a representation of the Heisenberg like algebra whose states are constructed by applying creation operators to a vacuum state. "Twisted" means that creation operators are not Hermitian conjugate of annihilation operators in this representation. In deformation quantization of Kähler manifolds with separation of variables formulated by Karabegov, local complex coordinates and partial derivatives of the Kähler potential with respect to coordinates satisfy the commutation relations between the creation and annihilation operators. Based on these relations, we construct the twisted Fock representation of noncommutative Kähler manifolds and give a dictionary to translate between the twisted Fock representations and functions on noncommutative Kähler manifolds concretely.
Particle phenomenology on noncommutative spacetime
Joseph, Anosh
2009-05-01
We introduce particle phenomenology on the noncommutative spacetime called the Groenewold-Moyal plane. The length scale of spacetime noncommutativity is constrained from the CPT violation measurements in the K{sup 0}-K{sup 0} system and g-2 difference of {mu}{sup +}-{mu}{sup -}. The K{sup 0}-K{sup 0} system provides an upper bound on the length scale of spacetime noncommutativity of the order of 10{sup -32} m, corresponding to a lower energy bound E of the order of E > or approx. 10{sup 16} GeV. The g-2 difference of {mu}{sup +}-{mu}{sup -} constrains the noncommutativity length scale to be of the order of 10{sup -20} m, corresponding to a lower energy bound E of the order of E > or approx. 10{sup 3} GeV. We also present the phenomenology of the electromagnetic interaction of electrons and nucleons at the tree level on the noncommutative spacetime. We show that the distributions of charge and magnetization of nucleons are affected by spacetime noncommutativity. The analytic properties of electromagnetic form factors are also changed and it may give rise to interesting experimental signals.
Conformal quantum mechanics and holography in noncommutative space-time
NASA Astrophysics Data System (ADS)
Gupta, Kumar S.; Harikumar, E.; Zuhair, N. S.
2017-09-01
We analyze the effects of noncommutativity in conformal quantum mechanics (CQM) using the κ-deformed space-time as a prototype. Up to the first order in the deformation parameter, the symmetry structure of the CQM algebra is preserved but the coupling in a canonical model of the CQM gets deformed. We show that the boundary conditions that ensure a unitary time evolution in the noncommutative CQM can break the scale invariance, leading to a quantum mechanical scaling anomaly. We calculate the scaling dimensions of the two and three point functions in the noncommutative CQM which are shown to be deformed. The AdS2 / CFT1 duality for the CQM suggests that the corresponding correlation functions in the holographic duals are modified. In addition, the Breitenlohner-Freedman bound also picks up a noncommutative correction. The strongly attractive regime of a canonical model of the CQM exhibit quantum instability. We show that the noncommutativity softens this singular behaviour and its implications for the corresponding holographic duals are discussed.
Oscillators in a (2+1)-dimensional noncommutative space
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.
Noncommutative field theory and Lorentz violation.
Carroll, S M; Harvey, J A; Kostelecký, V A; Lane, C D; Okamoto, T
2001-10-01
The role of Lorentz symmetry in noncommutative field theory is considered. Any realistic noncommutative theory is found to be physically equivalent to a subset of a general Lorentz-violating standard-model extension involving ordinary fields. Some theoretical consequences are discussed. Existing experiments bound the scale of the noncommutativity parameter to (10 TeV)(-2).
Quanta of geometry: noncommutative aspects.
Chamseddine, Ali H; Connes, Alain; Mukhanov, Viatcheslav
2015-03-06
In the construction of spectral manifolds in noncommutative geometry, a higher degree Heisenberg commutation relation involving the Dirac operator and the Feynman slash of real scalar fields naturally appears and implies, by equality with the index formula, the quantization of the volume. We first show that this condition implies that the manifold decomposes into disconnected spheres, which will represent quanta of geometry. We then refine the condition by involving the real structure and two types of geometric quanta, and show that connected spin manifolds with large quantized volume are then obtained as solutions. The two algebras M_{2}(H) and M_{4}(C) are obtained, which are the exact constituents of the standard model. Using the two maps from M_{4} to S^{4} the four-manifold is built out of a very large number of the two kinds of spheres of Planckian volume. We give several physical applications of this scheme such as quantization of the cosmological constant, mimetic dark matter, and area quantization of black holes.
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.
Space-time symmetries of noncommutative spaces
Calmet, Xavier
2005-04-15
We define a noncommutative Lorentz symmetry for canonical noncommutative spaces. The noncommutative vector fields and the derivatives transform under a deformed Lorentz transformation. We show that the star product is invariant under noncommutative Lorentz transformations. We then apply our idea to the case of actions obtained by expanding the star product and the fields taken in the enveloping algebra via the Seiberg-Witten maps and verify that these actions are invariant under these new noncommutative Lorentz transformations. We finally consider general coordinate transformations and show that the metric is undeformed.
Asymptotic Analysis of the Ponzano-Regge Model with Non-Commutative Metric Boundary Data
NASA Astrophysics Data System (ADS)
Oriti, Daniele; Raasakka, Matti
2014-06-01
We apply the non-commutative Fourier transform for Lie groups to formulate the non-commutative metric representation of the Ponzano-Regge spin foam model for 3d quantum gravity. The non-commutative representation allows to express the amplitudes of the model as a first order phase space path integral, whose properties we consider. In particular, we study the asymptotic behavior of the path integral in the semi-classical limit. First, we compare the stationary phase equations in the classical limit for three different non-commutative structures corresponding to the symmetric, Duflo and Freidel-Livine-Majid quantization maps. We find that in order to unambiguously recover discrete geometric constraints for non-commutative metric boundary data through the stationary phase method, the deformation structure of the phase space must be accounted for in the variational calculus. When this is understood, our results demonstrate that the non-commutative metric representation facilitates a convenient semi-classical analysis of the Ponzano-Regge model, which yields as the dominant contribution to the amplitude the cosine of the Regge action in agreement with previous studies. We also consider the asymptotics of the SU(2) 6j-symbol using the non-commutative phase space path integral for the Ponzano-Regge model, and explain the connection of our results to the previous asymptotic results in terms of coherent states.
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.
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.
Structural insights into transcription complexes.
Berger, Imre; Blanco, Alexandre G; Boelens, Rolf; Cavarelli, Jean; Coll, Miquel; Folkers, Gert E; Nie, Yan; Pogenberg, Vivian; Schultz, Patrick; Wilmanns, Matthias; Moras, Dino; Poterszman, Arnaud
2011-08-01
Control of transcription allows the regulation of cell activity in response to external stimuli and research in the field has greatly benefited from efforts in structural biology. In this review, based on specific examples from the European SPINE2-COMPLEXES initiative, we illustrate the impact of structural proteomics on our understanding of the molecular basis of gene expression. While most atomic structures were obtained by X-ray crystallography, the impact of solution NMR and cryo-electron microscopy is far from being negligible. Here, we summarize some highlights and illustrate the importance of specific technologies on the structural biology of protein-protein or protein/DNA transcription complexes: structure/function analysis of components the eukaryotic basal and activated transcription machinery with focus on the TFIID and TFIIH multi-subunit complexes as well as transcription regulators such as members of the nuclear hormone receptor families. We also discuss molecular aspects of promoter recognition and epigenetic control of gene expression. Copyright © 2011 Elsevier Inc. All rights reserved.
Complex DNA structures and structures of DNA complexes
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.
SHM in complex structural components
NASA Astrophysics Data System (ADS)
Croxford, Anthony J.; Wilcox, Paul D.; Courtney, Charles R. P.; Drinkwater, Bruce W.
2009-03-01
The use of permanently attached arrays of sensors has made it clear that guided waves can be used for the SHM of structures. The approaches developed have relied on the use of reference signal subtraction to indicate changes to the state of the structure, such as the appearance of damage. The limit of performance of any system is defined by the post subtraction noise. In order to confirm the basic principles at work the majority of this work has been carried out on simple metallic plates. While important to confirm the levels of understanding, this is not sufficient for practical use. This paper looks at the application of SHM techniques in more complex structures, more typical of those any system would be used on in practise. A rib from a BaE 146 aircraft is used to demonstrate the practical difficulties of applying guided wave SHM methods to densely featured structures. A model system comprising a plate with a single stringer is used to demonstrate a method for normalizing signals to give responses directly related to the scattering properties of the change in the system, mitigating the effect of the position of the change, and a method is proposed to generalize the approach to complex systems. Preliminary tests in the region of the stringer are used to identify the experimental challenges to realizing the calibration on complex systems.
Noncommuting momenta of topological solitons.
Watanabe, Haruki; Murayama, Hitoshi
2014-05-16
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.
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.
Structural Complexity of DNA Sequence
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
Noncommutativity from exact renormalization group dualities
NASA Astrophysics Data System (ADS)
Gangopadhyay, Sunandan; Scholtz, Frederik G.
2014-08-01
Here we demonstrate, first, the construction of dualities using the exact renormalization group approach and, second, that spatial noncommutativity can emerge as such a duality. This is done in a simple quantum mechanical setting that establishes an exact duality between the commutative and noncommutative quantum Hall systems with harmonic interactions. It is also demonstrated that this link can be understood as a blocking (coarse graining) transformation in time that relates commutative and noncommutative degrees of freedom.
Twisted covariant noncommutative self-dual gravity
Estrada-Jimenez, S.; Garcia-Compean, H.; Obregon, O.; Ramirez, C.
2008-12-15
A twisted covariant formulation of noncommutative self-dual gravity is presented. The formulation for constructing twisted noncommutative Yang-Mills theories is used. It is shown that the noncommutative torsion is solved at any order of the {theta} expansion in terms of the tetrad and some extra fields of the theory. In the process the first order expansion in {theta} for the Plebanski action is explicitly obtained.
Laser intensity effects in noncommutative QED
Heinzl, Thomas; Ilderton, Anton; Marklund, Mattias
2010-03-01
We discuss a twofold extension of QED assuming the presence of strong external fields provided by an ultraintense laser and noncommutativity of spacetime. While noncommutative effects leave the electron's intensity induced mass shift unchanged, photons change significantly in character: they acquire a quasimomentum that is no longer lightlike. We study the consequences of this combined noncommutative strong-field effect for the basic lepton-photon interactions.
Tree amplitudes of noncommutative U(N) Yang-Mills theory
NASA Astrophysics Data System (ADS)
Huang, Jia-Hui; Huang, Rijun; Jia, Yin
2011-10-01
Following the spirit of the S-matrix program, we propose a modified Britto-Cachazo-Feng-Witten recursion relation for tree amplitudes of noncommutative U(N) Yang-Mills theory. Starting from three-point amplitudes, one can use this modified BCFW recursion relation to compute or analyze color-ordered tree amplitudes without relying on any detailed information of noncommutative Yang-Mills theory. After clarifying the color structure of noncommutative tree amplitudes, we write down the noncommutative analogies of Kleiss-Kuijf and Bern-Carrasco-Johansson relations for color-ordered tree amplitudes and prove them using the modified BCFW recursion relation. This checks the consistency of the relation.
Late time acceleration in a non-commutative model of modified cosmology
NASA Astrophysics Data System (ADS)
Malekolkalami, B.; Atazadeh, K.; Vakili, B.
2014-12-01
We investigate the effects of non-commutativity between the position-position, position-momentum and momentum-momentum of a phase space corresponding to a modified cosmological model. We show that the existence of such non-commutativity results in a Moyal Poisson algebra between the phase space variables in which the product law between the functions is of the kind of an α-deformed product. We then transform the variables in such a way that the Poisson brackets between the dynamical variables take the form of a usual Poisson bracket but this time with a noncommutative structure. For a power law expression for the function of the Ricci scalar with which the action of the gravity model is modified, the exact solutions in the commutative and noncommutative cases are presented and compared. In terms of these solutions we address the issue of the late time acceleration in cosmic evolution.
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.
Noncommutative magnetic moment of charged particles
Adorno, T. C.; Gitman, D. M.; Shabad, A. E.; Vassilevich, D. V.
2011-10-15
It has been argued that in noncommutative field theories, the sizes of physical objects cannot be taken smaller than an ''elementary length'' related to noncommutativity parameters. By gauge covariantly extending field equations of noncommutative U(1){sub *} theory to cover the presence of external sources, we find electric and magnetic fields produced by an extended static charge. We find that such a charge, apart from being an ordinary electric monopole, is also a magnetic dipole. By writing off the existing experimental clearance in the value of the lepton magnetic moments for the present effect, we get the bound on noncommutativity at the level of 10{sup 4} TeV.
Noncommutative Circle Bundles and New Dirac Operators
NASA Astrophysics Data System (ADS)
Dąbrowski, Ludwik; Sitarz, Andrzej
2013-02-01
We study spectral triples over noncommutative principal U(1) bundles. Basing on the classical situation and the abstract algebraic approach, we propose an operatorial definition for a connection and compatibility between the connection and the Dirac operator on the total space and on the base space of the bundle. We analyze in details the example of the noncommutative three-torus viewed as a U(1) bundle over the noncommutative two-torus and find all connections compatible with an admissible Dirac operator. Conversely, we find a family of new Dirac operators on the noncommutative tori, which arise from the base-space Dirac operator and a suitable connection.
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).
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).
Weak equivalence principle in noncommutative phase space and the parameters of noncommutativity
NASA Astrophysics Data System (ADS)
Gnatenko, Kh. P.; Tkachuk, V. M.
2017-08-01
The weak equivalence principle is studied in a space with noncommutativity of coordinates and noncommutativity of momenta. We find conditions on the parameters of noncommutativity which give the possibility to recover the equivalence principle in two-dimensional noncommutative phase space. It is also shown that in the case when these conditions are satisfied the motion of the center-of-mass of a composite system in noncommutative phase space and the relative motion are independent, the kinetic energy of composite system has additivity property and is independent on the systems composition. So, we propose conditions on the parameters of noncommutativity which give the possibility to solve the list of problems in noncommutative phase space.
Noncommutativity Parameter and Composite Fermions
NASA Astrophysics Data System (ADS)
Jellal, Ahmed
We determine some particular values of the noncommutativity parameter θ and show that the Murthy Shankar approach is in fact a particular case of a more general one. Indeed, using the fractional quantum Hall effect (FQHE) experimental data, we give a measurement of θ. This measurement can be obtained by considering some values of the filling factor ν and other ingredients, magnetic field B and electron density ρ. Moreover, it is found that θ can be quantized either fractionally or integrally in terms of the magnetic length l0 and the quantization is exactly what Murthy and Shankar formulated recently for the FQHE. On the other hand, we show that the mapping of the FQHE in terms of the composite fermion basis has a noncommutative geometry nature and therefore there is a more general way than the Murthy Shankar method to do this mapping.
Non-commutative Nash inequalities
Kastoryano, Michael; Temme, Kristan
2016-01-15
A set of functional inequalities—called Nash inequalities—are introduced and analyzed in the context of quantum Markov process mixing. The basic theory of Nash inequalities is extended to the setting of non-commutative L{sub p} spaces, where their relationship to Poincaré and log-Sobolev inequalities is fleshed out. We prove Nash inequalities for a number of unital reversible semigroups.
Non-commutative Nash inequalities
NASA Astrophysics Data System (ADS)
Kastoryano, Michael; Temme, Kristan
2016-01-01
A set of functional inequalities—called Nash inequalities—are introduced and analyzed in the context of quantum Markov process mixing. The basic theory of Nash inequalities is extended to the setting of non-commutative 𝕃p spaces, where their relationship to Poincaré and log-Sobolev inequalities is fleshed out. We prove Nash inequalities for a number of unital reversible semigroups.
Noncommutativity in the early universe
NASA Astrophysics Data System (ADS)
Oliveira-Neto, G.; Silva de Oliveira, M.; Monerat, G. A.; Corrêa Silva, E. V.
In the present work, we study the noncommutative version of a quantum cosmology model. The model has a Friedmann-Robertson-Walker (FRW) geometry, the matter content is a radiative perfect fluid and the spatial sections have zero constant curvature. In this model, the scale factor takes values in a bounded domain. Therefore, its quantum mechanical version has a discrete energy spectrum. We compute the discrete energy spectrum and the corresponding eigenfunctions. The energies depend on a noncommutative parameter β. We compute the scale factor expected value () for several values of β. For all of them, oscillates between maxima and minima values and never vanishes. It gives an initial indication that those models are free from singularities, at the quantum level. We improve this result by showing that if we subtract a quantity proportional to the standard deviation of a from , this quantity is still positive. The behavior, for the present model, is a drastic modification of the behavior in the corresponding commutative version of the present model. There, grows without limits with the time variable. Therefore, if the present model may represent the early stages of the universe, the results of the present paper give an indication that may have been, initially, bounded due to noncommutativity. We also compute the Bohmian trajectories for a, which are in accordance with , and the quantum potential Q. From Q, we may understand why that model is free from singularities, at the quantum level.
From noncommutative spacetimes to Lorentz symmetry violation
NASA Astrophysics Data System (ADS)
Schreck, M.
2014-11-01
The current article provides a brief review on noncommutative spacetimes in light of Lorentz invariance violation and especially on how these models are linked to the Lorentz- violating Standard-Model Extension. By embedding a general noncommutative spacetime with a constant background tensor into the Standard-Model Extension, a couple of implications are drawn on Lorentz violation in such models.
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.
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.
Wormhole solutions in f(T) gravity with noncommutative geometry
NASA Astrophysics Data System (ADS)
Sharif, M.; Rani, Shamaila
2013-12-01
The objective of this paper is to study static spherically symmetric noncommutative wormhole solutions in the framework of f(T) gravity. We construct f(T) field equations in covariant and effective energy-momentum tensor forms to make a correspondence with general relativity. It is observed that the violation of energy conditions to support the nonstandard wormhole is due to the effective energy-momentum tensor. We explore the noncommutative wormhole solutions for two cases: (i) assume a viable power-law f(T) model to construct the shape function and (ii) a particular shape function is taken to construct the f(T) model. In the first case, only exotic matter forms a wormhole structure in teleparallel gravity, whereas for f(T) gravity, normal matter threads these structures except for a particular range of r. For the constructed f(T) model, there does not exist a physically acceptable wormhole solution similar to the teleparallel case.
Noncommutative spaces and Poincaré symmetry
NASA Astrophysics Data System (ADS)
Meljanac, Stjepan; Meljanac, Daniel; Mercati, Flavio; Pikutić, Danijel
2017-03-01
We present a framework which unifies a large class of noncommutative spacetimes that can be described in terms of a deformed Heisenberg algebra. The commutation relations between spacetime coordinates are up to linear order in the coordinates, with structure constants depending on the momenta plus terms depending only on the momenta. The possible implementations of the action of Lorentz transformations on these deformed phase spaces are considered, together with the consistency requirements they introduce. It is found that Lorentz transformations in general act nontrivially on tensor products of momenta. In particular the Lorentz group element which acts on the left and on the right of a composition of two momenta is different, and depends on the momenta involved in the process. We conclude with two representative examples, which illustrate the mentioned effect.
Noncommutativity of closed string zero modes
NASA Astrophysics Data System (ADS)
Freidel, Laurent; Leigh, Robert G.; Minic, Djordje
2017-09-01
We explore several consequences of the recently discovered intrinsic noncommutativity of the zero-mode sector of closed string theory. In particular, we illuminate the relation between T-duality and this intrinsic noncommutativity and also note that there is a simple closed string product, equivalent to the splitting-joining interaction of the pants diagram, that respects this noncommutativity and is covariant with respect to T-duality. We emphasize the central role played by the symplectic form ω on the space of zero modes. Furthermore, we begin an exploration of new noncommutative string backgrounds. In particular, we show that a constant nongeometric background field leads to a noncommutative space-time. We also comment on the nonassociativity that consequently arises in the presence of nontrivial flux. In this formulation, the H flux as well as the "nongeometric"Q , R , and F fluxes are simply the various components of the flux of an almost symplectic form.
Noncommutative Skyrmions in Quantum Hall Systems
NASA Astrophysics Data System (ADS)
Ezawa, Z. F.; Tsitsishvili, G.
Charged excitations in quantum Hall (QH) systems are noncommutative skyrmions. QH systems represent an ideal system equipped with noncommutative geometry. When an electron is confined within the lowest Landau level, its position is described solely by the guiding center, whose X and Y coordinates do not commute with one another. Topological excitations in such a noncommutative plane are noncommutative skyrmions flipping several spins coherently. We construct a microscopic skyrmion state by applying a certain unitary transformation to an electron or hole state. A remarkable property is that a noncommutative skyrmion carries necessarily the electron number proportional to the topological charge. More remarkable is the bilayer QH system with the layer degree of freedom acting as the pseudospin, where the quasiparticle is a topological soliton to be identified with the pseudospin skyrmion. Such a skyrmion is deformed into a bimeron (a pair of merons) by the parallel magnetic field penetrated between the two layers. Each meron carries the electric charge ±e/2.
Batalin-Fradkin-Tyutin embedding of noncommutative chiral bosons
Kim, Wontae; Park, Young-Jai; Shin, Hyeonjoon; Yoon, Myung Seok
2007-04-15
A two dimensional model of chiral bosons in noncommutative field space is considered in the framework of the Batalin-Fradkin-Tyutin Hamiltonian embedding method converting the second-class constrained system into the first-class one. The symmetry structure associated with the first-class constraints is explored and the propagation speed of fields is equivalent to that of the second-class constraint system.
Group theoretical construction of planar noncommutative phase spaces
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.
Causality in noncommutative two-sheeted space-times
NASA Astrophysics Data System (ADS)
Franco, Nicolas; Eckstein, Michał
2015-10-01
We investigate the causal structure of two-sheeted space-times using the tools of Lorentzian spectral triples. We show that the noncommutative geometry of these spaces allows for causal relations between the two sheets. The computation is given in detail when the sheet is a 2- or 4-dimensional globally hyperbolic spin manifold. The conclusions are then generalised to a point-dependent distance between the two sheets resulting from the fluctuations of the Dirac operator.
Structurally Complex Surface of Europa
NASA Technical Reports Server (NTRS)
1997-01-01
This is a composite of two images of Jupiter's icy moon Europa obtained from a range of 2119 miles (3410 kilometers) by the Galileo spacecraft during its fourth orbit around Jupiter and its first close pass of Europa. The mosaic spans 11 miles by 30 miles (17 km by 49 km) and shows features as small as 230 feet (70 meters) across. This mosaic is the first very high resolution image data obtained of Europa, and has a resolution more than 50 times better than the best Voyager coverage and 500 times better than Voyager coverage in this area. The mosaic shows the surface of Europa to be structurally complex. The sun illuminates the scene from the right, revealing complex overlapping ridges and fractures in the upper and lower portions of the mosaic, and rugged, more chaotic terrain in the center. Lateral faulting is revealed where ridges show offsets along their lengths (upper left of the picture). Missing ridge segments indicate obliteration of pre-existing materials and emplacement of new terrain (center of the mosaic). Only a small number of impact craters can be seen, indicating the surface is not geologically ancient.
The Jet Propulsion Laboratory, Pasadena, CA manages the mission for NASA's Office of Space Science, Washington, DC.
This image and other images and data received from Galileo are posted on the Galileo mission home page on the World Wide Web at http://galileo.jpl.nasa.gov. Background information and educational context for the images can be found at URL http://www.jpl.nasa.gov/galileo/sepo
Operator Algebras and Noncommutative Geometric Aspects in Conformal Field Theory
NASA Astrophysics Data System (ADS)
Longo, Roberto
2010-03-01
The Operator Algebraic approach to Conformal Field Theory has been particularly fruitful in recent years (leading for example to the classification of all local conformal nets on the circle with central charge c < 1, jointly with Y. Kawahigashi). On the other hand the Operator Algebraic viewpoint offers a natural perspective for a Noncommutative Geometric context within Conformal Field Theory. One basic point here is to uncover the relevant structures. In this talk I will explain some of the basic steps in this "Noncommutative Geometrization program" up to the recent construction of a spectral triple associated with certain Ramond representations of the Supersymmetric Virasoro net. So Alain Connes framework enters into play. This is a joint work with S. Carpi, Y. Kawahigashi, and R. Hillier.
Signature change in p-adic and noncommutative FRW cosmology
NASA Astrophysics Data System (ADS)
Djordjevic, Goran S.; Nesic, Ljubisa; Radovancevic, Darko
2014-10-01
The significant matter for the construction of the so-called no-boundary proposal is the assumption of signature transition, which has been a way to deal with the problem of initial conditions of the universe. On the other hand, results of Loop Quantum Gravity indicate that the signature change is related to the discrete nature of space at the Planck scale. Motivated by possibility of non-Archimedean and/or noncommutative structure of space-time at the Planck scale, in this work we consider the classical, p-adic and (spatial) noncommutative form of a cosmological model with Friedmann-Robertson-Walker (FRW) metric coupled with a self-interacting scalar field.
Quantum mechanics on SO(3) via noncommutative dual variables
NASA Astrophysics Data System (ADS)
Oriti, Daniele; Raasakka, Matti
2011-07-01
We formulate quantum mechanics on the group SO(3) using a noncommutative dual space representation for the quantum states, inspired by recent work in quantum gravity. The new noncommutative variables have a clear connection to the corresponding classical variables, and our analysis confirms them as the natural phase space variables, both mathematically and physically. In particular, we derive the first order (Hamiltonian) path integral in terms of the noncommutative variables, as a formulation of the transition amplitudes alternative to that based on harmonic analysis. We find that the nontrivial phase space structure gives naturally rise to quantum corrections to the action for which we find a closed expression. We then study both the semiclassical approximation of the first order path integral and the example of a free particle on SO(3). On the basis of these results, we comment on the relevance of similar structures and methods for more complicated theories with group-based configuration spaces, such as loop quantum gravity and spin foam models.
Noncommutative spaces from matrix models
NASA Astrophysics Data System (ADS)
Lu, Lei
Noncommutative (NC) spaces commonly arise as solutions to matrix model equations of motion. They are natural generalizations of the ordinary commutative spacetime. Such spaces may provide insights into physics close to the Planck scale, where quantum gravity becomes relevant. Although there has been much research in the literature, aspects of these NC spaces need further investigation. In this dissertation, we focus on properties of NC spaces in several different contexts. In particular, we study exact NC spaces which result from solutions to matrix model equations of motion. These spaces are associated with finite-dimensional Lie-algebras. More specifically, they are two-dimensional fuzzy spaces that arise from a three-dimensional Yang-Mills type matrix model, four-dimensional tensor-product fuzzy spaces from a tensorial matrix model, and Snyder algebra from a five-dimensional tensorial matrix model. In the first part of this dissertation, we study two-dimensional NC solutions to matrix equations of motion of extended IKKT-type matrix models in three-space-time dimensions. Perturbations around the NC solutions lead to NC field theories living on a two-dimensional space-time. The commutative limit of the solutions are smooth manifolds which can be associated with closed, open and static two-dimensional cosmologies. One particular solution is a Lorentzian fuzzy sphere, which leads to essentially a fuzzy sphere in the Minkowski space-time. In the commutative limit, this solution leads to an induced metric that does not have a fixed signature, and have a non-constant negative scalar curvature, along with singularities at two fixed latitudes. The singularities are absent in the matrix solution which provides a toy model for resolving the singularities of General relativity. We also discussed the two-dimensional fuzzy de Sitter space-time, which has irreducible representations of su(1,1) Lie-algebra in terms of principal, complementary and discrete series. Field
On noncommutative Levi-Civita connections
NASA Astrophysics Data System (ADS)
Peterka, Mira A.; Sheu, Albert Jeu-Liang
We make some observations about Rosenberg’s Levi-Civita connections on noncommutative tori, noting the non-uniqueness of general torsion-free metric-compatible connections without prescribed connection operator for the inner *-derivations, the nontrivial curvature form of the inner *-derivations, and the validity of the Gauss-Bonnet theorem for two classes of nonconformal deformations of the flat metric on the noncommutative two-tori, including the case of noncommuting scalings along the principal directions of a two-torus.
Design space for complex DNA structures.
Wei, Bryan; Dai, Mingjie; Myhrvold, Cameron; Ke, Yonggang; Jungmann, Ralf; Yin, Peng
2013-12-04
Nucleic acids have emerged as effective materials for assembling complex nanoscale structures. To tailor the structures to function optimally for particular applications, a broad structural design space is desired. Despite the many discrete and extended structures demonstrated in the past few decades, the design space remains to be fully explored. In particular, the complex finite-sized structures produced to date have been typically based on a small number of structural motifs. Here, we perform a comprehensive study of the design space for complex DNA structures, using more than 30 distinct motifs derived from single-stranded tiles. These motifs self-assemble to form structures with diverse strand weaving patterns and specific geometric properties, such as curvature and twist. We performed a systematic study to control and characterize the curvature of the structures, and constructed a flat structure with a corrugated strand pattern. The work here reveals the broadness of the design space for complex DNA nanostructures.
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.
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.
Noncommutative geometry and fluid dynamics
NASA Astrophysics Data System (ADS)
Das, Praloy; Ghosh, Subir
2016-11-01
In the present paper we have developed a Non-Commutative (NC) generalization of perfect fluid model from first principles, in a Hamiltonian framework. The noncommutativity is introduced at the Lagrangian (particle) coordinate space brackets and the induced NC fluid bracket algebra for the Eulerian (fluid) field variables is derived. Together with a Hamiltonian this NC algebra generates the generalized fluid dynamics that satisfies exact local conservation laws for mass and energy, thereby maintaining mass and energy conservation. However, nontrivial NC correction terms appear in the charge and energy fluxes. Other non-relativistic spacetime symmetries of the NC fluid are also discussed in detail. This constitutes the study of kinematics and dynamics of NC fluid. In the second part we construct an extension of the Friedmann-Robertson-Walker (FRW) cosmological model based on the NC fluid dynamics presented here. We outline the way in which NC effects generate cosmological perturbations bringing about anisotropy and inhomogeneity in the model. We also derive a NC extended Friedmann equation.
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.
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.
Dynamic testing of complex structures
NASA Technical Reports Server (NTRS)
Birs, C.; Anderson, P.
1973-01-01
Response of structure is determined under impulses large enough to create severe strains. Electrodynamic shaker can provide impulses to nearly any point on structure and can deliver repeated pulses of varying force and duration.
Constraining noncommutative spacetime from GW150914
NASA Astrophysics Data System (ADS)
Kobakhidze, Archil; Lagger, Cyril; Manning, Adrian
2016-09-01
The gravitational wave signal GW150914, recently detected by LIGO and Virgo collaborations, is used to place a bound on the scale of quantum fuzziness of noncommutative space-time. We show that the leading noncommutative correction to the phase of the gravitational waves produced by a binary system appears at the second order of the post-Newtonian expansion. This correction is proportional to Λ2≡|θ0 i|2/(lPtP)2, where θμ ν is the antisymmetric tensor of noncommutativity. To comply with GW150914 data, we find that √{Λ }≲3.5 , namely at the order of the Planck scale. This is the most stringent bound on the noncommutative scale, exceeding the previous constraints from particle physics processes by ˜15 orders of magnitude.
Higgs couplings in noncommutative Standard Model
NASA Astrophysics Data System (ADS)
Batebi, S.; Haghighat, M.; Tizchang, S.; Akafzade, H.
2015-06-01
We consider the Higgs and Yukawa parts of the Noncommutative Standard Model (NCSM). We explore the NC-action to give all Feynman rules for couplings of the Higgs boson to electroweak gauge fields and fermions.
Entropic force, noncommutative gravity, and ungravity
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.
Noncommutative Gauge Theory with Covariant Star Product
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.
Orientifolds of matrix theory and noncommutative geometry
NASA Astrophysics Data System (ADS)
Kim, Nakwoo
1999-06-01
We study explicit solutions for orientifolds of matrix theory compactified on a noncommutative torus. As quotients of the torus, a cylinder, Klein bottle, and Möbius strip are applicable as orientifolds. We calculate the solutions using the Connes-Douglas-Schwarz projective module solution, and investigate the twisted gauge bundle on quotient spaces as well. These solutions are of Yang-Mills theory on a noncommutative torus with proper boundary conditions which define the geometry of the dual space.
The noncommutative sine-Gordon breather
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.
Noncommutative Scalar Field Minimally Coupled to Gravity
NASA Astrophysics Data System (ADS)
Bertolami, Orfeu
A model for noncommutative scalar fields coupled to gravity based on the generalization of the Moyal product is proposed. Solutions compatible with homogeneous and isotropic flat Robertson-Walker spaces to first non-trivial order in the perturbation of the star-product are presented. It is shown that in the context of a typical chaotic inflationary scenario, at least in the slow-roll regime, noncommutativity yields no observable effect.
Haag's theorem in noncommutative quantum field theory
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.
Quantum mechanics with coordinate dependent noncommutativity
NASA Astrophysics Data System (ADS)
Kupriyanov, V. G.
2013-11-01
Noncommutative quantum mechanics can be considered as a first step in the construction of quantum field theory on noncommutative spaces of generic form, when the commutator between coordinates is a function of these coordinates. In this paper we discuss the mathematical framework of such a theory. The noncommutativity is treated as an external antisymmetric field satisfying the Jacobi identity. First, we propose a symplectic realization of a given Poisson manifold and construct the Darboux coordinates on the obtained symplectic manifold. Then we define the star product on a Poisson manifold and obtain the expression for the trace functional. The above ingredients are used to formulate a nonrelativistic quantum mechanics on noncommutative spaces of general form. All considered constructions are obtained as a formal series in the parameter of noncommutativity. In particular, the complete algebra of commutation relations between coordinates and conjugated momenta is a deformation of the standard Heisenberg algebra. As examples we consider a free particle and an isotropic harmonic oscillator on the rotational invariant noncommutative space.
Quantum mechanics with coordinate dependent noncommutativity
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.
Lexical Structure and Parsing Complexity.
ERIC Educational Resources Information Center
Stevenson, Suzanne; Merlo, Paolo
1997-01-01
Focuses on the consequences that the structural configuration of lexical knowledge has for the timecourse of parsing. Discusses reduced relative clauses and proposes a new lexical-structural analysis for manner of motion verbs. The article examines consequences for frequency-based models and all models whose difficulty derives from the ambiguity…
Structure of DNA-liposome complexes
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.
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.
Predicting complex mineral structures using genetic algorithms.
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.
TASI Lectures on Complex Structures
NASA Astrophysics Data System (ADS)
Denef, Frederik
2012-11-01
These lecture notes give an introduction to a number of ideas and methods that have been useful in the study of complex systems ranging from spin glasses to D-branes on Calabi-Yau manifolds. Topics include the replica formalism, Parisi's solution of the Sherrington-Kirkpatrick model, overlap order parameters, supersymmetric quantum mechanics, D-brane landscapes and their black hole duals.
Argument structure frames: a lexical complexity metric?
Schmauder, A R
1991-01-01
The number of semantic argument structure frames associated with a verb has been reported to influence ease of processing during language comprehension. The present experiments tested the generality of the argument structure complexity effect with three dependent measures: eye-fixation times, naming latencies, and lexical decision latencies. Two eye-movement experiments and two experiments using cross-modal tasks failed to provide evidence supporting the argument structure complexity effect. The present experiments indicated that results reflecting verbs' argument structure complexity are not generalizable.
Deformation of noncommutative quantum mechanics
NASA Astrophysics Data System (ADS)
Jiang, Jian-Jian; Chowdhury, S. Hasibul Hassan
2016-09-01
In this paper, the Lie group GNC α , β , γ , of which the kinematical symmetry group GNC of noncommutative quantum mechanics (NCQM) is a special case due to fixed nonzero α, β, and γ, is three-parameter deformation quantized using the method suggested by Ballesteros and Musso [J. Phys. A: Math. Theor. 46, 195203 (2013)]. A certain family of QUE algebras, corresponding to GNC α , β , γ with two of the deformation parameters approaching zero, is found to be in agreement with the existing results of the literature on quantum Heisenberg group. Finally, we dualize the underlying QUE algebra to obtain an expression for the underlying star-product between smooth functions on GNC α , β , γ .
Computational complexity in electronic structure.
Whitfield, James Daniel; Love, Peter John; Aspuru-Guzik, Alán
2013-01-14
In quantum chemistry, the price paid by all known efficient model chemistries is either the truncation of the Hilbert space or uncontrolled approximations. Theoretical computer science suggests that these restrictions are not mere shortcomings of the algorithm designers and programmers but could stem from the inherent difficulty of simulating quantum systems. Extensions of computer science and information processing exploiting quantum mechanics has led to new ways of understanding the ultimate limitations of computational power. Interestingly, this perspective helps us understand widely used model chemistries in a new light. In this article, the fundamentals of computational complexity will be reviewed and motivated from the vantage point of chemistry. Then recent results from the computational complexity literature regarding common model chemistries including Hartree-Fock and density functional theory are discussed.
Structure Formation in Complex Plasma
2011-08-24
electrically levitated above the wafer and fell on the wafer when the applied voltage on the wafer was turned off. The Coulomb lattice discovered...such an extreme condition as cryogenic temperature. We also developed an experimental device to study the flow effects of microparticles levitated at...Research Conference (JAXA, Sagamihara, 2011.3.3-3.4) (in Japanese) 5. Y. Nakamura, N. Toma, Y. Saito, and . O. Ishihara, Dust acoustic wave in a complex
Structure-Based Characterization of Multiprotein Complexes
Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J.
2014-01-01
Summary Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies. PMID:24954616
Structure-based characterization of multiprotein complexes.
Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J
2014-07-08
Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies.
Complex ceramic structures. I. Weberites.
Cai, Lu; Nino, Juan C
2009-06-01
The weberite structure (A2B2X7) is an anion-deficient fluorite-related superstructure. Compared with fluorites, the reduction in the number of anions leads to a decrease in the coordination number of the B cations (VI coordination) with respect to the A cations (VIII coordination), thus allowing the accommodation of diverse cations. As a result, weberite compounds have a broad range of chemical and physical properties and great technological potential. This article summarizes the structural features of weberite and describes the structure in several different ways. This is the first time that the stacking vector and stacking angle are used to represent the weberite structure. This paper also discusses the crystallographic relationship between weberite, fluorite and pyrochlore (another fluorite-related structure). The cation sublattices of weberite and pyrochlore are correlated by an axial transformation. It has been shown that the different coordination environment of anions is due to the alternating layering of the AB3 and A3B close-packed cation layers. A stability field of weberite oxides is proposed in terms of the ratio of ionic radius of cations and relative bond ionicity. In addition, a selection of weberite compounds with interesting properties is discussed.
Novel gene complex structure determination
Gatewood, J.M.
1997-08-01
This is the final report of a one-year, Laboratory-Directed Research and Development (LORD) project at the Los Alamos National Laboratory. `Operative` chromatin containing exclusively the minor hasten variants was successfully isolated. Linker hasten H1 is quantitatively missing from operative chromatin. One of the aims of this proposal was to determine the proteins responsible for stabilizing operative chromatin. This chromatin is stabilized by microtubule proteins tar and tubulin. Another goal of this project was the structural characterization of operate chromatin nucleosomes. Using solution scattering, nucleosomes containing the minor variants were shown to be structurally distinct from major variant containing nucleosomes. The unusual structure and stabilization of operative chromatin by microtubule proteins provides a possible mechanism for direct interaction of transcription machinery with specific chromatin domains.
Thermodynamics of the Schwarzschild Black Hole in Noncommutative Space
Perez-Payan, S.; Sabido, M.
2009-04-20
In this paper we study noncommutative black holes. In particular, we use a deform Schwarzschild solution in noncommutative gauge theory of gravity. By means of euclidean quantum gravity we obtain the entropy, temperatute and the time of evaporation of the noncommutative black hole.
Non-commutative relativistic equation with a Coulomb potential
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.
Mapping spaces and automorphism groups of toric noncommutative spaces
NASA Astrophysics Data System (ADS)
Barnes, Gwendolyn E.; Schenkel, Alexander; Szabo, Richard J.
2017-09-01
We develop a sheaf theory approach to toric noncommutative geometry which allows us to formalize the concept of mapping spaces between two toric noncommutative spaces. As an application, we study the `internalized' automorphism group of a toric noncommutative space and show that its Lie algebra has an elementary description in terms of braided derivations.
Measures of Complexity to quantify Bone Structure
NASA Astrophysics Data System (ADS)
Saparin, Peter; Gowin, Wolfgang; Kurths, Jürgen; Felsenberg, Dieter
1998-03-01
We propose a technique to assess structure of the bone in its spatial distribution by describing and quantifying the structural architecture as a whole. The concept of measures of complexity based on symbolic dynamics is applied to computed tomography (CT) - images obtained from human lumbar vertebra. CT-images have been transformed into images consisting of 5 different symbols, whereby both statical and dynamical coding are included. Different aspects of the bone structure are quantified by several measures which have been introduced: index of global ensemble of elements composing the bone; complexity, homogeneity and dynamics within the bone architecture; complexity and inhomogeneity of the trabecular net. This leads to new insides to the understanding of bone's internal structure. The results give the first experimental and quantitative evidence of the theoretical prediction that complexity of bone structure declines rapidly with the increased disintegration of bone structures leading to the loss of bone mass and specify experimentally that bone structure is exponentially related to its density. Especially, osteoporotic vertebrae are less complex organized than normal ones. In addition, this method is significantly sensitive to changes in bone structure and provides improvements of diagnostic of pathological structural loss.
Structural entanglements in protein complexes
NASA Astrophysics Data System (ADS)
Zhao, Yani; Chwastyk, Mateusz; Cieplak, Marek
2017-06-01
We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both termini of each chain simultaneously in the two chains. We have identified about 900 entangled systems in the Protein Data Bank and provided a more detailed analysis for several of them. We argue that entanglement enhances the thermodynamic stability of the system but it may have other functions: burying the hydrophobic residues at the interface and increasing the DNA or RNA binding area. We also study the folding and stretching properties of the knotted dimeric proteins MJ0366, YibK, and bacteriophytochrome. These proteins have been studied theoretically in their monomeric versions so far. The dimers are seen to separate on stretching through the tensile mechanism and the characteristic unraveling force depends on the pulling direction.
Noncommutative Differential Geometry of Generalized Weyl Algebras
NASA Astrophysics Data System (ADS)
Brzeziński, Tomasz
2016-06-01
Elements of noncommutative differential geometry of Z-graded generalized Weyl algebras A(p;q) over the ring of polynomials in two variables and their zero-degree subalgebras B(p;q), which themselves are generalized Weyl algebras over the ring of polynomials in one variable, are discussed. In particular, three classes of skew derivations of A(p;q) are constructed, and three-dimensional first-order differential calculi induced by these derivations are described. The associated integrals are computed and it is shown that the dimension of the integral space coincides with the order of the defining polynomial p(z). It is proven that the restriction of these first-order differential calculi to the calculi on B(p;q) is isomorphic to the direct sum of degree 2 and degree -2 components of A(p;q). A Dirac operator for B(p;q) is constructed from a (strong) connection with respect to this differential calculus on the (free) spinor bimodule defined as the direct sum of degree 1 and degree -1 components of A(p;q). The real structure of KO-dimension two for this Dirac operator is also described.
Protein complex compositions predicted by structural similarity
Davis, Fred P.; Braberg, Hannes; Shen, Min-Yi; Pieper, Ursula; Sali, Andrej; Madhusudhan, M.S.
2006-01-01
Proteins function through interactions with other molecules. Thus, the network of physical interactions among proteins is of great interest to both experimental and computational biologists. Here we present structure-based predictions of 3387 binary and 1234 higher order protein complexes in Saccharomyces cerevisiae involving 924 and 195 proteins, respectively. To generate candidate complexes, comparative models of individual proteins were built and combined together using complexes of known structure as templates. These candidate complexes were then assessed using a statistical potential, derived from binary domain interfaces in PIBASE (). The statistical potential discriminated a benchmark set of 100 interface structures from a set of sequence-randomized negative examples with a false positive rate of 3% and a true positive rate of 97%. Moreover, the predicted complexes were also filtered using functional annotation and sub-cellular localization data. The ability of the method to select the correct binding mode among alternates is demonstrated for three camelid VHH domain—porcine α–amylase interactions. We also highlight the prediction of co-complexed domain superfamilies that are not present in template complexes. Through integration with MODBASE, the application of the method to proteomes that are less well characterized than that of S.cerevisiae will contribute to expansion of the structural and functional coverage of protein interaction space. The predicted complexes are deposited in MODBASE (). PMID:16738133
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.
Noncommutative geometrical origin of the energy-momentum dispersion relation
NASA Astrophysics Data System (ADS)
Watcharangkool, A.; Sakellariadou, M.
2017-01-01
We investigate a link between the energy-momentum dispersion relation and the spectral distance in the context of a Lorentzian almost-commutative spectral geometry, defined by the product of Minkowski spacetime and an internal discrete noncommutative space. Using the causal structure, the almost-commutative manifold can be identified with a pair of four-dimensional Minkowski spacetimes embedded in a five-dimensional Minkowski geometry. Considering fermions traveling within the light cone of the ambient five-dimensional spacetime, we then derive the energy-momentum dispersion relation.
Very Special Relativity and Noncommutative Space-Time
NASA Astrophysics Data System (ADS)
Sheikh-Jabbari, M. M.; Tureanu, A.
The Very Special Relativity (VSR) introduced by Cohen and Glashow [16] has a robust mathematical realization on noncommutative space-time, in particular on noncommutative Moyal plane, with light-like noncommutativity [35]. The realization is essentially connected to the twisted Poincaré algebra and its role as symmetry of noncommutative space-time and the corresponding quantum field theories [11, 12]. In our setting the VSR invariant theories are specified with a single deformation parameter, the noncommutativity scaleΛ_{NC} Preliminary analysis with the available data leads to Λ_{NC} ≥ 1 - 10 Te V
Noncommutative Dirac quantization condition using the Seiberg-Witten map
NASA Astrophysics Data System (ADS)
Maceda, Marco; Martínez-Carbajal, Daniel
2016-11-01
The Dirac quantization condition (DQC) for magnetic monopoles in noncommutative space-time is analyzed. For this a noncommutative generalization of the method introduced by Wu and Yang is considered; the effects of noncommutativity are analyzed using the Seiberg-Witten map and the corresponding deformed Maxwell's equations are discussed. By using a perturbation expansion in the noncommutativity parameter θ , we show first that the DQC remains unmodified up to the first and second order. This result is then generalized to all orders in the expansion parameter for a class of noncommutative electric currents induced by the Seiberg-Witten map; these currents reduce to the Dirac delta function in the commutative limit.
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.
Structure of mammalian respiratory complex I
Hirst, Judy
2016-01-01
Complex I (NADH:ubiquinone oxidoreductase), one of the largest membrane-bound enzymes in the cell, powers ATP synthesis in mammalian mitochondria by using the reducing potential of NADH to drive protons across the inner membrane. Mammalian complex I1 contains 45 subunits, comprising 14 core subunits that house the catalytic machinery and are conserved from bacteria to humans, and a mammalian-specific cohort of 31 supernumerary subunits1,2. Knowledge about the structures and functions of the supernumerary subunits is fragmentary. Here, we describe a 4.2 Å resolution single-particle cryoEM structure of complex I from Bos taurus. We locate and model all 45 subunits to provide the entire structure of the mammalian complex. Furthermore, computational sorting of the particles identified different structural classes, related by subtle domain movements, which reveal conformationally-dynamic regions and match biochemical descriptions of the ‘active-to-deactive’ enzyme transition that occurs during hypoxia3,4. Thus, our structures provide a foundation for understanding complex I assembly5 and the effects of mutations that cause clinically-relevant complex I dysfunctions6, insights into the structural and functional roles of the supernumerary subunits, and new information on the mechanism and regulation of catalysis. PMID:27509854
Structure and function of cytochrome bc complexes
Berry, E.A.; Guergova-Kuras, M.; Huang, Li-Shar; Crofts, A.R.
2000-05-01
The cytochrome bc complexes represent a phylogenetically diverse group of electron-transfer membrane protein complexes, most familiarly represented by the mitochondrial and bacterial bc1 complexes and the chloroplast and cyanobacterial b6f complex. All these complexes couple electron transfer to protein translocation across a closed lipid bilayer membrane, conserving the free energy released by the oxidation-reduction process in the form of an electrochemical proton gradient across the membrane. Recent exciting developments include the application of site-directed mutagenesis to define the role of conserved residues, and the emergence over the past 5 years of x-ray structures for several mitochondrial complexes, and for two important domains of the b6f complex.
Noncommutative Geometry in M-Theory and Conformal Field Theory
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_{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_{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.
Non-commutativity in polar coordinates
NASA Astrophysics Data System (ADS)
Edwards, James P.
2017-05-01
We reconsider the fundamental commutation relations for non-commutative R2 described in polar coordinates with non-commutativity parameter θ . Previous analysis found that the natural transition from Cartesian coordinates to the traditional polar system led to a representation of [\\hat{r}, \\hat{φ}] as an everywhere diverging series. In this article we compute the Borel resummation of this series, showing that it can subsequently be extended throughout parameter space and hence provide an interpretation of this commutator. Our analysis provides a complete solution for arbitrary r and θ that reproduces the earlier calculations at lowest order and benefits from being generally applicable to problems in a two-dimensional non-commutative space. We compare our results to previous literature in the (pseudo-)commuting limit, finding a surprising spatial dependence for the coordinate commutator when θ ≫ r2. Finally, we raise some questions for future study in light of this progress.
Deconstructing Noncommutativity with a Giant Fuzzy Moose
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.
Non-Pauli transitions from spacetime noncommutativity.
Balachandran, A P; Joseph, Anosh; Padmanabhan, Pramod
2010-07-30
The consideration of noncommutative spacetimes in quantum theory can be plausibly advocated from physics at the Planck scale. Typically, this noncommutativity is controlled by fixed "vectors" or "tensors" with numerical entries like θμν for the Moyal spacetime. In approaches enforcing Poincaré invariance, these deform or twist the method of (anti)symmetrization of identical particle state vectors. We argue that the Earth's rotation and movements in the cosmos are "sudden" events to Pauli-forbidden processes. This induces (twisted) bosonic components in state vectors of identical spinorial particles. These components induce non-Pauli transitions. From known limits on such transitions, we infer that the energy scale for noncommutativity is ≳10(24) TeV. This suggests a new energy scale beyond the Planck scale.
Shadow of noncommutative geometry inspired black hole
Wei, Shao-Wen; Cheng, Peng; Zhong, Yi; Zhou, Xiang-Nan E-mail: pcheng14@lzu.edu.cn E-mail: zhouxn10@lzu.edu.cn
2015-08-01
In this paper, the shadow casted by the rotating black hole inspired by noncommutative geometry is investigated. In addition to the dimensionless spin parameter a/M{sub 0} with M{sub 0} black hole mass and inclination angle i, the dimensionless noncommutative parameter √θ/M{sub 0} is also found to affect the shape of the black hole shadow. The result shows that the size of the shadow slightly decreases with the parameter √θ/M{sub 0}, while the distortion increases with it. Compared to the Kerr black hole, the parameter √θ/M{sub 0} increases the deformation of the shadow. This may offer a way to distinguish noncommutative geometry inspired black hole from Kerr one via astronomical instruments in the near future.
Natural discretization in noncommutative field theory
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.
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.
Renormalization group flow for noncommutative Fermi liquids
Estrada-Jimenez, Sendic; Garcia-Compean, Hugo; Wu Yongshi
2011-06-15
Some recent studies of the AdS/CFT correspondence for condensed matter systems involve the Fermi liquid theory as a boundary field theory. Adding B-flux to the boundary D-branes leads in a certain limit to the noncommutative Fermi liquid, which calls for a field theory description of its critical behavior. As a preliminary step to more general consideration, the modification of the Landau's Fermi liquid theory due to noncommutativity of spatial coordinates is studied in this paper. We carry out the renormalization of interactions at tree level and one loop in a weakly coupled fermion system in two spatial dimensions. Channels ZS, ZS' and BCS are discussed in detail. It is shown that while the Gaussian fixed-point remains unchanged, the BCS instability is modified due to the space noncommutativity.
Structure of nucleosome-HMG complexes
Paton, A.E.
1982-12-01
This dissertation concentrates on the structure of HMG-nucleosome complexes, and how they differ from nucleosomes alone. The first chapter provides an introduction to chromatin and an overview of the field. The second and third chapters describe what kinds of nucleosome-HMG protein complexes form in solution, and where the HMG proteins may bind on the nucleosome. A model is proposed that locates the HMG binding sites on the nucleosome core particle. The fourth chapter describes the biophysical characterization of the complex. The methods include thermal denaturation, circular dichroism and sedimentation velocity, all done under variety of solvent conditions. These methods reveal a great deal of information on the stability and interactions of the complex. The fifth chapter describes conformational probes of the complex. These results reveal the structural transitions that occur when HMG protein binds to the nucleosome as well as the parts of the nucleosome essential for the binding reaction.
Structural Studies of Protein-Surfactant Complexes
Chodankar, S. N.; Aswal, V. K.; Wagh, A. G.
2008-03-17
The structure of protein-surfactant complexes of two proteins bovine serum albumin (BSA) and lysozyme in presence of anionic surfactant sodium dodecyl sulfate (SDS) has been studied using small-angle neutron scattering (SANS). It is observed that these two proteins form different complex structures with the surfactant. While BSA protein undergoes unfolding on addition of surfactant, lysozyme does not show any unfolding even up to very high surfactant concentrations. The unfolding of BSA protein is caused by micelle-like aggregation of surfactant molecules in the complex. On the other hand, for lysozyme protein there is only binding of individual surfactant molecules to protein. Lysozyme in presence of higher surfactant concentrations has protein-surfactant complex structure coexisting with pure surfactant micelles.
Complex II from a structural perspective.
Horsefield, Rob; Iwata, So; Byrne, Bernadette
2004-04-01
The super-macromolecular complex, succinate:quinone oxidoreductase (SQR, Complex II, succinate dehydrogenase) couples the oxidation of succinate in the matrix / cytoplasm to the reduction of quinone in the membrane. This function directly connects the Krebs cycle and the aerobic respiratory chain. Until the recent first report of the structure of SQR from Escherichia coli (E. coli) the structure-function relationships in SQR have been inferred from the structures of the homologous QFR, which catalyses the same reaction in the opposite direction. The structure of SQR from E. coli, analogous to the mitochondrial respiratory Complex II, has provided new insight into SQR's molecular design and mechanism, revealing the electron transport pathway through the enzyme. Comparison of the structures of SQR, QFR and other related flavoproteins shows how common amino acid residues at the interface of two domains facilitate the inter-conversion of succinate and fumarate. Additionally, the structure has provided a possible explanation as to why certain organisms utilise both SQR and QFR despite the fact that both can catalyse the inter-conversion of succinate and fumarate, in vitro and in vivo. Here we review how this structure has advanced our knowledge of this important enzyme and compare the structural information to other members of the Complex II superfamily and related flavoproteins.
Stochastic transport through complex comb structures
Zaburdaev, V. Yu.; Popov, P. V.; Romanov, A. S.; Chukbar, K. V.
2008-05-15
A unified rigorous approach is used to derive fractional differential equations describing subdiffusive transport through comb structures of various geometrical complexity. A general nontrivial effect of the initial particle distribution on the subsequent evolution is exposed. Solutions having qualitative features of practical importance are given for joined structures with widely different fractional exponents.
Braneworld cosmology and noncommutative inflation
NASA Astrophysics Data System (ADS)
Calcagni, Gianluca
2005-03-01
In this work we develop the patch formalism, an approach providing a very simple and compact description of braneworld-motivated cosmologies with nonstandard effective Friedmann equations. In particular, the Hubble parameter is assumed to depend on some power of the brane energy density, H^2 propto rho^q. The high-energy limit of Randall-Sundrum (q=2) and Gauss-Bonnet (q=2/3) braneworlds are considered, during an accelerating era triggered by a single ordinary or tachyonic scalar field. The inflationary dynamics, solutions, and spectra are provided. Using the latest results from WMAP and other experiments for estimates of cosmological observables, it is shown that future data and missions can in principle discriminate between standard four-dimensional and braneworld scenarios. The issue of non-Gaussianity is also studied within nonlinear perturbation theory. The introduction of a fundamental energy scale reinforces these results. Several classes of noncommutative inflationary models are considered and their features analyzed in a number of ways and energy regimes. Finally, we establish dual relations between inflationary, cyclic/ekpyrotic and phantom cosmologies, as well as between scalar-driven and tachyon-driven cosmologies. The exact dualities relating the four-dimensional spectra are broken in favour of their braneworld counterparts. The dual solutions display new interesting features because of the modification of the effective Friedmann equation on the brane.
On quantum algorithms for noncommutative hidden subgroups
Ettinger, M.; Hoeyer, P.
1998-12-01
Quantum algorithms for factoring and discrete logarithm have previously been generalized to finding hidden subgroups of finite Abelian groups. This paper explores the possibility of extending this general viewpoint to finding hidden subgroups of noncommutative groups. The authors present a quantum algorithm for the special case of dihedral groups which determines the hidden subgroup in a linear number of calls to the input function. They also explore the difficulties of developing an algorithm to process the data to explicitly calculate a generating set for the subgroup. A general framework for the noncommutative hidden subgroup problem is discussed and they indicate future research directions.
Noncommutative FRW Apparent Horizon and Hawking Radiation
NASA Astrophysics Data System (ADS)
Bouhallouf, H.; Mebarki, N.; Aissaoui, H.
2017-09-01
In the context of noncommutative (NCG) gauge gravity, and using a cosmic time power law formula for the scale factor, a Friedman-Robertson-Walker (FRW) like metric is obtained. Within the fermions tunneling effect approach and depending on the various intervals of the power parameter, expressions of the apparent horizon are also derived. It is shown that in some regions of the parameter space, a pure NCG trapped horizon does exist leading to new interpretation of the role played by the noncommutativity of the space-time.
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.
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.
The Electronic Structure of Heavy Element Complexes
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.
Structural polymorphism of DNA-dendrimer complexes
NASA Astrophysics Data System (ADS)
Evans, Heather M.; Ahmad, A.; Ewert, K.; Pfohl, T.; Martin-Herranz, A.; Bruinsma, R. F.; Safinya, C. R.
2003-08-01
DNA condensation in vivo relies on electrostatic complexation with small cations or large histones. We report a synchrotron x-ray study of the phase behavior of DNA complexed with synthetic cationic dendrimers of intermediate size and charge. We encounter unexpected structural transitions between columnar mesophases with in-plane square and hexagonal symmetries, as well as liquidlike disorder. The isoelectric point is a locus of structural instability. A simple model is proposed based on competing long-range electrostatic interactions and short-range entropic adhesion by counterion release.
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
Towards a noncommutative version of Gravitation
Franco, Nicolas
2010-06-23
Alain Connes' noncommutative theory led to an interesting model including both Standard Model of particle physics and Euclidean Gravity. Nevertheless, an hyperbolic version of the gravitational part would be necessary to make physical predictions, but it is still under research. We shall present the difficulties to generalize the model from Riemannian to Lorentzian Geometry and discuss key ideas and current attempts.
Recent structural insights into transcription preinitiation complexes.
Nogales, E
2000-12-01
Our understanding of the elaborate mechanism of gene transcription initiation in eukaryotes has been widened by recent structural information on some of the key components of the complex preinitiation transcriptional machinery. The high-resolution structures of both bacterial and eukaryotic polymerases are technical landmarks of great biological significance that have given us the first molecular insight into the mechanism of this large enzyme. While new atomic structures of different domains of general transcription factors, such as the double bromodomain of TAF250, have become available by means of X-ray crystallography and NMR studies, more global pictures of multisubunit transcription complexes, such as TFIID, TFIIH or the yeast mediator, have now been obtained by electron microscopy and image-reconstruction techniques. A combination of methodologies may prove essential for a complete structural description of the initial steps in the expression of eukaryotic genes.
Impulse Response Operators for Structural Complexes
1990-05-12
systems of the complex. The statistical energy analysis (SEA) is one such a device [ 13, 14]. The rendering of SEA from equation (21) and/or (25) lies...Propagation.] 13. L. Cremer, M. Heckl, and E.E. Ungar 1973 Structure-Borne Sound (Springer Verlag). 14. R. H. Lyon 1975 Statistical Energy Analysis of
Structure of Complex Verb Forms in Meiteilon
ERIC Educational Resources Information Center
Singh, Lourembam Surjit
2016-01-01
This piece of work proposes to descriptively investigate the structures of complex verbs in Meiteilon. The categorization of such verbs is based on the nature of semantic and syntactic functions of a lexeme or verbal lexeme. A lexeme or verbal lexeme in Meiteilon may have multifunctional properties in the nature of occurrence. Such lexical items…
From Feynman proof of Maxwell equations to noncommutative quantum mechanics
NASA Astrophysics Data System (ADS)
Bérard, A.; Mohrbach, H.; Lages, J.; Gosselin, P.; Grandati, Y.; Boumrar, H.; Ménas, F.
2007-05-01
In 1990, Dyson published a proof due to Feynman of the Maxwell equations assuming only the commutation relations between position and velocity. With this minimal assumption, Feynman never supposed the existence of Hamiltonian or Lagrangian formalism. In the present communication, we review the study of a relativistic particle using "Feynman brackets." We show that Poincaré's magnetic angular momentum and Dirac magnetic monopole are the consequences of the structure of the Lorentz Lie algebra defined by the Feynman's brackets. Then, we extend these ideas to the dual momentum space by considering noncommutative quantum mechanics. In this context, we show that the noncommutativity of the coordinates is responsible for a new effect called the spin Hall effect. We also show its relation with the Berry phase notion. As a practical application, we found an unusual spin-orbit contribution of a nonrelativistic particle that could be experimentally tested. Another practical application is the Berry phase effect on the propagation of light in inhomogeneous media.
COMPLEX STRUCTURE IN CLASS 0 PROTOSTELLAR ENVELOPES
Tobin, John J.; Hartmann, Lee; Looney, Leslie W.; Chiang, Hsin-Fang
2010-04-01
We use archived Infrared Array Camera images from the Spitzer Space Telescope to show that many Class 0 protostars exhibit complex, irregular, and non-axisymmetric structure within their dusty envelopes. Our 8 {mu}m extinction maps probe some of the densest regions in these protostellar envelopes. Many of the systems are observed to have highly irregular and non-axisymmetric morphologies on scales {approx}>1000 AU, with a quarter of the sample exhibiting filamentary or flattened dense structures. Complex envelope structure is observed in regions spatially distinct from outflow cavities, and the densest structures often show no systematic alignment perpendicular to the cavities. These results indicate that mass ejection is not responsible for much of the irregular morphologies we detect; rather, we suggest that the observed envelope complexity is mostly the result of collapse from protostellar cores with initially non-equilibrium structures. The striking non-axisymmetry in many envelopes could provide favorable conditions for the formation of binary systems. We also note that protostars in the sample appear to be formed preferentially near the edges of clouds or bends in filaments, suggesting formation by gravitational focusing.
Commuting flows and conservation laws for noncommutative Lax hierarchies
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.
Strong gravitational lensing in a noncommutative black-hole spacetime
Ding Chikun; Kang Shuai; Chen Changyong; Chen Songbai; Jing Jiliang
2011-04-15
Noncommutative geometry may be a starting point to a quantum gravity. We study the influence of the spacetime noncommutative parameter on the strong field gravitational lensing in the noncommutative Schwarzschild black-hole spacetime and obtain the angular position and magnification of the relativistic images. Supposing that the gravitational field of the supermassive central object of the galaxy can be described by this metric, we estimate the numerical values of the coefficients and observables for strong gravitational lensing. In comparison to the Reissner-Norstroem black hole, we find that the influences of the spacetime noncommutative parameter is similar to those of the charge, but these influences are much smaller. This may offer a way to distinguish a noncommutative black hole from a Reissner-Norstroem black hole, and may permit us to probe the spacetime noncommutative constant {theta} by the astronomical instruments in the future.
Structural complexity of a composite amyloid fibril.
Lewandowski, Józef R; van der Wel, Patrick C A; Rigney, Mike; Grigorieff, Nikolaus; Griffin, Robert G
2011-09-21
The molecular structure of amyloid fibrils and the mechanism of their formation are of substantial medical and biological importance, but present an ongoing experimental and computational challenge. An early high-resolution view of amyloid-like structure was obtained on amyloid-like crystals of a small fragment of the yeast prion protein Sup35p: the peptide GNNQQNY. As GNNQQNY also forms amyloid-like fibrils under similar conditions, it has been theorized that the crystal's structural features are shared by the fibrils. Here we apply magic-angle-spinning (MAS) NMR to examine the structure and dynamics of these fibrils. Previously multiple NMR signals were observed for such samples, seemingly consistent with the presence of polymorphic fibrils. Here we demonstrate that peptides with these three distinct conformations instead assemble together into composite protofilaments. Electron microscopy (EM) of the ribbon-like fibrils indicates that these protofilaments combine in differing ways to form striations of variable widths, presenting another level of structural complexity. Structural and dynamic NMR data reveal the presence of highly restricted side-chain conformations involved in interfaces between differently structured peptides, likely comprising interdigitated steric zippers. We outline molecular interfaces that are consistent with the observed EM and NMR data. The rigid and uniform structure of the GNNQQNY crystals is found to contrast distinctly with the more complex structural and dynamic nature of these "composite" amyloid fibrils. These results provide insight into the fibril-crystal distinction and also indicate a necessary caution with respect to the extrapolation of crystal structures to the study of fibril structure and formation.
Solution Structures of PPARγ2/RXRα Complexes.
Osz, Judit; Pethoukhov, Maxim V; Sirigu, Serena; Svergun, Dmitri I; Moras, Dino; Rochel, Natacha
2012-01-01
PPARγ is a key regulator of glucose homeostasis and insulin sensitization. PPARγ must heterodimerize with its dimeric partner, the retinoid X receptor (RXR), to bind DNA and associated coactivators such as p160 family members or PGC-1α to regulate gene networks. To understand how coactivators are recognized by the functional heterodimer PPARγ/RXRα and to determine the topological organization of the complexes, we performed a structural study using small angle X-ray scattering of PPARγ/RXRα in complex with DNA from regulated gene and the TIF2 receptor interacting domain (RID). The solution structures reveal an asymmetry of the overall structure due to the crucial role of the DNA in positioning the heterodimer and indicate asymmetrical binding of TIF2 to the heterodimer.
Solution Structures of PPARγ2/RXRα Complexes
Osz, Judit; Pethoukhov, Maxim V.; Sirigu, Serena; Svergun, Dmitri I.; Moras, Dino; Rochel, Natacha
2012-01-01
PPARγ is a key regulator of glucose homeostasis and insulin sensitization. PPARγ must heterodimerize with its dimeric partner, the retinoid X receptor (RXR), to bind DNA and associated coactivators such as p160 family members or PGC-1α to regulate gene networks. To understand how coactivators are recognized by the functional heterodimer PPARγ/RXRα and to determine the topological organization of the complexes, we performed a structural study using small angle X-ray scattering of PPARγ/RXRα in complex with DNA from regulated gene and the TIF2 receptor interacting domain (RID). The solution structures reveal an asymmetry of the overall structure due to the crucial role of the DNA in positioning the heterodimer and indicate asymmetrical binding of TIF2 to the heterodimer. PMID:23319938
Complex structures of dense lithium: Electronic origin
NASA Astrophysics Data System (ADS)
Degtyareva, V. F.
2016-11-01
Lithium—the lightest alkali metal exhibits unexpected structures and electronic behavior at high pressures. Like the heavier alkali metals, Li is bcc at ambient pressure and transforms first to fcc (at 7.5 GPa). The post-fcc high-pressure form Li-cI 16 (at 40-60 GPa) is similar to Na-cI 16 and related to more complex structures of heavy alkalis Rb-oC52 and Cs- oC84. The other high pressure phases for Li (oC88, oC40, oC24) observed at pressures up to 130 GPa are found only in Li. The different route of Li high-pressure structures correlates with its special electronic configuration containing the only 3 electrons (at 1s and 2s levels). Crystal structures for Li are analyzed within the model of Fermi sphere-Brillouin zone interactions. Stability of post-fcc structures for Li are supported by the Hume-Rothery arguments when new diffraction plains appear close to the Fermi level producing pseudogaps near the Fermi level and decreasing the crystal energy. The filling of Brillouin-Jones zones by electron states for a given structure defines the physical properties as optical reflectivity, electrical resistivity and superconductivity. To understand the complexity of structural and physical properties of Li above 60 GPa it is necessary to assume the valence electron band overlap with the core electrons and increase the valence electron count under compression.
Dirac Oscillator in a Galilean Covariant Non-commutative Space
NASA Astrophysics Data System (ADS)
de Melo, G. R.; de Montigny, M.; Pompeia, P. J.; Santos, E. S.
2013-02-01
We study the Galilean Dirac oscillator in a non-commutative situation, with space-space and momentum-momentum non-commutativity. The wave equation is obtained via a `Galilean covariant' approach, which consists in projecting the covariant equations from a (4,1)-dimensional manifold with light-cone coordinates, to a (3,1)-dimensional Galilean space-time. We obtain the exact wave functions and their energy levels for the plane and discuss the effects of non-commutativity.
Exponential convergence rates for weighted sums in noncommutative probability space
NASA Astrophysics Data System (ADS)
Choi, Byoung Jin; Ji, Un Cig
2016-11-01
We study exponential convergence rates for weighted sums of successive independent random variables in a noncommutative probability space of which the weights are in a von Neumann algebra. Then we prove a noncommutative extension of the result for the exponential convergence rate by Baum, Katz and Read. As applications, we first study a large deviation type inequality for weighted sums in a noncommutative probability space, and secondly we study exponential convergence rates for weighted free additive convolution sums of probability measures.
Imaging beneath complex structure: a case history
Gibson, B.; Larner, K.; Chambers, R.
1983-08-01
Migration is recognized as the essential step in converting seismic data into a representation of the earth's subsurface structure. Ironically, conventional migration often fails where migration is needed most - when the data are recorded over complex structures. In the Central American example, velocities increase nearly two-fold across an arched and thrust-faulted interface. Wave-front distortion introduced by this feature gives rise to distorted reflection from depth. Even with interval velocity known perfectly, no velocity is proper for time migrating the data here; time migration is the wrong process because it does not honor Snell's law. Depth migration of the stacked data, on the other hand, produces a reasonable image of the deeper section. The depth migration, however, leaves artifacts that could be attributed to problems that are common in structurally complicated areas: (1) departures of the stacked section from the ideal, a zero-offset section, (2) incorrect specification of velocities, and (3) loss of energy transmitted through the complex zone. For such an inhomogeneous velocity structure, shortcoming in CDP stacking are related directly to highly nonhyperbolic moveout. As with migration velocity, no proper stacking velocity can be developed for these data, even from the known interval-velocity model. Proper treatment of nonzero-offset reflection data could be accomplished by depth migration before stacking. Simple ray-theoretical correction of the complex moveouts, however, can produce a stack that is similar to the desired zero-offset section.
Structure of bacterial respiratory complex I.
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.
Classical mechanics in non-commutative phase space
NASA Astrophysics Data System (ADS)
Wei, Gao-Feng; Long, Chao-Yun; Long, Zheng-Wen; Qin, Shui-Jie; Fu, Qiang
2008-05-01
In this paper the laws of motion of classical particles have been investigated in a non-commutative phase space. The corresponding non-commutative relations contain not only spatial non-commutativity but also momentum non-commutativity. First, new Poisson brackets have been defined in non-commutative phase space. They contain corrections due to the non-commutativity of coordinates and momenta. On the basis of this new Poisson brackets, a new modified second law of Newton has been obtained. For two cases, the free particle and the harmonic oscillator, the equations of motion are derived on basis of the modified second law of Newton and the linear transformation (Phys. Rev. D, 2005, 72: 025010). The consistency between both methods is demonstrated. It is shown that a free particle in commutative space is not a free particle with zero-acceleration in the non-commutative phase space, but it remains a free particle with zero-acceleration in non-commutative space if only the coordinates are non-commutative. Supported by National Natural Science Foundation of China (10347003, 60666001), Planned Training Excellent Scientific and Technological Youth Foundation of Guizhou Province, China (2002,2013), Science Foundation of Guizhou Province, China, and Creativity Foundation for Graduate Guizhou University, China (2006031)
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.
Variable Complexity Structural Optimization of Shells
NASA Technical Reports Server (NTRS)
Haftka, Raphael T.; Venkataraman, Satchi
1998-01-01
Structural designers today face both opportunities and challenges in a vast array of available analysis and optimization programs. Some programs such as NASTRAN, are very general, permitting the designer to model any structure, to any degree of accuracy, but often at a higher computational cost. Additionally, such general procedures often do not allow easy implementation of all constraints of interest to the designer. Other programs, based on algebraic expressions used by designers one generation ago, have limited applicability for general structures with modem materials. However, when applicable, they provide easy understanding of design decisions trade-off. Finally, designers can also use specialized programs suitable for designing efficiently a subset of structural problems. For example, PASCO and PANDA2 are panel design codes, which calculate response and estimate failure much more efficiently than general-purpose codes, but are narrowly applicable in terms of geometry and loading. Therefore, the problem of optimizing structures based on simultaneous use of several models and computer programs is a subject of considerable interest. The problem of using several levels of models in optimization has been dubbed variable complexity modeling. Work under NASA grant NAG1-1808 has been concerned with the development of variable complexity modeling strategies with special emphasis on response surface techniques. In addition several modeling issues for the design of shells of revolution were studied.
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.
Structural investigations into microtubule-MAP complexes.
Hoenger, Andreas; Gross, Heinz
2008-01-01
Microtubules interact with a large variety of factors commonly referred to as either molecular motors (kinesins, dyneins) or structural microtubule-associated proteins (MAPs). MAPs do not exhibit motor activity, but regulate microtubule dynamics and their interactions with molecular motors, and organelles such as kinetochores or centrosomes. Structural investigations into microtubule-kinesin motor complexes are quite advanced today and by helical three-dimensional (3-D) analysis reveal a resolution of the motor-tubulin interface at <1.0 nm. However, due to their flexible structure MAPs like tau or MAP2C cannot be visualized in the same straightforward manner. Helical averaging usually reveals only the location of strong binding sites while the overall structure of the MAP remains unsolved. Other MAPs such as EB1 bind very selectively only to some parts of the microtubule lattice such as the lattice seam. Thus, they do not reveal a stoichiometric tubulin:MAP-binding ratio that would allow for a quantitative helical 3-D analysis. Therefore, to get a better view on the structure of microtubule-MAP complexes we often used a strategy that combined cryo-electron microscopy and helical or tomographic 3-D analysis with freeze-drying and high-resolution unidirectional surface shadowing. 3-D analysis of ice-embedded specimens reveals their full 3-D volume. This relies either on a repetitive structure following a helical symmetry that can be used for averaging or suffers from the limited resolution that is currently achievable with cryotomography. Surface metal shadowing exclusively images surface-exposed features at very high contrast, adding highly valuable information to 2-D or 3-D data of vitrified structures.
Noncommutative S O (2 , 3 )⋆ gravity: Noncommutativity as a source of curvature and torsion
NASA Astrophysics Data System (ADS)
Dimitrijević Ćirić, Marija; Nikolić, Biljana; Radovanović, Voja
2017-09-01
Noncommutative (NC) gravity is constructed on the canonical noncommutative (Moyal-Weyl) spacetime as a noncommutative S O (2 ,3 )⋆ gauge theory. The NC gravity action consists of three different terms: the first term is of Mac-Dowell Mansouri type, while the other two are generalizations of the Einstein-Hilbert action and the cosmological constant term. The expanded NC gravity action is then calculated using the Seiberg-Witten (SW) map and the expansion is done up second order in the deformation parameter. We analyze in details the low energy sector of the full model. We calculate the equations of motion, discuss their general properties and present one solution: the NC correction to Minkowski spacetime. Using this solution, we explain breaking of the diffeomorphism symmetry as a consequence of working in a particular coordinate system given by the Fermi normal coordinates.
Quantum Hall Physics Equals Noncommutive Field Theory
Rammsdonk , Mark van
2001-08-09
In this note, we study a matrix-regularized version of non-commutative U(1) Chern-Simons theory proposed recently by Polychronakos. We determine a complete minimal basis of exact wavefunctions for the theory at arbitrary level k and rank N and show that these are in one-to-one correspondence with Laughlin-type wavefunctions describing excitations of a quantum Hall droplet composed of N electrons at filling fraction 1/k. The finite matrix Chern-Simons theory is shown to be precisely equivalent to the theory of composite fermions in the lowest Landau level, believed to provide an accurate description of the filling fraction 1/k fractional quantum Hall state. In the large N limit, this implies that level k noncommutative U(1) Chern-Simons theory is equivalent to the Laughlin theory of the filling fraction 1k quantum Hall fluid, as conjectured recently by Susskind.
Paraquantum strings in noncommutative space-time
NASA Astrophysics Data System (ADS)
Seridi, M. A.; Belaloui, N.
2015-10-01
A parabosonic string is assumed to propagate in a total noncommutative target phase space. Three models are investigated: open strings, open strings between two parallel Dp-Dq branes and closed ones. This leads to a generalization of the oscillators algebra of the string and the corresponding Virasoro algebra. The mass operator is no more diagonal in the ordinary Fock space, a redefinition of this later will modify the mass spectrum, so that, neither massless vector state nor massless tensor state are present. The restoration of the photon and the graviton imposes specific forms of the noncommutativity parameter matrices, partially removes the mass degeneracy and gives new additional ones. In particular, for the D-branes, one can have a tachyon free model with a photon state when more strict conditions on these parameters are imposed, while, the match level condition of the closed string model induces the reduction of the spectrum.
Hamiltonian Approach To Dp-Brane Noncommutativity
NASA Astrophysics Data System (ADS)
Nikolic, B.; Sazdovic, B.
2010-07-01
In this article we investigate Dp-brane noncommutativity using Hamiltonian approach. We consider separately open bosonic string and type IIB superstring which endpoints are attached to the Dp-brane. From requirement that Hamiltonian, as the time translation generator, has well defined derivatives in the coordinates and momenta, we obtain boundary conditions directly in the canonical form. Boundary conditions are treated as canonical constraints. Solving them we obtain initial coordinates in terms of the effective ones as well as effective momenta. Presence of momenta implies noncommutativity of the initial coordinates. Effective theory, defined as initial one on the solution of boundary conditions, is its Ω even projection, where Ω is world-sheet parity transformation Ω:σ→-σ. The effective background fields are expressed in terms of Ω even and squares of the Ω odd initial background fields.
Structures of the CRISPR genome integration complex.
Wright, Addison V; Liu, Jun-Jie; Knott, Gavin J; Doxzen, Kevin W; Nogales, Eva; Doudna, Jennifer A
2017-09-15
CRISPR-Cas systems depend on the Cas1-Cas2 integrase to capture and integrate short foreign DNA fragments into the CRISPR locus, enabling adaptation to new viruses. We present crystal structures of Cas1-Cas2 bound to both donor and target DNA in intermediate and product integration complexes, as well as a cryo-electron microscopy structure of the full CRISPR locus integration complex, including the accessory protein IHF (integration host factor). The structures show unexpectedly that indirect sequence recognition dictates integration site selection by favoring deformation of the repeat and the flanking sequences. IHF binding bends the DNA sharply, bringing an upstream recognition motif into contact with Cas1 to increase both the specificity and efficiency of integration. These results explain how the Cas1-Cas2 CRISPR integrase recognizes a sequence-dependent DNA structure to ensure site-selective CRISPR array expansion during the initial step of bacterial adaptive immunity. Copyright © 2017, American Association for the Advancement of Science.
Structure of the haptoglobin-haemoglobin complex.
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
Sigma-Model Solitons on Noncommutative Spaces
NASA Astrophysics Data System (ADS)
Dabrowski, Ludwik; Landi, Giovanni; Luef, Franz
2015-12-01
We use results from time-frequency analysis and Gabor analysis to construct new classes of sigma-model solitons over the Moyal plane and over noncommutative tori, taken as source spaces, with a target space made of two points. A natural action functional leads to self-duality equations for projections in the source algebra. Solutions, having nontrivial topological content, are constructed via suitable Morita duality bimodules.
Coherent states in noncommutative quantum mechanics
Ben Geloun, J.; Scholtz, F. G.
2009-04-15
Gazeau-Klauder coherent states in noncommutative quantum mechanics are considered. We find that these states share similar properties to those of ordinary canonical coherent states in the sense that they saturate the related position uncertainty relation, obey a Poisson distribution, and possess a flat geometry. Using the natural isometry between the quantum Hilbert space of Hilbert-Schmidt operators and the tensor product of the classical configuration space and its dual, we reveal the inherent vector feature of these states.
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.
Structural alignment of RNA with complex pseudoknot structure.
Wong, Thomas K F; Lam, T W; Sung, Wing-Kin; Cheung, Brenda W Y; Yiu, S M
2011-01-01
The secondary structure of an ncRNA molecule is known to play an important role in its biological functions. Aligning a known ncRNA to a target candidate to determine the sequence and structural similarity helps in identifying de novo ncRNA molecules that are in the same family of the known ncRNA. However, existing algorithms cannot handle complex pseudoknot structures which are found in nature. In this article, we propose algorithms to handle two types of complex pseudoknots: simple non-standard pseudoknots and recursive pseudoknots. Although our methods are not designed for general pseudoknots, it already covers all known ncRNAs in both Rfam and PseudoBase databases. An evaluation of our algorithms shows that it is useful to identify ncRNA molecules in other species which are in the same family of a known ncRNA.
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.
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.
Deformed symmetries in noncommutative and multifractional spacetimes
NASA Astrophysics Data System (ADS)
Calcagni, Gianluca; Ronco, Michele
2017-02-01
We clarify the relation between noncommutative spacetimes and multifractional geometries, two quantum-gravity-related approaches where the fundamental description of spacetime is not given by a classical smooth geometry. Despite their different conceptual premises and mathematical formalisms, both research programs allow for the spacetime dimension to vary with the probed scale. This feature and other similarities led to ask whether there is a duality between these two independent proposals. In the absence of curvature and comparing the symmetries of both position and momentum space, we show that κ -Minkowski spacetime and the commutative multifractional theory with q -derivatives are physically inequivalent but they admit several contact points that allow one to describe certain aspects of κ -Minkowski noncommutative geometry as a multifractional theory and vice versa. Contrary to previous literature, this result holds without assuming any specific measure for κ -Minkowski. More generally, no well-defined ⋆-product can be constructed from the q -theory, although the latter does admit a natural noncommutative extension with a given deformed Poincaré algebra. A similar no-go theorem may be valid for all multiscale theories with factorizable measures. Turning gravity on, we write the algebras of gravitational first-class constraints in the multifractional theories with q - and weighted derivatives and discuss their differences with respect to the deformed algebras of κ -Minkowski spacetime and of loop quantum gravity.
Structure of a human translation termination complex
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
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.
Morphologically complex protostellar envelopes : structure and kinematics
NASA Astrophysics Data System (ADS)
Tobin, John J.
I present an in-depth study of protostars and their surrounding envelopes of dense gas and dust, using a multitude of observational methods to reveal new details of the star formation process. I use mid-infrared imaging from the Spitzer Space Telescope, combined with photometry spanning the near-infrared to millimeter wavelengths, to construct a model of the L1527 protostellar system. I modeled both the spectral energy distribution and resolved scattered light images to determine physical properties of the protostellar system. The nature of the apparent central point source in the Spitzer images was uncertain until high-resolution L-band imaging from the Gemini observatory resolved the point source into a disk in scattered light, having a radius of 200 AU. Protostellar envelopes are also often found to cast shadows against the 8 micron Galactic background in Spitzer imaging, enabling direct probes of envelope structure. The shadow images show that the dense envelopes around twenty-two Class 0 protostars are generally morphologically complex from 0.1 pc scales down to ˜1000 AU; they are often filamentary, and frequently non-axisymmetric. The observed envelope structure indicates a likely origin in turbulent cloud structure rather than a quasi-static/equilibrium formation. The complex envelope structure also may indicate an increased likelihood of fragmentation during collapse, forming close binaries. To further characterize these envelopes, I have observed them in the dense molecular gas tracers nthp and nht, both of which closely follow the 8 micron extinction morphology. The magnitude of the velocity gradients and envelope complexity on ˜10000 AU scales indicates that the velocity structure may reflect large-scale infall in addition to the often assumed rotation. Comparisons with three-dimensional filamentary and symmetric rotating collapse models reinforce the interpretation of velocities reflecting large-scale infall, showing that the structure of the envelope
The Structure and Dynamics of Economic Complexity
NASA Astrophysics Data System (ADS)
Hidalgo, Cesar A.
2011-03-01
Can network science help us understand the structure and evolution of the global economy? In this talk I summarize recent research that uses networks and complexity science to describe and explain the evolution of the mix of products that countries, and cities, produce and export. First, I show how to use information on the network connecting industries to locations to measure the complexity of an economy. Using these measures I demonstrate that countries tend to approach a level of income that is dictated by the complexity of their economies. Next, I study the evolution of economic complexity by showing that it is constrained by a coordination problem that countries, and cities, deal with using three different channels: First, they move to products that are close by, in the Product Space, to the products that they already do. Second, they are more likely to develop a product if a geographical neighbor has already developed it. And third, they follow the nestedness of the network connecting industries to locations. Finally, I introduce a simple model to account for the stylized facts uncovered in the previous sections.
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.
Topological structural classes of complex networks
NASA Astrophysics Data System (ADS)
Estrada, Ernesto
2007-01-01
We use theoretical principles to study how complex networks are topologically organized at large scale. Using spectral graph theory we predict the existence of four different topological structural classes of networks. These classes correspond, respectively, to highly homogenous networks lacking structural bottlenecks, networks organized into highly interconnected modules with low inter-community connectivity, networks with a highly connected central core surrounded by a sparser periphery, and networks displaying a combination of highly connected groups (quasicliques) and groups of nodes partitioned into disjoint subsets (quasibipartites). Here we show by means of the spectral scaling method that these classes really exist in real-world ecological, biological, informational, technological, and social networks. We show that neither of three network growth mechanisms—random with uniform distribution, preferential attachment, and random with the same degree sequence as real network—is able to reproduce the four structural classes of complex networks. These models reproduce two of the network classes as a function of the average degree but completely fail in reproducing the other two classes of networks.
Hydrogen atom spectrum and the lamb shift in noncommutative QED.
Chaichian, M; Sheikh-Jabbari, M M; Tureanu, A
2001-03-26
We have calculated the energy levels of the hydrogen atom as well as the Lamb shift within the noncommutative quantum electrodynamics theory. The results show deviations from the usual QED both on the classical and the quantum levels. On both levels, the deviations depend on the parameter of space/space noncommutativity.
Warped Products and Yang-Mills Equations on Noncommutative Spaces
NASA Astrophysics Data System (ADS)
Zampini, Alessandro
2015-02-01
This paper presents a non-self-dual solution of the Yang-Mills equations on a noncommutative version of the classical , so generalizing the classical meron solution first introduced by de Alfaro et al. (Phys Lett B 65:163-166, 1976). The basic tool for that is a generalization to noncommutative spaces of the classical notion of warped products between metric spaces.
Parity-dependent non-commutative quantum mechanics
NASA Astrophysics Data System (ADS)
Chung, Won Sang
2017-01-01
In this paper, we consider the non-commutative quantum mechanics (NCQM) with parity (or space reflection) in two dimensions. Using the parity operators Ri, we construct the deformed Heisenberg algebra with parity in the non-commutative plane. We use this algebra to discuss the isotropic harmonic Hamiltonian with parity.
Noncommutative anisotropic oscillator in a homogeneous magnetic field
NASA Astrophysics Data System (ADS)
Nath, D.; Roy, P.
2017-02-01
We study anisotropic oscillator in the presence of a homogeneous magnetic field and other related systems in the noncommutative plane. Energy values as function of the noncommutative parameter θ and the magnetic field B have been obtained. Some features of the spectrum, for example, formation of energy bands etc. have been examined. The effect of anisotropy on the energy levels has also been discussed.
Stabilization of Internal Space in Noncommutative Multidimensional Cosmology
NASA Astrophysics Data System (ADS)
Khosravi, N.; Jalalzadeh, S.; Sepangi, H. R.
We study the cosmological aspects of a noncommutative, multidimensional universe where the matter source is assumed to be a scalar field which does not commute with the internal scale factor. We show that such noncommutativity results in the internal dimensions being stabilized.
Parabosonic string and space-time non-commutativity
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.
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.
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
Non-commutative geometry, the Bohm interpretation and the mind-matter relationship
NASA Astrophysics Data System (ADS)
Hiley, B. J.
2001-06-01
It is argued that in order to address the mind/matter relationship, we will have to radically change the conceptual structure normally assumed in physics. Rather than fields and/or particles-in-interaction described in the traditional Cartesian order based a local evolution in spacetime, we need to introduce a more general notion of process described by a non-commutative algebra. This will have radical implications for both for physical processes and for geometry. By showing how the Bohm interpretation of quantum mechanics can be understood within a non-commutative structure, we can give a much clearer meaning to the implicate order introduced by Bohm. It is through this implicate order that mind and matter can be seen as different aspects of the same general process.
Complexity and the relaxation of hierarchical structures
NASA Astrophysics Data System (ADS)
Bachas, Constantin P.; Huberman, Bernardo A.
1986-10-01
We solve exactly the problem of diffusion in an arbitrary hierarchical space. We prove that for a given ``tree silhouette'' 0complexity. We conclude that uniform trees are optimal for information diffusion, that in thermally activated processes the temperature dependence of ν varies with the underlying tree structure, and that thin elongated trees are the only ones capable of producing a 1/f spectrum.
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.
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.
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.
Classical electrodynamics in a space with spin noncommutativity of coordinates
NASA Astrophysics Data System (ADS)
Vasyuta, V. M.; Tkachuk, V. M.
2016-10-01
We propose a relativistic Lorentz-invariant spin-noncommutative algebra. Using the Weyl ordering of noncommutative position operators, we find a mapping from a space of commutative functions into space of noncommutative functions. The Lagrange function of an electromagnetic field in the space with spin noncommutativity is constructed. In such a space electromagnetic field becomes non-abelian. A gauge transformation law of this field is also obtained. Exact nonlinear field equations of noncommutative electromagnetic field are derived from the least action principle. Within the perturbative approach we consider field of a point charge in a constant magnetic field and interaction of two plane waves. An exact solution of a plane wave propagation in a constant magnetic and electric fields is found.
On matrix model formulations of noncommutative Yang-Mills theories
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.
A note on nonlinear σ-models in noncommutative geometry
NASA Astrophysics Data System (ADS)
Lee, Hyun Ho
2016-03-01
We study nonlinear σ-models defined on a noncommutative torus as a two-dimensional string worldsheet. We consider (i) a two-point space, (ii) a circle, (iii) a noncommutative torus, (iv) a classical group SU(2, ℂ) as examples of space-time. Based on established results, the trivial harmonic unitaries of the noncommutative chiral model known as local minima are shown not to be global minima by comparing them to the symmetric unitaries derived from instanton solutions of the noncommutative Ising model corresponding to a two-point space. In addition, a ℤ2-action on field maps is introduced to a noncommutative torus, and its action on solutions of various Euler-Lagrange equations is described.
C, P, and T invariance of noncommutative gauge theories
Sheikh-Jabbari
2000-06-05
In this paper we study the invariance of the noncommutative gauge theories under C, P, and T transformations. For the noncommutative space (when only the spatial part of straight theta is nonzero) we show that noncommutative QED (NCQED) is parity invariant. In addition, we show that under charge conjugation the theory on noncommutative R(4)(straight theta) is transformed to the theory on R(4)(-straight theta), so NCQED is a CP violating theory. The theory remains invariant under time reversal if, together with proper changes in fields, we also change straight theta by -straight theta. Hence altogether NCQED is CPT invariant. Moreover, we show that the CPT invariance holds for general noncommutative space-time.
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).
Hawking-Moss tunneling in non-commutative eternal inflation
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.
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.
Garcia, J. Antonio
2007-08-15
The aim of this Comment is to call to the attention of double special relativity (DSR) readers a basic fact. The introduction of noncommutative structures in problems like the one addressed by Ghosh [ Phys. Rev. D 74, 084019 (2006)] is not necessary for the understanding of DSR physics. It can be described just as the relativistic free particle problem in a different parametrization.
Energy-Complexity Relations by Structural Complexity Methods
NASA Astrophysics Data System (ADS)
Ricca, Renzo L.
2011-09-01
In this paper we shall review some of the most recent developments and results on work on energy-complexity relations and, if time will allow it, we shall provide an analytical proof of eq. (3) below, a fundamental relation between energy and complexity established by numerical experiments.
Laplace-Runge-Lenz vector in quantum mechanics in noncommutative space
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.
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.
Geomechanical numerical simulations of complex geologic structures
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.
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.
Transcription initiation complex structures elucidate DNA opening.
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.
Electronic structures of ytterbocene-imine complexes
Da Re, R. E.; Kuehl, C. J.; John, K. D.; Morris, D. E.
2004-01-01
The electronic structures of complexes of the form [(C{sub 5}Me{sub 5}){sub 2}Yb(L)]{sup +/0} (L = bipyridine, phenanthroline, terpyridine) have been probed using cyclic voltammetry and electronic spectroscopy. Remarkably, the voltammetric data reveal that the imine-based LUMO is stabilized and the redox-active metal f orbital is destabilized by ca. 1 V each upon formation of the ytterbocene-imine adduct, which is presumably responsible for the [(f){sup 13}({pi}*(L)){sup 1}] charge-transfer ground state characteristic of these complexes. The ca. 0.8 V separation between ligand-based oxidation and metal-based reduction waves for each ytterbocene adduct correlates with the energy of its optically promoted {pi}*(L)-f(Yb) charge transfer (LMCT) transition (ca. 5000 cm{sup -1}). The coupling between this LMCT excited state and the {sup 2}F{sub 7/2} ground and {sup 2}F{sub 5/2} excited states of Yb(III) leads to unusually large intensities ({var_epsilon} {approx} 1000) for the metal-localized f-f bands, which will be discussed in the context of an intensity borrowing mechanism that invokes exchange between the ligand-based {sup 2}S and metal-based {sup 2}F spin states.
Noncommutative cosmological model in the presence of a phantom fluid
NASA Astrophysics Data System (ADS)
Oliveira-Neto, G.; Vaz, A. R.
2017-03-01
We study noncommutative classical Friedmann-Robertson-Walker cosmological models. The constant curvature of the spatial sections can be positive (k=1), negative (k=-1) or zero (k=0). The matter is represented by a perfect fluid with negative pressure, phantom fluid, which satisfies the equation of state p =α ρ, with α < -1, where p is the pressure and ρ is the energy density. We use Schutz's formalism in order to write the perfect fluid Hamiltonian. The noncommutativity is introduced by nontrivial Poisson brackets between few variables of the models. In order to recover a description in terms of commutative variables, we introduce variables transformations that depend on a noncommutative parameter (γ). The main motivation for the introduction of the noncommutativity is trying to explain the present accelerated expansion of the universe. We obtain the dynamical equations for these models and solve them. The solutions have four constants: γ, a parameter associated with the fluid energy C, k, α and the initial conditions of the models variables. For each value of α, we obtain different equations of motion. Then, we compare the evolution of the universe in the noncommutative models with the corresponding commutative ones (γ → 0). The results show that γ is very useful for describing an accelerating universe. We also obtain estimates for the noncommutative parameter γ . Then, using those values of γ, in one of the noncommutative cosmological models with a specific value of α, we compute the amount of time those universes would take to reach the big rip.
Thermal transport in a noncommutative hydrodynamics
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.
Noncommutative approach to the cosmological constant problem
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.
Pair creation in noncommutative space-time
NASA Astrophysics Data System (ADS)
Hamil, B.; Chetouani, L.
2016-09-01
By taking two interactions, the Volkov plane wave and a constant electromagnetic field, the probability related to the process of pair creation from the vacuum is exactly and analytically determined via the Schwinger method in noncommutative space-time. For the plane wave, it is shown that the probability is simply null and for the electromagnetic wave it is found that the expression of the probability has a similar form to that obtained by Schwinger in a commutative space-time. For a certain critical value of H, the probability is simply equal to 1.
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.
Coherent structures in a supersonic complex nozzle
NASA Astrophysics Data System (ADS)
Magstadt, Andrew; Berry, Matthew; Glauser, Mark
2016-11-01
The jet flow from a complex supersonic nozzle is studied through experimental measurements. The nozzle's geometry is motivated by future engine designs for high-performance civilian and military aircraft. This rectangular jet has a single plane of symmetry, an additional shear layer (referred to as a wall jet), and an aft deck representative of airframe integration. The core flow operates at a Mach number of Mj , c = 1 . 6 , and the wall jet is choked (Mj , w = 1 . 0). This high Reynolds number jet flow is comprised of intense turbulence levels, an intricate shock structure, shear and boundary layers, and powerful corner vortices. In the present study, stereo PIV measurements are simultaneously sampled with high-speed pressure measurements, which are embedded in the aft deck, and far-field acoustics in the anechoic chamber at Syracuse University. Time-resolved schlieren measurements have indicated the existence of strong flow events at high frequencies, at a Strouhal number of St = 3 . 4 . These appear to result from von Kàrmàn vortex shedding within the nozzle and pervade the entire flow and acoustic domain. Proper orthogonal decomposition is applied on the current data to identify coherent structures in the jet and study the influence of this vortex street. AFOSR Turbulence and Transition Program (Grant No. FA9550-15-1-0435) with program managers Dr. I. Leyva and Dr. R. Ponnappan.
Characterizing the Community Structure of Complex Networks
Lancichinetti, Andrea; Kivelä, Mikko; Saramäki, Jari; Fortunato, Santo
2010-01-01
Background Community structure is one of the key properties of complex networks and plays a crucial role in their topology and function. While an impressive amount of work has been done on the issue of community detection, very little attention has been so far devoted to the investigation of communities in real networks. Methodology/Principal Findings We present a systematic empirical analysis of the statistical properties of communities in large information, communication, technological, biological, and social networks. We find that the mesoscopic organization of networks of the same category is remarkably similar. This is reflected in several characteristics of community structure, which can be used as “fingerprints” of specific network categories. While community size distributions are always broad, certain categories of networks consist mainly of tree-like communities, while others have denser modules. Average path lengths within communities initially grow logarithmically with community size, but the growth saturates or slows down for communities larger than a characteristic size. This behaviour is related to the presence of hubs within communities, whose roles differ across categories. Also the community embeddedness of nodes, measured in terms of the fraction of links within their communities, has a characteristic distribution for each category. Conclusions/Significance Our findings, verified by the use of two fundamentally different community detection methods, allow for a classification of real networks and pave the way to a realistic modelling of networks' evolution. PMID:20711338
Sequences from zero entropy noncommutative toral automorphisms and Sarnak Conjecture
NASA Astrophysics Data System (ADS)
Huang, Wen; Lian, Zhengxing; Shao, Song; Ye, Xiangdong
2017-07-01
In this paper we study C*-algebra version of Sarnak Conjecture for noncommutative toral automorphisms. Let AΘ be a noncommutative torus and αΘ be the noncommutative toral automorphism arising from a matrix S ∈ GL (d , Z). We show that if the Voiculescu-Brown entropy of αΘ is zero, then the sequence { ρ (αΘn u) } n ∈ Z is a sum of a nilsequence and a zero-density-sequence, where u ∈AΘ and ρ is any state on AΘ. Then by a result of Green and Tao [9], this sequence is linearly disjoint from the Möbius function.
Lie algebra type noncommutative phase spaces are Hopf algebroids
NASA Astrophysics Data System (ADS)
Meljanac, Stjepan; Škoda, Zoran; Stojić, Martina
2016-11-01
For a noncommutative configuration space whose coordinate algebra is the universal enveloping algebra of a finite-dimensional Lie algebra, it is known how to introduce an extension playing the role of the corresponding noncommutative phase space, namely by adding the commuting deformed derivatives in a consistent and nontrivial way; therefore, obtaining certain deformed Heisenberg algebra. This algebra has been studied in physical contexts, mainly in the case of the kappa-Minkowski space-time. Here, we equip the entire phase space algebra with a coproduct, so that it becomes an instance of a completed variant of a Hopf algebroid over a noncommutative base, where the base is the enveloping algebra.
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.
Constraining spacetime noncommutativity with primordial nucleosynthesis
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.
Nonclassicality versus entanglement in a noncommutative space
NASA Astrophysics Data System (ADS)
Dey, Sanjib; Fring, Andreas; Hussin, Véronique
2017-01-01
Nonclassicality is an interesting property of light having applications in many different contexts of quantum optics, quantum information and computation. Nonclassical states produce substantial amount of reduced noise in optical communications. Furthermore, they often behave as sources of entangled quantum states, which are the most elementary requirement for quantum teleportation. We study various nonclassical properties of coherent states and Schrödinger cat states in a setting of noncommutative space resulting from the generalized uncertainty relation, first, in a complete analytical fashion and, later, by computing their entanglement entropies, which in turn provide supporting arguments behind our analytical results. By using standard theoretical frameworks, they are shown to produce considerably improved squeezing and nonclassicality and, hence, significantly higher amount of entanglement in comparison to the usual quantum mechanical models. Both the nonclassicality and the entanglement can be enhanced further by increasing the noncommutativity of the underlying space. In addition, we find as a by-product some rare explicit minimum uncertainty quadrature and number squeezed states, i.e., ideal squeezed states.
Scalar field theory on noncommutative Snyder spacetime
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.
Noncommutative accelerated multidimensional universe dominated by quintessence
NASA Astrophysics Data System (ADS)
El-Nabulsi, Ahmad Rami
2010-04-01
Noncommutative Geometry recently attracted growing interest of cosmologists, mainly after the greatest success of unifying the forces of nature into a single gravitational spectral action in a purely algebraic way, rather than as being an entirely new formalism. In the present work, we discuss a multidimensional Friedmann-Robertson-Walker flat universe in which the perfect fluid has a Gaussian profile in time and depends on a fundamental minimal length sqrt{θ} like ρ= ρ(0)exp (- t 2/4 θ) for some positive constant ρ(0). This special form is motivated by a more recent noncommutative inflationary cosmological model, which was found to be able to drive the universe through a bounce without the need of any scalar field. Furthermore, we conjecture that the generalized equation of state has the special form p= ω a m ρ- ρ,( ω, m)∈ℝ where a( t) is the scale factor. It was found that the expansion of the multidimensional universe accelerates in time and is dominated for very large time by quintessence. Many additional consequences are revealed and discussed in some detail.
On the non-commutative CP{sup 1} model
Lechtenfeld, Olaf; Maceda, Marco
2010-07-12
We present some results on the moduli space for the charge two-soliton solution of the non-commutative CP{sup 1} model. The associated Kaehler potential and its relation to the commutative case are discussed.
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.
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.
Exact master equation for a noncommutative Brownian particle
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.
Strong Planck constraints on braneworld and non-commutative inflation
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.
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
Cosmology and the noncommutative approach to the standard model
Nelson, William; Sakellariadou, Mairi
2010-04-15
We study cosmological consequences of the noncommutative approach to the standard model of particle physics. Neglecting the nonminimal coupling of the Higgs field to the curvature, noncommutative corrections to Einstein's equations are present only for inhomogeneous and anisotropic space-times. Considering the nonminimal coupling however, corrections are obtained even for background cosmologies. Links with dilatonic gravity as well as chameleon cosmology are briefly discussed, and potential experimental consequences are mentioned.
Casimir force in noncommutative Randall-Sundrum models revisited
Teo, L. P.
2010-07-15
We propose another method to compute the Casimir force in noncommutative Randall-Sundrum braneworld model considered by K. Nouicer and Y. Sabri, Phys. Rev. D 80, 086013 (2009). recently. Our method can be used to compute the Casimir force to any order in the noncommutative parameter. Contrary to the claim made by K. Nouicer and Y. Sabri that repulsive Casimir force can appear in the first order approximation, we show that the Casimir force is always attractive at any order of approximation.
Energy-dependent harmonic oscillator in noncommutative space
NASA Astrophysics Data System (ADS)
Benchikha, A.; Merad, M.; Birkandan, T.
2017-06-01
In noncommutative quantum mechanics, the energy-dependent harmonic oscillator problem is studied by solving the Schrödinger equation in polar coordinates. The presence of the noncommutativity in space coordinates and the dependence on energy for the potential yield energy-dependent mass and potential. The correction of normalization condition is calculated and the parameter-dependences of the results are studied graphically.
Background independent noncommutative gravity from Fedosov quantization of endomorphism bundle
NASA Astrophysics Data System (ADS)
Dobrski, Michał
2017-04-01
A model of noncommutative gravity is constructed by means of Fedosov deformation quantization of an endomorphism bundle. The fields describing noncommutativity—symplectic form and symplectic connection—are dynamical, and the resulting theory is coordinate covariant and background independent. Its interpretation in terms of a Seiberg–Witten map is provided. Also, a new action for ordinary (commutative) general relativity is given, which in the present context appears as a commutative limit of noncommutative theory.
Spectral functionals, nonholonomic Dirac operators, and noncommutative Ricci flows
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.
Fractional Zero-Point Angular Momenta in Noncommutative Quantum Mechanics
NASA Astrophysics Data System (ADS)
Liu, Si-Jia; Zhang, Yu-Fei; Long, Zheng-Wen; Jing, Jian
2016-09-01
The charged particle confined by a harmonic potential in a noncommutative planar phase space interacting with a homogeneous dynamical magnetic field and Aharonov-Bohm potentials is studied. We find that the canonical orbital angular momenta of the reduced models, which are obtained by setting the mass and a dimensionless parameter to zero, take fractional values. These fractional angular momenta are not only determined by the flux inside the thin long solenoid but also affected by the noncommutativities of phase space.
Wedge-local quantum fields on a nonconstant noncommutative spacetime
Much, A.
2012-08-15
Within the framework of warped convolutions we deform the massless free scalar field. The deformation is performed by using the generators of the special conformal transformations. The investigation shows that the deformed field turns out to be wedge-local. Furthermore, it is shown that the spacetime induced by the deformation with the special conformal operators is nonconstant noncommutative. The noncommutativity is obtained by calculating the deformed commutator of the coordinates.
Non-commutativity and Local Indistinguishability of Quantum States
Ma, Teng; Zhao, Ming-Jing; Wang, Yao-Kun; Fei, Shao-Ming
2014-01-01
We study the local indistinguishability problem of quantum states. By introducing an easily calculated quantity, non-commutativity, we present an criterion which is both necessary and sufficient for the local indistinguishability of a complete set of pure orthogonal product states. A constructive distinguishing procedure to obtain the concrete local measurements and classical communications is given. The non-commutativity of ensembles can be also used to characterize the quantumness for classical-quantum or quantum-classical correlated states. PMID:25208830
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.
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
Structure, dynamics, assembly, and evolution of protein complexes.
Marsh, Joseph A; Teichmann, Sarah A
2015-01-01
The assembly of individual proteins into functional complexes is fundamental to nearly all biological processes. In recent decades, many thousands of homomeric and heteromeric protein complex structures have been determined, greatly improving our understanding of the fundamental principles that control symmetric and asymmetric quaternary structure organization. Furthermore, our conception of protein complexes has moved beyond static representations to include dynamic aspects of quaternary structure, including conformational changes upon binding, multistep ordered assembly pathways, and structural fluctuations occurring within fully assembled complexes. Finally, major advances have been made in our understanding of protein complex evolution, both in reconstructing evolutionary histories of specific complexes and in elucidating general mechanisms that explain how quaternary structure tends to evolve. The evolution of quaternary structure occurs via changes in self-assembly state or through the gain or loss of protein subunits, and these processes can be driven by both adaptive and nonadaptive influences.
Thermodynamics of a Charged Particle in a Noncommutative Plane in a Background Magnetic Field
NASA Astrophysics Data System (ADS)
Halder, Aslam; Gangopadhyay, Sunandan
2017-03-01
Landau system in noncommutative space has been considered. To take into account the issue of gauge invariance in noncommutative space, we incorporate the Seiberg-Witten map in our analysis. Generalised Bopp-shift transformation is then used to map the noncommutative system to its commutative equivalent system. In particular we have computed the partition function of the system and from this we obtained the susceptibility of the Landau system and found that the result gets modified by the spatial noncommutative parameter θ. We also investigate the de Hass-van Alphen effect in noncommutative space and observe that the oscillation of the magnetization and the susceptibility gets noncommutative corrections. Interestingly, the susceptibility in the noncommutative scenario is non-zero in the range of the magnetic field greater than the threshold value which is in contrast to its commutative counterpart. The results obtained are valid upto all orders in the noncommutative parameter θ.
Thermodynamics of a Charged Particle in a Noncommutative Plane in a Background Magnetic Field
NASA Astrophysics Data System (ADS)
Halder, Aslam; Gangopadhyay, Sunandan
2017-06-01
Landau system in noncommutative space has been considered. To take into account the issue of gauge invariance in noncommutative space, we incorporate the Seiberg-Witten map in our analysis. Generalised Bopp-shift transformation is then used to map the noncommutative system to its commutative equivalent system. In particular we have computed the partition function of the system and from this we obtained the susceptibility of the Landau system and found that the result gets modified by the spatial noncommutative parameter θ. We also investigate the de Hass-van Alphen effect in noncommutative space and observe that the oscillation of the magnetization and the susceptibility gets noncommutative corrections. Interestingly, the susceptibility in the noncommutative scenario is non-zero in the range of the magnetic field greater than the threshold value which is in contrast to its commutative counterpart. The results obtained are valid upto all orders in the noncommutative parameter θ.
A non-commuting stabilizer formalism
Ni, Xiaotong; Van den Nest, Maarten; Buerschaper, Oliver
2015-05-15
We propose a non-commutative extension of the Pauli stabilizer formalism. The aim is to describe a class of many-body quantum states which is richer than the standard Pauli stabilizer states. In our framework, stabilizer operators are tensor products of single-qubit operators drawn from the group 〈αI, X, S〉, where α = e{sup iπ/4} and S = diag(1, i). We provide techniques to efficiently compute various properties related to bipartite entanglement, expectation values of local observables, preparation by means of quantum circuits, parent Hamiltonians, etc. We also highlight significant differences compared to the Pauli stabilizer formalism. In particular, we give examples of states in our formalism which cannot arise in the Pauli stabilizer formalism, such as topological models that support non-Abelian anyons.
Cosmological power spectrum in a noncommutative spacetime
NASA Astrophysics Data System (ADS)
Kothari, Rahul; Rath, Pranati K.; Jain, Pankaj
2016-09-01
We propose a generalized star product that deviates from the standard one when the fields are considered at different spacetime points by introducing a form factor in the standard star product. We also introduce a recursive definition by which we calculate the explicit form of the generalized star product at any number of spacetime points. We show that our generalized star product is associative and cyclic at linear order. As a special case, we demonstrate that our recursive approach can be used to prove the associativity of standard star products for same or different spacetime points. The introduction of a form factor has no effect on the standard Lagrangian density in a noncommutative spacetime because it reduces to the standard star product when spacetime points become the same. We show that the generalized star product leads to physically consistent results and can fit the observed data on hemispherical anisotropy in the cosmic microwave background radiation.
Spacetime singularity resolution in Snyder noncommutative space
NASA Astrophysics Data System (ADS)
Gorji, M. A.; Nozari, K.; Vakili, B.
2014-04-01
Inspired by quantum gravity proposals, we construct a deformed phase space which supports the UV and IR cutoffs. We show that the Liouville theorem is satisfied in the deformed phase space which allows us to formulate the thermodynamics of the early universe in the semiclassical regime. Applying the proposed method to the Snyder noncommutative space, we find a temperature dependent equation of state which opens a new window for the natural realization of inflation as a phase transition from the quantum gravity regime to the standard radiation dominated era. Also, we obtain finite energy and entropy densities for the Universe when at least the weak energy condition is satisfied. We show that there is a minimum size for the Universe which is proportional to the Planck length and consequently the big bang singularity is removed.
Structurally simple complexes of CO2.
Murphy, Luke J; Robertson, Katherine N; Kemp, Richard A; Tuononen, Heikki M; Clyburne, Jason A C
2015-03-07
The ability to bind CO2 through the formation of low-energy, easily-broken, bonds could prove invaluable in a variety of chemical contexts. For example, weak bonds to CO2 would greatly decrease the cost of the energy-intensive sorbent-regeneration step common to most carbon capture technologies. Furthermore, exploration of this field could lead to the discovery of novel CO2 chemistry. Reduction of complexed carbon dioxide might generate chemical feedstocks for the preparation of value-added products, particularly transportation fuels or fuel precursors. Implementation on a large scale could help to drastically reduce CO2 concentrations in the atmosphere. However, literature examples of weakly bonded complexes of CO2 are relatively few and true coordination complexes to a 'naked' CO2 fragment are nearly unheard of. In this review article, a variety of complexes of CO2 featuring diverse binding modes and reactivity will be examined. Topics covered include: (A) inclusion complexes of CO2 in porous materials. (B) Zwitterionic carbamates produced from the reaction of CO2 with polyamines. (C) Carbamate salts produced from reaction of CO2 with two equivalents of an amine. (D) Insertion products of CO2 into acid-base adducts (e.g., metal complexes). (E) Lewis acid-base activated CO2, such as frustrated Lewis pair complexes. (F) Simple base-CO2 adducts, wherein the base-CO2 bond is the only interaction formed. Complexes in the last category are of particular interest, and include imidazol-2-carboxylates (N-heterocyclic carbene adducts of CO2) as well as a few other examples that lie outside NHC chemistry.
Classical limits of quantum mechanics on a non-commutative configuration space
Benatti, Fabio; Gouba, Laure
2013-06-15
We consider a model of non-commutative quantum mechanics given by two harmonic oscillators over a non-commutative two dimensional configuration space. We study possible ways of removing the non-commutativity based on the classical limit context known as anti-Wick quantization. We show that removal of non-commutativity from the configuration space and from the canonical operators is not commuting operation.
A structural snapshot of the rhodopsin–arrestin complex
Kang, Yanyong; Gao, Xiang; Zhou, X. Edward; He, Yuanzheng; Melcher, Karsten; Xu, H. Eric
2015-01-01
The crystal structure of the rhodopsin–arrestin complex provides important insights into how G protein–coupled receptor signaling is terminated by arrestin and a structural basis for understanding the mechanism of arrestin-biased signaling. PMID:26467309
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…
Atomic structure of the Y complex of the nuclear pore
Kelley, Kotaro; Knockenhauer, Kevin E.; Kabachinski, Greg; Schwartz, Thomas U.
2015-03-30
The nuclear pore complex (NPC) is the principal gateway for transport into and out of the nucleus. Selectivity is achieved through the hydrogel-like core of the NPC. The structural integrity of the NPC depends on ~15 architectural proteins, which are organized in distinct subcomplexes to form the >40-MDa ring-like structure. In this paper, we present the 4.1-Å crystal structure of a heterotetrameric core element ('hub') of the Y complex, the essential NPC building block, from Myceliophthora thermophila. Using the hub structure together with known Y-complex fragments, we built the entire ~0.5-MDa Y complex. Our data reveal that the conserved core of the Y complex has six rather than seven members. Finally, evolutionarily distant Y-complex assemblies share a conserved core that is very similar in shape and dimension, thus suggesting that there are closely related architectural codes for constructing the NPC in all eukaryotes.
Gelled Complex Fluids: Combining Unique Structures with Mechanical Stability.
Stubenrauch, Cosima; Gießelmann, Frank
2016-03-01
Gelled complex fluids are soft materials in which the microstructure of the complex fluid is combined with the mechanical stability of a gel. To obtain a gelled complex fluid one either adds a gelator to a complex fluid or replaces the solvent in a gel by a complex fluid. The most prominent example of a "natural" gelled complex fluid is the cell. There are various strategies by which one can form a gelled complex fluid; one such strategy is orthogonal self-assembly, that is, the independent but simultaneous formation of two coexisting self-assembled structures within one system. The aim of this Review is to describe the structure and potential applications of various man-made gelled complex fluids and to clarify whether or not the respective system is formed by orthogonal self-assembly.
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)
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.
Calculus structure on the Lie conformal algebra complex and the variational complex
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.
Noncommutative quantum mechanics in a time-dependent background
NASA Astrophysics Data System (ADS)
Dey, Sanjib; Fring, Andreas
2014-10-01
We investigate a quantum mechanical system on a noncommutative space for which the structure constant is explicitly time dependent. Any autonomous Hamiltonian on such a space acquires a time-dependent form in terms of the conventional canonical variables. We employ the Lewis-Riesenfeld method of invariants to construct explicit analytical solutions for the corresponding time-dependent Schrödinger equation. The eigenfunctions are expressed in terms of the solutions of variants of the nonlinear Ermakov-Pinney equation and discussed in detail for various types of background fields. We utilize the solutions to verify a generalized version of Heisenberg's uncertainty relations for which the lower bound becomes a time-dependent function of the background fields. We study the variance for various states, including standard Glauber coherent states with their squeezed versions and Gaussian Klauder coherent states resembling a quasiclassical behavior. No type of coherent state appears to be optimal in general with regard to achieving minimal uncertainties, as this feature turns out to be background field dependent.
Stability analysis of lower dimensional gravastars in noncommutative geometry
NASA Astrophysics Data System (ADS)
Banerjee, Ayan; Hansraj, Sudan
2016-11-01
The Bañados et al. (Phys. Rev. Lett 69:1849, 1992), black hole solution is revamped from the Einstein field equations in (2 + 1)-dimensional anti-de Sitter spacetime, in a context of noncommutative geometry (Phys. Rev. D 87:084014, 2013). In this article, we explore the exact gravastar solutions in three-dimensional anti-de Sitter space given in the same geometry. As a first step we derive BTZ solution assuming the source of energy density as point-like structures in favor of smeared objects, where the particle mass M, is diffused throughout a region of linear size √{α } and is described by a Gaussian function of finite width rather than a Dirac delta function. We matched our interior solution to an exterior BTZ spacetime at a junction interface situated outside the event horizon. Furthermore, a stability analysis is carried out for the specific case when χ < 0. 214 under radial perturbations about the static equilibrium solutions. To give theoretical support we are also trying to explore their physical properties and characteristics.
Instantons, quivers and noncommutative Donaldson-Thomas theory
NASA Astrophysics Data System (ADS)
Cirafici, Michele; Sinkovics, Annamaria; Szabo, Richard J.
2011-12-01
We construct noncommutative Donaldson-Thomas invariants associated with abelian orbifold singularities by analyzing the instanton contributions to a six-dimensional topological gauge theory. The noncommutative deformation of this gauge theory localizes on noncommutative instantons which can be classified in terms of three-dimensional Young diagrams with a colouring of boxes according to the orbifold group. We construct a moduli space for these gauge field configurations which allows us to compute its virtual numbers via the counting of representations of a quiver with relations. The quiver encodes the instanton dynamics of the noncommutative gauge theory, and is associated to the geometry of the singularity via the generalized McKay correspondence. The index of BPS states which compute the noncommutative Donaldson-Thomas invariants is realized via topological quantum mechanics based on the quiver data. We illustrate these constructions with several explicit examples, involving also higher rank Coulomb branch invariants and geometries with compact divisors, and connect our approach with other ones in the literature.
Relationships between structural complexity, coral traits, and reef fish assemblages
NASA Astrophysics Data System (ADS)
Darling, Emily S.; Graham, Nicholas A. J.; Januchowski-Hartley, Fraser A.; Nash, Kirsty L.; Pratchett, Morgan S.; Wilson, Shaun K.
2017-06-01
With the ongoing loss of coral cover and the associated flattening of reef architecture, understanding the links between coral habitat and reef fishes is of critical importance. Here, we investigate whether considering coral traits and functional diversity provides new insights into the relationship between structural complexity and reef fish communities, and whether coral traits and community composition can predict structural complexity. Across 157 sites in Seychelles, Maldives, the Chagos Archipelago, and Australia's Great Barrier Reef, we find that structural complexity and reef zone are the strongest and most consistent predictors of reef fish abundance, biomass, species richness, and trophic structure. However, coral traits, diversity, and life histories provided additional predictive power for models of reef fish assemblages, and were key drivers of structural complexity. Our findings highlight that reef complexity relies on living corals—with different traits and life histories—continuing to build carbonate skeletons, and that these nuanced relationships between coral assemblages and habitat complexity can affect the structure of reef fish assemblages. Seascape-level estimates of structural complexity are rapid and cost effective with important implications for the structure and function of fish assemblages, and should be incorporated into monitoring programs.
Higher order structure in a complex plasma
NASA Astrophysics Data System (ADS)
Donkó, Z.; Hartmann, P.; Magyar, P.; Kalman, G. J.; Golden, K. I.
2017-10-01
The direct experimental determination of the 3-point static structure function S(3)(k1, k2, k0) of a 2-dimensional dusty plasma liquid is presented. The measurements are complemented by molecular dynamics simulations of the system, using parameters (dust charge, plasma frequency, coupling and screening coefficients), which are derived from the experimentally obtained 2-point static structure function S(2), as well as the dynamic structure function and current-current fluctuation spectra. The experimental results of S(3) are in good agreement with those of the simulations, including the (low wavenumber) domain, where S(3) acquires negative values. The "Convolution Approximation" (giving S(3) in a factorized form of S(2) functions) clearly breaks down in this domain; however, it is found to be a useful aid for explaining the main features of the S(3)(k1, k2, k0) functions, for which (experimental and simulation) maps are presented at selected values of one of its arguments.
Structural Determination of Certain Novel ER Complexes
2005-09-01
and Parker, T. M. (1992). Hydrophobicity-induced pK shifts in elastin protein-based polymers . Biopolymers 32, 373-379. Webb, P., Nguyen, P., and...between the aligned H12 from different complex struc- Chemicals, Materials, and Plasmids tures (OHT-ER and GW-ER) were calculated using a python script...buffer consisting of 1.5%-2% ethylene were used. 100 nM of GW7604 were added to the cells 18-24 hr imine polymer , 100 mM trisodium citrate (pH 5.6-5.7
In situ structural analysis of the human nuclear pore complex.
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.
Does Structural Complexity Necessarily Imply Processing Difficulty?
ERIC Educational Resources Information Center
Gayraud, Frederique; Martinie, Bruno
2008-01-01
Our goal is to establish a link between the time needed to plan a sentence containing an embedded clause and the structure of this sentence. Contrary to a traditional monolithic conception of subordination, three types of embeddings were considered, depending on their degree of syntactic integration: subcategorized, modifier and pseudo-embedded…
Supramolecular Multiblock Copolymers Featuring Complex Secondary Structures.
Elacqua, Elizabeth; Manning, Kylie B; Lye, Diane S; Pomarico, Scott K; Morgia, Federica; Weck, Marcus
2017-09-06
This contribution introduces main-chain supramolecular ABC and ABB'A block copolymers sustained by orthogonal metal coordination and hydrogen bonding between telechelic polymers that feature distinct secondary structure motifs. Controlled polymerization techniques in combination with supramolecular assembly are used to engineer heterotelechelic π-sheets that undergo high-fidelity association with both helical and coil-forming synthetic polymers. Our design features multiple advances to achieve our targeted structures, in particular, those emulating sheet-like structural aspects using poly(p-phenylenevinylene)s (PPVs). To engineer heterotelechelic PPVs in a sheet-like design, we engineer an iterative one-pot cross metathesis-ring-opening metathesis polymerization (CM-ROMP) strategy that affords functionalized Grubbs-II initiators that subsequently polymerize a paracyclophanediene. Supramolecular assembly of two heterotelechelic PPVs is used to realize a parallel π-sheet, wherein further orthogonal assembly with helical motifs is possible. We also construct an antiparallel π-sheet, wherein terminal PPV blocks are adjacent to a flexible coil-like poly(norbornene) (PNB). The PNB is designed, through supramolecular chain collapse, to expose benzene and perfluorobenzene motifs that promote a hairpin turn via charge-transfer-aided folding. We demonstrate that targeted helix-(π-sheet)-helix and helix-(π-sheet)-coil assemblies occur without compromising intrinsic helicity, while both parallel and antiparallel β-sheet-like structures are realized. Our main-chain orthogonal assembly approach allows the engineering of multiblock copolymer scaffolds featuring diverse secondary structures via the directional assembly of telechelic building blocks. The targeted assemblies, a mix of sequence-defined helix-sheet-coil and helix-sheet-helix architectures, are Nature-inspired synthetic mimics that expose α/β and α+β protein classes via de novo design and cooperative assembly
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.
Structure, dynamics and function of nuclear pore complexes
D’Angelo, M. A.; Hetzer, M. W.
2009-01-01
Nuclear pore complexes are large aqueous channels that penetrate the nuclear envelope, connecting the nuclear interior with the cytoplasm. Until recently, these macromolecular complexes were viewed as static structures whose only function was to control the molecular trafficking between the two compartments. It has now become evident that this simplistic scenario is inaccurate and that nuclear pore complexes are highly dynamic multiprotein assemblies involved in diverse cellular processes ranging from the organization of the cytoskeleton to gene expression. In this review, we will discuss the most recent developments in the nuclear pore complex field, focusing in the assembly, disassembly, maintenance and function of this macromolecular structure. PMID:18786826
Community structure of complex networks based on continuous neural network
NASA Astrophysics Data System (ADS)
Dai, Ting-ting; Shan, Chang-ji; Dong, Yan-shou
2017-09-01
As a new subject, the research of complex networks has attracted the attention of researchers from different disciplines. Community structure is one of the key structures of complex networks, so it is a very important task to analyze the community structure of complex networks accurately. In this paper, we study the problem of extracting the community structure of complex networks, and propose a continuous neural network (CNN) algorithm. It is proved that for any given initial value, the continuous neural network algorithm converges to the eigenvector of the maximum eigenvalue of the network modularity matrix. Therefore, according to the stability of the evolution of the network symbol will be able to get two community structure.
Structure and function of complex brain networks.
Sporns, Olaf
2013-09-01
An increasing number of theoretical and empirical studies approach the function of the human brain from a network perspective. The analysis of brain networks is made feasible by the development of new imaging acquisition methods as well as new tools from graph theory and dynamical systems. This review surveys some of these methodological advances and summarizes recent findings on the architecture of structural and functional brain networks. Studies of the structural connectome reveal several modules or network communities that are interlinked by hub regions mediating communication processes between modules. Recent network analyses have shown that network hubs form a densely linked collective called a "rich club," centrally positioned for attracting and dispersing signal traffic. In parallel, recordings of resting and task-evoked neural activity have revealed distinct resting-state networks that contribute to functions in distinct cognitive domains. Network methods are increasingly applied in a clinical context, and their promise for elucidating neural substrates of brain and mental disorders is discussed.
Reinforcing Visual Grouping Cues to Communicate Complex Informational Structure.
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.
Analysis of Progressive Collapse of Complex Structures.
1982-12-01
discussion included catenary action of slabs, beam ac- tion of adequately tied ceiling-wall-floor systems actinq as wide flange sections, and the in...plane arching of walls over damage (4, 7, 9 through 14). A third cateqory was an effort to develop codes which mate the first two areas into economically...Building Criteria and Loading. New York: American Society of Civil Engineers, 1980. (9) Regan, P. E. " Catenary Action in Damaged Concrete Structures
Complexity and dynamics of topological and community structure in complex networks
NASA Astrophysics Data System (ADS)
Berec, Vesna
2017-01-01
Complexity is highly susceptible to variations in the network dynamics, reflected on its underlying architecture where topological organization of cohesive subsets into clusters, system's modular structure and resulting hierarchical patterns, are cross-linked with functional dynamics of the system. Here we study connection between hierarchical topological scales of the simplicial complexes and the organization of functional clusters - communities in complex networks. The analysis reveals the full dynamics of different combinatorial structures of q-th-dimensional simplicial complexes and their Laplacian spectra, presenting spectral properties of resulting symmetric and positive semidefinite matrices. The emergence of system's collective behavior from inhomogeneous statistical distribution is induced by hierarchically ordered topological structure, which is mapped to simplicial complex where local interactions between the nodes clustered into subcomplexes generate flow of information that characterizes complexity and dynamics of the full system.
Complexity and dynamics of topological and community structure in complex networks
NASA Astrophysics Data System (ADS)
Berec, Vesna
2017-07-01
Complexity is highly susceptible to variations in the network dynamics, reflected on its underlying architecture where topological organization of cohesive subsets into clusters, system's modular structure and resulting hierarchical patterns, are cross-linked with functional dynamics of the system. Here we study connection between hierarchical topological scales of the simplicial complexes and the organization of functional clusters - communities in complex networks. The analysis reveals the full dynamics of different combinatorial structures of q-th-dimensional simplicial complexes and their Laplacian spectra, presenting spectral properties of resulting symmetric and positive semidefinite matrices. The emergence of system's collective behavior from inhomogeneous statistical distribution is induced by hierarchically ordered topological structure, which is mapped to simplicial complex where local interactions between the nodes clustered into subcomplexes generate flow of information that characterizes complexity and dynamics of the full system.
A deformation quantization theory for noncommutative quantum mechanics
Costa Dias, Nuno; Prata, Joao Nuno; Gosson, Maurice de; Luef, Franz
2010-07-15
We show that the deformation quantization of noncommutative quantum mechanics previously considered by Dias and Prata ['Weyl-Wigner formulation of noncommutative quantum mechanics', J. Math. Phys. 49, 072101 (2008)] and Bastos, Dias, and Prata ['Wigner measures in non-commutative quantum mechanics', e-print arXiv:math-ph/0907.4438v1; Commun. Math. Phys. (to appear)] can be expressed as a Weyl calculus on a double phase space. We study the properties of the star-product thus defined and prove a spectral theorem for the star-genvalue equation using an extension of the methods recently initiated by de Gosson and Luef ['A new approach to the *-genvalue equation', Lett. Math. Phys. 85, 173-183 (2008)].
Noncommutative topology and the world’s simplest index theorem
van Erp, Erik
2010-01-01
In this article we outline an approach to index theory on the basis of methods of noncommutative topology. We start with an explicit index theorem for second-order differential operators on 3-manifolds that are Fredholm but not elliptic. This low-brow index formula is expressed in terms of winding numbers. We then proceed to show how it is derived as a special case of an index theorem for hypoelliptic operators on contact manifolds. Finally, we discuss the noncommutative topology that is employed in the proof of this theorem. The article is intended to illustrate that noncommutative topology can be a powerful tool for proving results in classical analysis and geometry. PMID:20418506
Black hole evaporation in a noncommutative charged Vaidya model
Sharif, M. Javed, W.
2012-06-15
We study the black hole evaporation and Hawking radiation for a noncommutative charged Vaidya black hole. For this purpose, we determine a spherically symmetric charged Vaidya model and then formulate a noncommutative Reissner-Nordstroem-like solution of this model, which leads to an exact (t - r)-dependent metric. The behavior of the temporal component of this metric and the corresponding Hawking temperature are investigated. The results are shown in the form of graphs. Further, we examine the tunneling process of charged massive particles through the quantum horizon. We find that the tunneling amplitude is modified due to noncommutativity. Also, it turns out that the black hole evaporates completely in the limits of large time and horizon radius. The effect of charge is to reduce the temperature from a maximum value to zero. We note that the final stage of black hole evaporation is a naked singularity.
Casimir force in noncommutative Randall-Sundrum models
Nouicer, Khireddine; Sabri, Youssef
2009-10-15
In this paper we study the effect of spacetime noncommutativity in the five-dimensional Randall-Sundrum braneworlds on the Casimir force acting on a pair of parallel plates. We show that the presence of a noncommutative scale length affects the nature of the Casimir force for small plate separation. Using accurate experimental bounds for the Casimir force in parallel plate geometry, we find an upper bound for the noncommutative cutoff of the order of 10{sup 3} TeV; we also find that the size of the interbrane distance in the first Randall-Sundrum model is approximately given by kR < or approx. 20.5 and kR < or approx. 18.4 for k=10{sup 19} GeV and k=10{sup 16} GeV, respectively.
k-Inflation in noncommutative space-time
NASA Astrophysics Data System (ADS)
Feng, Chao-Jun; Li, Xin-Zhou; Liu, Dao-Jun
2015-02-01
The power spectra of the scalar and tensor perturbations in the noncommutative k-inflation model are calculated in this paper. In this model, all the modes created when the stringy space-time uncertainty relation is satisfied, and they are generated inside the sound/Hubble horizon during inflation for the scalar/tensor perturbations. It turns out that a linear term describing the noncommutative space-time effect contributes to the power spectra of the scalar and tensor perturbations. Confronting the general noncommutative k-inflation model with latest results from Planck and BICEP2, and taking and as free parameters, we find that it is well consistent with observations. However, for the two specific models, i.e. the tachyon and DBI inflation models, it is found that the DBI model is not favored, while the tachyon model lies inside the contour, when the e-folding number is assumed to be around.
Toward structural elucidation of the γ-secretase complex
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
An Algebraic Approach to Inference in Complex Networked Structures
2015-07-09
AFRL-AFOSR-VA-TR-2015-0265 An Algebraic Approach to Inference in Complex Networked Structures Jose Moura CARNEGIE MELLON UNIVERSITY Final Report 07...31-03-2015 4. TITLE AND SUBTITLE An Algebraic Approach to Inference in Complex Networked Structures 5a. CONTRACT NUMBER 5b. GRANT NUMBER FA9550-12-1...Final Report: An Algebraic Approach to Inference in Complex Networked Structures FA9550-12-1-0087 4/1/2012-3/31/2015 José M F Moura Carnegie Mellon
A Structurally Characterized Organometallic Plutonium(IV) Complex.
Apostolidis, Christos; Walter, Olaf; Vogt, Jochen; Liebing, Phil; Maron, Laurent; Edelmann, Frank T
2017-03-30
The blood-red plutonocene complex Pu(1,3-COT'')(1,4-COT'') (4; COT''=η(8) -bis(trimethylsilyl)cyclooctatetraenyl) has been synthesized by oxidation of the anionic sandwich complex Li[Pu(1,4-COT'')2 ] (3) with anhydrous cobalt(II) chloride. The first crystal structure determination of an organoplutonium(IV) complex revealed an asymmetric sandwich structure for 4 where one COT'' ring is 1,3-substituted while the other retains the original 1,4-substitution pattern. The electronic structure of 4 has been elucidated by a computational study, revealing a probable cause for the unexpected silyl group migration.
Toward structural elucidation of the gamma-secretase complex
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.
Quantum dynamics of simultaneously measured non-commuting observables
NASA Astrophysics Data System (ADS)
Hacohen-Gourgy, Shay; Martin, Leigh S.; Flurin, Emmanuel; Ramasesh, Vinay V.; Whaley, K. Birgitta; Siddiqi, Irfan
2016-10-01
In quantum mechanics, measurements cause wavefunction collapse that yields precise outcomes, whereas for non-commuting observables such as position and momentum Heisenberg’s uncertainty principle limits the intrinsic precision of a state. Although theoretical work has demonstrated that it should be possible to perform simultaneous non-commuting measurements and has revealed the limits on measurement outcomes, only recently has the dynamics of the quantum state been discussed. To realize this unexplored regime, we simultaneously apply two continuous quantum non-demolition probes of non-commuting observables to a superconducting qubit. We implement multiple readout channels by coupling the qubit to multiple modes of a cavity. To control the measurement observables, we implement a ‘single quadrature’ measurement by driving the qubit and applying cavity sidebands with a relative phase that sets the observable. Here, we use this approach to show that the uncertainty principle governs the dynamics of the wavefunction by enforcing a lower bound on the measurement-induced disturbance. Consequently, as we transition from measuring identical to measuring non-commuting observables, the dynamics make a smooth transition from standard wavefunction collapse to localized persistent diffusion and then to isotropic persistent diffusion. Although the evolution of the state differs markedly from that of a conventional measurement, information about both non-commuting observables is extracted by keeping track of the time ordering of the measurement record, enabling quantum state tomography without alternating measurements. Our work creates novel capabilities for quantum control, including rapid state purification, adaptive measurement, measurement-based state steering and continuous quantum error correction. As physical systems often interact continuously with their environment via non-commuting degrees of freedom, our work offers a way to study how notions of contemporary
Effective action for noncommutative Bianchi I model
NASA Astrophysics Data System (ADS)
Rosenbaum, M.; Vergara, J. D.; Minzoni, A. A.
2013-06-01
Quantum Mechanics, as a mini-superspace of Field Theory has been assumed to provide physically relevant information on quantum processes in Field Theory. In the case of Quantum Gravity this would imply using Cosmological models to investigate quantum processes at distances of the order of the Planck scale. However because of the Stone-von Neuman Theorem, it is well known that quantization of Cosmological models by the Wheeler-DeWitt procedure in the context of a Heisenberg-Weyl group with piecewise continuous parameters leads irremediably to a volume singularity. In order to avoid this information catastrophe it has been suggested recently the need to introduce in an effective theory of the quantization some form of reticulation in 3-space. On the other hand, since in the geometry of the General Relativistic formulation of Gravitation space can not be visualized as some underlying static manifold in which the physical system evolves, it would be interesting to investigate whether the effective reticulation which removes the singularity in such simple cosmologies as the Bianchi models has a dynamical origin manifested by a noncommutativity of the generators of the Heisenberg-Weyl algebra, as would be expected from an operational point of view at the Planck length scale.
Effective action for noncommutative Bianchi I model
Rosenbaum, M.; Vergara, J. D.; Minzoni, A. A.
2013-06-12
Quantum Mechanics, as a mini-superspace of Field Theory has been assumed to provide physically relevant information on quantum processes in Field Theory. In the case of Quantum Gravity this would imply using Cosmological models to investigate quantum processes at distances of the order of the Planck scale. However because of the Stone-von Neuman Theorem, it is well known that quantization of Cosmological models by the Wheeler-DeWitt procedure in the context of a Heisenberg-Weyl group with piecewise continuous parameters leads irremediably to a volume singularity. In order to avoid this information catastrophe it has been suggested recently the need to introduce in an effective theory of the quantization some form of reticulation in 3-space. On the other hand, since in the geometry of the General Relativistic formulation of Gravitation space can not be visualized as some underlying static manifold in which the physical system evolves, it would be interesting to investigate whether the effective reticulation which removes the singularity in such simple cosmologies as the Bianchi models has a dynamical origin manifested by a noncommutativity of the generators of the Heisenberg-Weyl algebra, as would be expected from an operational point of view at the Planck length scale.
In situ structural analysis of the human nuclear pore complex
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
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
Structure and function of complex brain networks
Sporns, Olaf
2013-01-01
An increasing number of theoretical and empirical studies approach the function of the human brain from a network perspective. The analysis of brain networks is made feasible by the development of new imaging acquisition methods as well as new tools from graph theory and dynamical systems. This review surveys some of these methodological advances and summarizes recent findings on the architecture of structural and functional brain networks. Studies of the structural connectome reveal several modules or network communities that are interlinked by hub regions mediating communication processes between modules. Recent network analyses have shown that network hubs form a densely linked collective called a “rich club,” centrally positioned for attracting and dispersing signal traffic. In parallel, recordings of resting and task-evoked neural activity have revealed distinct resting-state networks that contribute to functions in distinct cognitive domains. Network methods are increasingly applied in a clinical context, and their promise for elucidating neural substrates of brain and mental disorders is discussed. PMID:24174898
MATERIALS WITH COMPLEX ELECTRONIC/ATOMIC STRUCTURES
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.
Microbial mediation of complex subterranean mineral structures.
Tisato, Nicola; Torriani, Stefano F F; Monteux, Sylvain; Sauro, Francesco; De Waele, Jo; Tavagna, Maria Luisa; D'Angeli, Ilenia M; Chailloux, Daniel; Renda, Michel; Eglinton, Timothy I; Bontognali, Tomaso R R
2015-10-29
Helictites--an enigmatic type of mineral structure occurring in some caves--differ from classical speleothems as they develop with orientations that defy gravity. While theories for helictite formation have been forwarded, their genesis remains equivocal. Here, we show that a remarkable suite of helictites occurring in Asperge Cave (France) are formed by biologically-mediated processes, rather than abiotic processes as had hitherto been proposed. Morphological and petro-physical properties are inconsistent with mineral precipitation under purely physico-chemical control. Instead, microanalysis and molecular-biological investigation reveals the presence of a prokaryotic biofilm intimately associated with the mineral structures. We propose that microbially-influenced mineralization proceeds within a gliding biofilm which serves as a nucleation site for CaCO3, and where chemotaxis influences the trajectory of mineral growth, determining the macroscopic morphology of the speleothems. The influence of biofilms may explain the occurrence of similar speleothems in other caves worldwide, and sheds light on novel biomineralization processes.
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.
When complex neuronal structures may not matter
Otopalik, Adriane G; Sutton, Alexander C; Banghart, Matthew; Marder, Eve
2017-01-01
Much work has explored animal-to-animal variability and compensation in ion channel expression. Yet, little is known regarding the physiological consequences of morphological variability. We quantify animal-to-animal variability in cable lengths (CV = 0.4) and branching patterns in the Gastric Mill (GM) neuron, an identified neuron type with highly-conserved physiological properties in the crustacean stomatogastric ganglion (STG) of Cancer borealis. We examined passive GM electrotonic structure by measuring the amplitudes and apparent reversal potentials (Erevs) of inhibitory responses evoked with focal glutamate photo-uncaging in the presence of TTX. Apparent Erevs were relatively invariant across sites (mean CV ± SD = 0.04 ± 0.01; 7–20 sites in each of 10 neurons), which ranged between 100–800 µm from the somatic recording site. Thus, GM neurons are remarkably electrotonically compact (estimated λ > 1.5 mm). Electrotonically compact structures, in consort with graded transmission, provide an elegant solution to observed morphological variability in the STG. DOI: http://dx.doi.org/10.7554/eLife.23508.001 PMID:28165322
Microbial mediation of complex subterranean mineral structures
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
Infinite volume of noncommutative black hole wrapped by finite surface
NASA Astrophysics Data System (ADS)
Zhang, Baocheng; You, Li
2017-02-01
The volume of a black hole under noncommutative spacetime background is found to be infinite, in contradiction with the surface area of a black hole, or its Bekenstein-Hawking (BH) entropy, which is well-known to be finite. Our result rules out the possibility of interpreting the entropy of a black hole by counting the number of modes wrapped inside its surface if the final evaporation stage can be properly treated. It implies the statistical interpretation for the BH entropy can be independent of the volume, provided spacetime is noncommutative. The effect of radiation back reaction is found to be small and doesn't influence the above conclusion.
Relativistic Hydrogen-Like Atom on a Noncommutative Phase Space
NASA Astrophysics Data System (ADS)
Masum, Huseyin; Dulat, Sayipjamal; Tohti, Mutallip
2017-09-01
The energy levels of hydrogen-like atom on a noncommutative phase space were studied in the framework of relativistic quantum mechanics. The leading order corrections to energy levels 2 S 1/2, 2 P 1/2 and 2 P 3/2 were obtained by using the 𝜃 and the \\bar θ modified Dirac Hamiltonian of hydrogen-like atom on a noncommutative phase space. The degeneracy of the energy levels 2 P 1/2 and 2 P 3/2 were removed completely by 𝜃-correction. And the \\bar θ -correction shifts these energy levels.
Curvature and geometric modules of noncommutative spheres and tori
Arnlind, Joakim
2014-04-15
When considered as submanifolds of Euclidean space, the Riemannian geometry of the round sphere and the Clifford torus may be formulated in terms of Poisson algebraic expressions involving the embedding coordinates, and a central object is the projection operator, projecting tangent vectors in the ambient space onto the tangent space of the submanifold. In this note, we point out that there exist noncommutative analogues of these projection operators, which implies a very natural definition of noncommutative tangent spaces as particular projective modules. These modules carry an induced connection from Euclidean space, and we compute its scalar curvature.
Noncommutative geometry modified non-Gaussianities of cosmological perturbation
Fang Kejie; Xue Wei; Chen Bin
2008-03-15
We investigate the noncommutative effect on the non-Gaussianities of primordial cosmological perturbation. In the lowest order of string length and slow-roll parameter, we find that in the models with small speed of sound the noncommutative modifications could be observable if assuming a relatively low string scale. In particular, the dominant modification of the non-Gaussianity estimator f{sub NL} could reach O(1) in Dirac-Born-Infeld (DBI) inflation and K-inflation. The corrections are sensitive to the speed of sound and the choice of string length scale. Moreover the shapes of the corrected non-Gaussianities are distinct from that of ordinary ones.
Charged thin-shell gravastars in noncommutative geometry
NASA Astrophysics Data System (ADS)
Övgün, Ali; Banerjee, Ayan; Jusufi, Kimet
2017-08-01
In this paper we construct a charged thin-shell gravastar model within the context of noncommutative geometry. To do so, we choose the interior of the nonsingular de Sitter spacetime with an exterior charged noncommutative solution by cut-and-paste technique and apply the generalized junction conditions. We then investigate the stability of a charged thin-shell gravastar under linear perturbations around the static equilibrium solutions as well as the thermodynamical stability of the charged gravastar. We find the stability regions, by choosing appropriate parameter values, located sufficiently close to the event horizon.
Noncommutative scalar field minimally coupled to nonsymmetric gravity
Kouadik, S.; Sefai, D.
2012-06-27
We construct a non-commutative non symmetric gravity minimally coupled model (the star product only couples matter). We introduce the action for the system considered namely a non-commutative scalar field propagating in a nontrivial gravitational background. We expand the action in powers of the anti-symmetric field and the graviton to second order adopting the assumption that the scalar is weekly coupled to the graviton. We compute the one loop radiative corrections to the self-energy of a scalar particle.
NASA Astrophysics Data System (ADS)
Chowdhury, S. Hasibul Hassan
2017-06-01
We construct a 2-parameter family of unitarily equivalent irreducible representations of the triply extended group GNC of translations of R4 associated with a family of its 4-dimensional coadjoint orbits and show how a continuous 2-parameter family of gauge potentials emerges from these unitarily equivalent representations. We show that the Landau and the symmetric gauges of noncommutative quantum mechanics, widely used in the literature, in fact, belong to this 2-parameter family of gauges. We also provide an explicit construction of noncommutative 4-tori and compute the associated star products using the unitary dual of the group GNC that was studied at length in an earlier paper [S. H. H. Chowdhury and S. T. Ali, J. Phys. A: Math. Theor. 47, 085301 (2014)]. Finally, we construct projective modules over such noncommutative 4-tori and compute constant curvature connections on them using Rieffel's method.
Remarkable luminescence properties of lanthanide complexes with asymmetric dodecahedron structures.
Miyata, Kohei; Nakagawa, Tetsuya; Kawakami, Ryuhei; Kita, Yuki; Sugimoto, Katsufumi; Nakashima, Takuya; Harada, Takashi; Kawai, Tsuyoshi; Hasegawa, Yasuchika
2011-01-10
The distorted coordination structures and luminescence properties of novel lanthanide complexes with oxo-linked bidentate phosphane oxide ligands--4,5-bis(diphenylphosphoryl)-9,9-dimethylxanthene (xantpo), 4,5-bis(di-tert-butylphosphoryl)-9,9-dimethylxanthene (tBu-xantpo), and bis[(2-diphenylphosphoryl)phenyl] ether (dpepo)--and low-vibrational frequency hexafluoroacetylacetonato (hfa) ligands are reported. The lanthanide complexes exhibit characteristic square antiprism and trigonal dodecahedron structures with eight-coordinated oxygen atoms. The luminescence properties of these complexes are characterized by their emission quantum yields, emission lifetimes, and their radiative and nonradiative rate constants. Lanthanide complexes with dodecahedron structures offer markedly high emission quantum yields (Eu: 55-72 %, Sm: 2.4-5.0 % in [D(6)]acetone) due to enhancement of the electric dipole transition and suppression of vibrational relaxation. These remarkable luminescence properties are elucidated in terms of their distorted coordination structures.
Electroluminescence of Zinc Complexes in Various OLED Structures
NASA Astrophysics Data System (ADS)
Odod, A. V.; Nikonova, E. N.; Nikonov, S. Yu.; Kopylova, T. N.; Kaplunov, M. G.; Krasnikova, S. S.; Nikitenko, S. L.; Yakushchenko, I. K.
2017-05-01
Results of spectral-luminescent and electroluminescent studies of organic semiconductor zinc complexes in light-emitting diode devices are presented. A displacement of the electroluminescence band maximum toward longer wavelengths with structure complication is shown. Devices based on zinc metal organic complexes have low threshold voltage (from 2.5 V) and brightness above 100 cd/m2.
Nanoparticle Controlled Soft Complex Structures with Topological Defects
2013-10-01
topological defects stabilized by adaptive targeting nanoparticles. In our experiments we used as NPs magic quantum dots CdSe [19] exhibiting size...AFRL-AFOSR-UK-TR-2014-0002 Nanoparticle controlled soft complex structures with topological defects Samo Kralj...From – To) 15 July 2012 – 14 October 2013 4. TITLE AND SUBTITLE Nanoparticle controlled soft complex structures with topological defects 5a
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.
The Structure Inventory of the Nuclear Pore Complex.
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.
Calculus structure on the Lie conformal algebra complex and the variational complex
NASA Astrophysics Data System (ADS)
De Sole, Alberto; Hekmati, Pedram; Kac, Victor G.
2011-05-01
We construct a calculus structure on the Lie conformal algebra cochain complex. By restricting to degree one chains, we recover the structure of a {mathfrak g}-complex introduced in [A. De Sole and V. G. Kac, Commun. Math. Phys. 292, 667 (2009), 10.1007/s00220-009-0886-1]. A special case of this construction is the variational calculus, for which we provide explicit formulas.
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.
Quantum groups, non-commutative differential geometry and applications
Schupp, Peter
1993-12-09
The topic of this thesis is the development of a versatile and geometrically motivated differential calculus on non-commutative or quantum spaces, providing powerful but easy-to-use mathematical tools for applications in physics and related sciences. A generalization of unitary time evolution is proposed and studied for a simple 2-level system, leading to non-conservation of microscopic entropy, a phenomenon new to quantum mechanics. A Cartan calculus that combines functions, forms, Lie derivatives and inner derivations along general vector fields into one big algebra is constructed for quantum groups and then extended to quantum planes. The construction of a tangent bundle on a quantum group manifold and an BRST type approach to quantum group gauge theory are given as further examples of applications. The material is organized in two parts: Part I studies vector fields on quantum groups, emphasizing Hopf algebraic structures, but also introducing a ``quantum geometric`` construction. Using a generalized semi-direct product construction we combine the dual Hopf algebras A of functions and U of left-invariant vector fields into one fully bicovariant algebra of differential operators. The pure braid group is introduced as the commutant of {Delta}(U). It provides invariant maps A {yields} U and thereby bicovariant vector fields, casimirs and metrics. This construction allows the translation of undeformed matrix expressions into their less obvious quantum algebraic counter parts. We study this in detail for quasitriangular Hopf algebras, giving the determinant and orthogonality relation for the ``reflection`` matrix. Part II considers the additional structures of differential forms and finitely generated quantum Lie algebras -- it is devoted to the construction of the Cartan calculus, based on an undeformed Cartan identity.
Modeling of Protein Binary Complexes Using Structural Mass Spectrometry Data
Amisha Kamal,J.; Chance, M.
2008-01-01
In this article, we describe a general approach to modeling the structure of binary protein complexes using structural mass spectrometry data combined with molecular docking. In the first step, hydroxyl radical mediated oxidative protein footprinting is used to identify residues that experience conformational reorganization due to binding or participate in the binding interface. In the second step, a three-dimensional atomic structure of the complex is derived by computational modeling. Homology modeling approaches are used to define the structures of the individual proteins if footprinting detects significant conformational reorganization as a function of complex formation. A three-dimensional model of the complex is constructed from these binary partners using the ClusPro program, which is composed of docking, energy filtering, and clustering steps. Footprinting data are used to incorporate constraints--positive and/or negative--in the docking step and are also used to decide the type of energy filter--electrostatics or desolvation--in the successive energy-filtering step. By using this approach, we examine the structure of a number of binary complexes of monomeric actin and compare the results to crystallographic data. Based on docking alone, a number of competing models with widely varying structures are observed, one of which is likely to agree with crystallographic data. When the docking steps are guided by footprinting data, accurate models emerge as top scoring. We demonstrate this method with the actin/gelsolin segment-1 complex. We also provide a structural model for the actin/cofilin complex using this approach which does not have a crystal or NMR structure.
Preparation and Structural Properties of InIII–H Complexes
Sickerman, Nathaniel S.; Henry, Renée M.; Ziller, Joseph W.
2013-01-01
The use of the tripodal ligands tris[(N'-tert-butylureaylato)-N-ethyl]aminato ([H3buea]3−) and the sulfonamide-based N,N',N"-[2,2',2"-nitrilotris(ethane-2,1-diyl)]tris(2,4,6-trimethylbenzene-sulfonamidato) ([MST]3−) has led to the synthesis of two structurally distinct In(III)–OH complexes. The first example of a five-coordinate indium(III) complex with a terminal hydroxide ligand, K[InIIIH3buea(OH)], was prepared by addition of In(OAc)3 and water to a deprotonated solution of H6buea. X-ray diffraction analysis, as well as FTIR and 1H NMR spectroscopic methods, provided evidence for the formation of a monomeric In(III)–OH complex. The complex contains an intramolecular hydrogen bonding (H-bonding) network involving the In(III)–OH unit and [H3buea]3− ligand, which aided in isolation of the complex. Isotope labeling studies verified the source of the hydroxo ligand as water. Treatment of the [InIIIMST] complex with a mixture of 15-crown-5 ether and NaOH led to isolation of the complex [15-crown-5⊃NaI-(μ-OH)-InIIIMST], whose solid-state structure was confirmed using X-ray diffraction methods. Nuclear magnetic resonance studies on this complex suggest it retains its heterobimetallic structure in solution. PMID:25309019
On the complexity and the information content of cosmic structures
NASA Astrophysics Data System (ADS)
Vazza, F.
2017-03-01
The emergence of cosmic structure is commonly considered one of the most complex phenomena in nature. However, this complexity has never been defined nor measured in a quantitative and objective way. In this work, we propose a method to measure the information content of cosmic structure and to quantify the complexity that emerges from it, based on Information Theory. The emergence of complex evolutionary patterns is studied with a statistical symbolic analysis of the datastream produced by state-of-the-art cosmological simulations of forming galaxy clusters. This powerful approach allows us to measure how many bits of information is necessary to predict the evolution of energy fields in a statistical way, and it offers a simple way to quantify when, where and how the cosmic gas behaves in complex ways. The most complex behaviours are found in the peripheral regions of galaxy clusters, where supersonic flows drive shocks and large energy fluctuations over a few tens of million years. Describing the evolution of magnetic energy requires at least twice as large amount of bits as required for the other energy fields. When radiative cooling and feedback from galaxy formation are considered, the cosmic gas is overall found to double its degree of complexity. In the future, Cosmic Information Theory can significantly increase our understanding of the emergence of cosmic structure as it represents an innovative framework to design and analyse complex simulations of the Universe in a simple, yet powerful way.
Structure and Dynamics of Antigenic Peptides in Complex with TAP
Lehnert, Elisa; Tampé, Robert
2017-01-01
The transporter associated with antigen processing (TAP) selectively translocates antigenic peptides into the endoplasmic reticulum. Loading onto major histocompatibility complex class I molecules and proofreading of these bound epitopes are orchestrated within the macromolecular peptide-loading complex, which assembles on TAP. This heterodimeric ABC-binding cassette (ABC) transport complex is therefore a major component in the adaptive immune response against virally or malignantly transformed cells. Its pivotal role predestines TAP as a target for infectious diseases and malignant disorders. The development of therapies or drugs therefore requires a detailed comprehension of structure and function of this ABC transporter, but our knowledge about various aspects is still insufficient. This review highlights recent achievements on the structure and dynamics of antigenic peptides in complex with TAP. Understanding the binding mode of antigenic peptides in the TAP complex will crucially impact rational design of inhibitors, drug development, or vaccination strategies. PMID:28194151
Structural and evolutionary versatility in protein complexes with uneven stoichiometry.
Marsh, Joseph A; Rees, Holly A; Ahnert, Sebastian E; Teichmann, Sarah A
2015-03-16
Proteins assemble into complexes with diverse quaternary structures. Although most heteromeric complexes of known structure have even stoichiometry, a significant minority have uneven stoichiometry--that is, differing numbers of each subunit type. To adopt this uneven stoichiometry, sequence-identical subunits must be asymmetric with respect to each other, forming different interactions within the complex. Here we first investigate the occurrence of uneven stoichiometry, demonstrating that it is common in vitro and is likely to be common in vivo. Next, we elucidate the structural determinants of uneven stoichiometry, identifying six different mechanisms by which it can be achieved. Finally, we study the frequency of uneven stoichiometry across evolution, observing a significant enrichment in bacteria compared with eukaryotes. We show that this arises due to a general increased tendency for bacterial proteins to self-assemble and form homomeric interactions, even within the context of a heteromeric complex.
Probing the noncommutative effects of phase space in the time-dependent Aharonov-Bohm effect
NASA Astrophysics Data System (ADS)
Ma, Kai; Wang, Jian-Hua
2017-08-01
We study the noncommutative corrections on the time-dependent Aharonov-Bohm effect when both the coordinate-coordinate and momentum-momentum noncommutativities are considered. On the noncommutative phase space, while the ordinary gauge symmetry can be kept by the Seiberg-Witten map, but the Lorentz symmetry is broken. Therefore nontrivial noncommutative corrections are expected. We find there are three kinds of noncommutative corrections in general: (1) ξ-dependent correction which comes from the noncommutativity among momentum operators; (2) momentum-dependent correction which is rooted in the nonlocal interactions in the noncommutative extended model; (3) momentum-independent correction which emerges become of the gauge invariant condition on the nonlocal interactions in the noncommutative model. We proposed two dimensionless quantities, which are based on the distributions of the measured phase shift with respect to the external magnetic field and to the cross section enclosed by the particle trajectory, to extract the noncommutative parameters. We find that stronger (weaker) magnetic field strength can give better bounds on the coordinate-coordinate (momentum-momentum) noncommutative parameter, and large parameter space region can be explored by the time-dependent AB effect.
Structural evaluation of crystalline ternary γ-cyclodextrin complex.
Higashi, Kenjirou; Ideura, Saori; Waraya, Haruka; Moribe, Kunikazu; Yamamoto, Keiji
2011-01-01
The structure of a crystalline γ-cyclodextrin (γ-CD) ternary complex containing salicylic acid (SA) and flurbiprofen (FBP) prepared by sealed heating was investigated. FBP/γ-CD inclusion complex was prepared by coprecipitation; its molar ratio was determined as 1/1. Powder X-ray diffraction measurements showed that the molecular packing of γ-CD changed from hexagonal to monoclinic columnar form by sealed heating of SA with dried FBP/γ-CD inclusion complex, indicating ternary complex formation. The stoichiometry of SA/FBP/γ-CD was estimated as 2/1/1. Solid-state transformation of γ-CD molecular packing upon water vapor adsorption and desorption was irreversible for this ternary complex, in contrast to the reversible transition for the FBP/γ-CD inclusion complex. The ternary complex contained one FBP molecule in the cavity of γ-CD and two SA molecules in the intermolecular space between neighboring γ-CD column stacks. Infrared and (13) C solid-state NMR spectroscopies revealed that the molecular states of SA and FBP changed upon ternary complex formation. In the complex, dimer FBP molecules were sandwiched between two γ-CD molecules whereas each monomer SA molecule was present in the intermolecular space of γ-CD. Ternary complex formation was also observed for other drug-guest systems using naproxen and ketoprofen. Thus, the complex can be used to formulate variety of drugs.
Solution structure of the luzopeptin-DNA complex
Zhang, Xiaolu; Patel, D.J. )
1991-04-23
The luzopeptin-d(C-A-T-G) complex (1 drug/duplex) has been generated in aqueous solution and its structure characterized by a combined application of two-dimensional NMR experiments and molecular dynamics calculations. Once equivalent of luzopeptin binds to the self-complementary tetranucleotide duplex with the 2-fold symmetry of the antitumor agent and the DNA oligomer retained on complex formation. The authors have assigned the exchangeable and nonexchangeable proton resonances of luzopeptin and the d(C-A-T-G) duplex in the complex and identified the intermolecular proton-proton NOEs that define the alignment of the antitumor agent at its binding site in duplex DNA. The analysis was greatly aided by a large number of intermolecular NOEs involving exchangeable protons on both the luzopeptin and the DNA in the complex. The formation of cis peptide bonds for luzopeptin in the complex results in an increased separation of the long sides of the rectangular cyclic depsipeptide backbone and reorients in the glycine amide proton so that it can form an intermolecular hydrogen bond with the 2-carbonyl of T3 in the complex. This observation explains, in part, the requirement for Watson-Crick A{center dot}T pairs to be sandwiched between the quinolines at the bisintercalation site in the luzopeptin-DNA complex. The NMR studies on the luzopeptin-d(C-A-T-G) complex unequivocally establish that antitumor agents can undergo conformational transitions on complex formation with DNA, and it is the conformation of the drug in the complex that should serve as the starting point for drug design studies. The above structural details on the solution structure of the luzopeptin-DNA complex also explain the sequence selectivity of luzopeptin for bisintercalation at d(C-A){center dot}d(T-G) steps in the d(C-A-T-G) duplex in solution.
On supermatrix models, Poisson geometry, and noncommutative supersymmetric gauge theories
Klimčík, Ctirad
2015-12-15
We construct a new supermatrix model which represents a manifestly supersymmetric noncommutative regularisation of the UOSp(2|1) supersymmetric Schwinger model on the supersphere. Our construction is much simpler than those already existing in the literature and it was found by using Poisson geometry in a substantial way.
A perspective on non-commutative quantum gravity
NASA Astrophysics Data System (ADS)
Martins, Rachel A. D.
2015-06-01
In this paper, we present some of the concepts underlying a program of non-commutative quantum gravity and recall some of the results. This program includes a novel approach to spectral triple categorification and also a precise connection between Fell bundles and Connes' non-commutative geometry. Motivated by topics in quantization of the non-commutative standard model and introduction of algebraic techniques and concepts into quantum gravity (following for example Crane, Baez and Barrett), we define spectral C*-categories, which are deformed spectral triples in a sense made precise. This definition gives to representations of a C*-category on a small category of Hilbert spaces and bounded linear maps, the interpretation of a topological quantum field theory. The construction passes two mandatory tests: (i) there is a classical limit theorem reproducing a Riemannian spin manifold manifesting Connes' and Schücker's non-commutative counterpart of Einstein's equivalence principle, and (ii) there is consistency with the experimental fermion mass matrix. We also present an algebra invariant taking the form of a partition function arising from a C*-bundle dynamical system in connection with C*-subalgebra theory.
Born-Infeld inspired bosonic action in a noncommutative geometry
Serie, Emmanuel; Masson, Thierry; Kerner, Richard
2004-09-15
The Born-Infeld Lagrangian for non-Abelian gauge theory is adapted to the case of the generalized gauge fields arising in noncommutative matrix geometry. Basic properties of static and time-dependent solutions of the scalar sector of this model are investigated.
The left spectrum, the Levitzki radical, and noncommutative schemes.
Rosenberg, A L
1990-01-01
This note contains a brief exposition of the basics of a noncommutative version of affine, quasi-affine, and projective algebraic geometry. In this version, to any associative ring (with unity) a quasi-affine (resp. affine) left scheme is assigned. The notion of the left spectrum of a ring plays the key role. PMID:11607114
Curved noncommutative tori as Leibniz quantum compact metric spaces
Latrémolière, Frédéric
2015-12-15
We prove that curved noncommutative tori are Leibniz quantum compact metric spaces and that they form a continuous family over the group of invertible matrices with entries in the image of the quantum tori for the conjugation by modular conjugation operator in the regular representation, when this group is endowed with a natural length function.
3D quantum gravity and effective noncommutative quantum field theory.
Freidel, Laurent; Livine, Etera R
2006-06-09
We show that the effective dynamics of matter fields coupled to 3D quantum gravity is described after integration over the gravitational degrees of freedom by a braided noncommutative quantum field theory symmetric under a kappa deformation of the Poincaré group.
Noncommuting observables in quantum detection and estimation theory
NASA Technical Reports Server (NTRS)
Helstrom, C. W.
1971-01-01
In quantum detection theory, the optimum detection operators must commute; admitting simultaneous approximate measurement of noncommuting observables cannot yield a lower Bayes cost. In addition, the lower bounds on mean square errors of parameter estimates, predicted by the quantum mechanical Cramer-Rao inequality, cannot be reduced by such means.
Effects of the Noncommutative Standard Model in WW Scattering
Conley, John A.; Hewett, JoAnne L.
2008-12-02
We examine W pair production in the Noncommutative Standard Model constructed with the Seiberg-Witten map. Consideration of partial wave unitarity in the reactions WW {yields} WW and e{sup +}e{sup -} {yields} WW shows that the latter process is more sensitive and that tree-level unitarity is violated when scattering energies are of order a TeV and the noncommutative scale is below about a TeV. We find that WW production at the LHC is not sensitive to scales above the unitarity bounds. WW production in e{sup +}e{sup -} annihilation, however, provides a good probe of such effects with noncommutative scales below 300-400 GeV being excluded at LEP-II, and the ILC being sensitive to scales up to 10-20 TeV. In addition, we find that the ability to measure the helicity states of the final state W bosons at the ILC provides a diagnostic tool to determine and disentangle the different possible noncommutative contributions.
A comparative review of four formulations of noncommutative quantum mechanics
NASA Astrophysics Data System (ADS)
Gouba, Laure
2016-07-01
Four formulations of quantum mechanics on noncommutative Moyal phase spaces are reviewed. These are the canonical, path-integral, Weyl-Wigner and systematic formulations. Although all these formulations represent quantum mechanics on a phase space with the same deformed Heisenberg algebra, there are mathematical and conceptual differences which we discuss.
Extremal noncommutative black holes as dark matter furnaces
NASA Astrophysics Data System (ADS)
Kawamoto, Shoichi; Wei, Chun-Yu; Wen, Wen-Yu
2017-09-01
In this paper, we consider dark matter annihilation in the gravitational field of noncommutative black holes. Instead of a violent fate predicted in the usual Hawking radiation, we propose a thermal equilibrium state where a mildly burning black hole relic is fueled by dark matter accretion at the final stage of evaporation.
Fuzzy Physics: A Brief Overview of Noncommutative Geometry in Physics
NASA Astrophysics Data System (ADS)
Maceda, Marco
2011-10-01
Noncommutative geometry (NCG) is a mathematical tool which has been used in the search for a quantum theory of gravity. However, its application is not limited to this field. In this brief note we present different uses of NCG in Theoretical Physics.
Slavnov-Taylor identities for noncommutative QED{sub 4}
Charneski, B.; Gomes, M.; Silva, A. J. da; Mariz, T.; Nascimento, J. R.
2010-05-15
In this work we present an analysis of the one-loop Slavnov-Taylor identities in noncommutative QED{sub 4}. The vectorial fermion-photon and the triple photon vertex functions were studied, with the conclusion that no anomalies arise.
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.
Repression and activation by multiprotein complexes that alter chromatin structure.
Kingston, R E; Bunker, C A; Imbalzano, A N
1996-04-15
Recent studies have provided strong evidence that macromolecular complexes are used in the cell to remodel chromatin structure during activation and to create an inaccessible structure during repression, Although there is not yet any rigorous demonstration that modification of chromatin structure plays a direct, causal role in either activation or repression, there is sufficient smoke to indicate the presence of a blazing inferno nearby. It is clear that complexes that remodel chromatin are tractable in vitro; hopefully this will allow the establishment of systems that provide a direct analysis of the role that remodeling might play in activation. These studies indicate that establishment of functional systems to corroborate the elegant genetic studies on repression might also be tractable. As the mechanistic effects of these complexes are sorted out, it will become important to understand how the complexes are regulated. In many of the instances discussed above, the genes whose products make up these complexes were identified in genetic screens for effects on developmental processes. This implies a regulation of the activity of these complexes in response to developmental cues and further implies that the work to fully understand these complexes will occupy a generation of scientists.
Atomic structure of the Y complex of the nuclear pore
Kelley, Kotaro; Knockenhauer, Kevin E.; Kabachinski, Greg; ...
2015-03-30
The nuclear pore complex (NPC) is the principal gateway for transport into and out of the nucleus. Selectivity is achieved through the hydrogel-like core of the NPC. The structural integrity of the NPC depends on ~15 architectural proteins, which are organized in distinct subcomplexes to form the >40-MDa ring-like structure. In this paper, we present the 4.1-Å crystal structure of a heterotetrameric core element ('hub') of the Y complex, the essential NPC building block, from Myceliophthora thermophila. Using the hub structure together with known Y-complex fragments, we built the entire ~0.5-MDa Y complex. Our data reveal that the conserved coremore » of the Y complex has six rather than seven members. Finally, evolutionarily distant Y-complex assemblies share a conserved core that is very similar in shape and dimension, thus suggesting that there are closely related architectural codes for constructing the NPC in all eukaryotes.« less
Family Structure and Child Well-Being: Integrating Family Complexity
Brown, Susan L.; Manning, Wendy D.; Stykes, J. Bart
2014-01-01
Although children’s family lives are diverse, the measurement of children’s living arrangements has lagged, focusing on the relationships of children to parents while largely ignoring sibling composition. Using data from the 2008 Survey of Income and Program Participation (N = 23,985) the authors documented patterns of family complexity among a nationally representative sample of children ages 0–17 living in a range of family structures. They also examined the independent and joint associations of family structure and family complexity on child economic well-being. Family complexity was independently related to economic disadvantage, namely, a lower income-to-needs ratio and a higher likelihood of public assistance receipt. The role of family complexity was partially contingent on family structure, with the positive association between family complexity and receipt of public assistance more pronounced for children in families with 2 married biological parents. This study demonstrates the utility of integrating family structure and family complexity in studies of children’s well-being. PMID:25620810
The Ccr4-Not Complex: Architecture and Structural Insights.
Collart, Martine A; Panasenko, Olesya O
2017-01-01
The Ccr4-Not complex is an essential multi-subunit protein complex that plays a fundamental role in eukaryotic mRNA metabolism and has a multitude of different roles that impact eukaryotic gene expression . It has a conserved core of three Not proteins, the Ccr4 protein, and two Ccr4 associated factors, Caf1 and Caf40. A fourth Not protein, Not4, is conserved, but is only a stable subunit of the complex in yeast. Certain subunits have been duplicated during evolution, with functional divergence, such as Not3 in yeast, and Ccr4 or Caf1 in human. However the complex includes only one homolog for each protein. In addition, species-specific subunits are part of the complex, such as Caf130 in yeast or Not10 and Not11 in human. Two conserved catalytic functions are associated with the complex, deadenylation and ubiquitination . The complex adopts an L-shaped structure, in which different modules are bound to a large Not1 scaffold protein. In this chapter we will summarize our current knowledge of the architecture of the complex and of the structure of its constituents.
Geometric modeling of subcellular structures, organelles, and multiprotein complexes
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
Geometric modeling of subcellular structures, organelles, and multiprotein complexes.
Feng, Xin; Xia, Kelin; Tong, Yiying; Wei, Guo-Wei
2012-12-01
Recently, the structure, function, stability, and dynamics of subcellular structures, organelles, and multiprotein complexes have emerged as a leading interest in structural biology. Geometric modeling not only provides visualizations of shapes for large biomolecular complexes but also fills the gap between structural information and theoretical modeling, and enables the understanding of function, stability, and dynamics. This paper introduces a suite of computational tools for volumetric data processing, information extraction, surface mesh rendering, geometric measurement, and curvature estimation of biomolecular complexes. Particular emphasis is given to the modeling of cryo-electron microscopy data. Lagrangian-triangle meshes are employed for the surface presentation. On the basis of this representation, algorithms are developed for surface area and surface-enclosed volume calculation, and curvature estimation. Methods for volumetric meshing have also been presented. Because the technological development in computer science and mathematics has led to multiple choices at each stage of the geometric modeling, we discuss the rationales in the design and selection of various algorithms. Analytical models are designed to test the computational accuracy and convergence of proposed algorithms. Finally, we select a set of six cryo-electron microscopy data representing typical subcellular complexes to demonstrate the efficacy of the proposed algorithms in handling biomolecular surfaces and explore their capability of geometric characterization of binding targets. This paper offers a comprehensive protocol for the geometric modeling of subcellular structures, organelles, and multiprotein complexes. Copyright © 2012 John Wiley & Sons, Ltd.
Surprise maximization reveals the community structure of complex networks
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
Revealing and exploiting hierarchical material structure through complex atomic networks
NASA Astrophysics Data System (ADS)
Ahnert, Sebastian E.; Grant, William P.; Pickard, Chris J.
2017-08-01
One of the great challenges of modern science is to faithfully model, and understand, matter at a wide range of scales. Starting with atoms, the vastness of the space of possible configurations poses a formidable challenge to any simulation of complex atomic and molecular systems. We introduce a computational method to reduce the complexity of atomic configuration space by systematically recognising hierarchical levels of atomic structure, and identifying the individual components. Given a list of atomic coordinates, a network is generated based on the distances between the atoms. Using the technique of modularity optimisation, the network is decomposed into modules. This procedure can be performed at different resolution levels, leading to a decomposition of the system at different scales, from which hierarchical structure can be identified. By considering the amount of information required to represent a given modular decomposition we can furthermore find the most succinct descriptions of a given atomic ensemble. Our straightforward, automatic and general approach is applied to complex crystal structures. We show that modular decomposition of these structures considerably simplifies configuration space, which in turn can be used in discovery of novel crystal structures, and opens up a pathway towards accelerated molecular dynamics of complex atomic ensembles. The power of this approach is demonstrated by the identification of a possible allotrope of boron containing 56 atoms in the primitive unit cell, which we uncover using an accelerated structure search, based on a modular decomposition of a known dense phase of boron, γ-B28.
NASA Astrophysics Data System (ADS)
Harrington, James M.; Parker, Dorothy L.; Bargar, John R.; Jarzecki, Andrzej A.; Tebo, Bradley M.; Sposito, Garrison; Duckworth, Owen W.
2012-07-01
Siderophores traditionally have been viewed as solely being involved in the biogeochemical cycling of Fe(III). This paradigm, however, ignores the diverse roles siderophores may play in the cycling of other trace metals, such as Mn, Co, Mo, and V. Recent work has shown that siderophores form complexes with high stability constants with Mn(III), which are in some cases higher than that of the corresponding Fe(III) complex. Herein, we report on a structural analysis of the dissolved Fe(III)- and Mn(III)-siderophore complexes of rhizoferrin and two pyoverdin-type siderophores using X-ray spectroscopic techniques. Additionally, the stability constants of the Mn(III)-pyoverdinPaA and Mn(III)-rhizoferrin complexes have been quantified as log β111 = 47.5 ± 0.3 and log β110 = 29.8 ± 0.3, respectively. Comparisons of thermodynamic stability and solution structures of Fe(III)- and Mn(III)-complexes with a variety of siderophores demonstrate the relationship between donor group identity, siderophore structure, and strength of complex formation. Rhizoferrin and two mixed-moiety pyoverdins bind with a higher affinity for Mn(III) than Fe(III), possibly because of binding moiety composition which makes them better able to accommodate Jahn-Teller distortion. In contrast, Fe(III) forms complexes of higher relative stability with siderophores that contain hydroxamate and catecholate moieties, more rigid donor groups that form five-membered chelate rings.
Noncommutative correction to the Cornell potential in heavy-quarkonium atoms
NASA Astrophysics Data System (ADS)
Mirjalili, A.; Taki, M.
2016-02-01
We investigate the effect of space-time noncommutativity on the Cornell potential in heavy-quarkonium systems. It is known that the space-time noncommutativity can create bound states, and we therefore consider the noncommutative geometry of the space-time as a correction in quarkonium models. Furthermore, we take the experimental hyperfine measurements of the bottomium ground state as an upper limit on the noncommutative energy correction and derive the maximum possible value of the noncommutative parameter θ, obtaining θ ≤ 37.94 · 10-34 m2. Finally, we use our model to calculate the maximum value of the noncommutative energy correction for energy levels of charmonium and bottomium in 1S and 2S levels. The energy correction as a binding effect in quarkonium system is smaller for charmonium than for bottomium, as expected.
RNA polymerase II structure, and organization of the preinitiation complex.
Asturias, Francisco J
2004-04-01
Recent X-ray and cryo-electron microscopy studies have provided information about the basal eukaryotic transcription machinery and about Mediator, the complex involved in transcription regulation during initiation. On the basis of this structural information, a model describing the minimal transcription complex and its interaction with Mediator has been proposed. The model provides insight into the possible mechanisms of transcription initiation and regulation.
Navigation signal structure based on complex carrier modulation
NASA Astrophysics Data System (ADS)
Xu, Ying; Yuan, Hong
2011-06-01
Signal structure design is an important part of satellite navigation system research, which directly affects navigation performance. Signal performance parameters are analyzed and performances of BPSK modulated signals and BOC modulated signals are compared. Aiming at requirements of high navigation precision and high anti-jamming ability, a new navigation signal structure based on complex carrier modulation is proposed and performances of the signal are researched with different parameters. A synchronization algorithm is put forward according to the signal characteristics, and the synchronization performance is qualitatively analyzed. Next, the applications of the complex carrier modulated signal are discussed, which include anti-jamming, navigation enhancement, power combing and so on. Simulations and analysis show that the proposed navigation signal structure based on complex carrier modulation has good navigation capabilities and anti-jamming abilities, which deserves further study.
Structures and Activities of the Elongator Complex and Its Cofactors.
Kolaj-Robin, Olga; Séraphin, Bertrand
2017-01-01
Elongator is a highly conserved eukaryotic protein complex consisting of two sets of six Elp proteins, while homologues of its catalytic subunit Elp3 are found in all the kingdoms of life. Although it was originally described as a transcription elongation factor, cumulating evidence suggests that its primary function is catalyzing tRNA modifications. In humans, defects in Elongator subunits are associated with neurological disorders and cancer. Although further studies are still required, a clearer picture of the molecular mechanism of action of Elongator and its cofactors has started to emerge within recent years that have witnessed significant development in the field. In this review we summarize recent Elongator-related findings provided largely by crystal structures of several subunits of the complex, the electron microscopy structure of the entire yeast holoenzyme, as well as the structure of the Elongator cofactor complex Kti11/Kti13. © 2017 Elsevier Inc. All rights reserved.
Stoichiometry and structure of a lantibiotic maturation complex
Reiners, Jens; Abts, André; Clemens, Rebecca; Smits, Sander H. J.; Schmitt, Lutz
2017-01-01
Lantibiotics are ribosomally synthesized antimicrobial peptides secreted by mainly Gram-positive bacteria. Class 1 lantibiotics mature via two modification steps introduced by a modification LanBC complex. For the lantibiotic nisin, the dehydratase NisB catalyzes the dehydration of serine and threonine residues in the so-called core peptide. Second, five (methyl)-lanthionine rings are introduced in a regio- and stereospecific manner by the cyclase NisC. Here, we characterized the assembly of the NisBC complex in vitro, which is only formed in the presence of the substrate. The complex is composed of a NisB dimer, a monomer of NisC and one prenisin molecule. Interestingly, the presence of the last lanthionine ring prevented complex formation. This stoichiometry was verified by small-angle X-ray scattering measurements, which revealed the first structural glimpse of a LanBC complex in solution. PMID:28169337
Solvent structure improves docking prediction in lectin-carbohydrate complexes.
Gauto, Diego F; Petruk, Ariel A; Modenutti, Carlos P; Blanco, Juan I; Di Lella, Santiago; Martí, Marcelo A
2013-02-01
Recognition and complex formation between proteins and carbohydrates is a key issue in many important biological processes. Determination of the three-dimensional structure of such complexes is thus most relevant, but particularly challenging because of their usually low binding affinity. In silico docking methods have a long-standing tradition in predicting protein-ligand complexes, and allow a potentially fast exploration of a number of possible protein-carbohydrate complex structures. However, determining which of these predicted complexes represents the correct structure is not always straightforward. In this work, we present a modification of the scoring function provided by AutoDock4, a widely used docking software, on the basis of analysis of the solvent structure adjacent to the protein surface, as derived from molecular dynamics simulations, that allows the definition and characterization of regions with higher water occupancy than the bulk solvent, called water sites. They mimic the interaction held between the carbohydrate -OH groups and the protein. We used this information for an improved docking method in relation to its capacity to correctly predict the protein-carbohydrate complexes for a number of tested proteins, whose ligands range in size from mono- to tetrasaccharide. Our results show that the presented method significantly improves the docking predictions. The resulting solvent-structure-biased docking protocol, therefore, appears as a powerful tool for the design and optimization of development of glycomimetic drugs, while providing new insights into protein-carbohydrate interactions. Moreover, the achieved improvement also underscores the relevance of the solvent structure to the protein carbohydrate recognition process.
Computational RNA secondary structure design: empirical complexity and improved methods
Aguirre-Hernández, Rosalía; Hoos, Holger H; Condon, Anne
2007-01-01
Background We investigate the empirical complexity of the RNA secondary structure design problem, that is, the scaling of the typical difficulty of the design task for various classes of RNA structures as the size of the target structure is increased. The purpose of this work is to understand better the factors that make RNA structures hard to design for existing, high-performance algorithms. Such understanding provides the basis for improving the performance of one of the best algorithms for this problem, RNA-SSD, and for characterising its limitations. Results To gain insights into the practical complexity of the problem, we present a scaling analysis on random and biologically motivated structures using an improved version of the RNA-SSD algorithm, and also the RNAinverse algorithm from the Vienna package. Since primary structure constraints are relevant for designing RNA structures, we also investigate the correlation between the number and the location of the primary structure constraints when designing structures and the performance of the RNA-SSD algorithm. The scaling analysis on random and biologically motivated structures supports the hypothesis that the running time of both algorithms scales polynomially with the size of the structure. We also found that the algorithms are in general faster when constraints are placed only on paired bases in the structure. Furthermore, we prove that, according to the standard thermodynamic model, for some structures that the RNA-SSD algorithm was unable to design, there exists no sequence whose minimum free energy structure is the target structure. Conclusion Our analysis helps to better understand the strengths and limitations of both the RNA-SSD and RNAinverse algorithms, and suggests ways in which the performance of these algorithms can be further improved. PMID:17266771
Effect of Lanthanide Complex Structure on Cell Viability and Association
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
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.
Complex quantum networks as structured environments: engineering and probing
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
Fractional angular momentum in noncommutative generalized Chern-Simons quantum mechanics
NASA Astrophysics Data System (ADS)
Zhang, Xi-Lun; Sun, Yong-Li; Wang, Qing; Long, Zheng-Wen; Jing, Jian
2016-07-01
The noncommutative generalized Chern-Simons quantum mechanics, i.e., the Chern-Simons quantum mechanics on the noncommutative plane in the presence of Aharonov-Bohm magnetic vector potentials, is studied in this paper. We focus our attention on the canonical orbital angular momentum and show that there are two different approaches to produce the fractional angular momentum in the noncommutative generalized Chern-Simons quantum mechanics.
Quantum speed limit for a relativistic electron in the noncommutative phase space
NASA Astrophysics Data System (ADS)
Wang, Kang; Zhang, Yu-Fei; Wang, Qing; Long, Zheng-Wen; Jing, Jian
2017-08-01
The influence of the noncommutativity on the average speed of a relativistic electron interacting with a uniform magnetic field within the minimum evolution time is investigated. We find that it is possible for the wave packet of the electron to travel faster than the speed of light in vacuum because of the noncommutativity. It is a clear signature of violating Lorentz invariance in the noncommutative relativistic quantum mechanical region.
Pair production of Dirac particles in a -dimensional noncommutative space-time
NASA Astrophysics Data System (ADS)
Ousmane Samary, Dine; N'Dolo, Emanonfi Elias; Hounkonnou, Mahouton Norbert
2014-11-01
This work addresses the computation of the probability of fermionic particle pair production in -dimensional noncommutative Moyal space. Using Seiberg-Witten maps, which establish relations between noncommutative and commutative field variables, up to the first order in the noncommutative parameter , we derive the probability density of vacuum-vacuum pair production of Dirac particles. The cases of constant electromagnetic, alternating time-dependent, and space-dependent electric fields are considered and discussed.
Solving complex and disordered surface structures with electron diffraction
Van Hove, M.A.
1987-10-01
The past of surface structure determination with low-energy electron diffraction (LEED) will be briefly reviewed, setting the stage for a discussion of recent and future developments. The aim of these developments is to solve complex and disordered surface structures. Some efficient solutions to the theoretical and experimental problems will be presented. Since the theoretical problems dominate, the emphasis will be on theoretical approaches to the calculation of the multiple scattering of electrons through complex and disordered surfaces. 49 refs., 13 figs., 1 tab.
Zhang, Weizhe; Zhang, Hongmin; Zhang, Tao; Fan, Haifu; Hao, Quan
2015-07-01
Protein complexes are essential components in many cellular processes. In this study, a procedure to determine the protein-complex structure from a partial molecular-replacement (MR) solution is demonstrated using a direct-method-aided dual-space iterative phasing and model-building program suite, IPCAS (Iterative Protein Crystal structure Automatic Solution). The IPCAS iteration procedure involves (i) real-space model building and refinement, (ii) direct-method-aided reciprocal-space phase refinement and (iii) phase improvement through density modification. The procedure has been tested with four protein complexes, including two previously unknown structures. It was possible to use IPCAS to build the whole complex structure from one or less than one subunit once the molecular-replacement method was able to give a partial solution. In the most challenging case, IPCAS was able to extend to the full length starting from less than 30% of the complex structure, while conventional model-building procedures were unsuccessful.
Target selection of soluble protein complexes for structural proteomics studies
Shen, Weiping; Yun, Steven; Tam, Bonny; Dalal, Kush; Pio, Frederic F
2005-01-01
Background Protein expression in E. coli is the most commonly used system to produce protein for structural studies, because it is fast and inexpensive and can produce large quantity of proteins. However, when proteins from other species such as mammalian are produced in this system, problems of protein expression and solubility arise [1]. Structural genomics project are currently investigating proteomics pipelines that would produce sufficient quantities of recombinant proteins for structural studies of protein complexes. To investigate how the E. coli protein expression system could be used for this purpose, we purified apoptotic binary protein complexes formed between members of the Caspase Associated Recruitment Domain (CARD) family. Results A combinatorial approach to the generation of protein complexes was performed between members of the CARD domain protein family that have the ability to form hetero-dimers between each other. In our method, each gene coding for a specific protein partner is cloned in pET-28b (Novagen) and PGEX2T (Amersham) expression vectors. All combinations of protein complexes are then obtained by reconstituting complexes from purified components in native conditions, after denaturation-renaturation or co-expression. Our study applied to 14 soluble CARD domain proteins revealed that co-expression studies perform better than native and denaturation-renaturation methods. In this study, we confirm existing interactions obtained in vivoin mammalian cells and also predict new interactions. Conclusion The simplicity of this screening method could be easily scaled up to identify soluble protein complexes for structural genomic projects. This study reports informative statistics on the solubility of human protein complexes expressed in E.coli belonging to the human CARD protein family. PMID:15904526
Self-Assembly of Structures with Addressable Complexity.
Jacobs, William M; Frenkel, Daan
2016-03-02
The self-assembly of structures with "addressable complexity", where every component is distinct and is programmed to occupy a specific location within a target structure, is a promising route to engineering materials with precisely defined morphologies. Because systems with many components are inherently complicated, one might assume that the chances of successful self-assembly are extraordinarily small. Yet recent advances suggest otherwise: addressable structures with hundreds of distinct building blocks have been designed and assembled with nanometer precision. Despite this remarkable success, it is often challenging to optimize a self-assembly reaction to ensure that the intended structure is kinetically accessible. In this Perspective, we focus on the prediction of kinetic pathways for self-assembly and implications for the design of robust experimental protocols. The development of general principles to predict these pathways will enable the engineering of complex materials using a much wider range of building blocks than is currently possible.
Realization of Cohen-Glashow very special relativity on noncommutative space-time.
Sheikh-Jabbari, M M; Tureanu, A
2008-12-31
We show that the Cohen-Glashow very special relativity (VSR) theory [A. G. Cohen and S. L. Glashow, Phys. Rev. Lett. 97, 021601 (2006)] can be realized as the part of the Poincaré symmetry preserved on a noncommutative Moyal plane with lightlike noncommutativity. Moreover, we show that the three subgroups relevant to VSR can also be realized in the noncommutative space-time setting. For all of these three cases, the noncommutativity parameter theta(mu upsilon) should be lightlike (theta(mu upsilon) theta mu upsilon = 0). We discuss some physical implications of this realization of the Cohen-Glashow VSR.
Structural Changes in the Antennapedia Complex of Drosophila Pseudoobscura
Randazzo, F. M.; Seeger, M. A.; Huss, C. A.; Sweeney, M. A.; Cecil, J. K.; Kaufman, T. C.
1993-01-01
The discovery of the striking positional conservation between the Antennapedia and Bithorax homeotic gene complexes (ANT-C and BX-C) in Drosophila melanogaster and the murine Hox and human HOX clusters has had a substantial impact on our understanding of the evolution of development and its genetic regulation. Structural differences do exist among the mammalian Hox complexes and the ANT-C in D. melanogaster. To gain further insight into the evolutionary changes among these complexes, the ANT-C was cloned in the closely related species, Drosophila pseudoobscura. The overall structure of the ANT-C in D. pseudoobscura is highly similar to its D. melanogaster counterpart; however, two differences in the organization of the ANT-C have been identified. First, the z2 gene, a member of the ANT-C in D. melanogaster, is not present in the D. pseudoobscura ANT-C and is possibly absent from the D. pseudoobscura genome. Second, the orientation of the Deformed gene is inverted in D. pseudoobscura, providing it with a 5' to 3' direction of transcription identical to the remaining ANT-C homeobox genes with the exception of fushi tarazu. These differences demonstrate that subtle changes can occur in ANT-C structure during relatively short periods of evolutionary divergence, although the fundamental organization of the complex is conserved. These observations and others suggest that the complex is not absolutely rigid but that selective pressures have maintained this organization of genes for some functional reason that remains elusive. PMID:8099892
Structural evolution of Mesozoic complexes in Western Chukotka
NASA Astrophysics Data System (ADS)
Golionko, B. G.; Vatrushkina, E. V.; Verzhbitsky, V. E.; Degtiarev, K. E.
2017-07-01
Detailed structural investigations were carried out in the Pevek area in order to verify the tectonic evolution of the Mesozoic thrust and fold belt in Chukotka. South-vergent F1 folds in Triassic rocks were proved to be the earliest structures formed during the first deformation stage DI. These structures were deformed by north-vergent folds F2 that were formed during the second deformation stage DII. North-vergent folds are the main structures of the Jurassic-Lower Cretaceous complex. The fold structures of the first two stages are deformed by shear folds F3 finishing the stage DII. All these structures are deformed by submeridionally trending normal faults referred to the deformation stage DIII.
Structural study of coacervation in protein-polyelectrolyte complexes
NASA Astrophysics Data System (ADS)
Chodankar, S.; Aswal, V. K.; Kohlbrecher, J.; Vavrin, R.; Wagh, A. G.
2008-09-01
Coacervation is a dense liquid-liquid phase separation and herein we report coacervation of protein bovine serum albumin (BSA) in the presence of polyelectrolyte sodium polystyrene sulfonate (NaPSS) under varying solution conditions. Small-angle neutron scattering (SANS) measurements have been performed on above protein-polyelectrolyte complexes to study the structural evolution of the process that leads to coacervation and the phase separated coacervate as a function of solution pH , protein-polyelectrolyte ratio and ionic strength. SANS study prior to phase separation on the BSA-NaPSS complex shows a fractal structure representing a necklace model of protein macromolecules randomly distributed along the polystyrene sulfonate chain. The fractal dimension of the complex decreases as pH is shifted away from the isoelectric point (˜4.7) of BSA protein, which indicates the decrease in the compactness of the complex structure due to increase in the charge repulsion between the protein macromolecules bound to the polyelectrolyte. Concentration-dependence studies of the polyelectrolyte in the complex suggest coexistence of two populations of polyelectrolytes, first one fully saturated with proteins and another one free from proteins. Coacervation phase has been obtained through the turbidity measurement by varying pH of the aqueous solution containing protein and polyelectrolyte from neutral to acidic regime to get them to where the two components are oppositely charged. The spontaneous formation of coacervates is observed for pH values less than 4. SANS study on coacervates shows two length scales related to complex aggregations (mesh size and overall extent of the complex) hierarchically branched to form a larger network. The mesh size represents the distance between cross-linked points in the primary complex, which decreases with increase in ionic strength and remains the same on varying the protein-polyelectrolyte ratio. On the other hand, the overall extent of the
Structural Basis for TSC-1 TSC-2 Complex Formation
2008-03-01
Cancer 4, 665-676. 3. Irminger-Finger, I., Leung, W. C., Li, J., Dubois- Dauphin , M., Harb, J., Feki, A., Jefford, C. E., Soriano, J. V., Jaconi, M...Brookhaven National Laboratory, Long Island , NY. The structure of the FE65 WW–Mn10 complex was solved by MAD methods, using SeMet-substituted FE65 WW
School Structures: Transforming Urban Complex Schools into Better Learning Communities
ERIC Educational Resources Information Center
Haimendorf, Max; Kestner, Jacob
2008-01-01
This article, which forms part of the policy booklet "Lessons from the Front" written by participants and Ambassadors of the Teach First scheme, argues that educational outcomes are often adversely affected by the size and structure of many urban complex schools. Rather than multiplying the efforts of teachers, too often the…
Structure, Agency, Complexity Theory and Interdisciplinary Research in Education Studies
ERIC Educational Resources Information Center
Smith, John A.
2013-01-01
This article argues that Education Studies needs to develop its existing interdisciplinarity understanding of structures and agencies by giving greater attention to the modern process theories of self-organisation in the physical, biological, psychological and social sciences, sometimes given the umbrella term "complexity theory". The…
Structure, Agency, Complexity Theory and Interdisciplinary Research in Education Studies
ERIC Educational Resources Information Center
Smith, John A.
2013-01-01
This article argues that Education Studies needs to develop its existing interdisciplinarity understanding of structures and agencies by giving greater attention to the modern process theories of self-organisation in the physical, biological, psychological and social sciences, sometimes given the umbrella term "complexity theory". The…
Fitting Meta-Analytic Structural Equation Models with Complex Datasets
ERIC Educational Resources Information Center
Wilson, Sandra Jo; Polanin, Joshua R.; Lipsey, Mark W.
2016-01-01
A modification of the first stage of the standard procedure for two-stage meta-analytic structural equation modeling for use with large complex datasets is presented. This modification addresses two common problems that arise in such meta-analyses: (a) primary studies that provide multiple measures of the same construct and (b) the correlation…
Structure of a trimeric nucleoporin complex reveals alternate oligomerization states
Nagy, Vivien; Hsia, Kuo-Chiang; Debler, Erik W.; Kampmann, Martin; Davenport, Andrew M.; Blobel, Günter; Hoelz, André
2009-01-01
The heptameric Nup84 complex constitutes an evolutionarily conserved building block of the nuclear pore complex. Here, we present the crystal structure of the heterotrimeric Sec13·Nup145C·Nup84 complex, the centerpiece of the heptamer, at 3.2-Å resolution. Nup84 forms a U-shaped α-helical solenoid domain, topologically similar to two other members of the heptamer, Nup145C and Nup85. The interaction between Nup84 and Nup145C is mediated via a hydrophobic interface located in the kink regions of the two solenoids that is reinforced by additional interactions of two long Nup84 loops. The Nup84 binding site partially overlaps with the homo-dimerization interface of Nup145C, suggesting competing binding events. Fitting of the elongated Z-shaped heterotrimer into electron microscopy (EM) envelopes of the heptamer indicates that structural changes occur at the Nup145C·Nup84 interface. Docking the crystal structures of all heptamer components into the EM envelope constitutes a major advance toward the completion of the structural characterization of the Nup84 complex. PMID:19805193
Fitting Meta-Analytic Structural Equation Models with Complex Datasets
ERIC Educational Resources Information Center
Wilson, Sandra Jo; Polanin, Joshua R.; Lipsey, Mark W.
2016-01-01
A modification of the first stage of the standard procedure for two-stage meta-analytic structural equation modeling for use with large complex datasets is presented. This modification addresses two common problems that arise in such meta-analyses: (a) primary studies that provide multiple measures of the same construct and (b) the correlation…
Argument Structure of Tsou: Simplex and Complex Predicates
ERIC Educational Resources Information Center
Lin, Gujing
2010-01-01
This thesis investigates the argument structure of Tsou, a Formosan language within the Austronesian family. The investigation studies both simplex and complex predicates as well as describes the valency groupings and alignment patterns emerging from various clausal configurations. Assuming the stance that language description should respect…
Hybrid Structural Model of the Complete Human ESCRT-0 Complex
Ren, Xuefeng; Kloer, Daniel P.; Kim, Young C.; Ghirlando, Rodolfo; Saidi, Layla F.; Hummer, Gerhard; Hurley, James H.
2009-03-31
The human Hrs and STAM proteins comprise the ESCRT-0 complex, which sorts ubiquitinated cell surface receptors to lysosomes for degradation. Here we report a model for the complete ESCRT-0 complex based on the crystal structure of the Hrs-STAM core complex, previously solved domain structures, hydrodynamic measurements, and Monte Carlo simulations. ESCRT-0 expressed in insect cells has a hydrodynamic radius of R{sub H} = 7.9 nm and is a 1:1 heterodimer. The 2.3 {angstrom} crystal structure of the ESCRT-0 core complex reveals two domain-swapped GAT domains and an antiparallel two-stranded coiled-coil, similar to yeast ESCRT-0. ESCRT-0 typifies a class of biomolecular assemblies that combine structured and unstructured elements, and have dynamic and open conformations to ensure versatility in target recognition. Coarse-grained Monte Carlo simulations constrained by experimental R{sub H} values for ESCRT-0 reveal a dynamic ensemble of conformations well suited for diverse functions.
Effects of Structural Complexity on Administrative Role Demands.
ERIC Educational Resources Information Center
Carr, John C.
This report of a 1986 survey conducted in Maine addresses the relationship between stated time use demands on principals and superintendents and the structural complexity of the organizations in which they work. Researchers, comparing single with multiple schools and districts of supervisory responsibility, mailed the Maine Administrative…
Structural and functional clusters of complex brain networks
NASA Astrophysics Data System (ADS)
Zemanová, Lucia; Zhou, Changsong; Kurths, Jürgen
2006-12-01
Recent research using the complex network approach has revealed a rich and complicated network topology in the cortical connectivity of mammalian brains. It is of importance to understand the implications of such complex network structures in the functional organization of the brain activities. Here we study this problem from the viewpoint of dynamical complex networks. We investigate synchronization dynamics on the corticocortical network of the cat by modeling each node (cortical area) of the network with a sub-network of interacting excitable neurons. We find that the network displays clustered synchronization behavior, and the dynamical clusters coincide with the topological community structures observed in the anatomical network. Our results provide insights into the relationship between the global organization and the functional specialization of the brain cortex.
One Single Static Measurement Predicts Wave Localization in Complex Structures.
Lefebvre, Gautier; Gondel, Alexane; Dubois, Marc; Atlan, Michael; Feppon, Florian; Labbé, Aimé; Gillot, Camille; Garelli, Alix; Ernoult, Maxence; Mayboroda, Svitlana; Filoche, Marcel; Sebbah, Patrick
2016-08-12
A recent theoretical breakthrough has brought a new tool, called the localization landscape, for predicting the localization regions of vibration modes in complex or disordered systems. Here, we report on the first experiment which measures the localization landscape and demonstrates its predictive power. Holographic measurement of the static deformation under uniform load of a thin plate with complex geometry provides direct access to the landscape function. When put in vibration, this system shows modes precisely confined within the subregions delineated by the landscape function. Also the maxima of this function match the measured eigenfrequencies, while the minima of the valley network gives the frequencies at which modes become extended. This approach fully characterizes the low frequency spectrum of a complex structure from a single static measurement. It paves the way for controlling and engineering eigenmodes in any vibratory system, especially where a structural or microscopic description is not accessible.
The structure of the β-barrel assembly machinery complex
Bakelar, Jeremy; Buchanan, Susan K.; Noinaj, Nicholas
2016-01-08
β-Barrel outer membrane proteins (OMPs) are found in the outer membranes of Gram-negative bacteria and are essential for nutrient import, signaling, and adhesion. A 200-kilodalton five-component complex called the β-barrel assembly machinery (BAM) complex has been implicated in the biogenesis of OMPs. In this paper, we report the structure of the BAM complex from Escherichia coli, revealing that binding of BamCDE modulates the conformation of BamA, the central component, which may serve to regulate the BAM complex. The periplasmic domain of BamA was in a closed state that prevents access to the barrel lumen, which indicates substrate OMPs may not be threaded through the barrel during biogenesis. Finally and further, conformational shifts in the barrel domain lead to opening of the exit pore and rearrangement at the lateral gate.
The structure of the β-barrel assembly machinery complex
Bakelar, Jeremy; Buchanan, Susan K.; Noinaj, Nicholas
2016-01-08
β-Barrel outer membrane proteins (OMPs) are found in the outer membranes of Gram-negative bacteria and are essential for nutrient import, signaling, and adhesion. A 200-kilodalton five-component complex called the β-barrel assembly machinery (BAM) complex has been implicated in the biogenesis of OMPs. In this paper, we report the structure of the BAM complex from Escherichia coli, revealing that binding of BamCDE modulates the conformation of BamA, the central component, which may serve to regulate the BAM complex. The periplasmic domain of BamA was in a closed state that prevents access to the barrel lumen, which indicates substrate OMPs may notmore » be threaded through the barrel during biogenesis. Finally and further, conformational shifts in the barrel domain lead to opening of the exit pore and rearrangement at the lateral gate.« less
2. View, structures in Systems Integration Laboratory complex, looking north. ...
2. View, structures in Systems Integration Laboratory complex, looking north. The Components Test Laboratory (T-27) is located in the immediate foreground. Immediately uphill to the left of T-27 is the Boiler Chiller Plant (T-28H). To the left of T-28H is the Oxidizer Conditioning Structure (T-28D). Behind the T-28D is the Long-Term Oxidizer Silo (T-28B). The twin gantry structure at the left is the Systems Integration Laboratory (T-28). - Air Force Plant PJKS, Systems Integration Laboratory, Waterton Canyon Road & Colorado Highway 121, Lakewood, Jefferson County, CO
Complex Nano-Scale Structures for Unprecedented Properties in Steels
Caballero, Francisca G.; Poplawsky, Jonathan D.; Yen, Hung Wei; Rementeria, Rosalia; Morales-Rivas, Lucia; Yang, Jer-Ren; García-Mateo, Carlos
2016-11-01
Processing bulk nanoscrystalline materials for structural applications still poses a rather large challenge, particularly in achieving an industrially viable process. In this context, recent work has proved that complex nanoscale steel structures can be formed by solid reaction at low temperatures. These nanocrystalline bainitic steels present the highest strength ever recorded, unprecedented ductility, fatigue on par with commercial bearing steels and exceptional rolling-sliding wear performances. In this paper, a description of the characteristics and significance of these remarkable structures in the context of the atomic mechanism of transformation is provided.
Complex Nano-Scale Structures for Unprecedented Properties in Steels
Caballero, Francisca G.; Poplawsky, Jonathan D.; Yen, Hung Wei; ...
2016-11-01
Processing bulk nanoscrystalline materials for structural applications still poses a rather large challenge, particularly in achieving an industrially viable process. In this context, recent work has proved that complex nanoscale steel structures can be formed by solid reaction at low temperatures. These nanocrystalline bainitic steels present the highest strength ever recorded, unprecedented ductility, fatigue on par with commercial bearing steels and exceptional rolling-sliding wear performances. In this paper, a description of the characteristics and significance of these remarkable structures in the context of the atomic mechanism of transformation is provided.
On complexity of trellis structure of linear block codes
NASA Technical Reports Server (NTRS)
Lin, Shu
1990-01-01
The trellis structure of linear block codes (LBCs) is discussed. The state and branch complexities of a trellis diagram (TD) for a LBC is investigated. The TD with the minimum number of states is said to be minimal. The branch complexity of a minimal TD for a LBC is expressed in terms of the dimensions of specific subcodes of the given code. Then upper and lower bounds are derived on the number of states of a minimal TD for a LBC, and it is shown that a cyclic (or shortened cyclic) code is the worst in terms of the state complexity among the LBCs of the same length and dimension. Furthermore, it is shown that the structural complexity of a minimal TD for a LBC depends on the order of its bit positions. This fact suggests that an appropriate permutation of the bit positions of a code may result in an equivalent code with a much simpler minimal TD. Boolean polynomial representation of codewords of a LBC is also considered. This representation helps in study of the trellis structure of the code. Boolean polynomial representation of a code is applied to construct its minimal TD. Particularly, the construction of minimal trellises for Reed-Muller codes and the extended and permuted binary primitive BCH codes which contain Reed-Muller as subcodes is emphasized. Finally, the structural complexity of minimal trellises for the extended and permuted, and double-error-correcting BCH codes is analyzed and presented. It is shown that these codes have relatively simple trellis structure and hence can be decoded with the Viterbi decoding algorithm.
Structural Architecture of SNP Effects on Complex Traits
Gamazon, Eric R.; Cox, Nancy J.; Davis, Lea K.
2014-01-01
Despite the discovery of copy-number variation (CNV) across the genome nearly 10 years ago, current SNP-based analysis methodologies continue to collapse the homozygous (i.e., A/A), hemizygous (i.e., A/0), and duplicative (i.e., A/A/A) genotype states, treating the genotype variable as irreducible or unaltered by other colocalizing forms of genetic (e.g., structural) variation. Our understanding of common, genome-wide CNVs suggests that the canonical genotype construct might belie the enormous complexity of the genome. Here we present multiple analyses of several phenotypes and provide methods supporting a conceptual shift that embraces the structural dimension of genotype. We comprehensively investigate the impact of the structural dimension of genotype on (1) GWAS methods, (2) interpretation of rare LOF variants, (3) characterization of genomic architecture, and (4) implications for mapping loci involved in complex disease. Taken together, these results argue for the inclusion of a structural dimension and suggest that some portion of the “missing” heritability might be recovered through integration of the structural dimension of SNP effects on complex traits. PMID:25307299
Informational Complexity and Functional Activity of RNA Structures
Carothers, James M.; Oestreich, Stephanie C.; Davis, Jonathan H.
2004-01-01
Very little is known about the distribution of functional DNA, RNA, and protein molecules in sequence space. The question of how the number and complexity of distinct solutions to a particular biochemical problem varies with activity is an important aspect of this general problem. Here we present a comparison of the structures and activities of eleven distinct GTP-binding RNAs (aptamers). By experimentally measuring the amount of information required to specify each optimal binding structure, we show that defining a structure capable of 10-fold tighter binding requires approximately 10 additional bits of information. This increase in information content is equivalent to specifying the identity of five additional nucleotide positions and corresponds to an ∼1000-fold decrease in abundance in a sample of random sequences. We observe a similar relationship between structural complexity and activity in a comparison of two catalytic RNAs (ribozyme ligases), raising the possibility of a general relationship between the complexity of RNA structures and their functional activity. Describing how information varies with activity in other heteropolymers, both biological and synthetic, may lead to an objective means of comparing their functional properties. This approach could be useful in predicting the functional utility of novel heteropolymers. PMID:15099096
Significance tests for functional data with complex dependence structure.
Staicu, Ana-Maria; Lahiri, Soumen N; Carroll, Raymond J
2015-01-01
We propose an L(2)-norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a multilevel structure of the form groups-clusters or subjects-units, where the unit-level profiles are spatially correlated within the cluster, and the cluster-level data are independent. Orthogonal series expansions are used to approximate the group mean functions and the test statistic is estimated using the basis coefficients. The asymptotic null distribution of the test statistic is developed, under mild regularity conditions. To our knowledge this is the first work that studies hypothesis testing, when data have such complex multilevel functional and spatial structure. Two small-sample alternatives, including a novel block bootstrap for functional data, are proposed, and their performance is examined in simulation studies. The paper concludes with an illustration of a motivating experiment.
Significance tests for functional data with complex dependence structure
Lahiri, Soumen N.; Carroll, Raymond J.
2015-01-01
We propose an L2-norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a multilevel structure of the form groups–clusters or subjects–units, where the unit-level profiles are spatially correlated within the cluster, and the cluster-level data are independent. Orthogonal series expansions are used to approximate the group mean functions and the test statistic is estimated using the basis coefficients. The asymptotic null distribution of the test statistic is developed, under mild regularity conditions. To our knowledge this is the first work that studies hypothesis testing, when data have such complex multilevel functional and spatial structure. Two small-sample alternatives, including a novel block bootstrap for functional data, are proposed, and their performance is examined in simulation studies. The paper concludes with an illustration of a motivating experiment. PMID:26023253
Structure of the Rigor Actin-Tropomyosin-Myosin Complex
Behrmann, Elmar; Müller, Mirco; Penczek, Pawel A.; Mannherz, Hans Georg; Manstein, Dietmar J.; Raunser, Stefan
2014-01-01
The interaction of myosin with actin filaments is the central feature of muscle contraction and cargo movement along actin filaments of the cytoskeleton. Myosin converts the chemical energy stored in ATP into force and movement along actin filaments. Myosin binding to actin induces conformational changes that are coupled to the nucleotide-binding pocket and amplified by a specialized region of the motor domain for efficient force generation. Tropomyosin plays a key role in regulating the productive interaction between myosins and actin. Here, we report the 8 Å resolution structure of the actin-tropomyosin-myosin complex determined by cryo electron microscopy. The pseudo-atomic model of the complex obtained from fitting crystal structures into the map defines the large actin-myosin-tropomyosin interface and the molecular interactions between the proteins in detail and allows us to propose a structural model for tropomyosin dependent myosin binding to actin and actin-induced nucleotide release from myosin. PMID:22817895
Geometric and electronic structures of potassium-adsorbed rubrene complexes
Li, Tsung-Lung; Lu, Wen-Cai
2015-06-28
The geometric and electronic structures of potassium-adsorbed rubrene complexes are studied in this article. It is found that the potassium-rubrene (K{sub 1}RUB) complexes inherit the main symmetry characteristics from their pristine counterparts and are thus classified into D{sub 2}- and C{sub 2h}-like complexes according to the relative orientations of the four phenyl side groups. The geometric structures of K{sub 1}RUB are governed by two general effects on the total energy: Deformation of the carbon frame of the pristine rubrene increases the total energy, while proximity of the potassium ion to the phenyl ligands decreases the energy. Under these general rules, the structures of D{sub 2}- and C{sub 2h}-like K{sub 1}RUB, however, exhibit their respective peculiarities. These peculiarities can be illustrated by their energy profiles of equilibrium structures. For the potassium adsorption-sites, the D{sub 2}-like complexes show minimum-energy basins, whereas the C{sub 2h}-like ones have single-point minimum-energies. If the potassium atom ever has the energy to diffuse from the minimum-energy site, the potassium diffusion path on the D{sub 2}-like complexes is most likely along the backbone in contrast to the C{sub 2h}-like ones. Although the electronic structures of the minimum-energy structures of D{sub 2}- and C{sub 2h}-like K{sub 1}RUB are very alike, decompositions of their total spectra reveal insights into the electronic structures. First, the spectral shapes are mainly determined by the facts that, in comparison with the backbone carbons, the phenyl carbons have more uniform chemical environments and far less contributions to the electronic structures around the valence-band edge. Second, the electron dissociated from the potassium atom mainly remains on the backbone and has little effects on the electronic structures of the phenyl groups. Third, the two phenyls on the same side of the backbone as the potassium atom have more similar chemical environments
Solution structures of antimalarial drug-heme complexes.
Leed, Alison; DuBay, Kateri; Ursos, Lyann M B; Sears, Devin; De Dios, Angel C; Roepe, Paul D
2002-08-13
Paramagnetic metal centers [such as Fe(III) found within ferriprotoporphyrin IX heme (FPIX)] exert through space effects on the relaxation rate of nearby proton spins that depend critically on the metal-proton distance. We have measured these effects for all protons of several antimalarial drugs that bind to FPIX by systematically varying the drug:heme molar ratio in high field NMR experiments. These measurements allow us to determine precise FPIX Fe-drug H distances for the solution structures of noncovalent complexes formed between FPIX mu-oxo dimers and the antimalarial drugs chloroquine (CQ), quinine (QN), and quinidine (QD). Using these distances, we then performed distance restraint calculations to determine the lowest-energy solution structures of these complexes. Structures were solved for neutral, monoprotic (+1), and diprotic (+2) forms of the drugs. Analysis of these structures allows us to visualize for the first time the stereospecific differences between QN and QD binding to FPIX and the differences in populations of QN and QD solution structures upon changes in digestive vacuolar pH for drug resistant malarial parasites [Dzekunov, S. M., et al. (2000) Mol. Biochem. Parasitol. 110, 107-124]. The data indicate a previously unrecognized key role for the CQ aliphatic chain in stabilizing FPIX-CQ complexes, and suggest how lengthening or shortening the chain might perturb stability. We also define FPIX:drug stoichiometries of 2:1 for the complexes formed at physiological FPIX concentrations, in contrast to the 4:1 and 5:1 stoichiometries previously determined at higher FPIX concentrations [Dorn, A., et al. (1998) Biochem. Pharmacol. 55, 727-736]. These atomic resolution antimalarial drug-heme structures should help elucidate how these drugs inhibit formation of hemozoin during metabolism of heme within the malarial parasite Plasmodium falciparum and assist ongoing development of strategies for circumventing antimalarial drug resistance.
q -deformed noncommutative cat states and their nonclassical properties
NASA Astrophysics Data System (ADS)
Dey, Sanjib
2015-02-01
We study several classical-like properties of q -deformed nonlinear coherent states as well as nonclassical behaviors of q -deformed version of the Schrödinger cat states in noncommutative space. Coherent states in q -deformed space are found to be minimum uncertainty states together with the squeezed photon distributions unlike the ordinary systems, where the photon distributions are always Poissonian. Several advantages of utilizing cat states in noncommutative space over the standard quantum mechanical spaces have been reported here. For instance, the q -deformed parameter has been utilized to improve the squeezing of the quadrature beyond the ordinary case. Most importantly, the parameter provides an extra degree of freedom by which we achieve both quadrature squeezed and number squeezed cat states at the same time in a single system, which is impossible to achieve from ordinary cat states.
Noncommutative geometry and the primordial dipolar imaginary power spectrum
NASA Astrophysics Data System (ADS)
Jain, Pankaj; Rath, Pranati K.
2015-03-01
We argue that noncommutative space-times lead to an anisotropic dipolar imaginary primordial power spectrum. We define a new product rule, which allows us to consistently extract the power spectrum in such space-times. The precise nature of the power spectrum depends on the model of noncommutative geometry. We assume a simple dipolar model which has a power dependence on the wave number, , with a spectral index, . We show that such a spectrum provides a good description of the observed dipole modulation in the cosmic microwave background radiation (CMBR) data with . We extract the parameters of this model from the data. The dipole modulation is related to the observed hemispherical anisotropy in the CMBR data, which might represent the first signature of quantum gravity.
Noncommutative QED+QCD and the {beta} function for QED
Ettefaghi, M. M.; Haghighat, M.; Mohammadi, R.
2010-11-15
QED based on {theta}-unexpanded noncomutative space-time in contrast with the noncommutative QED based on {theta}-expanded U(1) gauge theory via the Seiberg-Witten map is one-loop renormalizable. Meanwhile it suffers from asymptotic freedom that is not in agreement with the experiment. We show that the QED part of the U{sub *}(3)xU{sub *}(1) gauge group as an appropriate gauge group for the noncommutative QED+QCD is not only one-loop renormalizable but also has a {beta} function that can be positive, negative and even zero. In fact the {beta} function depends on the mixing parameter {delta}{sub 13} as a free parameter and it will be equal to its counterpart in the ordinary QED for {delta}{sub 13}=0.367{pi}.
Bim Automation: Advanced Modeling Generative Process for Complex Structures
NASA Astrophysics Data System (ADS)
Banfi, F.; Fai, S.; Brumana, R.
2017-08-01
The new paradigm of the complexity of modern and historic structures, which are characterised by complex forms, morphological and typological variables, is one of the greatest challenges for building information modelling (BIM). Generation of complex parametric models needs new scientific knowledge concerning new digital technologies. These elements are helpful to store a vast quantity of information during the life cycle of buildings (LCB). The latest developments of parametric applications do not provide advanced tools, resulting in time-consuming work for the generation of models. This paper presents a method capable of processing and creating complex parametric Building Information Models (BIM) with Non-Uniform to NURBS) with multiple levels of details (Mixed and ReverseLoD) based on accurate 3D photogrammetric and laser scanning surveys. Complex 3D elements are converted into parametric BIM software and finite element applications (BIM to FEA) using specific exchange formats and new modelling tools. The proposed approach has been applied to different case studies: the BIM of modern structure for the courtyard of West Block on Parliament Hill in Ottawa (Ontario) and the BIM of Masegra Castel in Sondrio (Italy), encouraging the dissemination and interaction of scientific results without losing information during the generative process.
On the structure of thorium and americium adenosine triphosphate complexes.
Mostapha, Sarah; Fontaine-Vive, Fabien; Berthon, Laurence; Boubals, Nathalie; Zorz, Nicole; Solari, Pier Lorenzo; Charbonnel, Marie Christine; Den Auwer, Christophe
2014-11-01
The actinides are chemical poisons and radiological hazards. One challenge to better appraise their toxicity and develop countermeasures in case of exposure of living organisms is to better assess pathways of contamination. Because of the high chemical affinity of those actinide elements for phosphate groups and the ubiquity of such chemical functions in biochemistry, nucleotides and in particular adenosine triphosphate nucleotide (ATP) may be considered critical target building blocks for actinides. Combinations of spectroscopic techniques (Fourier transformed Infra Red [FTIR], Electrospray Ionization Mass Spectrometry [ESI-MS], and Extended X-ray Absorption Fine Structure [EXAFS]) with quantum chemical calculations have been implemented in order to assess the actinides coordination arrangement with ATP. We describe and compare herein the interaction of ATP with thorium and americium; thorium(IV) as a representative of actinide(IV) like plutonium(IV) and americium(III) as a representative of all heavier actinides. In the case of thorium, an insoluble complex is readily formed. In the case of americium, a behavior identical to that described previously for lutetium has been observed with insoluble and soluble complexes. The comparative study of ATP complexation with Th(IV) and Am(III) shows their ability to form insoluble complexes for which a structural model has been proposed by analogy with previously described Lu(III) complexes.
Structural Allostery and Binding of the Transferring Receptor Complex
Xu,G.; Liu, R.; Zak, O.; Aisen, P.; Chance, M.
2005-01-01
The structural allostery and binding interface for the human serum transferrin (Tf){center_dot}transferrin receptor (TfR) complex were identified using radiolytic footprinting and mass spectrometry. We have determined previously that the transferrin C-lobe binds to the receptor helical domain. In this study we examined the binding interactions of full-length transferrin with receptor and compared these data with a model of the complex derived from cryoelectron microscopy (cryo-EM) reconstructions. The footprinting results provide the following novel conclusions. First, we report characteristic oxidations of acidic residues in the C-lobe of native Tf and basic residues in the helical domain of TfR that were suppressed as a function of complex formation; this confirms ionic interactions between these protein segments as predicted by cryo-EM data and demonstrates a novel method for detecting ion pair interactions in the formation of macromolecular complexes. Second, the specific side-chain interactions between the C-lobe and N-lobe of transferrin and the corresponding interactions sites on the transferrin receptor predicted from cryo-EM were confirmed in solution. Last, the footprinting data revealed allosteric movements of the iron binding C- and N-lobes of Tf that sequester iron as a function of complex formation; these structural changes promote tighter binding of the metal ion and facilitate efficient ion transport during endocytosis.
Three-dimensional structure of the {gamma}-secretase complex
Ogura, Toshihiko; Mio, Kazuhiro; Hayashi, Ikuo; Miyashita, Hiroyuki; Iwastubo, Takeshi; Fukuda, Rie; Kopan, Raphael |; Kodama, Tatsuhiko; Hamakubo, Takao; Tomita, Taisuke . E-mail: taisuke@mol.f.u-tokyo.ac.jp; Sato, Chikara . E-mail: ti-sato@aist.go.jp
2006-05-05
{gamma}-Secretase belongs to an atypical class of aspartic proteases that hydrolyzes peptide bonds within the transmembrane domain of substrates, including amyloid-{beta} precursor protein and Notch. {gamma}-Secretase is comprised of presenilin, nicastrin, APH-1, and PEN-2 which form a large multimeric membrane protein complex, the three-dimensional structure of which is unknown. To gain insight into the structure of this complex enzyme, we purified functional {gamma}-secretase complex reconstituted in Sf9 cells and analyzed it using negative stain electron microscopy and 3D reconstruction techniques. Analysis of 2341 negatively stained particle images resulted in the three-dimensional representation of {gamma}-secretase at a resolution of 48 A. The structure occupies a volume of 560 x 320 x 240 A and resembles a flat heart comprised of two oppositely faced, dimpled domains. A low density space containing multiple pores resides between the domains. Some of the dimples in the putative transmembrane region may house the catalytic site. The large dimensions are consistent with the observation that {gamma}-secretase activity resides within a high molecular weight complex.
Structure of the rigor actin-tropomyosin-myosin complex.
Behrmann, Elmar; Müller, Mirco; Penczek, Pawel A; Mannherz, Hans Georg; Manstein, Dietmar J; Raunser, Stefan
2012-07-20
Regulation of myosin and filamentous actin interaction by tropomyosin is a central feature of contractile events in muscle and nonmuscle cells. However, little is known about molecular interactions within the complex and the trajectory of tropomyosin movement between its "open" and "closed" positions on the actin filament. Here, we report the 8 Å resolution structure of the rigor (nucleotide-free) actin-tropomyosin-myosin complex determined by cryo-electron microscopy. The pseudoatomic model of the complex, obtained from fitting crystal structures into the map, defines the large interface involving two adjacent actin monomers and one tropomyosin pseudorepeat per myosin contact. Severe forms of hereditary myopathies are linked to mutations that critically perturb this interface. Myosin binding results in a 23 Å shift of tropomyosin along actin. Complex domain motions occur in myosin, but not in actin. Based on our results, we propose a structural model for the tropomyosin-dependent modulation of myosin binding to actin. Copyright © 2012 Elsevier Inc. All rights reserved.
Structural mechanisms of DREAM complex assembly and regulation
Guiley, Keelan Z.; Liban, Tyler J.; Felthousen, Jessica G.; Ramanan, Parameshwaran
2015-01-01
The DREAM complex represses cell cycle genes during quiescence through scaffolding MuvB proteins with E2F4/5 and the Rb tumor suppressor paralog p107 or p130. Upon cell cycle entry, MuvB dissociates from p107/p130 and recruits B-Myb and FoxM1 for up-regulating mitotic gene expression. To understand the biochemical mechanisms underpinning DREAM function and regulation, we investigated the structural basis for DREAM assembly. We identified a sequence in the MuvB component LIN52 that binds directly to the pocket domains of p107 and p130 when phosphorylated on the DYRK1A kinase site S28. A crystal structure of the LIN52–p107 complex reveals that LIN52 uses a suboptimal LxSxExL sequence together with the phosphate at nearby S28 to bind the LxCxE cleft of the pocket domain with high affinity. The structure explains the specificity for p107/p130 over Rb in the DREAM complex and how the complex is disrupted by viral oncoproteins. Based on insights from the structure, we addressed how DREAM is disassembled upon cell cycle entry. We found that p130 and B-Myb can both bind the core MuvB complex simultaneously but that cyclin-dependent kinase phosphorylation of p130 weakens its association. Together, our data inform a novel target interface for studying MuvB and p130 function and the design of inhibitors that prevent tumor escape in quiescence. PMID:25917549
Structure, bonding, and reactivity of reactant complexes and key intermediates.
Soriano, Elena; Marco-Contelles, José
2011-01-01
Complexes of Pt and Au (gold(III) and cationic gold(I)) have shown an exceptional ability to promote a variety of organic transformations of unsaturated precursors due to their peculiar Lewis acid properties: the alkynophilic character of these soft metals and the π-acid activation of unsaturated groups promotes the intra- or intermolecular attack of a nucleophile. In this chapter we summarize the computational data reported on the structure, bonding, and reactivity of the reactant π-complexes and also on the key intermediate species.
Vacuum structure of the Higgs complex singlet-doublet model
NASA Astrophysics Data System (ADS)
Ferreira, P. M.
2016-11-01
The complex singlet-doublet model is a popular theory to account for dark matter and electroweak baryogenesis, wherein the Standard Model particle content is supplemented by a complex scalar gauge singlet, with certain discrete symmetries imposed. The scalar potential which results thereof can have seven different types of minima at tree level, which may coexist for specific choices of parameters. There is therefore the possibility that a given minimum is not global but rather a local one, and may tunnel to a deeper extremum, thus causing vacuum instability. This rich vacuum structure is explained and discussed in detail.
A uranium (VI) complex: Synthesis, structural and thermal kinetic analysis
NASA Astrophysics Data System (ADS)
Goel, Nidhi
2016-08-01
A new complex [UO2(2,6-DNP)2phen] (1) (2,6-DNP = 2,6-dinitrophenol, phen = 1,10-phenanthroline) was synthesized, and identified by elemental analysis, IR, Powder XRD and single crystal X-ray crystallography. Crystal structure provides the abundant information's about the bonding and geometry around the U(VI) metal center. The thermal decomposition was studied by TG-DSC, and the kinetics of thermolysis was investigated by applying model fitting as well as isoconversional methods. Explosion delay measurement (De) was also evaluated to determine the response of this complex under the condition of rapid heating.
Reduction chemistry of neptunium cyclopentadienide complexes: from structure to understanding.
Dutkiewicz, Michał S; Apostolidis, Christos; Walter, Olaf; Arnold, Polly L
2017-04-01
Neptunium complexes in the formal oxidation states II, III, and IV supported by cyclopentadienyl ligands are explored, and significant differences between Np and U highlighted as a result. A series of neptunium(iii) cyclopentadienyl (Cp) complexes [Np(Cp)3], its bis-acetonitrile adduct [Np(Cp)3(NCMe)2], and its KCp adduct K[Np(Cp)4] and [Np(Cp')3] (Cp' = C5H4SiMe3) have been made and characterised providing the first single crystal X-ray analyses of Np(III) Cp complexes. In all NpCp3 derivatives there are three Cp rings in η(5)-coordination around the Np(III) centre; additionally in [Np(Cp)3] and K[Np(Cp)4] one Cp ring establishes a μ-η(1)-interaction to one C atom of a neighbouring Np(Cp)3 unit. The solid state structure of K[Np(Cp)4] is unique in containing two different types of metal-Cp coordination geometries in the same crystal. Np(III)(Cp)4 units are found exhibiting four units of η(5)-coordinated Cp rings like in the known complex [Np(IV)(Cp)4], the structure of which is now reported. A detailed comparison of the structures gives evidence for the change of ionic radii of ca. -8 pm associated with change in oxidation state between Np(III) and Np(IV). The rich redox chemistry associated with the syntheses is augmented by the reduction of [Np(Cp')3] by KC8 in the presence of 2.2.2-cryptand to afford a neptunium(ii) complex that is thermally unstable above -10 °C like the U(II) and Th(II) complexes K(2.2.2-cryptand)[Th/U(Cp')3]. Together, these spontaneous and controlled redox reactions of organo-neptunium complexes, along with information from structural characterisation, show the relevance of organometallic Np chemistry to understanding fundamental structure and bonding in the minor actinides.
Can noncommutativity affect the whole history of the universe?
NASA Astrophysics Data System (ADS)
Monerat, G. A.; Corrêa Silva, E. V.; Neves, C.; Oliveira-Neto, G.; Rezende Rodrigues, L. G.; Silva de Oliveira, M.
We study a classical, noncommutative (NC), Friedmann-Robertson-Walker (FRW) cosmological model. The spatial sections may have positive, negative or zero constant curvatures. The matter content is a generic perfect fluid. The initial noncommutativity between some canonical variables is rewritten, such that, we end up with commutative variables and a NC parameter. Initially, we derive the scale factor dynamic equations for the general situation, without specifying the perfect fluid or the curvature of the spatial sections. Next, we consider two concrete situations: a radiation perfect fluid and dust. We study all possible scale factor behaviors, for both cases. We compare them with the corresponding commutative cases and one with the other. We obtain, some cases, where the NC model predicts a scale factor expansion which may describe the present expansion of our universe. Those cases are not present in the corresponding commutative models. Finally, we compare our model with another NC model, where the noncommutativity is between different canonical variables. We show that, in general, it leads to a scale factor behavior that is different from our model.
Canonical quantum gravity on noncommutative space-time
NASA Astrophysics Data System (ADS)
Kober, Martin
2015-06-01
In this paper canonical quantum gravity on noncommutative space-time is considered. The corresponding generalized classical theory is formulated by using the Moyal star product, which enables the representation of the field quantities depending on noncommuting coordinates by generalized quantities depending on usual coordinates. But not only the classical theory has to be generalized in analogy to other field theories. Besides, the necessity arises to replace the commutator between the gravitational field operator and its canonical conjugated quantity by a corresponding generalized expression on noncommutative space-time. Accordingly the transition to the quantum theory has also to be performed in a generalized way and leads to extended representations of the quantum theoretical operators. If the generalized representations of the operators are inserted to the generalized constraints, one obtains the corresponding generalized quantum constraints including the Hamiltonian constraint as dynamical constraint. After considering quantum geometrodynamics under incorporation of a coupling to matter fields, the theory is transferred to the Ashtekar formalism. The holonomy representation of the gravitational field as it is used in loop quantum gravity opens the possibility to calculate the corresponding generalized area operator.
Regular black holes and noncommutative geometry inspired fuzzy sources
NASA Astrophysics Data System (ADS)
Kobayashi, Shinpei
2016-05-01
We investigated regular black holes with fuzzy sources in three and four dimensions. The density distributions of such fuzzy sources are inspired by noncommutative geometry and given by Gaussian or generalized Gaussian functions. We utilized mass functions to give a physical interpretation of the horizon formation condition for the black holes. In particular, we investigated three-dimensional BTZ-like black holes and four-dimensional Schwarzschild-like black holes in detail, and found that the number of horizons is related to the space-time dimensions, and the existence of a void in the vicinity of the center of the space-time is significant, rather than noncommutativity. As an application, we considered a three-dimensional black hole with the fuzzy disc which is a disc-shaped region known in the context of noncommutative geometry as a source. We also analyzed a four-dimensional black hole with a source whose density distribution is an extension of the fuzzy disc, and investigated the horizon formation condition for it.
Reaction-diffusion controlled growth of complex structures
NASA Astrophysics Data System (ADS)
Noorduin, Willem; Mahadevan, L.; Aizenberg, Joanna
2013-03-01
Understanding how the emergence of complex forms and shapes in biominerals came about is both of fundamental and practical interest. Although biomineralization processes and organization strategies to give higher order architectures have been studied extensively, synthetic approaches to mimic these self-assembled structures are highly complex and have been difficult to emulate, let alone replicate. The emergence of solution patterns has been found in reaction-diffusion systems such as Turing patterns and the BZ reaction. Intrigued by this spontaneous formation of complexity we explored if similar processes can lead to patterns in the solid state. We here identify a reaction-diffusion system in which the shape of the solidified products is a direct readout of the environmental conditions. Based on insights in the underlying mechanism, we developed a toolbox of engineering strategies to deterministically sculpt patterns and shapes, and combine different morphologies to create a landscape of hierarchical multi scale-complex tectonic architectures with unprecedented levels of complexity. These findings may hold profound implications for understanding, mimicking and ultimately expanding upon nature's morphogenesis strategies, allowing the synthesis of advanced highly complex microscale materials and devices. WLN acknowledges the Netherlands Organization for Scientific Research for financial support
STRIPAK complexes: structure, biological function, and involvement in human diseases.
Hwang, Juyeon; Pallas, David C
2014-02-01
The mammalian striatin family consists of three proteins, striatin, S/G2 nuclear autoantigen, and zinedin. Striatin family members have no intrinsic catalytic activity, but rather function as scaffolding proteins. Remarkably, they organize multiple diverse, large signaling complexes that participate in a variety of cellular processes. Moreover, they appear to be regulatory/targeting subunits for the major eukaryotic serine/threonine protein phosphatase 2A. In addition, striatin family members associate with germinal center kinase III kinases as well as other novel components, earning these assemblies the name striatin-interacting phosphatase and kinase (STRIPAK) complexes. Recently, there has been a great increase in functional and mechanistic studies aimed at identifying and understanding the roles of STRIPAK and STRIPAK-like complexes in cellular processes of multiple organisms. These studies have identified novel STRIPAK and STRIPAK-like complexes and have explored their roles in specific signaling pathways. Together, the results of these studies have sparked increased interest in striatin family complexes because they have revealed roles in signaling, cell cycle control, apoptosis, vesicular trafficking, Golgi assembly, cell polarity, cell migration, neural and vascular development, and cardiac function. Moreover, STRIPAK complexes have been connected to clinical conditions, including cardiac disease, diabetes, autism, and cerebral cavernous malformation. In this review, we discuss the expression, localization, and protein domain structure of striatin family members. Then we consider the diverse complexes these proteins and their homologs form in various organisms, emphasizing what is known regarding function and regulation. Finally, we explore possible roles of striatin family complexes in disease, especially cerebral cavernous malformation.
Minimizing ambiguities in stream classification of complex drainage structures
NASA Astrophysics Data System (ADS)
Sah, Rajesh Kumar; Das, Apurba Kumar
2017-10-01
In hydrological studies complex drainage structures in river systems are open to ambiguous subjectivity when conventional classification systems are followed. We suggest rules that compliment both Strahler's and Shreve's methods of stream numbering and their extent consideration to reduce this subjective uncertainty. We delineated three possible complex distributary conditions followed by individual application of Strahler's and Shreve's rationales for stream classifications with concurrent verification in real river situations. As a result, for Strahler's method, we derived the decisive criteria in designating correct stream number in complex stream interconnections by plotting minimum number of segments along with the concept of primary and secondary flow. On the other hand, for Shreve's method, splitting the magnitude of the streams at divides of the distributaries yielded precise results. Final real world verification from both applications substantiated the potential of our proposed methodologies to reduce subjectivity in stream classification.
Polyacrylic acids-bovine serum albumin complexation: Structure and dynamics.
Othman, Mohamed; Aschi, Adel; Gharbi, Abdelhafidh
2016-01-01
The study of the mixture of BSA with polyacrylic acids at different masses versus pH allowed highlighting the existence of two regimes of weak and strong complexation. These complexes were studied in diluted regime concentration, by turbidimetry, dynamic light scattering (DLS), zeta-potential measurements and nuclear magnetic resonance (NMR). We have followed the pH effect on the structure and properties of the complex. This allowed refining the interpretation of the phase diagram and understanding the observed phenomena. The NMR measurements allowed probing the dynamics of the constituents versus the pH. The computational method was used to precisely determine the electrostatic potential of BSA and how the polyelectrolyte binds to it at different pH.
Parallel Structural Evolution of Mitochondrial Ribosomes and OXPHOS Complexes
van der Sluis, Eli O.; Bauerschmitt, Heike; Becker, Thomas; Mielke, Thorsten; Frauenfeld, Jens; Berninghausen, Otto; Neupert, Walter; Herrmann, Johannes M.; Beckmann, Roland
2015-01-01
The five macromolecular complexes that jointly mediate oxidative phosphorylation (OXPHOS) in mitochondria consist of many more subunits than those of bacteria, yet, it remains unclear by which evolutionary mechanism(s) these novel subunits were recruited. Even less well understood is the structural evolution of mitochondrial ribosomes (mitoribosomes): while it was long thought that their exceptionally high protein content would physically compensate for their uniquely low amount of ribosomal RNA (rRNA), this hypothesis has been refuted by structural studies. Here, we present a cryo-electron microscopy structure of the 73S mitoribosome from Neurospora crassa, together with genomic and proteomic analyses of mitoribosome composition across the eukaryotic domain. Surprisingly, our findings reveal that both structurally and compositionally, mitoribosomes have evolved very similarly to mitochondrial OXPHOS complexes via two distinct phases: A constructive phase that mainly acted early in eukaryote evolution, resulting in the recruitment of altogether approximately 75 novel subunits, and a reductive phase that acted during metazoan evolution, resulting in gradual length-reduction of mitochondrially encoded rRNAs and OXPHOS proteins. Both phases can be well explained by the accumulation of (slightly) deleterious mutations and deletions, respectively, in mitochondrially encoded rRNAs and OXPHOS proteins. We argue that the main role of the newly recruited (nuclear encoded) ribosomal- and OXPHOS proteins is to provide structural compensation to the mutationally destabilized mitochondrially encoded components. While the newly recruited proteins probably provide a selective advantage owing to their compensatory nature, and while their presence may have opened evolutionary pathways toward novel mitochondrion-specific functions, we emphasize that the initial events that resulted in their recruitment was nonadaptive in nature. Our framework is supported by population genetic
Parallel Structural Evolution of Mitochondrial Ribosomes and OXPHOS Complexes.
van der Sluis, Eli O; Bauerschmitt, Heike; Becker, Thomas; Mielke, Thorsten; Frauenfeld, Jens; Berninghausen, Otto; Neupert, Walter; Herrmann, Johannes M; Beckmann, Roland
2015-04-09
The five macromolecular complexes that jointly mediate oxidative phosphorylation (OXPHOS) in mitochondria consist of many more subunits than those of bacteria, yet, it remains unclear by which evolutionary mechanism(s) these novel subunits were recruited. Even less well understood is the structural evolution of mitochondrial ribosomes (mitoribosomes): while it was long thought that their exceptionally high protein content would physically compensate for their uniquely low amount of ribosomal RNA (rRNA), this hypothesis has been refuted by structural studies. Here, we present a cryo-electron microscopy structure of the 73S mitoribosome from Neurospora crassa, together with genomic and proteomic analyses of mitoribosome composition across the eukaryotic domain. Surprisingly, our findings reveal that both structurally and compositionally, mitoribosomes have evolved very similarly to mitochondrial OXPHOS complexes via two distinct phases: A constructive phase that mainly acted early in eukaryote evolution, resulting in the recruitment of altogether approximately 75 novel subunits, and a reductive phase that acted during metazoan evolution, resulting in gradual length-reduction of mitochondrially encoded rRNAs and OXPHOS proteins. Both phases can be well explained by the accumulation of (slightly) deleterious mutations and deletions, respectively, in mitochondrially encoded rRNAs and OXPHOS proteins. We argue that the main role of the newly recruited (nuclear encoded) ribosomal- and OXPHOS proteins is to provide structural compensation to the mutationally destabilized mitochondrially encoded components. While the newly recruited proteins probably provide a selective advantage owing to their compensatory nature, and while their presence may have opened evolutionary pathways toward novel mitochondrion-specific functions, we emphasize that the initial events that resulted in their recruitment was nonadaptive in nature. Our framework is supported by population genetic
Upper-mantle structures beneath USArray derived from waveform complexity
NASA Astrophysics Data System (ADS)
Sun, Daoyuan; Helmberger, Don
2011-01-01
Tomographic imaging of the crust and upper mantle beneath the western United States has greatly improved with the addition of USArray data. These models display many detailed images of both fast and slow blobs penetrating into the transition zone. To study such features, we apply a newly developed technique, called MultiPath Detector analysis, to the SH waveform data. The method simulates each observed body waveform by performing a decomposition; by [S(t)+C×S(t-ΔLR)]/2, where S(t) is the synthetics for a reference model. Time separation ΔLR and amplitude ratio C are needed to obtain a high cross-correlation between a simulated waveform and data. The travel time of the composite waveform relative to the reference model synthetics is defined as ΔT. A simulated annealing algorithm is used to determine the parameters ΔLR and C. We also record the amplitude ratio (Amp) between the synthetics for the reference model relative to the data. Generally, large ΔLR values are associated with low Amp's. Whereas the conventional tomography yields a travel time correction (ΔT), our analysis yields an extra parameter (ΔLR), which describes the waveform complexity. With the array, we can construct a mapping of the gradient of ΔLR with complexity patterns. A horizontal structure introduces waveform complexity along the distance profile (in-plane multipathing). An azimuthally orientation ΔLR pattern indicates a vertical structure with out-of-plane multipathing. Using such maps generated from artificial data, we can easily recognize features produced by dipping fast structures and slow structures (DSS). Many of these features display organized waveform complexity that are distinctly directional indicative of dipping sharp-edges. Here, we process the array data for events arriving from various azimuths and construct maps of multipathing patterns. The similarity between tomographic features and complexity maps is striking. When features are dipping such as the slab structures
Integrated structural analysis of the human nuclear pore complex scaffold.
Bui, Khanh Huy; von Appen, Alexander; DiGuilio, Amanda L; Ori, Alessandro; Sparks, Lenore; Mackmull, Marie-Therese; Bock, Thomas; Hagen, Wim; Andrés-Pons, Amparo; Glavy, Joseph S; Beck, Martin
2013-12-05
The nuclear pore complex (NPC) is a fundamental component of all eukaryotic cells that facilitates nucleocytoplasmic exchange of macromolecules. It is assembled from multiple copies of about 30 nucleoporins. Due to its size and complex composition, determining the structure of the NPC is an enormous challenge, and the overall architecture of the NPC scaffold remains elusive. In this study, we have used an integrated approach based on electron tomography, single-particle electron microscopy, and crosslinking mass spectrometry to determine the structure of a major scaffold motif of the human NPC, the Nup107 subcomplex, in both isolation and integrated into the NPC. We show that 32 copies of the Nup107 subcomplex assemble into two reticulated rings, one each at the cytoplasmic and nuclear face of the NPC. This arrangement may explain how changes of the diameter are realized that would accommodate transport of huge cargoes.
Structural insights into the YAP and TEAD complex.
Li, Ze; Zhao, Bin; Wang, Ping; Chen, Fei; Dong, Zhenghong; Yang, Huirong; Guan, Kun-Liang; Xu, Yanhui
2010-02-01
The Yes-associated protein (YAP) transcriptional coactivator is a key regulator of organ size and a candidate human oncogene inhibited by the Hippo tumor suppressor pathway. The TEAD family of transcription factors binds directly to and mediates YAP-induced gene expression. Here we report the three-dimensional structure of the YAP (residues 50-171)-TEAD1 (residues 194-411) complex, in which YAP wraps around the globular structure of TEAD1 and forms extensive interactions via three highly conserved interfaces. Interface 3, including YAP residues 86-100, is most critical for complex formation. Our study reveals the biochemical nature of the YAP-TEAD interaction, and provides a basis for pharmacological intervention of YAP-TEAD hyperactivation in human diseases.
Structural insights into the YAP and TEAD complex
Li, Ze; Zhao, Bin; Wang, Ping; Chen, Fei; Dong, Zhenghong; Yang, Huirong; Guan, Kun-Liang; Xu, Yanhui
2010-01-01
The Yes-associated protein (YAP) transcriptional coactivator is a key regulator of organ size and a candidate human oncogene inhibited by the Hippo tumor suppressor pathway. The TEAD family of transcription factors binds directly to and mediates YAP-induced gene expression. Here we report the three-dimensional structure of the YAP (residues 50–171)–TEAD1 (residues 194–411) complex, in which YAP wraps around the globular structure of TEAD1 and forms extensive interactions via three highly conserved interfaces. Interface 3, including YAP residues 86–100, is most critical for complex formation. Our study reveals the biochemical nature of the YAP–TEAD interaction, and provides a basis for pharmacological intervention of YAP–TEAD hyperactivation in human diseases. PMID:20123905
The nuclear pore complex: understanding its function through structural insight.
Beck, Martin; Hurt, Ed
2017-02-01
Nuclear pore complexes (NPCs) fuse the inner and outer nuclear membranes to form channels across the nuclear envelope. They are large macromolecular assemblies with a complex composition and diverse functions. Apart from facilitating nucleocytoplasmic transport, NPCs are involved in chromatin organization, the regulation of gene expression and DNA repair. Understanding the molecular mechanisms underlying these functions has been hampered by a lack of structural knowledge about the NPC. The recent convergence of crystallographic and biochemical in vitro analysis of nucleoporins (NUPs), the components of the NPC, with cryo-electron microscopic imaging of the entire NPC in situ has provided first pseudo-atomic view of its central core and revealed that an unexpected network of short linear motifs is an important spatial organization principle. These breakthroughs have transformed the way we understand NPC structure, and they provide an important base for functional investigations, including the elucidation of the molecular mechanisms underlying clinically manifested mutations of the nucleocytoplasmic transport system.
Community structure from spectral properties in complex networks
NASA Astrophysics Data System (ADS)
Servedio, V. D. P.; Colaiori, F.; Capocci, A.; Caldarelli, G.
2005-06-01
We analyze the spectral properties of complex networks focusing on their relation to the community structure, and develop an algorithm based on correlations among components of different eigenvectors. The algorithm applies to general weighted networks, and, in a suitably modified version, to the case of directed networks. Our method allows to correctly detect communities in sharply partitioned graphs, however it is useful to the analysis of more complex networks, without a well defined cluster structure, as social and information networks. As an example, we test the algorithm on a large scale data-set from a psychological experiment of free word association, where it proves to be successful both in clustering words, and in uncovering mental association patterns.
Emergence of hierarchical structural complexities in nanoparticles and their assembly
NASA Astrophysics Data System (ADS)
Zeng, Chenjie; Chen, Yuxiang; Kirschbaum, Kristin; Lambright, Kelly J.; Jin, Rongchao
2016-12-01
We demonstrate that nanoparticle self-assembly can reach the same level of hierarchy, complexity, and accuracy as biomolecules. The precise assembly structures of gold nanoparticles (246 gold core atoms with 80 p-methylbenzenethiolate surface ligands) at the atomic, molecular, and nanoscale levels were determined from x-ray diffraction studies. We identified the driving forces and rules that guide the multiscale assembly behavior. The protecting ligands self-organize into rotational and parallel patterns on the nanoparticle surface via C-Hṡṡṡπ interaction, and the symmetry and density of surface patterns dictate directional packing of nanoparticles into crystals with orientational, rotational, and translational orders. Through hierarchical interactions and symmetry matching, the simple building blocks evolve into complex structures, representing an emergent phenomenon in the nanoparticle system.
On the index of noncommutative elliptic operators over C*-algebras
Savin, Anton Yu; Sternin, Boris Yu
2010-05-11
We consider noncommutative elliptic operators over C*-algebras, associated with a discrete group of isometries of a manifold. The main result of the paper is a formula expressing the Chern characters of the index (Connes invariants) in topological terms. As a corollary to this formula a simple proof of higher index formulae for noncommutative elliptic operators is obtained. Bibliography: 36 titles.
Noncommutative Integrability of the Klein-Gordon and Dirac Equations in (2+1)-Dimensional Spacetime
NASA Astrophysics Data System (ADS)
Breev, A. I.; Shapovalov, A. V.
2017-03-01
Noncommutative integration of the Klein-Gordon and Dirac relativistic wave equations in (2+1)-dimensional Minkowski space is considered. It is shown that for all non-Abelian subalgebras of the (2+1)-dimensional Poincaré algebra the condition of noncommutative integrability is satisfied.
Seiberg-Witten map and quantum phase effects for neutral Dirac particle on noncommutative plane
NASA Astrophysics Data System (ADS)
Ma, Kai; Wang, Jian-Hua; Yang, Huan-Xiong
2016-05-01
We provide a new approach to study the noncommutative effects on the neutral Dirac particle with anomalous magnetic or electric dipole moment on the noncommutative plane. The advantages of this approach are demonstrated by investigating the noncommutative corrections on the Aharonov-Casher and He-McKellar-Wilkens effects. This approach is based on the effective U (1) gauge symmetry for the electrodynamics of spin on the two dimensional space. The Seiberg-Witten map for this symmetry is then employed when we study the noncommutative corrections. Because the Seiberg-Witten map preserves the gauge symmetry, the noncommutative corrections can be defined consistently with the ordinary phases. Based on this approach we find the noncommutative corrections on the Aharonov-Casher and He-McKellar-Wilkens phases consist of two terms. The first one depends on the beam particle velocity and consistence with the previous results. However the second term is velocity-independent and then completely new. Therefore our results indicate it is possible to investigate the noncommutative space by using ultra-cold neutron interferometer in which the velocity-dependent term is negligible. Furthermore, both these two terms are proportional to the ratio between the noncommutative parameter θ and the cross section Ae/m of the electrical/magnetic charged line enclosed by the trajectory of beam particles. Therefore the experimental sensitivity can be significantly enhanced by reducing the cross section of the charge line Ae/m.
Retroviral integrase protein and intasome nucleoprotein complex structures
Grawenhoff, Julia; Engelman, Alan N
2017-01-01
Retroviral replication proceeds through the integration of a DNA copy of the viral RNA genome into the host cellular genome, a process that is mediated by the viral integrase (IN) protein. IN catalyzes two distinct chemical reactions: 3’-processing, whereby the viral DNA is recessed by a di- or trinucleotide at its 3’-ends, and strand transfer, in which the processed viral DNA ends are inserted into host chromosomal DNA. Although IN has been studied as a recombinant protein since the 1980s, detailed structural understanding of its catalytic functions awaited high resolution structures of functional IN-DNA complexes or intasomes, initially obtained in 2010 for the spumavirus prototype foamy virus (PFV). Since then, two additional retroviral intasome structures, from the α-retrovirus Rous sarcoma virus (RSV) and β-retrovirus mouse mammary tumor virus (MMTV), have emerged. Here, we briefly review the history of IN structural biology prior to the intasome era, and then compare the intasome structures of PFV, MMTV and RSV in detail. Whereas the PFV intasome is characterized by a tetrameric assembly of IN around the viral DNA ends, the newer structures harbor octameric IN assemblies. Although the higher order architectures of MMTV and RSV intasomes differ from that of the PFV intasome, they possess remarkably similar intasomal core structures. Thus, retroviral integration machineries have adapted evolutionarily to utilize disparate IN elements to construct convergent intasome core structures for catalytic function. PMID:28289517
1. View, structures in Systems Integration Laboratory complex, looking northwest. ...
1. View, structures in Systems Integration Laboratory complex, looking northwest. The twin gantry structure in the center is the Systems Integration Laboratory (T-28). To its immediate left in the foreground is a truck well, concrete retaining wall, piping, and stack associated with the oxidizer vault storage area. To the immediate right of T-28 is the concrete Signal Transfer Building (T-28A). At the extreme right is the Long-Term Hydrazine Silo (T-28E). - Air Force Plant PJKS, Systems Integration Laboratory, Waterton Canyon Road & Colorado Highway 121, Lakewood, Jefferson County, CO
Structure and function analysis of protein-nucleic acid complexes
NASA Astrophysics Data System (ADS)
Kuznetsova, S. A.; Oretskaya, T. S.
2016-05-01
The review summarizes published data on the results and achievements in the field of structure and function analysis of protein-nucleic acid complexes by means of main physical and biochemical methods, including X-ray diffraction, nuclear magnetic resonance spectroscopy, electron and atomic force microscopy, small-angle X-ray and neutron scattering, footprinting and cross-linking. Special attention is given to combined approaches. The advantages and limitations of each method are considered, and the prospects of their application for wide-scale structural studies in vivo are discussed. The bibliography includes 145 references.
Block-structured grids for complex aerodynamic configurations: Current status
NASA Technical Reports Server (NTRS)
Vatsa, Veer N.; Sanetrik, Mark D.; Parlette, Edward B.
1995-01-01
The status of CFD methods based on the use of block-structured grids for analyzing viscous flows over complex configurations is examined. The objective of the present study is to make a realistic assessment of the usability of such grids for routine computations typically encountered in the aerospace industry. It is recognized at the very outset that the total turnaround time, from the moment the configuration is identified until the computational results have been obtained and postprocessed, is more important than just the computational time. Pertinent examples will be cited to demonstrate the feasibility of solving flow over practical configurations of current interest on block-structured grids.
Ultrathin conformal coating for complex magneto-photonic structures.
Pascu, Oana; Caicedo, José Manuel; López-García, Martín; Canalejas, Víctor; Blanco, Álvaro; López, Cefe; Arbiol, Jordi; Fontcuberta, Josep; Roig, Anna; Herranz, Gervasi
2011-11-01
We report on an extremely fast and versatile synthetic approach, based on microwave assisted sol-gel chemistry, that allows a conformal nanometric coating of intricate three-dimensional structures. Using this methodology, we have achieved a conformal coverage of large areas of three-dimensional opals with a superparamagnetic manganese ferrite layer, yielding magneto-photonic crystals with excellent quality. The use of a ternary oxide for the ultrathin coating demonstrates the potential of this methodology to realize three-dimensional structures with complex materials that may find applications beyond photonics, such as energy, sensing or catalysis.
Methods for SAXS-Based Structure Determination of Biomolecular Complexes
Yang, Sichun
2014-05-30
Measurements from small-angle X-ray scattering (SAXS) are highly informative to determine the structures of bimolecular complexes in solution. Here, we describe current and recent SAXS-driven developments, with an emphasis on computational modeling. In particular, accurate methods to computing one theoretical scattering profile from a given structure model are discussed, with a key focus on structure factor coarse-graining and hydration contribution. Methods for reconstructing topological structures from an experimental SAXS profile are currently under active development. We report on several modeling tools designed for conformation generation that make use of either atomic-level or coarse-grained representations. Furthermore, since large, flexible biomolecules can adopt multiple well-defined conformations, a traditional single-conformation SAXS analysis is inappropriate, so we also discuss recent methods that utilize the concept of ensemble optimization, weighing in on the SAXS contributions of a heterogeneous mixture of conformations. These tools will ultimately posit the usefulness of SAXS data beyond a simple space-filling approach by providing a reliable structure characterization of biomolecular complexes under physiological conditions.
Potassium under pressure: Electronic origin of complex structures
NASA Astrophysics Data System (ADS)
Degtyareva, V. F.
2014-10-01
Recent high-pressure X-ray diffraction studies of alkali metals revealed unusual complex structures that follow the body-centred and face-centred cubic structures on compression. The structural sequence of potassium under compression to 1 Mbar is as follows: bcc-fcc-h-g (tI19*), hP4-oP8-tI4-oC16. We consider configurations of Brillouin-Jones zones and the Fermi surface within a nearly-free-electron model in order to analyze the importance of these configurations for the crystal structure stability. Formation of Brillouin zone planes close to the Fermi surface is related to opening an energy gap at these planes and reduction of crystal energy. Under pressure, this mechanism becomes more important leading to appearance of complex low-symmetry structures. The stability of the post-fcc phases in K is attributed to the changes in the valence electron configuration under strong compression.
Crystal structure of the Mus81-Eme1 complex.
Chang, Jeong Ho; Kim, Jeong Joo; Choi, Jung Min; Lee, Jung Hoon; Cho, Yunje
2008-04-15
The Mus81-Eme1 complex is a structure-specific endonuclease that plays an important role in rescuing stalled replication forks and resolving the meiotic recombination intermediates in eukaryotes. We have determined the crystal structure of the Mus81-Eme1 complex. Both Mus81 and Eme1 consist of a central nuclease domain, two repeats of the helix-hairpin-helix (HhH) motif at their C-terminal region, and a linker helix. While each domain structure resembles archaeal XPF homologs, the overall structure is significantly different from those due to the structure of a linker helix. We show that a flexible intradomain linker that formed with 36 residues in the nuclease domain of Eme1 is essential for the recognition of DNA. We identified several basic residues lining the outer surface of the active site cleft of Mus81 that are involved in the interaction with a flexible arm of a nicked Holliday junction (HJ). These interactions might contribute to the optimal positioning of the opposite junction across the nick into the catalytic site, which provided the basis for the "nick and counternick" mechanism of Mus81-Eme1 and for the nicked HJ to be the favored in vitro substrate of this enzyme.
Control of complex networks requires both structure and dynamics
NASA Astrophysics Data System (ADS)
Gates, Alexander J.; Rocha, Luis M.
2016-04-01
The study of network structure has uncovered signatures of the organization of complex systems. However, there is also a need to understand how to control them; for example, identifying strategies to revert a diseased cell to a healthy state, or a mature cell to a pluripotent state. Two recent methodologies suggest that the controllability of complex systems can be predicted solely from the graph of interactions between variables, without considering their dynamics: structural controllability and minimum dominating sets. We demonstrate that such structure-only methods fail to characterize controllability when dynamics are introduced. We study Boolean network ensembles of network motifs as well as three models of biochemical regulation: the segment polarity network in Drosophila melanogaster, the cell cycle of budding yeast Saccharomyces cerevisiae, and the floral organ arrangement in Arabidopsis thaliana. We demonstrate that structure-only methods both undershoot and overshoot the number and which sets of critical variables best control the dynamics of these models, highlighting the importance of the actual system dynamics in determining control. Our analysis further shows that the logic of automata transition functions, namely how canalizing they are, plays an important role in the extent to which structure predicts dynamics.
Methods for SAXS-Based Structure Determination of Biomolecular Complexes
Yang, Sichun
2014-05-30
Measurements from small-angle X-ray scattering (SAXS) are highly informative to determine the structures of bimolecular complexes in solution. Here, we describe current and recent SAXS-driven developments, with an emphasis on computational modeling. In particular, accurate methods to computing one theoretical scattering profile from a given structure model are discussed, with a key focus on structure factor coarse-graining and hydration contribution. Methods for reconstructing topological structures from an experimental SAXS profile are currently under active development. We report on several modeling tools designed for conformation generation that make use of either atomic-level or coarse-grained representations. Furthermore, since large, flexible biomolecules canmore » adopt multiple well-defined conformations, a traditional single-conformation SAXS analysis is inappropriate, so we also discuss recent methods that utilize the concept of ensemble optimization, weighing in on the SAXS contributions of a heterogeneous mixture of conformations. These tools will ultimately posit the usefulness of SAXS data beyond a simple space-filling approach by providing a reliable structure characterization of biomolecular complexes under physiological conditions.« less
Complex Oxide Thin Film Metamaterial Structures for THz applications
NASA Astrophysics Data System (ADS)
Shreiber, D.; Cravey, R.; Cole, M. W.
2013-03-01
Metamaterials operating in the frequency range of 0.1-1.5 THz are of a special interest for multiple Army applications such as communications, NDE of materials, and detection of chem./bio hazards. Recently proposed dielectric metamaterials present an intriguing venue for the developments in this field due to their low propagation losses and ease of fabrication. These dielectric metamaterials were implemented in bulk and in thick films. Tunability of ferroelectric complex oxides is achieved by applied bias voltage and constitutes an additional benefit for multiple applications. However, real-life applications require usage of relatively low bias voltage which is achievable only by using a ferroelectric complex oxide thin-film. Although the physical dimensions of the thin film metamaterial structures suggest their usage in IR-optical spectrum, their very high dielectric constant provides a rare opportunity to lower their resonant frequency to the frequency range of interest. This presentation will discuss the opportunities and challenges associated with the metamaterial complex oxide thin film structures including numerical investigations of the resonant frequency shift as a function of the complex oxide thin film dielectric constant and thickness.
Control of cerium oxidation state through metal complex secondary structures
Levin, Jessica R.; Dorfner, Walter L.; Carroll, Patrick J.; Schelter, Eric J.
2015-08-11
A series of alkali metal cerium diphenylhydrazido complexes, M_{x}(py)_{y}[Ce(PhNNPh)_{4}], M = Li, Na, and K, x = 4 (Li and Na) or 5 (K), and y = 4 (Li), 8 (Na), or 7 (K), were synthesized to probe how a secondary coordination sphere would modulate electronic structures at a cerium cation. The resulting electronic structures of the heterobimetallic cerium diphenylhydrazido complexes were found to be strongly dependent on the identity of the alkali metal cations. When M = Li^{+ }or Na^{+}, the cerium(III) starting material was oxidized with concomitant reduction of 1,2-diphenylhydrazine to aniline. Reduction of 1,2-diphenylhydrazine was not observed when M = K^{+}, and the complex remained in the cerium(III) oxidation state. Oxidation of the cerium(III) diphenylhydrazido complex to the Ce(_{IV}) diphenylhydrazido one was achieved through a simple cation exchange reaction of the alkali metals. As a result, UV-Vis spectroscopy, FTIR spectroscopy, electrochemistry, magnetic susceptibility, and DFT studies were used to probe the oxidation state and the electronic changes that occurred at the metal centre.
Control of cerium oxidation state through metal complex secondary structures
Levin, Jessica R.; Dorfner, Walter L.; Carroll, Patrick J.; ...
2015-08-11
A series of alkali metal cerium diphenylhydrazido complexes, Mx(py)y[Ce(PhNNPh)4], M = Li, Na, and K, x = 4 (Li and Na) or 5 (K), and y = 4 (Li), 8 (Na), or 7 (K), were synthesized to probe how a secondary coordination sphere would modulate electronic structures at a cerium cation. The resulting electronic structures of the heterobimetallic cerium diphenylhydrazido complexes were found to be strongly dependent on the identity of the alkali metal cations. When M = Li+ or Na+, the cerium(III) starting material was oxidized with concomitant reduction of 1,2-diphenylhydrazine to aniline. Reduction of 1,2-diphenylhydrazine was not observedmore » when M = K+, and the complex remained in the cerium(III) oxidation state. Oxidation of the cerium(III) diphenylhydrazido complex to the Ce(IV) diphenylhydrazido one was achieved through a simple cation exchange reaction of the alkali metals. As a result, UV-Vis spectroscopy, FTIR spectroscopy, electrochemistry, magnetic susceptibility, and DFT studies were used to probe the oxidation state and the electronic changes that occurred at the metal centre.« less
Structural complexity and the quality of stepfather-stepchild relationships.
Clingempeel, W G; Ievoli, R; Brand, E
1984-12-01
This research examined the effects of structural complexity and sex of stepchild on the quality of stepfather-stepchild relationships. Sixteen simple stepfather families (the wife had custody of a child from a previous marriage, but the stepfather has no biological children) and 16 complex stepfather families (the wife had custody of a child from a previous marriage, and the stepfather was a noncustodial biological parent) with half of each type (N = 8) having a male and half having a female, 9-12-year-old target child participated in a multimethod-multimeasure assessment of the stepfather-stepchild relationship. Families were recruited from marriage license records, and data collection was accomplished in a single three-and-a-half-hour home visit. Dependent variables included: (a) questionnaire measures of love and detachment relationship dimensions independently obtained from parents, stepparents, and (step)children, and (b) proportions of positive and negative stepparent and stepchild communication behaviors derived from videotaped interaction tasks. Findings revealed that simple and complex stepfather families did not differ on any questionnaire or behavioral measures. Girls, however, engaged in a lower proportion of positive verbal and greater proportion of negative problem-solving behaviors toward their stepfathers than boys did. Stepfathers did not differ on proportions of communication behaviors emitted toward boys and girls. No sex-of-child differences were obtained on the questionnaire measures. Directions for future research on structural complexity and stepfather families are discussed.
Structure of the ESCRT-II endosomal trafficking complex.
Hierro, Aitor; Sun, Ji; Rusnak, Alexander S; Kim, Jaewon; Prag, Gali; Emr, Scott D; Hurley, James H
2004-09-09
The multivesicular-body (MVB) pathway delivers transmembrane proteins and lipids to the lumen of the endosome. The multivesicular-body sorting pathway has crucial roles in growth-factor-receptor downregulation, developmental signalling, regulation of the immune response and the budding of certain enveloped viruses such as human immunodeficiency virus. Ubiquitination is a signal for sorting into the MVB pathway, which also requires the functions of three protein complexes, termed ESCRT-I, -II and -III (endosomal sorting complex required for transport). Here we report the crystal structure of the core of the yeast ESCRT-II complex, which contains one molecule of the Vps protein Vps22, the carboxy-terminal domain of Vps36 and two molecules of Vps25, and has the shape of a capital letter 'Y'. The amino-terminal coiled coil of Vps22 and the flexible linker leading to the ubiquitin-binding NZF domain of Vps36 both protrude from the tip of one branch of the 'Y'. Vps22 and Vps36 form nearly equivalent interactions with the two Vps25 molecules at the centre of the 'Y'. The structure suggests how ubiquitinated cargo could be passed between ESCRT components of the MVB pathway through the sequential transfer of ubiquitinated cargo from one complex to the next.
DNA complexes with Ni nanoparticles: structural and functional properties
NASA Astrophysics Data System (ADS)
Tatarinova, Olga N.; Smirnov, Igor P.; Safenkova, Irina V.; Varizhuk, Anna M.; Pozmogova, Galina E.
2012-10-01
Supramolecular complexes of biopolymers based on magnetic nanoparticles play an important role in creation of biosensors, implementation of theragnostic and gene therapeutic methods and biosafety evaluation. We investigated the impact of DNA interactions with nanoparticles of nickel (nNi) on the integrity and functionality of DNA. Data obtained by mass spectrometry, electrophoresis, TEM and AFM microscopy techniques, bacterial transformation, and real-time PCR provide evidence that ssDNA and plasmid DNA (pDNA) efficiently form complexes with nNi. AFM data suggest that the complexes are necklace-type structures, in which nanoparticles are randomly distributed along the DNA chains, rather than highly entangled clot-type structures. After desorption, observed DNA characteristics in bioanalytical and biological systems remain unchanged. Only supercoiled pDNA was nicked, but remained, as well as a plasmid-nNi complex, active in expression vector assays. These results are very important for creation of new methods of DNA immobilization and controlled manipulation.
Optimal structure of complex networks for minimizing traffic congestion.
Zhao, Liang; Cupertino, Thiago Henrique; Park, Kwangho; Lai, Ying-Cheng; Jin, Xiaogang
2007-12-01
To design complex networks to minimize traffic congestion, it is necessary to understand how traffic flow depends on network structure. We study data packet flow on complex networks, where the packet delivery capacity of each node is not fixed. The optimal configuration of capacities to minimize traffic congestion is derived and the critical packet generating rate is determined, below which the network is at a free flow state but above which congestion occurs. Our analysis reveals a direct relation between network topology and traffic flow. Optimal network structure, free of traffic congestion, should have two features: uniform distribution of load over all nodes and small network diameter. This finding is confirmed by numerical simulations. Our analysis also makes it possible to theoretically compare the congestion conditions for different types of complex networks. In particular, we find that network with low critical generating rate is more susceptible to congestion. The comparison has been made on the following complex-network topologies: random, scale-free, and regular.
Structure sensitive normal coordinate analysis of metal-diethyldithiocarbamate - complexes
NASA Astrophysics Data System (ADS)
Mikosch, H.; Bauer, G.; Kellner, R.; Trendafilova, N. S.; St. Nikolov, G.
1986-03-01
Symmetry changes in the course of dissolution are assumed to produce frequency shifts in molecular spectra of N, N-Disubstituted Dithiocarbamates. Using (mass-weighted) cartesian coordinates it is possible to calculate eigenvalues both for the site- and the molecular symmetry. Calculated shifts for Cu- and Zn- complexes are of the same order of magnitude as experimental results and calculation of frequencies even for assumed structures is possible.
Generating a 2D Representation of a Complex Data Structure
NASA Technical Reports Server (NTRS)
James, Mark
2006-01-01
A computer program, designed to assist in the development and debugging of other software, generates a two-dimensional (2D) representation of a possibly complex n-dimensional (where n is an integer >2) data structure or abstract rank-n object in that other software. The nature of the 2D representation is such that it can be displayed on a non-graphical output device and distributed by non-graphical means.
18-crown-6-sodium cholate complex: thermochemistry, structure, and stability.
Mihelj, Tea; Tomašić, Vlasta; Biliškov, Nikola
2014-06-03
18-Crown-6, one of the most relevant crown ethers, and sodium cholate, a steroidal surfactant classified as a natural bile salt, are components of a novel, synthesized coordination complex: 18-crown-6-sodium cholate (18C6·NaCh). Like crown ethers, bile salts act as building blocks in supramolecular chemistry to design new functionalized materials with a desired structure and properties. In order to obtain thermal behavior of this 1:1 coordination complex, thermogravimetry and differential thermal analysis were used, as well as microscopic observations and differential scanning calorimetry. Temperature dependent infrared (IR) spectroscopy gave a detailed view into phase transitions. The structures during thermal treatment were observed with powder X-ray diffraction, and molecular models of the phases were made. Hard, glassy, colorless compound 18C6·NaCh goes through crystalline-crystalline polymorphic phase transitions at higher temperatures. The room temperature phase is indexed to a triclinic lattice, while in the high temperature phases molecules take randomly one of the two different configurations in the unit cell, resulting in the 2-fold symmetry. The formation of cholesteric liquid crystalline phase occurs simultaneously with partial decomposition, followed by the isotropization with simultaneous and complete decomposition at much higher temperature, as obtained by IR. The results provide valuable information about the relationship between molecular structure, thermal properties, and stability of the complex, indicating the importance of an appropriate choice of cation, amphiphilic, and crown ether unit in order to synthesize compounds with desired behavior.
Solution structure of the core SMN–Gemin2 complex
Sarachan, Kathryn L.; Valentine, Kathleen G.; Gupta, Kushol; Moorman, Veronica R.; Gledhill, John M.; Bernens, Matthew; Tommos, Cecilia; Wand, A. Joshua; Van Duyne, Gregory D.
2012-08-01
In humans, assembly of spliceosomal snRNPs (small nuclear ribonucleoproteins) begins in the cytoplasm where the multi-protein SMN (survival of motor neuron) complex mediates the formation of a seven-membered ring of Sm proteins on to a conserved site of the snRNA (small nuclear RNA). The SMN complex contains the SMN protein Gemin2 and several additional Gemins that participate in snRNP biosynthesis. SMN was first identified as the product of a gene found to be deleted or mutated in patients with the neurodegenerative disease SMA (spinal muscular atrophy), the leading genetic cause of infant mortality. In the present study, we report the solution structure of Gemin2 bound to the Gemin2-binding domain of SMN determined by NMR spectroscopy. This complex reveals the structure of Gemin2, how Gemin2 binds to SMN and the roles of conserved SMN residues near the binding interface. Surprisingly, several conserved SMN residues, including the sites of two SMA patient mutations, are not required for binding to Gemin2. Instead, they form a conserved SMN/Gemin2 surface that may be functionally important for snRNP assembly. The SMN–Gemin2 structure explains how Gemin2 is stabilized by SMN and establishes a framework for structure–function studies to investigate snRNP biogenesis as well as biological processes involving Gemin2 that do not involve snRNP assembly.
DMS Footprinting of Structured RNAs and RNA-Protein Complexes
Tijerina, Pilar; Mohr, Sabine; Russell, Rick
2008-01-01
We describe a protocol in which dimethyl sulfate (DMS) modification of the base-pairing faces of unpaired adenosine and cytidine nucleotides is used for structural analysis of RNAs and RNA-protein complexes (RNPs). The protocol is optimized for RNAs of small to moderate size (≤500 nucleotides). The RNA or RNP is first exposed to DMS under conditions that promote formation of the folded structure or complex, as well as ‘control’ conditions that do not allow folding or complex formation. The positions and extents of modification are then determined by primer extension, polyacrylamide gel electrophoresis (PAGE), and quantitative analysis. From changes in the extent of modification upon folding or protein binding (appearance of a ‘footprint’), it is possible to detect local changes in RNA secondary and tertiary structure, as well as the formation of RNA-protein contacts. This protocol takes 1.5–3 days to complete, depending on the type of analysis used. PMID:17948004
Complexation of Flavonoids with Iron: Structure and Optical Signatures
NASA Astrophysics Data System (ADS)
Ren, Jun; Meng, Sheng; Lekka, Ch. E.; Kaxiras, Efthimios
2008-03-01
Flavonoids exhibit antioxidant behavior believed to be related to their metal ion chelation ability. We investigate the complexation mechanism of several flavonoids, quercetin, luteolin, galangin, kaempferol and chrysin with iron, the most abundant type of metal ions in the body, through first- principles electronic structure calculations based on Density Functional Theory (DFT). We find that the most likely chelation site for Fe is the 3-hydroxyl-4-carbonyl group, followed by 4- carbonyl-5-hydroxyl group and the 3'-4' hydroxyl (if present) for all the flavonoid molecules studied. Three quercetin molecules are required to saturate the bonds of a single Fe ion by forming six orthogonal Fe-O bonds, though the binding energy per molecule is highest for complexes consisting of two quercetin molecules and one Fe atom, in agreement with experiment. Optical absorption spectra calculated with time- dependent DFT serve as signatures to identify various complexes. For the iron-quercetin complexes, we find a redshift of the first absorbance peak upon complexation in good agreement with experiment; this behavior is explained by the narrowing of the optical gap of quercetin due to Fe(d)--O(p) orbital hybridization.
Structure, bonding, and catecholase mechanism of copper bispidine complexes.
Comba, Peter; Martin, Bodo; Muruganantham, Amsaveni; Straub, Johannes
2012-09-03
Oxygen activation by copper(I) complexes with tetra- or pentadentate mono- or dinucleating bispidine ligands is known to lead to unusually stable end-on-[{(bispidine)Cu}(2)(O(2))](2+) complexes (bispidines are methyl-2,4-bis(2-pyridin-yl)-3,7-diazabicyclo-[3.3.1]-nonane-9-diol-1,5-dicarboxylates); catecholase activity of these dinuclear Cu(II/I) systems has been demonstrated experimentally, and the mechanism has been thoroughly analyzed. The present density functional theory (DFT) based study provides an analysis of the electronic structure and catalytic activity of [{(bispidine)Cu}(2)(O(2))](2+). As a result of the unique square pyramidal coordination geometry, the d(x(2)-y(2)) ground state leads to an unusual σ/π bonding pattern, responsible for the stability of the peroxo complex and the observed catecholase activity with a unique mechanistic pathway. The oxidation of catechol to ortho-quinone (one molecule per catalytic cycle and concomitant formation of one equivalent of H(2)O(2)) is shown to occur via an associative, stepwise pathway. The unusual stability of the end-on-peroxo-dicopper(II) complex and isomerization to copper(II) complexes with chelating catecholate ligands, which inhibit the catalytic cycle, are shown to be responsible for an only moderate catalytic activity.
Pyridylphosphinate metal complexes: synthesis, structural characterisation and biological activity.
Cross, Jasmine M; Gallagher, Natalie; Gill, Jason H; Jain, Mohit; McNeillis, Archibald W; Rockley, Kimberly L; Tscherny, Fiona H; Wirszycz, Natasha J; Yufit, Dmitry S; Walton, James W
2016-08-09
For the first time, a series of 25 pseudo-octahedral pyridylphosphinate metal complexes (Ru, Os, Rh, Ir) has been synthesised and assessed in biological systems. Each metal complex incorporates a pyridylphosphinate ligand, a monodentate halide and a capping η(6)-bound aromatic ligand. Solid- and solution-state analyses of two complexes reveal a structural preference for one of a possible two diastereomers. The metal chlorides hydrolyse rapidly in D2O to form a 1 : 1 equilibrium ratio between the aqua and chloride adducts. The pKa of the aqua adduct depends upon the pyridyl substituent and the metal but has little dependence upon the phosphinate R' group. Toxicity was measured in vitro against non-small cell lung carcinoma H460 cells, with the most potent complexes reporting IC50 values around 50 μM. Binding studies with selected amino acids and nucleobases provide a rationale for the variation in toxicity observed within the series. Finally, an investigation into the ability of the chelating amino acid l-His to displace the phosphinate O-metal bond shows the potential for phosphinate complexes to act as prodrugs that can be activated in the intracellular environment.
Special relativity as a noncommutative geometry: Lessons for deformed special relativity
Girelli, Florian; Livine, Etera R.
2010-04-15
Deformed special relativity (DSR) is obtained by imposing a maximal energy to special relativity and deforming the Lorentz symmetry (more exactly, the Poincare symmetry) to accommodate this requirement. One can apply the same procedure in the context of Galilean relativity by imposing a maximal speed (the speed of light). Effectively, one deforms the Galilean group and this leads to a noncommutative space structure, together with the deformations of composition of speed and conservation of energy momentum. In doing so, one runs into most of the ambiguities that one stumbles onto in the DSR context. However, this time, special relativity is there to tell us what is the underlying physics, in such a way we can understand and interpret these ambiguities. We use these insights to comment on the physics of DSR.
Anticancer activity of structurally related ruthenium(II) cyclopentadienyl complexes.
Côrte-Real, Leonor; Mendes, Filipa; Coimbra, Joana; Morais, Tânia S; Tomaz, Ana Isabel; Valente, Andreia; Garcia, M Helena; Santos, Isabel; Bicho, Manuel; Marques, Fernanda
2014-08-01
A set of structurally related Ru(η(5)-C5H5) complexes with bidentate N,N'-heteroaromatic ligands have been evaluated as prospective metallodrugs, with focus on exploring the uptake and cell death mechanisms and potential cellular targets. We have extended these studies to examine the potential of these complexes to target cancer cell metabolism, the energetic-related phenotype of cancer cells. The observations that these complexes can enter cells, probably facilitated by binding to plasma transferrin, and can be retained preferentially at the membranes prompted us to explore possible membrane targets involved in cancer cell metabolism. Most malignant tumors present the Warburg effect, which consists in increasing glycolytic rates with production of lactate, even in the presence of oxygen. The reliance of glycolytic cancer cells on trans-plasma-membrane electron transport (TPMET) systems for their continued survival raises the question of their appropriateness as a target for anticancer drug development strategies. Considering the interesting findings that some anticancer drugs in clinical use are cytotoxic even without entering cells and can inhibit TPMET activity, we investigated whether redox enzyme modulation could be a potential mechanism of action of antitumor ruthenium complexes. The results from this study indicated that ruthenium complexes can inhibit lactate production and TPMET activity in a way dependent on the cancer cell aggressiveness and the concentration of the complex. Combination approaches that target cell metabolism (glycolytic inhibitors) as well as proliferation are needed to successfully cure cancer. This study supports the potential use of some of these ruthenium complexes as adjuvants of glycolytic inhibitors in the treatment of aggressive cancers.
Fixed-point and implicit/inverse function theorems for free noncommutative functions
NASA Astrophysics Data System (ADS)
Abduvalieva, Gulnara K.
We establish a fixed-point theorem for mappings of square matrices of all sizes which respect the matrix sizes and direct sums of matrices. The conclusions are stronger if such a mapping is a free noncommutative function, i.e., if it respects matrix similarities. As a special case, we obtain the corresponding version of the Banach Contraction Mapping Theorem. This result is then applied to prove the existence and uniqueness of a solution of the initial value problem for ODEs in noncommutative spaces. As a by-product of the ideas developed in this paper, we establish a noncommutative version of the principle of nested closed sets. We prove the implicit function theorem and the inverse function theorem in two different settings: for free noncommutative functions over operator spaces and for free noncommutative functions on the set of nilpotent matrices.
Path-integral action of a particle in the noncommutative phase-space
NASA Astrophysics Data System (ADS)
Gangopadhyay, Sunandan; Halder, Aslam
2017-01-01
In this paper we construct a path integral formulation of quantum mechanics on noncommutative phase-space. We first map the system to an equivalent system on the noncommutative plane. Then by applying the formalism of representing a quantum system in the space of Hilbert-Schmidt operators acting on noncommutative configuration space, the path integral action of a particle is derived. It is observed that the action has a similar form to that of a particle in a magnetic field in the noncommutative plane. From this action the energy spectrum is obtained for the free particle and the harmonic-oscillator potential. We also show that the nonlocal nature (in time) of the action yields a second-class constrained system from which the noncommutative Heisenberg algebra can be recovered.
Crystal Structure of LGR4-Rspo1 Complex
Xu, Jin-Gen; Huang, Chunfeng; Yang, Zhengfeng; Jin, Mengmeng; Fu, Panhan; Zhang, Ni; Luo, Jian; Li, Dali; Liu, Mingyao; Zhou, Yan; Zhu, Yongqun
2015-01-01
Leucine-rich repeat G-protein-coupled receptors (LGRs) are a unique class of G-protein-coupled receptors characterized by a large extracellular domain to recognize ligands and regulate many important developmental processes. Among the three groups of LGRs, group B members (LGR4–6) recognize R-spondin family proteins (Rspo1–4) to stimulate Wnt signaling. In this study, we successfully utilized the “hybrid leucine-rich repeat technique,” which fused LGR4 with the hagfish VLR protein, to obtain two recombinant human LGR4 proteins, LGR415 and LGR49. We determined the crystal structures of ligand-free LGR415 and the LGR49-Rspo1 complex. LGR4 exhibits a twisted horseshoe-like structure. Rspo1 adopts a flat and β-fold architecture and is bound in the concave surface of LGR4 in the complex through electrostatic and hydrophobic interactions. All the Rspo1-binding residues are conserved in LGR4–6, suggesting that LGR4–6 bind R-spondins through an identical surface. Structural analysis of our LGR4-Rspo1 complex with the previously determined LGR4 and LGR5 structures revealed that the concave surface of LGR4 is the sole binding site for R-spondins, suggesting a one-site binding model of LGR4–6 in ligand recognition. The molecular mechanism of LGR4–6 is distinct from the two-step mechanism of group A receptors LGR1–3 and the multiple-interface binding model of group C receptors LGR7–8, suggesting LGRs utilize the divergent mechanisms for ligand recognition. Our structures, together with previous reports, provide a comprehensive understanding of the ligand recognition by LGRs. PMID:25480784
Complexity of Soils Porous Structure: A Simple Question
NASA Astrophysics Data System (ADS)
Benito, R. M.; Cardenas, J. P.; Santiago, A.; Borondo, F.; Losada, J. C.; Tarquis, A. M.; Grupo de Sistemas Complejos
2011-12-01
In the last decades scientist have realized that soil processes are implicated the biggest global challenges facing humanity such as soil aeration, sequestration or emission of greenhouse gasses, volatilization of volatile organic chemicals among other phenomena. Progress in these challenges will depend on being able to understand the integrated behavior of soil as a system, and dealing with the complexity in describing soil in these terms. In this work we focus in one of the critical soil issues: soil structure and pore connectivity. A quantitative and explicit characterization of soil structure is difficult because of the complexity of the pore space. We proposed a model to attempt to capture the complexity of the system in which we interpret porous soils as heterogeneous networks, where pores are represented by nodes and the links representing flows between them. Pore properties such as position and size are described by fixed states in a metric space, while an affinity function is introduced to bias the attachment probabilities of links according to these properties taking in account soil texture. These types of models are named as Heterogeneous Preferential Attachment (HPA). We perform an analytical study of the degree distributions in the soil model and show that under reasonable conditions all the model variants yield a multiscaling behavior in the connectivity degrees, leaving an empirically testable signature of heterogeneity in the topology of pore networks. With the aim to study in more detail topological properties of these networks, for different real soils samples an analysis of the community structure have been applied and studied depending on the values of the parameters of the porous soil model used. The detection of communities of pores, as groups densely connected with only sparser connections between groups, could contribute to understand the mechanisms of the diffusion phenomena in soils. References Cardenas, J. P. Cardenas, A. M. Tarquis, J. C
Bio-inspired Fabrication of Complex Hierarchical Structure in Silicon.
Gao, Yang; Peng, Zhengchun; Shi, Tielin; Tan, Xianhua; Zhang, Deqin; Huang, Qiang; Zou, Chuanping; Liao, Guanglan
2015-08-01
In this paper, we developed a top-down method to fabricate complex three dimensional silicon structure, which was inspired by the hierarchical micro/nanostructure of the Morpho butterfly scales. The fabrication procedure includes photolithography, metal masking, and both dry and wet etching techniques. First, microscale photoresist grating pattern was formed on the silicon (111) wafer. Trenches with controllable rippled structures on the sidewalls were etched by inductively coupled plasma reactive ion etching Bosch process. Then, Cr film was angled deposited on the bottom of the ripples by electron beam evaporation, followed by anisotropic wet etching of the silicon. The simple fabrication method results in large scale hierarchical structure on a silicon wafer. The fabricated Si structure has multiple layers with uniform thickness of hundreds nanometers. We conducted both light reflection and heat transfer experiments on this structure. They exhibited excellent antireflection performance for polarized ultraviolet, visible and near infrared wavelengths. And the heat flux of the structure was significantly enhanced. As such, we believe that these bio-inspired hierarchical silicon structure will have promising applications in photovoltaics, sensor technology and photonic crystal devices.
Structural characterization of polymorphs and molecular complexes of finasteride
NASA Astrophysics Data System (ADS)
Wawrzycka, Irena; Stȩpniak, Krystyna; Matyjaszczyk, Sławomir; Kozioł, Anna E.; Lis, Tadeusz; Abboud, Khalil A.
1999-01-01
The molecular structure of finasteride, 17 β-( N-tert-butylcarbamoyl)-4-aza-5 α-androst-1-en-3-one, and structures of three related crystalline forms have been determined by X-ray analysis. The rigid steroid skeleton of the molecule adopts a half-chair/chair/chair/half-chair conformation. Two peptide groups, one cyclic (lactam) in the ring A and a second being a part of the substituent at C17, are the main factors influencing intermolecular contacts. Different hydrogen-bond interactions of these hydrophilic groups are observed in the crystal structures. An infinite ribbon of finasteride molecules is formed between lactam groups in the orthorhombic homomolecular crystal ( 1) obtained from an ethanol solution. The linear molecular complex finasteride-acetic acid ( 1a) is connected by hydrogen bonds between the lactam of finasteride and the carboxyl group of acetic acid. The crystallization from an ethyl acetate solution gives a complex structure of bis-finasteride monohydrate ethyl acetate clathrate ( 1b) with guest molecule disordered in channels. Crystals of a second (monoclinic) finasteride polymorph ( 2) were obtained during thermal decomposition of 1a, and sublimation of 1, 1a and 1b. Two polymorphic forms show different IR spectra.
ISOLATION AND STRUCTURAL STUDIES ON SYNAPTIC COMPLEXES FROM RAT BRAIN
Cotman, Carl W.; Taylor, Dwan
1972-01-01
A fraction enriched in synaptic complexes has been isolated from rat brain. The major structural elements of synaptic complexes after isolation are a sector of pre- and postsynaptic plasma membranes joined together by a synaptic cleft and a postsynaptic density (PSD) located on the inner surface of the postsynaptic membrane. On its outer surface, the postsynaptic membrane has a series of projections which extend about halfway into the cleft and which occur along the entire length of the PSD. Proteolytic enzymes at high concentrations remove the PSD and open the synaptic cleft; at low concentrations the PSD is selectively destroyed. By contrast, the structural integrity of the PSD is resistant to treatment with NaCl, EGTA, and low concentrations of urea. Pre- and postsynaptic membranes also remain joined by the synaptic cleft after NaCl, EGTA, or mild urea treatment. High concentrations of urea cause the partial dissociation of the PSD. We conclude that polypeptides are probably one of the major components of the PSD and that the structural integrity of the PSD depends on polypeptides because disruption of the covalent or hydrophobic bonding of these polypeptides leads to a progressive loss of PSD structure. PMID:4656707
Probing the complex ionic structure of warm dense carbon
NASA Astrophysics Data System (ADS)
Kraus, Dominik
2014-10-01
The carbon phase diagram at extreme pressure conditions has received broad interest for modeling planetary interiors and high energy density laboratory experiments. Numerous theoretical models and simulations have recently been performed but critical experimental data at the phase boundaries and of the microscopic physical properties remain very scarce. In this work, we present novel experimental observations of the complex ion structure in warm dense carbon at pressures from 20 to 220 GPa and temperatures of several thousand Kelvins. Our experiments employ powerful x-ray sources at kilo-joule class laser facilities and at the Linac Coherent Light Source to perform spectrally and angularly resolved x-ray scattering from shock-compressed graphite samples; the absolute static ion structure factor is directly measured by resolving the ratio of elastically and inelastically scattered radiation. Using different types of graphite and varying drive laser intensity, we were able to probe conditions below and above the melting line, resolving the shock-induced graphite-to-diamond and graphite-to-liquid transitions on nanosecond time scale. Our results confirm a complex ionic structure predicted by QMD simulations and demonstrate the importance of chemical bonds at extreme conditions similar to those found in the interiors of giant planets. The evidence presented here thus provides a firmer ground for modeling the evolution and current structure of carbon-bearing icy giants like Neptune, Uranus, and a number of extra-solar planets.
Crystal structure of a nuclear actin ternary complex
Cao, Tingting; Sun, Lingfei; Jiang, Yuxiang; Huang, Shanjin; Wang, Jiawei; Chen, Zhucheng
2016-01-01
Actin polymerizes and forms filamentous structures (F-actin) in the cytoplasm of eukaryotic cells. It also exists in the nucleus and regulates various nucleic acid transactions, particularly through its incorporation into multiple chromatin-remodeling complexes. However, the specific structure of actin and the mechanisms that regulate its polymeric nature inside the nucleus remain unknown. Here, we report the crystal structure of nuclear actin (N-actin) complexed with actin-related protein 4 (Arp4) and the helicase-SANT–associated (HSA) domain of the chromatin remodeler Swr1. The inner face and barbed end of N-actin are sequestered by interactions with Arp4 and the HSA domain, respectively, which prevents N-actin from polymerization and binding to many actin regulators. The two major domains of N-actin are more twisted than those of globular actin (G-actin), and its nucleotide-binding pocket is occluded, freeing N-actin from binding to and regulation by ATP. These findings revealed the salient structural features of N-actin that distinguish it from its cytoplasmic counterpart and provide a rational basis for its functions and regulation inside the nucleus. PMID:27457955
Heo, Lim; Lee, Hasup; Seok, Chaok
2016-08-18
Protein-protein docking methods have been widely used to gain an atomic-level understanding of protein interactions. However, docking methods that employ low-resolution energy functions are popular because of computational efficiency. Low-resolution docking tends to generate protein complex structures that are not fully optimized. GalaxyRefineComplex takes such low-resolution docking structures and refines them to improve model accuracy in terms of both interface contact and inter-protein orientation. This refinement method allows flexibility at the protein interface and in the overall docking structure to capture conformational changes that occur upon binding. Symmetric refinement is also provided for symmetric homo-complexes. This method was validated by refining models produced by available docking programs, including ZDOCK and M-ZDOCK, and was successfully applied to CAPRI targets in a blind fashion. An example of using the refinement method with an existing docking method for ligand binding mode prediction of a drug target is also presented. A web server that implements the method is freely available at http://galaxy.seoklab.org/refinecomplex.
Heo, Lim; Lee, Hasup; Seok, Chaok
2016-01-01
Protein-protein docking methods have been widely used to gain an atomic-level understanding of protein interactions. However, docking methods that employ low-resolution energy functions are popular because of computational efficiency. Low-resolution docking tends to generate protein complex structures that are not fully optimized. GalaxyRefineComplex takes such low-resolution docking structures and refines them to improve model accuracy in terms of both interface contact and inter-protein orientation. This refinement method allows flexibility at the protein interface and in the overall docking structure to capture conformational changes that occur upon binding. Symmetric refinement is also provided for symmetric homo-complexes. This method was validated by refining models produced by available docking programs, including ZDOCK and M-ZDOCK, and was successfully applied to CAPRI targets in a blind fashion. An example of using the refinement method with an existing docking method for ligand binding mode prediction of a drug target is also presented. A web server that implements the method is freely available at http://galaxy.seoklab.org/refinecomplex. PMID:27535582
Jambhekar, Sunil S; Breen, Philip
2016-02-01
Cyclodextrins are cyclic oligosaccharides that have been recognized as pharmaceutical adjuvants for the past 20 years. The molecular structure of these glucose derivatives, which approximates a truncated cone, bucket, or torus, generates a hydrophilic exterior surface and a nonpolar interior cavity. Cyclodextrins can interact with appropriately sized drug molecules to yield an inclusion complex. These noncovalent inclusion complexes offer a variety of advantages over the noncomplexed form of a drug. Cyclodextrins are primarily used to enhance the aqueous solubility, physical chemical stability, and bioavailability of drugs. Their other applications include preventing drug-drug interactions, converting liquid drugs into microcrystalline powders, minimizing gastrointestinal and ocular irritation, and reducing or eliminating unpleasant taste and smell. Here, we discuss the physical chemical properties of various cyclodextrins, including the effects of substitutions on these properties. Additionally, we report on the regulatory status of their use, commercial products containing cyclodextrins, toxicological considerations, and the forces involved in complex formation. We also highlight the types of complex formed and discuss the methods used to determine the types of complex present.
The Bow City structure, southern Alberta, Canada: The deep roots of a complex impact structure?
NASA Astrophysics Data System (ADS)
Glombick, Paul; Schmitt, Douglas R.; Xie, Wei; Bown, Todd; Hathway, Ben; Banks, Christopher
2014-05-01
Geological and geophysical evidence is presented for a newly discovered, probable remnant complex impact structure. The structure, located near Bow City, southern Alberta, has no obvious morphological expression at surface. The geometry of the structure in the shallow subsurface, mapped using downhole geophysical well logs, is a semicircular structural depression approximately 8 km in diameter with a semicircular uplifted central region. Detailed subsurface mapping revealed evidence of localized duplication of stratigraphic section in the central uplift area and omission of strata within the surrounding annular region. Field mapping of outcrop confirmed an inlier of older rocks present within the center of the structure. Evidence of deformation along the eastern margin of the central uplift includes thrust faulting, folding, and steeply dipping bedding. Normal faults were mapped along the northern margin of the annular region. Isopach maps reveal that structural thickening and thinning were accommodated primarily within the Belly River Group. Evidence from legacy 2-D seismic data is consistent with the subsurface mapping and reveals additional insight into the geometry of the structure, including a series of listric normal faults in the annular region and complex faulting within the central uplift. The absence of any ejecta blanket, breccia, suevite, or melt sheet (based on available data) is consistent with the Bow City structure being the remnant of a deeply eroded, complex impact structure. Accordingly, the Bow City structure may provide rare access and insight into zones of deformation remaining beneath an excavated transient crater in stratified siliciclastic target rocks.
Complex Dynamic Flows in Solar Flare Sheet Structures
NASA Technical Reports Server (NTRS)
McKenzie, David E.; Reeves, Katharine K.; Savage, Sabrina
2012-01-01
Observations of high-energy emission from solar flares often reveal the presence of large sheet-like structures, sometimes extending over a space comparable to the Sun's radius. Given that these structures are found between a departing coronal mass ejection and the post-eruption flare arcade, it is natural to associate the structure with a current sheet; though the relationship is unclear. Moreover, recent high-resolution observations have begun to reveal that the motions in this region are highly complex, including reconnection outflows, oscillations, and apparent wakes and eddies. We present a detailed first look at the complicated dynamics within this supra-arcade plasma, and consider implications for the interrelationship between the plasma and its embedded magnetic field.
Structural Complexity and Phonon Physics in 2D Arsenenes.
Carrete, Jesús; Gallego, Luis J; Mingo, Natalio
2017-03-15
In the quest for stable 2D arsenic phases, four different structures have been recently claimed to be stable. We show that, due to phonon contributions, the relative stability of those structures differs from previous reports and depends crucially on temperature. We also show that one of those four phases is in fact mechanically unstable. Furthermore, our results challenge the common assumption of an inverse correlation between structural complexity and thermal conductivity. Instead, a richer picture emerges from our results, showing how harmonic interactions, anharmonicity, and symmetries all play a role in modulating thermal conduction in arsenenes. More generally, our conclusions highlight how vibrational properties are an essential element to be carefully taken into account in theoretical searches for new 2D materials.
The structure of the O2-N2O complex.
Salmon, Steven R; Lane, Joseph R
2015-09-28
We have investigated the lowest energy structures and interaction energies of the oxygen nitrous oxide complex (O2-N2O) using explicitly correlated coupled cluster theory. We find that the intermolecular potential energy surface of O2-N2O is very flat, with two minima of comparable energy separated by a low energy first order saddle point. Our results are able to conclusively distinguish between the two sets of experimental geometric parameters for O2-N2O that were previously determined from rotationally resolved infrared spectra. The global minimum structure of O2-N2O is therefore found to be planar with a distorted slipped parallel structure. Finally, we show that the very flat potential energy surface of O2-N2O is problematic when evaluating vibrational frequencies with a numerical Hessian and that consideration should be given as to whether results might change if the step-size is varied.
Measuring robustness of community structure in complex networks
NASA Astrophysics Data System (ADS)
Li, Hui-Jia; Wang, Hao; Chen, Luonan
2014-12-01
The theory of community structure is a powerful tool for real networks, which can simplify their topological and functional analysis considerably. However, since community detection methods have random factors and real social networks derived from complex systems always contain error edges, evaluating the robustness of community structure is an urgent and important task. In this letter, we employ the critical threshold of resolution parameter in Hamiltonian function, γC , to measure the robustness of a network. According to spectral theory, a rigorous proof shows that the index we proposed is inversely proportional to robustness of community structure. Furthermore, by utilizing the co-evolution model, we provides a new efficient method for computing the value of γC . The research can be applied to broad clustering problems in network analysis and data mining due to its solid mathematical basis and experimental effects.
Exceptional structural and mechanical flexibility of the nuclear pore complex.
Liashkovich, Ivan; Meyring, Anne; Kramer, Armin; Shahin, Victor
2011-03-01
Nuclear pore complexes (NPCs) mediate all transport between the cytosol and the nucleus and therefore take centre stage in physiology. While transport through NPCs has been extensively investigated little is known about their structural and barley anything about their mechanical flexibility. Structural and mechanical flexibility of NPCs, however, are presumably of key importance. Like the cell and the cell nucleus, NPCs themselves are regularly exposed to physiological mechanical forces. Besides, NPCs reveal striking transport properties which are likely to require fairly high structural flexibility. The NPC transports up to 1,000 molecules per second through a physically 9 nm wide channel which repeatedly opens to accommodate macromolecules significantly larger than its physical diameter. We hypothesised that NPCs possess remarkable structural and mechanical stability. Here, we tested this hypothesis at the single NPC level using the nano-imaging and probing approach atomic force microscopy (AFM). AFM presents the NPC as a highly flexible structure. The NPC channel dilates by striking 35% on exposure to trans-cyclohexane-1,2-diol (TCHD), which is known to transiently collapse the hydrophobic phase in the NPC channel like receptor-cargo complexes do in transit. It constricts again to its initial size after TCHD removal. AFM-based nano-indentation measurements show that the 50 nm long NPC basket can astonishingly be squeezed completely into the NPC channel on exposure to incremental mechanical loads but recovers its original vertical position within the nuclear envelope plane when relieved. We conclude that the NPC possesses exceptional structural and mechanical flexibility which is important to fulfilling its functions.
Manufacturing of a 3D complex hyperstable Cesic structure
NASA Astrophysics Data System (ADS)
Kroedel, Matthias; Courteau, Pascal; Poupinet, Anne; Sarri, Giuseppe
2007-09-01
Global astrometry requires extremely stable materials for instrument structures, such as optical benches. Cesic®, developed by ECM and Thales Alenia Space for mirrors and high stability structures, offers an excellent compromise in terms of structural strength, stability and very high lightweight capability, with a coefficient of thermal expansion that is virtually zero at cryogenic T°. The High-Stability Optical Bench (HSOB) GAIA study, realized by Thales Alenia Space under ESA contract, aimed to design, develop and test a full-scale representative of the HSOB bench, made entirely of Cesic®. The bench has been equipped with SAGEIS-CSO laser metrology system MOUSE1, a Michelson interferometer composed of integrated optics with nm-resolution. The HSOB bench has been submitted to a homogeneous T° step under vacuum to characterize 3-D expansion behavior of its two arms. The quite negligible interarm differential, measured with a nm-range reproducibility, demonstrates that a complete 3-D structure made of Cesic® has the same CTE homogeneity as do characterization samples, fully in line with the stringent GAIA requirements (1ppm at 120K). This demonstrates that Cesic® properties at cryogenic temperatures are fully appropriate to the manufacturing of complex highly stable optical structures. This successful study confirms ECM's and Thales Alenia Space's ability to design and manufacture monolithic lightweight highly stable optical structures, based on inner-cell triangular design made possible by the unique Cesic® manufacturing process.
Structural and Spectroscopic Insights into BolA-Glutaredoxin Complexes
Roret, Thomas; Tsan, Pascale; Couturier, Jérémy; Zhang, Bo; Johnson, Michael K.; Rouhier, Nicolas; Didierjean, Claude
2014-01-01
BolA proteins are defined as stress-responsive transcriptional regulators, but they also participate in iron metabolism. Although they can form [2Fe-2S]-containing complexes with monothiol glutaredoxins (Grx), structural details are lacking. Three Arabidopsis thaliana BolA structures were solved. They differ primarily by the size of a loop referred to as the variable [H/C] loop, which contains an important cysteine (BolA_C group) or histidine (BolA_H group) residue. From three-dimensional modeling and spectroscopic analyses of A. thaliana GrxS14-BolA1 holo-heterodimer (BolA_H), we provide evidence for the coordination of a Rieske-type [2Fe-2S] cluster. For BolA_C members, the cysteine could replace the histidine as a ligand. NMR interaction experiments using apoproteins indicate that a completely different heterodimer was formed involving the nucleic acid binding site of BolA and the C-terminal tail of Grx. The possible biological importance of these complexes is discussed considering the physiological functions previously assigned to BolA and to Grx-BolA or Grx-Grx complexes. PMID:25012657
Structural and spectroscopic insights into BolA-glutaredoxin complexes.
Roret, Thomas; Tsan, Pascale; Couturier, Jérémy; Zhang, Bo; Johnson, Michael K; Rouhier, Nicolas; Didierjean, Claude
2014-08-29
BolA proteins are defined as stress-responsive transcriptional regulators, but they also participate in iron metabolism. Although they can form [2Fe-2S]-containing complexes with monothiol glutaredoxins (Grx), structural details are lacking. Three Arabidopsis thaliana BolA structures were solved. They differ primarily by the size of a loop referred to as the variable [H/C] loop, which contains an important cysteine (BolA_C group) or histidine (BolA_H group) residue. From three-dimensional modeling and spectroscopic analyses of A. thaliana GrxS14-BolA1 holo-heterodimer (BolA_H), we provide evidence for the coordination of a Rieske-type [2Fe-2S] cluster. For BolA_C members, the cysteine could replace the histidine as a ligand. NMR interaction experiments using apoproteins indicate that a completely different heterodimer was formed involving the nucleic acid binding site of BolA and the C-terminal tail of Grx. The possible biological importance of these complexes is discussed considering the physiological functions previously assigned to BolA and to Grx-BolA or Grx-Grx complexes. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.
Linking structural features of protein complexes and biological function
Sowmya, Gopichandran; Breen, Edmond J; Ranganathan, Shoba
2015-01-01
Protein–protein interaction (PPI) establishes the central basis for complex cellular networks in a biological cell. Association of proteins with other proteins occurs at varying affinities, yet with a high degree of specificity. PPIs lead to diverse functionality such as catalysis, regulation, signaling, immunity, and inhibition, playing a crucial role in functional genomics. The molecular principle of such interactions is often elusive in nature. Therefore, a comprehensive analysis of known protein complexes from the Protein Data Bank (PDB) is essential for the characterization of structural interface features to determine structure–function relationship. Thus, we analyzed a nonredundant dataset of 278 heterodimer protein complexes, categorized into major functional classes, for distinguishing features. Interestingly, our analysis has identified five key features (interface area, interface polar residue abundance, hydrogen bonds, solvation free energy gain from interface formation, and binding energy) that are discriminatory among the functional classes using Kruskal-Wallis rank sum test. Significant correlations between these PPI interface features amongst functional categories are also documented. Salt bridges correlate with interface area in regulator-inhibitors (r = 0.75). These representative features have implications for the prediction of potential function of novel protein complexes. The results provide molecular insights for better understanding of PPIs and their relation to biological functions. PMID:26131659
Crystal Structure of the Eukaryotic Origin Recognition Complex
Bleichert, Franziska; Botchan, Michael R.; Berger, James M.
2015-01-01
Initiation of cellular DNA replication is tightly controlled to sustain genomic integrity. In eukaryotes, the heterohexameric origin recognition complex (ORC) is essential for coordinating replication onset. The 3.5 Å resolution crystal structure of Drosophila ORC reveals that the 270 kDa initiator core complex comprises a two-layered notched ring in which a collar of winged-helix domains from the Orc1-5 subunits sits atop a layer of AAA+ ATPase folds. Although canonical inter-AAA+ domain interactions exist between four of the six ORC subunits, unanticipated features are also evident, including highly interdigitated domain-swapping interactions between the winged-helix folds and AAA+ modules of neighboring protomers, and a quasi-spiral arrangement of DNA binding elements that circumnavigate a ~20 Å wide channel in the center of the complex. Comparative analyses indicate that ORC encircles DNA, using its winged-helix domain face to engage the MCM2-7 complex during replicative helicase loading; however, an observed >90° out-of-plane rotation for the Orc1 AAA+ domain disrupts interactions with catalytic amino acids in Orc4, narrowing and sealing off entry into the central channel. Prima facie, our data indicate that Drosophila ORC can switch between active and autoinhibited conformations, suggesting a novel means for cell cycle and/or developmental control of ORC functions. PMID:25762138
Structure of an extracellular gp130 cytokine receptor signaling complex.
Chow, D; He, X; Snow, A L; Rose-John, S; Garcia, K C
2001-03-16
The activation of gp130, a shared signal-transducing receptor for a family of cytokines, is initiated by recognition of ligand followed by oligomerization into a higher order signaling complex. Kaposi's sarcoma-associated herpesvirus encodes a functional homolog of human interleukin-6 (IL-6) that activates human gp130. In the 2.4 angstrom crystal structure of the extracellular signaling assembly between viral IL-6 and human gp130, two complexes are cross-linked into a tetramer through direct interactions between the immunoglobulin domain of gp130 and site III of viral IL-6, which is necessary for receptor activation. Unlike human IL-6 (which uses many hydrophilic residues), the viral cytokine largely uses hydrophobic amino acids to contact gp130, which enhances the complementarity of the viral IL-6-gp130 binding interfaces. The cross-reactivity of gp130 is apparently due to a chemical plasticity evident in the amphipathic gp130 cytokine-binding sites.
Structural Mechanism for Cargo Recognition by the Retromer Complex.
Lucas, María; Gershlick, David C; Vidaurrazaga, Ander; Rojas, Adriana L; Bonifacino, Juan S; Hierro, Aitor
2016-12-01
Retromer is a multi-protein complex that recycles transmembrane cargo from endosomes to the trans-Golgi network and the plasma membrane. Defects in retromer impair various cellular processes and underlie some forms of Alzheimer's disease and Parkinson's disease. Although retromer was discovered over 15 years ago, the mechanisms for cargo recognition and recruitment to endosomes have remained elusive. Here, we present an X-ray crystallographic analysis of a four-component complex comprising the VPS26 and VPS35 subunits of retromer, the sorting nexin SNX3, and a recycling signal from the divalent cation transporter DMT1-II. This analysis identifies a binding site for canonical recycling signals at the interface between VPS26 and SNX3. In addition, the structure highlights a network of cooperative interactions among the VPS subunits, SNX3, and cargo that couple signal-recognition to membrane recruitment.
The origin recognition complex: a biochemical and structural view
Li, Huilin; Stillman, Bruce
2013-01-01
The origin recognition complex (ORC) was first discovered in the baker’s yeast in 1992. Identification of ORC opened up a path for subsequent molecular level investigations on how eukaryotic cells initiate and control genome duplication each cell cycle. Twenty years after the first biochemical isolation, ORC is now taking on a three-dimensional shape, although a very blurry shape at the moment, thanks to the recent electron microscopy and image reconstruction efforts. In this chapter, we outline the current biochemical knowledge about ORC from several eukaryotic systems, with emphasis on the most recent structural and biochemical studies. Despite many species-specific properties, an emerging consensus is that ORC is a ATP-dependent machine that recruits other key proteins to form pre-Replicative Complexes (pre-RCs) at many origins of DNA replication, enabling the subsequent initiation of DNA replication in S phase. PMID:22918579
Structure and stability of oligomer/α-cyclodextrin inclusion complexes.
NASA Astrophysics Data System (ADS)
Hunt, Marcus; Villar, Silvia; Gomez, Marian; Tonelli, Alan; Balik, Maury
2007-03-01
Cyclomaltohexaose (α-cyclodextrin, α-CD) can form inclusion complexes (ICs) with polymer molecules in the columnar crystal in which α-CD molecules stack to form a molecular tube. Complementary water vapor sorption and wide-angle X-ray diffractomery (WAXD) were performed on oligomer/α-CD ICs to probe their structures and stabilities. To discern the effect of guest molecule hydrophobicity on water adsorption isotherms, polyethylene glycol (PEG, MW = 600 g/mol) and hexatriacontane (HTC) guests were used. Sorption isotherms for PEG/α-CD IC are similar to those obtained for pure α-CD and PEG, suggesting the presence of dethreaded PEG in the sample. WAXD collected before and after water vapor sorption of PEG/α-CD IC indicated a partial conversion from columnar to cage crystal structure, the thermodynamically preferred structure for pure α-CD, due to dethreading of PEG. This behavior does not occur for HTC/α-CD IC. Sorption isotherms collected at 20, 30, 40 and 50 C allowed the calculation of differential heats of adsorption and integral entropies of adsorbed water, while solid-state ^13C NMR suggested a dramatic increase in HTC and α-CD mobilities upon complexation.
Brain structural correlates of complex sentence comprehension in children.
Fengler, Anja; Meyer, Lars; Friederici, Angela D
2015-10-01
Prior structural imaging studies found initial evidence for the link between structural gray matter changes and the development of language performance in children. However, previous studies generally only focused on sentence comprehension. Therefore, little is known about the relationship between structural properties of brain regions relevant to sentence processing and more specific cognitive abilities underlying complex sentence comprehension. In this study, whole-brain magnetic resonance images from 59 children between 5 and 8 years were assessed. Scores on a standardized sentence comprehension test determined grammatical proficiency of our participants. A confirmatory factory analysis corroborated a grammar-relevant and a verbal working memory-relevant factor underlying the measured performance. Voxel-based morphometry of gray matter revealed that while children's ability to assign thematic roles is positively correlated with gray matter probability (GMP) in the left inferior temporal gyrus and the left inferior frontal gyrus, verbal working memory-related performance is positively correlated with GMP in the left parietal operculum extending into the posterior superior temporal gyrus. Since these areas are known to be differentially engaged in adults' complex sentence processing, our data suggest a specific correspondence between children's GMP in language-relevant brain regions and differential cognitive abilities that guide their sentence comprehension. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.
Crystal structure of the intraflagellar transport complex 25/27
Bhogaraju, Sagar; Taschner, Michael; Morawetz, Michaela; Basquin, Claire; Lorentzen, Esben
2011-01-01
The cilium is an important organelle that is found on many eukaryotic cells, where it serves essential functions in motility, sensory reception and signalling. Intraflagellar transport (IFT) is a vital process for the formation and maintenance of cilia. We have determined the crystal structure of Chlamydomonas reinhardtii IFT25/27, an IFT sub-complex, at 2.6 Å resolution. IFT25 and IFT27 interact via a conserved interface that we verify biochemically using structure-guided mutagenesis. IFT27 displays the fold of Rab-like small guanosine triphosphate hydrolases (GTPases), binds GTP and GDP with micromolar affinity and has very low intrinsic GTPase activity, suggesting that it likely requires a GTPase-activating protein (GAP) for robust GTP turnover. A patch of conserved surface residues contributed by both IFT25 and IFT27 is found adjacent to the GTP-binding site and could mediate the binding to other IFT proteins as well as to a potential GAP. These results provide the first step towards a high-resolution structural understanding of the IFT complex. PMID:21505417
Temporal Structure and Complexity Affect Audio-Visual Correspondence Detection
Denison, Rachel N.; Driver, Jon; Ruff, Christian C.
2013-01-01
Synchrony between events in different senses has long been considered the critical temporal cue for multisensory integration. Here, using rapid streams of auditory and visual events, we demonstrate how humans can use temporal structure (rather than mere temporal coincidence) to detect multisensory relatedness. We find psychophysically that participants can detect matching auditory and visual streams via shared temporal structure for crossmodal lags of up to 200 ms. Performance on this task reproduced features of past findings based on explicit timing judgments but did not show any special advantage for perfectly synchronous streams. Importantly, the complexity of temporal patterns influences sensitivity to correspondence. Stochastic, irregular streams – with richer temporal pattern information – led to higher audio-visual matching sensitivity than predictable, rhythmic streams. Our results reveal that temporal structure and its complexity are key determinants for human detection of audio-visual correspondence. The distinctive emphasis of our new paradigms on temporal patterning could be useful for studying special populations with suspected abnormalities in audio-visual temporal perception and multisensory integration. PMID:23346067