Noncommutative complex structures on quantum homogeneous spaces
NASA Astrophysics Data System (ADS)
Ó Buachalla, Réamonn
2016-01-01
A new framework for noncommutative complex geometry on quantum homogeneous spaces is introduced. The main ingredients used are covariant differential calculi and Takeuchi's categorical equivalence for quantum homogeneous spaces. A number of basic results are established, producing a simple set of necessary and sufficient conditions for noncommutative complex structures to exist. Throughout, the framework is applied to the quantum projective spaces endowed with the Heckenberger-Kolb calculus.
Construction of the noncommutative complex ball
Wang, Zhituo
2014-09-15
We describe the construction of the noncommutative complex ball whose commutative analog is the Hermitian symmetric space D = SU(m, 1)/U(m), with the method of coherent state quantization. In the commutative limit, we obtain the standard manifold. We also consider a quantum field theory model on the noncommutative manifold.
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.
Noncommutative Biology: Sequential Regulation of Complex Networks.
Letsou, William; Cai, Long
2016-08-01
Single-cell variability in gene expression is important for generating distinct cell types, but it is unclear how cells use the same set of regulatory molecules to specifically control similarly regulated genes. While combinatorial binding of transcription factors at promoters has been proposed as a solution for cell-type specific gene expression, we found that such models resulted in substantial information bottlenecks. We sought to understand the consequences of adopting sequential logic wherein the time-ordering of factors informs the final outcome. We showed that with noncommutative control, it is possible to independently control targets that would otherwise be activated simultaneously using combinatorial logic. Consequently, sequential logic overcomes the information bottleneck inherent in complex networks. We derived scaling laws for two noncommutative models of regulation, motivated by phosphorylation/neural networks and chromosome folding, respectively, and showed that they scale super-exponentially in the number of regulators. We also showed that specificity in control is robust to the loss of a regulator. Lastly, we connected these theoretical results to real biological networks that demonstrate specificity in the context of promiscuity. These results show that achieving a desired outcome often necessitates roundabout steps. PMID:27560383
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.
Classical mechanics on noncommutative space with Lie-algebraic structure
Miao Yangang; Wang Xudong; Yu Shaojie
2011-08-15
Highlights: > Suggest a useful method to look for new Lie-algebraic noncommutative spaces. > Find out two new Lie-algebraic noncommutative spaces. > Derive Newton and Hamilton equations that present unimaginable extra forces. > Analyse the source of unimaginable extra forces from space noncummutativity. > Provide various intriguing classical trajectories. - Abstract: We investigate the kinetics of a nonrelativistic particle interacting with a constant external force on a Lie-algebraic noncommutative space. The structure constants of a Lie algebra, also called noncommutative parameters, are constrained in general due to some algebraic properties, such as the antisymmetry and Jacobi identity. Through solving the constraint equations the structure constants satisfy, we obtain two new sorts of algebraic structures, each of which corresponds to one type of noncommutative spaces. Based on such types of noncommutative spaces as the starting point, we analyze the classical motion of the particle interacting with a constant external force by means of the Hamiltonian formalism on a Poisson manifold. Our results not only include that of a recent work as our special cases, but also provide new trajectories of motion governed mainly by marvelous extra forces. The extra forces with the unimaginable tx-dot-,(xx-dot)-, and (xx-double dot)-dependence besides with the usual t-, x-, and x-dot-dependence, originating from a variety of noncommutativity between different spatial coordinates and between spatial coordinates and momenta as well, deform greatly the particle's ordinary trajectories we are quite familiar with on the Euclidean (commutative) space.
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.
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.
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
Stern, A.
2008-02-15
We construct a perturbative solution to classical noncommutative gauge theory on R{sup 3} minus the origin using the Groenewald-Moyal star product. The result describes a noncommutative point charge. Applying it to the quantum mechanics of the noncommutative hydrogen atom gives shifts in the 1S hyperfine splitting which are first order in the noncommutativity parameter.
Noncommutative corrections to the Robertson-Walker metric
Fabi, S.; Harms, B.; Stern, A.
2008-09-15
Upon applying Chamseddine's noncommutative deformation of gravity, we obtain the leading order noncommutative corrections to the Robertson-Walker metric tensor. We get an isotropic inhomogeneous metric tensor for a certain choice of the noncommutativity parameters. Moreover, the singularity of the commutative metric at t=0 is replaced by a more involved space-time structure in the noncommutative theory. In a toy model we construct a scenario where there is no singularity at t=0 at leading order in the noncommutativity parameter. Although singularities may still be present for nonzero t, they need not be the source of all timelike geodesics and the result resembles a bouncing cosmology.
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 effects of spacetime on holographic superconductors
NASA Astrophysics Data System (ADS)
Ghorai, Debabrata; Gangopadhyay, Sunandan
2016-07-01
The Sturm-Liouville eigenvalue method is employed to analytically investigate the properties of holographic superconductors in higher dimensions in the framework of Born-Infeld electrodynamics incorporating the effects of noncommutative spacetime. In the background of pure Einstein gravity in noncommutative spacetime, we obtain the relation between the critical temperature and the charge density. We also obtain the value of the condensation operator and the critical exponent. Our findings suggest that the higher value of noncommutative parameter and Born-Infeld parameter make the condensate harder to form. We also observe that the noncommutative structure of spacetime makes the critical temperature depend on the mass of the black hole and higher value of black hole mass is favourable for the formation of the condensate.
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.
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.
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.
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.
Renormalization on noncommutative torus
NASA Astrophysics Data System (ADS)
D'Ascanio, D.; Pisani, P.; Vassilevich, D. V.
2016-04-01
We study a self-interacting scalar \\varphi ^4 theory on the d-dimensional noncommutative torus. We determine, for the particular cases d=2 and d=4, the counterterms required by one-loop renormalization. We discuss higher loops in two dimensions and two-loop contributions to the self-energy in four dimensions. Our analysis points toward the absence of any problems related to the ultraviolet/infrared mixing and thus to renormalizability of the theory. However, we find another potentially troubling phenomenon which is a wild behavior of the two-point amplitude as a function of the noncommutativity matrix θ.
Morita equivalence and spectral triples on noncommutative orbifolds
NASA Astrophysics Data System (ADS)
Harju, Antti J.
2016-08-01
Let G be a finite group. Noncommutative geometry of unital G-algebras is studied. A geometric structure is determined by a spectral triple on the crossed product algebra associated with the group action. This structure is to be viewed as a representative of a noncommutative orbifold. Based on a study of classical orbifold groupoids, a Morita equivalence for the crossed product spectral triples is developed. Noncommutative orbifolds are Morita equivalence classes of the crossed product spectral triples. As a special case of this Morita theory one can study freeness of the G-action on the noncommutative level. In the case of a free action, the crossed product formalism reduced to the usual spectral triple formalism on the algebra of G-invariant functions.
On the renormalization of non-commutative field theories
NASA Astrophysics Data System (ADS)
Blaschke, Daniel N.; Garschall, Thomas; Gieres, François; Heindl, Franz; Schweda, Manfred; Wohlgenannt, Michael
2013-01-01
This paper addresses three topics concerning the quantization of non-commutative field theories (as defined in terms of the Moyal star product involving a constant tensor describing the non-commutativity of coordinates in Euclidean space). To start with, we discuss the Quantum Action Principle and provide evidence for its validity for non-commutative quantum field theories by showing that the equation of motion considered as insertion in the generating functional Z c [ j] of connected Green functions makes sense (at least at one-loop level). Second, we consider the generalization of the BPHZ renormalization scheme to non-commutative field theories and apply it to the case of a self-interacting real scalar field: Explicit computations are performed at one-loop order and the generalization to higher loops is commented upon. Finally, we discuss the renormalizability of various models for a self-interacting complex scalar field by using the approach of algebraic renormalization.
Noncommutative Geometry and Physics
Connes, Alain
2006-11-03
In this very short essay we shall describe a 'spectral' point of view on geometry which allows to start taking into account the lessons from both renormalization and of general relativity. We shall first do that for renormalization and explain in rough outline the content of our recent collaborations with Dirk Kreimer and Matilde Marcolli leading to the universal Galois symmetry of renormalizable quantum field theories provided by the renormalization group in its cosmic Galois group incarnation. As far as general relativity is concerned, since the functional integral cannot be treated in the traditional perturbative manner, it relies heavily as a 'sum over geometries' on the chosen paradigm of geometric space. This will give us the occasion to discuss, in the light of noncommutative geometry, the issue of 'observables' in gravity and our joint work with Ali Chamseddine on the spectral action, with a first attempt to write down a functional integral on the space of noncommutative geometries.
Noncommutative SO(2,3) gauge theory and noncommutative gravity
NASA Astrophysics Data System (ADS)
Dimitrijević, Marija; Radovanović, Voja
2014-06-01
In this paper noncommutative gravity is constructed as a gauge theory of the noncommutative SO(2,3)⋆ group, while the noncommutativity is canonical (constant). The Seiberg-Witten map is used to express noncommutative fields in terms of the corresponding commutative fields. The commutative limit of the model is the Einstein-Hilbert action with the cosmological constant term and the topological Gauss-Bonnet term. We calculate the second order correction to this model and obtain terms that are of zeroth to fourth power in the curvature tensor and torsion. Trying to relate our results with f(R) and f(T) models, we analyze different limits of our model. In the limit of big cosmological constant and vanishing torsion we obtain an x-dependent correction to the cosmological constant; i.e. noncommutativity leads to an x-dependent cosmological constant. We also discuss the limit of small cosmological constant and vanishing torsion and the teleparallel limit.
Noncommutative fluid dynamics in the Kähler parametrization
NASA Astrophysics Data System (ADS)
Holender, L.; Santos, M. A.; Orlando, M. T. D.; Vancea, I. V.
2011-11-01
In this paper, we propose a first-order action functional for a large class of systems that generalize the relativistic perfect fluids in the Kähler parametrization to noncommutative spacetimes. The noncommutative action is parametrized by two arbitrary functions K(z,z¯) and f(-j2) that depend on the fluid potentials and represent the generalization of the Kähler potential of the complex surface parametrized by z and z¯, respectively, and the characteristic function of each model. We calculate the equations of motion for the fluid potentials and the energy-momentum tensor in the first order in the noncommutative parameter. The density current does not receive any noncommutative corrections and it is conserved under the action of the commutative generators Pμ but the energy-momentum tensor is not. Therefore, we determine the set of constraints under which the energy-momentum tensor is divergenceless. Another set of constraints on the fluid potentials is obtained from the requirement of the invariance of the action under the generalization of the volume preserving transformations of the noncommutative spacetime. We show that the proposed action describes noncommutative fluid models by casting the energy-momentum tensor in the familiar fluid form and identifying the corresponding energy and momentum densities. In the commutative limit, they are identical to the corresponding quantities of the relativistic perfect fluids. The energy-momentum tensor contains a dissipative term that is due to the noncommutative spacetime and vanishes in the commutative limit. Finally, we particularize the theory to the case when the complex fluid potentials are characterized by a function K(z,z¯) that is a deformation of the complex plane and show that this model has important common features with the commutative fluid such as infinitely many conserved currents and a conserved axial current that in the commutative case is associated to the topologically conserved linking number.
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.
Noncommutative quantum mechanics
NASA Astrophysics Data System (ADS)
Gamboa, J.; Loewe, M.; Rojas, J. C.
2001-09-01
A general noncommutative quantum mechanical system in a central potential V=V(r) in two dimensions is considered. The spectrum is bounded from below and, for large values of the anticommutative parameter θ, we find an explicit expression for the eigenvalues. In fact, any quantum mechanical system with these characteristics is equivalent to a commutative one in such a way that the interaction V(r) is replaced by V=V(HHO,Lz), where HHO is the Hamiltonian of the two-dimensional harmonic oscillator and Lz is the z component of the angular momentum. For other finite values of θ the model can be solved by using perturbation theory.
Plane waves in noncommutative fluids
NASA Astrophysics Data System (ADS)
Abdalla, M. C. B.; Holender, L.; Santos, M. A.; Vancea, I. V.
2013-08-01
We study the dynamics of the noncommutative fluid in the Snyder space perturbatively at the first order in powers of the noncommutative parameter. The linearized noncommutative fluid dynamics is described by a system of coupled linear partial differential equations in which the variables are the fluid density and the fluid potentials. We show that these equations admit a set of solutions that are monochromatic plane waves for the fluid density and two of the potentials and a linear function for the third potential. The energy-momentum tensor of the plane waves is calculated.
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.
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.
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.
Lifshitz field theories, Snyder noncommutative spacetime and momentum-dependent metric
NASA Astrophysics Data System (ADS)
Romero, Juan M.; Vergara, J. David
2015-08-01
In this paper, we propose three different modified relativistic particles. In the first case, we propose a particle with metrics depending on the momenta and we show that the quantum version of these systems includes different field theories, as Lifshitz field theories. As a second case, we propose a particle that implies a modified symplectic structure and we show that the quantum version of this system gives different noncommutative spacetimes, for example the Snyder spacetime. In the third case, we combine both structures before mentioned, namely noncommutative spacetimes and momentum-dependent metrics. In this last case, we show that anisotropic field theories can be seen as a limit of noncommutative field theory.
Structural complexity of DNA sequence.
Liou, Cheng-Yuan; Tseng, Shen-Han; 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
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
Quanta of geometry: noncommutative aspects.
Chamseddine, Ali H; Connes, Alain; Mukhanov, Viatcheslav
2015-03-01
In the construction of spectral manifolds in noncommutative geometry, a higher degree Heisenberg commutation relation involving the Dirac operator and the Feynman slash of real scalar fields naturally appears and implies, by equality with the index formula, the quantization of the volume. We first show that this condition implies that the manifold decomposes into disconnected spheres, which will represent quanta of geometry. We then refine the condition by involving the real structure and two types of geometric quanta, and show that connected spin manifolds with large quantized volume are then obtained as solutions. The two algebras M_{2}(H) and M_{4}(C) are obtained, which are the exact constituents of the standard model. Using the two maps from M_{4} to S^{4} the four-manifold is built out of a very large number of the two kinds of spheres of Planckian volume. We give several physical applications of this scheme such as quantization of the cosmological constant, mimetic dark matter, and area quantization of black holes. PMID:25793795
Noncommutative CPN and CHN and their physics
NASA Astrophysics Data System (ADS)
Sako, Akifumi; Suzuki, Toshiya; Umetsu, Hiroshi
2013-06-01
We study noncommutative deformation of manifolds by constructing star products. We start from a noncommutative Bbb Rd and discuss more genaral noncommutative manifolds. In general, star products can not be described in concrete expressions without some exceptions. In this article we introduce new examples of noncommutative manifolds with explicit star products. Karabegov's deformation quantization of Bbb CPN and Bbb CHN with separation of variables gives explicit calulable star products represented by gamma functions. Using the results of star products between inhomogeneous coordinates, we find creation and anihilation operators and obtain the Fock representation of the noncommutative Bbb CPN and Bbb CHN.
Landau problem in noncommutative quantum mechanics
NASA Astrophysics Data System (ADS)
Sayipjamal, Dulat; Li, Kang
2008-02-01
The Landau problem in non-commutative quantum mechanics (NCQM) is studied. First by solving the Schrödinger equations on noncommutative (NC) space we obtain the Landau energy levels and the energy correction that is caused by space-space noncommutativity. Then we discuss the noncommutative phase space case, namely, space-space and momentum-momentum non-commutative case, and we get the explicit expression of the Hamiltonian as well as the corresponding eigenfunctions and eigenvalues. Supported by National Natural Science Foundation of China (10465004, 10665001, 10575026) and Abdus Salam ICTP, Trieste, Italy
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).
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.
The complex structured singular value
NASA Technical Reports Server (NTRS)
Packard, A.; Doyle, J.
1993-01-01
A tutorial introduction to the complex structured singular value (mu) is presented, with an emphasis on the mathematical aspects of mu. The mu-based methods discussed here have been useful for analyzing the performance and robustness properties of linear feedback systems. Several tests for robust stability and performance with computable bounds for transfer functions and their state space realizations are compared, and a simple synthesis problem is studied. Uncertain systems are represented using linear fractional transformations which naturally unify the frequency-domain and state space methods.
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.
Noncommutative geometry inspired entropic inflation
NASA Astrophysics Data System (ADS)
Nozari, Kourosh; Akhshabi, Siamak
2011-06-01
Recently Verlinde proposed that gravity can be described as an emergent phenomena arising from changes in the information associated with the positions of material bodies. By using noncommutative geometry as a way to describe the microscopic microstructure of quantum spacetime, we derive modified Friedmann equation in this setup and study the entropic force modifications to the inflationary dynamics of early universe.
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
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.
Structure determination of transient transcription complexes.
Cramer, Patrick
2016-08-15
The determination of detailed 3D structures of large and transient multicomponent complexes remains challenging. Here I describe the approaches that were used and developed by our laboratory to achieve structure solution of eukaryotic transcription complexes. I hope this collection serves as a resource for structural biologists seeking solutions for difficult structure determination projects. PMID:27528766
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.
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.
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.
Fock modules and noncommutative line bundles
NASA Astrophysics Data System (ADS)
Landi, Giovanni
2016-09-01
To a line bundle over a noncommutative space there is naturally associated a Fock module. The algebra of corresponding creation and annihilation operators is the total space algebra of a principal U(1) -bundle over the noncommutative space. We describe the general construction and illustrate it with examples.
3D complex: a structural classification of protein complexes.
Levy, Emmanuel D; Pereira-Leal, Jose B; Chothia, Cyrus; Teichmann, Sarah A
2006-11-17
Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.
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.
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…
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.
Generalized complex structures on Kodaira surfaces
NASA Astrophysics Data System (ADS)
Brinzanescu, Vasile; Turcu, Oana Adela
2010-01-01
We compute the deformations in the sense of generalized complex structures of the standard classical complex structure on a primary Kodaira surface and we prove that the obtained family of deformations is a smooth locally complete family depending on four complex parameters. This family is the same as the extended deformations (in the sense of Kontsevich and Barannikov) in degree two, obtained by Poon using differential Gerstenhaber algebras.
Structure-based characterization of multiprotein complexes.
Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J
2014-07-01
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
Spin Hall effect on a noncommutative space
Ma Kai; Dulat, Sayipjamal
2011-07-15
We study the spin-orbital interaction and the spin Hall effect of an electron moving on a noncommutative space under the influence of a vector potential A(vector sign). On a noncommutative space, we find that the commutator between the vector potential A(vector sign) and the electric potential V{sub 1}(r(vector sign)) of the lattice induces a new term, which can be treated as an effective electric field, and the spin Hall conductivity obtains some correction. On a noncommutative space, the spin current and spin Hall conductivity have distinct values in different directions, and depend explicitly on the noncommutative parameter. Once this spin Hall conductivity in different directions can be measured experimentally with a high level of accuracy, the data can then be used to impose bounds on the value of the space noncommutativity parameter. We have also defined a new parameter, {sigma}={rho}{theta} ({rho} is the electron concentration, {theta} is the noncommutativity parameter), which can be measured experimentally. Our approach is based on the Foldy-Wouthuysen transformation, which gives a general Hamiltonian of a nonrelativistic electron moving on a noncommutative space.
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.
Imprecise probability for non-commuting observables
NASA Astrophysics Data System (ADS)
Allahverdyan, Armen E.
2015-08-01
It is known that non-commuting observables in quantum mechanics do not have joint probability. This statement refers to the precise (additive) probability model. I show that the joint distribution of any non-commuting pair of variables can be quantified via upper and lower probabilities, i.e. the joint probability is described by an interval instead of a number (imprecise probability). I propose transparent axioms from which the upper and lower probability operators follow. The imprecise probability depend on the non-commuting observables, is linear over the state (density matrix) and reverts to the usual expression for commuting observables.
Projectively adapted pattern representation using noncommutative harmonic analysis
NASA Astrophysics Data System (ADS)
Turski, Jacek
1996-03-01
Projectively invariant classification of patterns is constructed in terms of orbits of the group SL(2,C) acting on an extended complex line (image plane with complex coordinates) by Mobius transformations. It provides projectively adapted noncommutative harmonic analysis for patterns by decomposing a pattern into irreducible representations of the unitary principal series of SL(2,C). It is the projective analog of the classical (Euclidean) Fourier decomposition, well suited for the analysis of projectively distorted images such as aerial images of the same scene when taken from different vantage points.
Noncommutativity in (2+1)-dimensions and the Lorentz group
NASA Astrophysics Data System (ADS)
Falomir, H.; Vega, F.; Gamboa, J.; Méndez, F.; Loewe, M.
2012-11-01
In this article we considered models of particles living in a three-dimensional space-time with a nonstandard noncommutativity induced by shifting canonical coordinates and momenta with generators of a unitary irreducible representation of the Lorentz group. The Hilbert space gets the structure of a direct product with the representation space, where we are able to construct operators which realize the algebra of Lorentz transformations. We study the modified Landau problem for both Schrödinger and Dirac particles, whose Hamiltonians are obtained through a kind of non-Abelian Bopp’s shift of the dynamical variables from the ones of the usual problem in the normal space. The spectrum of these models are considered in perturbation theory, both for small and large noncommutativity parameters. We find no constraint between the parameters referring to noncommutativity in coordinates and momenta but they rather play similar roles. 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.
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.
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.
Structure of Mutualistic Complex Networks
NASA Astrophysics Data System (ADS)
Hwang, Jun Kyung; Maeng, Seong Eun; Cha, Moon Yong; Lee, Jae Woo
We consider the structures of six plant-pollinator mutualistic networks. The plants and pollinators are linked by the plant-pollinating relation. We assigned the visiting frequency of pollinators to a plant as a weight of each link. We calculated the cumulative distribution functions of the degree and strength for the networks. We observed a power-law, linear, and stretched exponential dependence of the cumulative distribution function. We also calculated the disparity and the strength of the nodes s(k) with degree k. We observed that the plant-pollinator networks exhibit an disassortative behaviors and nonlinear dependence of the strength on the nodes. In mutualistic networks links with large weight are connected to the neighbors with small degrees.
Structure of mammalian respiratory complex I.
Zhu, Jiapeng; Vinothkumar, Kutti R; Hirst, Judy
2016-08-18
Complex I (NADH:ubiquinone oxidoreductase), one of the largest membrane-bound enzymes in the cell, powers ATP synthesis in mammalian mitochondria by using the reducing potential of NADH to drive protons across the inner mitochondrial membrane. Mammalian complex I (ref. 1) contains 45 subunits, comprising 14 core subunits that house the catalytic machinery (and are conserved from bacteria to humans) and a mammalian-specific cohort of 31 supernumerary subunits. Knowledge of the structures and functions of the supernumerary subunits is fragmentary. Here we describe a 4.2-Å resolution single-particle electron cryomicroscopy structure of complex I from Bos taurus. We have located and modelled all 45 subunits, including the 31 supernumerary subunits, to provide the entire structure of the mammalian complex. Computational sorting of the particles identified different structural classes, related by subtle domain movements, which reveal conformationally dynamic regions and match biochemical descriptions of the 'active-to-de-active' enzyme transition that occurs during hypoxia. Our structures therefore provide a foundation for understanding complex I assembly and the effects of mutations that cause clinically relevant complex I dysfunctions, give insights into the structural and functional roles of the supernumerary subunits and reveal new information on the mechanism and regulation of catalysis. PMID:27509854
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.
Entropic force, noncommutative gravity, and ungravity
NASA Astrophysics Data System (ADS)
Nicolini, Piero
2010-08-01
After recalling the basic concepts of gravity as an emergent phenomenon, we analyze the recent derivation of Newton’s law in terms of entropic force proposed by Verlinde. By reviewing some points of the procedure, we extend it to the case of a generic quantum gravity entropic correction to get compelling deviations to the Newton’s law. More specifically, we study: (1) noncommutative geometry deviations and (2) ungraviton corrections. As a special result in the noncommutative case, we find that the noncommutative character of the manifold would be equivalent to the temperature of a thermodynamic system. Therefore, in analogy to the zero temperature configuration, the description of spacetime in terms of a differential manifold could be obtained only asymptotically. Finally, we extend the Verlinde’s derivation to a general case, which includes all possible effects, noncommutativity, ungravity, asymptotically safe gravity, electrostatic energy, and extra dimensions, showing that the procedure is solid versus such modifications.
Complex structures – smart solutions
2011-01-01
The siliceous skeletal elements of the sponges, the spicules, represent one of the very few examples from where the molecule toolkit required for the formation of an extracellular mineral-based skeleton, has been elucidated. The distinguished feature of the inorganic matrix, the bio-silica, is its enzymatic synthesis mediated by silicatein. Ortho-silicate undergoes in the presence of silicatein a polycondensation reaction and forms bio-silica under release of reaction water. The protein silicatein aggregates non-covalently to larger filaments, a process that is stabilized by the silicatein-associated protein, silintaphin-1. These structured clusters form the axial filament that is located in the center of the spicules, the axial canal. Surprisingly it has now been found that the initial axial orientation, in which the spicules grow, is guided by cell processes through evagination. The approximately two µm wide cell extensions release silicatein that forms the first organic axial filament, which then synthesizes the inner core of the siliceous spicule rods. In parallel, the radial growth of the spicules is controlled by a telescopic arrangement of organic layers, into which bio-silica and ortho-silicate are deposited. Hence, the formation of a mature siliceous spicule is completed by a centrifugal accretion of bio-silica mediated by the silicatein in the axial filament, and a centripetal bio-silica deposition catalyzed by the extra-spicular silicatein. Finally this contribution highlights that for the ultimate determination of the spicule shapes, their species-specific morphologies, bio-silica hardens during a process which removes reaction water. The data presented can also provide new blueprints for the fabrication of novel biomaterials for biomedical applications. PMID:22446527
Non-commutativity measure of quantum discord
NASA Astrophysics Data System (ADS)
Guo, Yu
2016-04-01
Quantum discord is a manifestation of quantum correlations due to non-commutativity rather than entanglement. Two measures of quantum discord by the amount of non-commutativity via the trace norm and the Hilbert-Schmidt norm respectively are proposed in this paper. These two measures can be calculated easily for any state with arbitrary dimension. It is shown by several examples that these measures can reflect the amount of the original quantum discord.
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.
Non-commutativity measure of quantum discord
Guo, Yu
2016-01-01
Quantum discord is a manifestation of quantum correlations due to non-commutativity rather than entanglement. Two measures of quantum discord by the amount of non-commutativity via the trace norm and the Hilbert-Schmidt norm respectively are proposed in this paper. These two measures can be calculated easily for any state with arbitrary dimension. It is shown by several examples that these measures can reflect the amount of the original quantum discord. PMID:27122226
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.
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.
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.
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 .
Noncommutative Geometry and Basic Physics
NASA Astrophysics Data System (ADS)
Kastler, Daniel
Alain Connes' noncommutative geometry, started in 1982 [0], widely developed in 1994 as expounded in his book at this date [0] (it has grown meanwhile) is a systematic quantization of mathematics parallel to the quantization of physics effected in the twenties.This theory widens the scope of mathematics in a manner congenial to physics, reorganizes the existing ("classical") mathematics of which it produces an hitherto unsuspected unification, and provides basic physics (the synthesis of elementary particles and gravitation) with a programme of renewal which has thus far achieved a clarification of the classical (tree-level) aspects of a new synthesis of the (Euclidean) standard model with gravitation [32],[33]: this is the subject of the present lectures - with the inherent tentative prediction of the Higgs mass.
Calabi-Yau manifolds from noncommutative Hermitian U (1 ) instantons
NASA Astrophysics Data System (ADS)
Yang, Hyun Seok
2015-05-01
We show that Calabi-Yau manifolds are emergent from the commutative limit of six-dimensional noncommutative Hermitian U (1 ) instantons. Therefore, we argue that the noncommutative Hermitian U (1 ) instantons correspond to quantized Calabi-Yau manifolds.
Chiral fermions in noncommutative electrodynamics: Renormalizability and dispersion
Buric, Maja; Latas, Dusko; Radovanovic, Voja; Trampetic, Josip
2011-02-15
We analyze quantization of noncommutative chiral electrodynamics in the enveloping algebra formalism in linear order in noncommutativity parameter {theta}. Calculations show that divergences exist and cannot be removed by ordinary renormalization; however, they can be removed by the Seiberg-Witten redefinition of fields. Performing redefinitions explicitly, we obtain renormalizable Lagrangian and discuss the influence of noncommutativity on field propagation. Noncommutativity affects the propagation of chiral fermions only: half of the fermionic modes become massive and birefringent.
NASA Astrophysics Data System (ADS)
Sakellariadou, Mairi
I will summarize Noncommutative Geometry Spectral Action, an elegant geometrical model valid at unification scale, which offers a purely gravitational explanation of the Standard Model, the most successful phenomenological model of particle physics. Noncommutative geometry states that close to the Planck energy scale, spacetime has a fine structure and proposes that it is given as the product of a four-dimensional continuum compact Riemaniann manifold by a tiny discrete finite noncommutative space. The spectral action principle, a universal action functional on spectral triples which depends only on the spectrum of the Dirac operator, applied to this almost commutative product geometry, leads to the full Standard Model, including neutrino mixing which has Majorana mass terms and a see-saw mechanism, minimally coupled to gravity. It also makes various predictions at unification scale. I will review some of the phenomenological and cosmological consequences of this beautiful and purely geometrical approach to unification.
Hawking radiation as tunneling from a Vaidya black hole in noncommutative gravity
Mehdipour, S. Hamid
2010-06-15
In the context of a noncommutative model of coordinate coherent states, we present a Schwarzschild-like metric for a Vaidya solution instead of the standard Eddington-Finkelstein metric. This leads to the appearance of an exact (t-r) dependent case of the metric. We analyze the resulting metric in three possible causal structures. In this setup, we find a zero remnant mass in the long-time limit, i.e. an instable black hole remnant. We also study the tunneling process across the quantum horizon of such a Vaidya black hole. The tunneling probability including the time-dependent part is obtained by using the tunneling method proposed by Parikh and Wilczek in terms of the noncommutative parameter {sigma}. After that, we calculate the entropy associated to this noncommutative black hole solution. However, the corrections are fundamentally trifling; one could respect this as a consequence of quantum inspection at the level of semiclassical quantum gravity.
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.
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.
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.
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
Structure of human PNP complexed with ligands.
Canduri, Fernanda; Silva, Rafael Guimarães; dos Santos, Denis Marangoni; Palma, Mário Sérgio; Basso, Luiz Augusto; Santos, Diógenes Santiago; de Azevedo, Walter Filgueira
2005-07-01
Purine nucleoside phosphorylase (PNP) is a key enzyme in the purine-salvage pathway, which allows cells to utilize preformed bases and nucleosides in order to synthesize nucleotides. PNP is specific for purine nucleosides in the beta-configuration and exhibits a strong preference for purines containing a 6-keto group and ribosyl-containing nucleosides relative to the corresponding analogues. PNP was crystallized in complex with ligands and data collection was performed using synchrotron radiation. This work reports the structure of human PNP in complex with guanosine (at 2.80 A resolution), 3'-deoxyguanosine (at 2.86 A resolution) and 8-azaguanine (at 2.85 A resolution). These structures were compared with the PNP-guanine, PNP-inosine and PNP-immucillin-H complexes solved previously.
On the structure of valiant's complexity classes
NASA Astrophysics Data System (ADS)
Bürgisser, Peter
In [25,27] Valiant developed an algebraic analogue of the theory of NP-completeness for computations with polynomials over a field. We further develop this theory in the spirit of structural complexity and obtain analogues of well-known results by Baker, Gill, and Solovay [1], Ladner [18], and Schöning [23,24].
Network quotients: Structural skeletons of complex systems
NASA Astrophysics Data System (ADS)
Xiao, Yanghua; MacArthur, Ben D.; Wang, Hui; Xiong, Momiao; Wang, Wei
2008-10-01
A defining feature of many large empirical networks is their intrinsic complexity. However, many networks also contain a large degree of structural repetition. An immediate question then arises: can we characterize essential network complexity while excluding structural redundancy? In this article we utilize inherent network symmetry to collapse all redundant information from a network, resulting in a coarse graining which we show to carry the essential structural information of the “parent” network. In the context of algebraic combinatorics, this coarse-graining is known as the “quotient.” We systematically explore the theoretical properties of network quotients and summarize key statistics of a variety of “real-world” quotients with respect to those of their parent networks. In particular, we find that quotients can be substantially smaller than their parent networks yet typically preserve various key functional properties such as complexity (heterogeneity and hub vertices) and communication (diameter and mean geodesic distance), suggesting that quotients constitute the essential structural skeletons of their parent networks. We summarize with a discussion of potential uses of quotients in analysis of biological regulatory networks and ways in which using quotients can reduce the computational complexity of network algorithms.
Structural complexity of a composite amyloid fibril
Lewandowski, Józef R.; van der Wel, Patrick C.A.; Rigney, Mike; Grigorieff, Nikolaus; Griffin, Robert G.
2011-01-01
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 dynamical 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. PMID:21766841
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{sub q}(SU(2)). I discuss the X-structure of SU(2)* and give a detailed description of its leaves using various parametrizations. Then, I will introduce a new reality structure on the Heisenberg double of Fun{sub q} (SL(N,C)) for q phase, which can be interpreted as the quantum phase space of a particle on the q-deformed mass-hyperboloid. I also present evidence that the above real form describes zero modes of certain non-compact WZNW-models.
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.
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.
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.
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.
Dilaton cosmology, noncommutativity, and generalized uncertainty principle
Vakili, Babak
2008-02-15
The effects of noncommutativity and of the existence of a minimal length on the phase space of a dilatonic cosmological model are investigated. The existence of a minimum length results in the generalized uncertainty principle (GUP), which is a deformed Heisenberg algebra between the minisuperspace variables and their momenta operators. I extend these deformed commutating relations to the corresponding deformed Poisson algebra. For an exponential dilaton potential, the exact classical and quantum solutions in the commutative and noncommutative cases, and some approximate analytical solutions in the case of GUP, are presented and compared.
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.
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
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.
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
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
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.
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.
Bogomolny equations for vortices in the noncommutative torus
NASA Astrophysics Data System (ADS)
Forgács, Peter; Lozano, Gustavo S.; Moreno, Enrique F.; Schaposnik, Fidel A.
2005-07-01
We derive Bogomolny-type equations for the abelian Higgs model defined on the noncommutative torus and discuss its vortex like solutions. To this end, we carefully analyze how periodic boundary conditions have to be handled in noncommutative space and discuss how vortex solutions are constructed. We also consider the extension to an U(2) × U(1) model, a simplified prototype of the noncommutative standard model.
Some Properties of Nonlinear σ-MODELS in Noncommutative Geometry
NASA Astrophysics Data System (ADS)
Dabrowski, Ludwik; Krajewski, Thomas; Landi, Giovanni
We introduce nonlinear σ-models in the framework of noncommutative geometry with special emphasis on models defined on the noncommutative torus. We choose as target spaces the two point space and the circle and illustrate some characteristic features of the corresponding σ-models. In particular we construct a σ-model instanton with topological charge equal to 1. We also define and investigate some properties of a noncommutative analogue of the Wess-Zumino-Witten model.
Higher order theories and their relationship with noncommutativity
NASA Astrophysics Data System (ADS)
Sánchez-Santos, Oscar; Vergara, José David
2014-06-01
We present a relationship between noncommutativity and higher order time derivative theories using a perturbation method. We make a generalization of the Chern-Simons quantum mechanics for higher order time derivatives. This model presents noncommutativity in a natural way when we project to low-energy physical states without the necessity of taking the strong field limit. We quantize the theory using a Bopp's shift of the noncommutative variables and we obtain a spectrum without negative energies, under the perturbation limits. In addition, we extent the model to high order time derivatives and noncommutativity with variable dependent parameter.
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.
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.
Supergravity dual of noncommutative /N=1 SYM
NASA Astrophysics Data System (ADS)
Mateos, Toni; Pons, Josep M.; Talavera, Pere
2003-02-01
We construct the noncommutative deformation of the Maldacena-Núñez supergravity solution. The background describes a bound state of D5-D3 branes wrapping an S2 inside a Calabi-Yau three-fold, and in the presence of a magnetic B-field. The dual field theory in the IR is an N=1 U( N) SYM theory with spatial noncommutativity. We show that, under certain conditions, the massive Kaluza-Klein states can be decoupled and that UV/IR mixing seems to be visible in our solution. By calculating the quark-antiquark potential via the Wilson loop we show confinement in the IR and strong repulsion at closer distances. We also compute the β-function and show that it coincides with the recently calculated commutative one.
Chirality and Dirac Operator on Noncommutative Sphere
NASA Astrophysics Data System (ADS)
Carow-Watamura, Ursula; Watamura, Satoshi
1997-01-01
We give a derivation of the Dirac operator on the noncommutative 2-sphere within the framework of the bosonic fuzzy sphere and define Connes' triple. It turns out that there are two different types of spectra of the Dirac operator and correspondingly there are two classes of quantized algebras. As a result we obtain a new restriction on the Planck constant in Berezin's quantization. The map to the local frame in noncommutative geometry is also discussed. Acknowledgement. The authors benefited from discussions with M. Bordemann, O. Grandjean and M. Pillin. S.W. would like to thank K. Osterwalder for his hospitality during the stay in ETH where this work began. He also thanks the Canon Foundation in Europe for supporting that stay. U.C. would like to acknowledge the Japan Society for Promotion of Science for financial support.-->
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.
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.
Exact BPS bound for noncommutative baby Skyrmions
NASA Astrophysics Data System (ADS)
Domrin, Andrei; Lechtenfeld, Olaf; Linares, Román; Maceda, Marco
2013-11-01
The noncommutative baby Skyrme model is a Moyal deformation of the two-dimensional sigma model plus a Skyrme term, with a group-valued or Grassmannian target. Exact abelian solitonic solutions have been identified analytically in this model, with a singular commutative limit. Inside any given Grassmannian, we establish a BPS bound for the energy functional, which is saturated by these baby Skyrmions. This asserts their stability for unit charge, as we also test in second-order perturbation theory.
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.
Conformal invariance in noncommutative geometry and mutually interacting Snyder particles
NASA Astrophysics Data System (ADS)
Pramanik, Souvik; Ghosh, Subir; Pal, Probir
2014-11-01
A system of relativistic Snyder particles with mutual two-body interaction that lives in a noncommutative Snyder geometry is studied. The underlying novel symplectic structure is a coupled and extended version of (single-particle) Snyder algebra. In a recent work by Casalbuoni and Gomis [Phys. Rev. D 90, 026001 (2014)], a system of interacting conventional particles (in commutative spacetime) was studied with special emphasis on its conformal invariance. Proceeding along the same lines, we have shown that our interacting Snyder particle model is also conformally invariant. Moreover, the conformal Killing vectors have been constructed. Our main emphasis is on the Hamiltonian analysis of the conformal symmetry generators. We demonstrate that the Lorentz algebra remains undeformed, but validity of the full conformal algebra requires further restrictions.
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.
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.
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.
Noncommutative Yang-Mills and noncommutative relativity: a bridge over troubled water
NASA Astrophysics Data System (ADS)
Carminati, L.; Iochum, B.; Schücker, T.
1999-05-01
Connes' view at Yang-Mills theories is reviewed with special emphasis on the gauge invariant scalar product. This landscape is shown to contain Chamseddine and Connes' noncommutative extension of general relativity restricted to flat spacetime, if the top mass is between 172 and 204 GeV. Then the Higgs mass is between 188 and 201 GeV.
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
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
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
Non-commutative tools for topological insulators
NASA Astrophysics Data System (ADS)
Prodan, Emil
2010-06-01
This paper reviews several analytic tools for the field of topological insulators, developed with the aid of non-commutative calculus and geometry. The set of tools includes bulk topological invariants defined directly in the thermodynamic limit and in the presence of disorder, whose robustness is shown to have nontrivial physical consequences for the bulk states. The set of tools also includes a general relation between the current of an observable and its edge index, a relation that can be used to investigate the robustness of the edge states against disorder. The paper focuses on the motivations behind creating such tools and on how to use them.
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.
Dixmier traces and non-commutative analysis
NASA Astrophysics Data System (ADS)
Sukochev, Fedor; Usachev, Alexandr
2016-07-01
In the present paper we review recent advances in the theory of Dixmier traces and aspects of their application to noncommutative analysis and geometry. We describe J. Dixmier's original construction of singular traces together with recent revisions of his ideas. We pay particular attention to subclasses of Dixmier traces related to exponentiation invariant extended limits and notions of measurability due to A. Connes. We discuss in detail the applications of Dixmier traces to the study of spectral properties of pseudo-differential operators and a very recent application of Dixmier traces in the study the Fréchet differentiability of Haagerup's Lp norm.
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.
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.
Structurally simple complexes of CO2.
Murphy, Luke J; Robertson, Katherine N; Kemp, Richard A; Tuononen, Heikki M; Clyburne, Jason A C
2015-03-01
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.
Noncommutative topology and the world's simplest index theorem.
van Erp, Erik
2010-05-11
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.
Location and direction dependent effects in collider physics from noncommutativity
Haghighat, Mansour; Okada, Nobuchika; Stern, Allen
2010-07-01
We examine the leading order noncommutative corrections to the differential and total cross sections for e{sup +}e{sup -{yields}}qq. After averaging over the Earth's rotation, the results depend on the latitude for the collider, as well as the direction of the incoming beam. They also depend on the scale and direction of the noncommutativity. Using data from LEP, we exclude regions in the parameter space spanned by the noncommutative scale and angle relative to the Earth's axis. We also investigate possible implications for phenomenology at the future International Linear Collider.
NASA Astrophysics Data System (ADS)
Jurić, Tajron; Samsarov, Andjelo
2016-05-01
In this work, we consider a noncommutative (NC) massless scalar field coupled to the classical nonrotational BTZ geometry. In a manner of the theories where the gravity emerges from the underlying scalar field theory, we study the effective action and the entropy derived from this noncommutative model. In particular, the entropy is calculated by making use of the two different approaches, the brick-wall method and the heat kernel method designed for spaces with conical singularity. We show that the UV divergent structures of the entropy obtained through these two different methods agree with each other. It is also shown that the same renormalization condition that removes the infinities from the effective action can also be used to renormalize the entanglement entropy for the same system. Besides, the interesting feature of the NC model considered here is that it allows an interpretation in terms of an equivalent system comprising a commutative massive scalar field but in a modified geometry: that of the rotational BTZ black hole, the result that hints at a duality between the commutative and noncommutative systems in the background of a BTZ black hole.
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…
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.
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.
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.
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.
Crystallization and Structure Determination of Superantigens and Immune Receptor Complexes.
Rödström, Karin E J; Lindkvist-Petersson, Karin
2016-01-01
Structure determination of superantigens and the complexes they form with immune receptors have over the years provided insight in their modes of action. This technique requires growing large and highly ordered crystals of the superantigen or receptor-superantigen complex, followed by exposure to X-ray radiation and data collection. Here, we describe methods for crystallizing superantigens and superantigen-receptor complexes using the vapor diffusion technique, how the crystals may be optimized, and lastly data collection and structure determination.
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.
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.
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.
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.
Quantum Tunneling and Spectroscopy of Noncommutative Inspired Kerr Black Hole
NASA Astrophysics Data System (ADS)
Miao, Yan-Gang; Xue, Zhao; Zhang, Shao-Jun
We discuss the thermodynamics of the noncommutative inspired Kerr black hole by means of a reformulated Hamilton-Jacobi method and a dimensional reduction technique. In order to investigate the effect of the angular momentum of the tunneling particle, we calculate the wave function to the first order of the WKB ansatz. Then, using a density matrix technique we derive the radiation spectrum from which the radiation temperature can be read out. Our results show that the radiation of this noncommutative inspired black hole corresponds to a modified temperature which involves the effect of noncommutativity. However, the angular momentum of the tunneling particle has no influence on the radiation temperature. Moreover, we analyze the entropy spectrum and verify that its quantization is modified neither by the noncommutativity of spacetime nor by the quantum correction of wave functions.
Vortex scattering and intercommuting cosmic strings on a noncommutative spacetime
Joseph, Anosh; Trodden, Mark
2010-02-15
We study the scattering of noncommutative vortices, based on the noncommutative field theory developed in [A. P. Balachandran, T. R. Govindarajan, G. Mangano, A. Pinzul, B. A. Qureshi, and ?>S. Vaidya, Phys. Rev. D 75, 045009 (2007).], as a way to understand the interaction of cosmic strings. In the center-of-mass frame, the effects of noncommutativity vanish, and therefore the reconnection of cosmic strings occurs in an identical manner to the commutative case. However, when scattering occurs in a frame other than the center-of-mass frame, strings still reconnect but the well-known 90 deg. scattering no longer need correspond to the head-on collision of the strings, due to the breakdown of Lorentz invariance in the underlying noncommutative field theory.
Noncommutative 3 Dimensional Soliton from Multi-instantons
NASA Astrophysics Data System (ADS)
Correa, D. H.; Forgacs, P.; Moreno, E. F.; Schaposnik, F. A.; Silva, G. A.
2004-07-01
We extend the relation between instanton and monopole solutions of the selfduality equations in SU(2) gauge theory to noncommutative space-times. Using this approach and starting from a noncommutative multi-instanton solution we construct a U(2) monopole configuration which lives in 3 dimensional ordinary space. This configuration resembles the Wu-Yang monopole and satisfies the selfduality (Bogomol'nyi) equations for a U(2) Yang-Mills-Higgs system.
Non-commutativity, teleology and GRB time delay
NASA Astrophysics Data System (ADS)
Li, Miao; Pang, Yi; Wang, Yi
2010-01-01
We propose a model in which an energy-dependent time delay of a photon originates from space-time non-commutativity, the time delay is due to a non-commutative coupling between dilaton and photon. We predict that in our model, high energy photons with different momentum can either be delayed or superluminal, this may be related to a possible time delay reported by the Fermi LAT and Fermi GBM Collaborations.
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.
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
Topics in Noncommutative Gauge Theories and Deformed Relativistic Theories
NASA Astrophysics Data System (ADS)
Chandra, Nitin
2013-01-01
This is my PhD thesis. In this thesis we study the gauge theories on noncommutative Moyal space. We find new static solitons and instantons in terms of the so called generalized Bose operators. Generalized Bose operators are constructed to describe reducible representation of the oscillator algebra. They create/annihilate k-quanta, k being a positive integer. We start with giving an alternative description to the already found static magnetic flux tube solutions of the noncommutative gauge theories in terms of generalized Bose operators. The Nielsen-Olesen vortex solutions found in terms of these operators reduce to the already found ones. On the contrary we find a class of new instaton solutions which are unitarily inequivalant to the the ones found from ADHM construction on noncommutative space. The charge of the instaton has a description in terms of the index representing the reducibility of the Fock space, i.e., k. After studying the static solitonic solutions in noncommutative Minkowski space and the instaton solutions in noncommutative Euclidean space we go on to study the implications of the time-space noncommutativity in Minkowski space. To understand it properly we study the time-dependent transitions of a forced harmonic oscillator in noncommutative 1+1 dimensional spacetime. We also try to understand the implications of the found results in the context of quantum optics. We then shift to the so called DSR theories which are related to a different kind of noncommutative (kappa-Minkowski) space. DSR (Doubly/Deformed Special Relativity) aims to search for an alternate relativistic theory which keeps a length/energy scale (the Planck scale) and a velocity scale (the speed of light scale) invariant. We study thermodynamics of an ideal gas in such a scenario.
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…
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.
Structural visualization of complex software systems
Vemuri, V.; Smart, J.C. |
1991-08-01
The design outline of an automatic, computer-based Abstract Visualization Utility (A-Vu) is presented. Although A-Vu is a general purpose tool, emphasis here is on its ability to visualize structural aspects of software design. Starting from a system definition, an Ada program library, or a directed graph definition, A-Vu proceeds to develop a variety of ``nice`` linear graphs, revealing different visual representations of the design. Formally, given a linear graph G=(V,E), A-Vu searches for a configuration C such that a suitably defined ``energy`` function J(C) is minimized. The definition of the energy function includes software engineering considerations such as layering, modularity as well as aesthetic considerations like visual appeal, cognitive correctness, and so on. Simulated annealing techniques are applied to linear graph representations of software structures to obtain the ``minimum energy`` configurations.
Structural visualization of complex software systems
Vemuri, V.; Smart, J.C. . Dept. of Applied Science Lawrence Livermore National Lab., CA )
1991-08-01
The design outline of an automatic, computer-based Abstract Visualization Utility (A-Vu) is presented. Although A-Vu is a general purpose tool, emphasis here is on its ability to visualize structural aspects of software design. Starting from a system definition, an Ada program library, or a directed graph definition, A-Vu proceeds to develop a variety of nice'' linear graphs, revealing different visual representations of the design. Formally, given a linear graph G=(V,E), A-Vu searches for a configuration C such that a suitably defined energy'' function J(C) is minimized. The definition of the energy function includes software engineering considerations such as layering, modularity as well as aesthetic considerations like visual appeal, cognitive correctness, and so on. Simulated annealing techniques are applied to linear graph representations of software structures to obtain the minimum energy'' configurations.
Complex banded structures in directional solidification processes.
Korzhenevskii, A L; Rozas, R E; Horbach, J
2016-01-27
A combination of theory and numerical simulation is used to investigate impurity superstructures that form in rapid directional solidification (RDS) processes in the presence of a temperature gradient and a pulling velocity with an oscillatory component. Based on a capillary wave model, we show that the RDS processes are associated with a rich morphology of banded structures, including frequency locking and the transition to chaos.
Complex eigenvalue analysis of rotating structures
NASA Technical Reports Server (NTRS)
Patel, J. S.; Seltzer, S. M.
1972-01-01
A FORTRAN subroutine to NASTRAN which constructs coriolis and centripetal acceleration matrices, and a centrifugal load vector due to spin about a selected point or about the mass center of the structure is discussed. The rigid translational degrees of freedom can be removed by using a transformation matrix T and its explicitly given inverse. These matrices are generated in the subroutine and their explicit expressions are given.
Complex banded structures in directional solidification processes.
Korzhenevskii, A L; Rozas, R E; Horbach, J
2016-01-27
A combination of theory and numerical simulation is used to investigate impurity superstructures that form in rapid directional solidification (RDS) processes in the presence of a temperature gradient and a pulling velocity with an oscillatory component. Based on a capillary wave model, we show that the RDS processes are associated with a rich morphology of banded structures, including frequency locking and the transition to chaos. PMID:26704726
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. PMID:26356911
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.
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.
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.
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.
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
CMB statistical anisotropy from noncommutative gravitational waves
NASA Astrophysics Data System (ADS)
Shiraishi, Maresuke; Mota, David F.; Ricciardone, Angelo; Arroja, Frederico
2014-07-01
Primordial statistical anisotropy is a key indicator to investigate early Universe models and has been probed by the cosmic microwave background (CMB) anisotropies. In this paper, we examine tensor-mode CMB fluctuations generated from anisotropic gravitational waves, parametrised by Ph(k) = Ph(0)(k) [ 1 + ∑LM fL(k) gLM YLM (hat k)], where Ph(0)(k) is the usual scale-invariant power spectrum. Such anisotropic tensor fluctuations may arise from an inflationary model with noncommutativity of fields. It is verified that in this model, an isotropic component and a quadrupole asymmetry with f0(k) = f2(k) propto k-2 are created and hence highly red-tilted off-diagonal components arise in the CMB power spectra, namely l2 = l1 ± 2 in TT, TE, EE and BB, and l2 = l1 ± 1 in TB and EB. We find that B-mode polarisation is more sensitive to such signals than temperature and E-mode polarisation due to the smallness of large-scale cosmic variance and we can potentially measure g00 = 30 and g2M = 58 at 68% CL in a cosmic-variance-limited experiment. Such a level of signal may be measured in a PRISM like experiment, while the instrumental noise contaminates it in the Planck experiment. These results imply that it is impossible to measure the noncommutative parameter if it is small enough for the perturbative treatment to be valid. Our formalism and methodology for dealing with the CMB tensor statistical anisotropy are general and straightforwardly applicable to other early Universe models.
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.
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.
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
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
2015-01-01
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
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.
The structure and function of bacterial light-harvesting complexes.
Law, Christopher J; Roszak, Aleksander W; Southall, June; Gardiner, Alastair T; Isaacs, Neil W; Cogdell, Richard J
2004-01-01
The harvesting of solar radiation by purple photosynthetic bacteria is achieved by circular, integral membrane pigment-protein complexes. There are two main types of light-harvesting complex, termed LH2 and LH1, that function to absorb light energy and to transfer that energy rapidly and efficiently to the photochemical reaction centres where it is trapped. This mini-review describes our present understanding of the structure and function of the purple bacterial light-harvesting complexes.
[Problems of formal organizational structure of industrial health care complexes].
Włodarczyk, C
1978-01-01
The author formulates the thesis that the description of organizational structure of industrial health care complex calls for isolation of the following aspects:--structure of territorial links--systemof organizational units and divisions--organization of basic functions--structure of management--structure of supervision of middle and lowe-level personnel--composition of health care complex council--system of accessibility ranges. Each of the above aspects has been considered on the basis of operative rules of law, using organizational analysis methods.
Complexation of Actinides in Solution: Thermodynamic Measurementsand Structural Characterization
Rao, L.
2007-02-01
This paper presents a brief introduction of the studies of actinide complexation in solution at Lawrence Berkeley National Laboratory. An integrated approach of thermodynamic measurements and structural characterization is taken to obtain fundamental understanding of actinide complexation in solution that is of importance in predicting the behavior of actinides in separation processes and environmental transport.
Mesoscopic hydrothermodynamics of complex-structured materials.
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. PMID:24229119
Dynamics of a complex streamer structure
NASA Astrophysics Data System (ADS)
Lehtinen, N. G.; Ostgaard, N.; Inan, U.
2014-12-01
Streamer corona formation and propagation is an important process in the development of lightning. In order to understand its dynamics, the streamer front velocity is calculated in a 1D model with curvature. We show that streamers may only propagate only the presence of mechanisms such as electron drift, electron diffusion and photoionization. The results indicate, in particular, that: (1) the effect of photoionization on the streamer velocity for both positive and negative streamers is mostly determined by the photoionization length, with a weaker dependence on the amount of photoionization; (2) the electron drift may increase the velocity of the negative streamers but has an opposite effect on the positive streamers; (3) the contributions of photoionization and electron diffusion to the velocity are decreased for positive curvature, i.e., convex fronts, while the contribution of electron drift is independent of curvature. These results are used in a fractal model in which the front propagation velocity is simulated as the cluster growth probability [Niemeyer et al, 1984, doi:10.1103/PhysRevLett.52.1033]. In the case when the photoionization is the main mechanism which determines the streamer propagation, the emerging transverse size of the streamers is of the order of the photoionization length, and at the larger scale the streamer structure is a fractal similar to the one obtained in a diffusion-limited aggregation system.
Noncommutative Chern-Simons gauge and gravity theories and their geometric Seiberg-Witten map
NASA Astrophysics Data System (ADS)
Aschieri, Paolo; Castellani, Leonardo
2014-11-01
We use a geometric generalization of the Seiberg-Witten map between noncommutative and commutative gauge theories to find the expansion of noncommutative Chern-Simons (CS) theory in any odd dimension D and at first order in the noncommutativity parameter θ. This expansion extends the classical CS theory with higher powers of the curvatures and their derivatives.
NASA Astrophysics Data System (ADS)
Benatti, Fabio; Gouba, Laure
2015-11-01
When dealing with the classical limit of two quantum mechanical oscillators on a noncommutative configuration space, the limits corresponding to the removal of configuration-space noncommutativity and position-momentum noncommutativity do not commute. We address this behaviour from the point of view of the phase-space localisation properties of the Wigner functions of coherent states under the two limits.
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.
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.
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.
Structure of Cationic Liposome DNA Complexes Incorporating PEG Lipids
NASA Astrophysics Data System (ADS)
Winkler, Kathrin; Subramanian, G.; Safinya, C. R.
1998-03-01
DNA cationic liposome complexes with PEG lipids are promising candidates for efficient transfection of DNA in vivo. The presence of PEG confers (a) colloidal stability and (b) increased circulation time of the complexes in the blood stream leading to long term transfection activity. However, there has been no elucidation of the structure of these complexes which is crucial for correlating the structure and transfection efficiency. We have carried out a systematic structural investigation of complexes incorporating PEG lipids using X-ray scattering. We have studied the structure of complexes made from DOTAP (a cationic lipid), DOPC (a neutral lipid), PEG-DMPE and λ-DNA both as a function of the PEG-DMPE and neutral lipid concentrations. We have produced stable complexes which form a multilamellar structure with alternating lipid bilayers and DNA molecules. The DNA molecules are ordered in a 2-D smectic array whose spacing is controlled by the concentrations of PEG-DMPE and the neutral lipid. Supported by NSF-DMR-9624091, PRF-31352-AC7, and Los Alamos-STB/UC:96-108.
Integrating Mass Spectrometry of Intact Protein Complexes into Structural Proteomics
Hyung, Suk-Joon; Ruotolo, Brandon T.
2013-01-01
Summary Mass spectrometry analysis of intact protein complexes has emerged as an established technology for assessing the composition and connectivity within dynamic, heterogeneous multiprotein complexes at low concentrations and in the context of mixtures. As this technology continues to move forward, one of the main challenges is to integrate the information content of such intact protein complex measurements with other mass spectrometry approaches in structural biology. Methods such as H/D exchange, oxidative foot-printing, chemical cross-linking, affinity purification, and ion mobility separation add complementary information that allows access to every level of protein structure and organization. Here, we survey the structural information that can be retrieved by such experiments, demonstrate the applicability of integrative mass spectrometry approaches in structural proteomics, and look to the future to explore upcoming innovations in this rapidly-advancing area. PMID:22611037
Noncommutative Inverse Scattering Method for the Kontsevich System
NASA Astrophysics Data System (ADS)
Arthamonov, Semeon
2015-09-01
We formulate an analog of Inverse Scattering Method for integrable systems on noncommutative associative algebras. In particular, we define Hamilton flows, Casimir elements and noncommutative analog of the Lax matrix. The noncommutative Lax element generates infinite family of commuting Hamilton flows on an associative algebra. The proposed approach to integrable systems on associative algebras satisfies certain universal property, in particular, it incorporates both classical and quantum integrable systems as well as provides a basis for further generalization. We motivate our definition by explicit construction of noncommutative analog of Lax matrix for a system of differential equations on associative algebra recently proposed by Kontsevich. First, we present these equations in the Hamilton form by defining a bracket of Loday type on the group algebra of the free group with two generators. To make the definition more constructive, we utilize (with certain generalizations) the Van den Bergh approach to Loday brackets via double Poisson brackets. We show that there exists an infinite family of commuting flows generated by the noncommutative Lax element.
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.
Colored Extensions of GLq(2) Quantum Group and Related Noncommutative Planes
NASA Astrophysics Data System (ADS)
Basu-Mallick, B.
An infinite-dimensional quantum group, containing the standard GLq(2) and GLp,q(2) cases as different subalgebras, is constructed by using a colored braid group representation. It turns out that all algebraic relations occurring in this “colored” quantum group can be expressed in the Heisenberg-Weyl form, for a nontrivial choice of corresponding basis elements. Moreover a novel quadratic algebra, defined through Kac-Moody-like generators, is obtained by making some power series expansion of related monodromy matrix elements. The structure of invariant noncommutative planes associated with this “colored” quantum group has also been investigated.
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.
CMB statistical anisotropy from noncommutative gravitational waves
Shiraishi, Maresuke; Ricciardone, Angelo; Mota, David F.; Arroja, Frederico E-mail: d.f.mota@astro.uio.no E-mail: arroja@pd.infn.it
2014-07-01
Primordial statistical anisotropy is a key indicator to investigate early Universe models and has been probed by the cosmic microwave background (CMB) anisotropies. In this paper, we examine tensor-mode CMB fluctuations generated from anisotropic gravitational waves, parametrised by P{sub h}(k) = P{sub h}{sup (0)}(k) [ 1 + ∑{sub LM} f{sub L}(k) g{sub LM} Y{sub LM} ( k-circumflex )], where P{sub h}{sup (0)}(k) is the usual scale-invariant power spectrum. Such anisotropic tensor fluctuations may arise from an inflationary model with noncommutativity of fields. It is verified that in this model, an isotropic component and a quadrupole asymmetry with f{sub 0}(k) = f{sub 2}(k) ∝ k{sup -2} are created and hence highly red-tilted off-diagonal components arise in the CMB power spectra, namely ℓ{sub 2} = ℓ{sub 1} ± 2 in TT, TE, EE and BB, and ℓ{sub 2} = ℓ{sub 1} ± 1 in TB and EB. We find that B-mode polarisation is more sensitive to such signals than temperature and E-mode polarisation due to the smallness of large-scale cosmic variance and we can potentially measure g{sub 00} = 30 and g{sub 2M} = 58 at 68% CL in a cosmic-variance-limited experiment. Such a level of signal may be measured in a PRISM like experiment, while the instrumental noise contaminates it in the Planck experiment. These results imply that it is impossible to measure the noncommutative parameter if it is small enough for the perturbative treatment to be valid. Our formalism and methodology for dealing with the CMB tensor statistical anisotropy are general and straightforwardly applicable to other early Universe models.
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.
Noncommutative topology and the world's simplest index theorem.
van Erp, Erik
2010-05-11
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
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 (supersymmetric) electrodynamics in the Yang-Feldman formalism
Zahn, Jochen
2010-11-15
We study quantum electrodynamics on the noncommutative Minkowski space (NCQED) in the Yang-Feldman formalism. Local observables are defined by using covariant coordinates. We compute the two-point function of the interacting field strength to second order and find the infrared divergent terms already known from computations using the so-called modified Feynman rules. It is shown that these lead to nonlocal renormalization ambiguities. Also new nonlocal divergences stemming from the covariant coordinates are found. Furthermore, we study the supersymmetric extension of the model. For this, the supersymmetric generalization of the covariant coordinates is introduced. We find that the nonlocal divergences cancel. At the one-loop level, the only effect of noncommutativity is then a momentum-dependent field strength normalization. We interpret it as an acausal effect and show that its range is independent of the noncommutativity scale.
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.
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.
Structural insight into the UNC-45-myosin complex.
Fratev, Filip; Osk Jónsdóttir, Svava; Pajeva, Ilza
2013-07-01
The UNC-45 chaperone protein interacts with and affects the folding, stability, and the ATPase activity of myosins. It plays a critical role in the cardiomyopathy development and in the breast cancer tumor growth. Here we propose the first structural model of the UNC-45-myosin complex using various in silico methods. Initially, the human UNC-45B binding epitope was identified and the protein was docked to the cardiac myosin (MYH7) motor domain. The final UNC45B-MYH7 structure was obtained by performing of total 630 ns molecular dynamics simulations. The results indicate a complex formation, which is mainly stabilized by electrostatic interactions. Remarkably, the contact surface area is similar to that of the myosin-actin complex. A significant interspecies difference in the myosin binding epitope is observed. Our results reveal the structural basis of MYH7 exons 15-16 hypertrophic cardiomyopathy mutations and provide directions for drug targeting. PMID:23408646
The Dystrophin Complex: structure, function and implications for therapy
Gao, Quan; McNally, Elizabeth M
2016-01-01
The dystrophin complex stabilizes the plasma membrane of striated muscle cells. Loss of function mutations in the genes encoding dystrophin, or the associated proteins, triggers instability of the plasma membrane and myofiber loss. Mutations in dystrophin have been extensively cataloged providing remarkable structure-function correlation between predicted protein structure and clinical outcomes. These data have highlighted dystrophin regions necessary for in vivo function and fueled the design of viral vectors and now, exon skipping approaches for use in dystrophin restoration therapies. However, dystrophin restoration is likely more complex, owing to the role of the dystrophin complex as a broad cytoskeletal integrator. This review will focus on dystrophin restoration, with emphasis on the regions of dystrophin essential for interacting with its associated proteins and discuss the structural implications of these approaches. PMID:26140716
Structural insights into the rhabdovirus transcription/replication complex.
Ivanov, Ivan; Yabukarski, Filip; Ruigrok, Rob W H; Jamin, Marc
2011-12-01
The rhabdoviruses have a non-segmented single stranded negative-sense RNA genome. Their multiplication in a host cell requires three viral proteins in addition to the viral RNA genome. The nucleoprotein (N) tightly encapsidates the viral RNA, and the N-RNA complex serves as the template for both transcription and replication. The viral RNA-dependent RNA polymerase is a two subunit complex that consists of a large subunit, L, and a non-catalytic cofactor, the phosphoprotein, P. P also acts as a chaperone of nascent RNA-free N by forming a N(0)-P complex that prevents N from binding to cellular RNAs and from polymerizing in the absence of RNA. Here, we discuss the recent molecular and structural studies of individual components and multi-molecular complexes that are involved in the transcription/replication complex of these viruses with regard to their implication in viral transcription and replication.
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.
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
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
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
2016-05-27
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.
Chelation-Induced Polymer Structural Hierarchy/Complexity in Water.
Han, Jie; Zhou, Kaiyi; Zhu, Xuechao; Yu, Qiuping; Ding, Yi; Lu, Xinhua; Cai, Yuanli
2016-08-01
Understanding nanoscale structural hierarchy/complexity of hydrophilic flexible polymers is imperative because it can be viewed as an analogue to protein-alike superstructures. However, current understanding is still in infancy. Herein the first demonstration of nanoscale structural hierarchy/complexity via copper chelation-induced self-assembly (CCISA) is presented. Hierarchically-ordered colloidal networks and disks can be achieved by deliberate control of spacer length and solution pH. Dynamic light scattering, transmission electron microscopy, and atomic force microscopy demonstrate that CCISA underwent supramolecular-to-supracolloidal stepwise-growth mechanism, and underline amazing prospects to the hierarchically-ordered superstructures of hydrophilic flexible polymers in water.
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.
Quantum-corrected finite entropy of noncommutative acoustic black holes
NASA Astrophysics Data System (ADS)
Anacleto, M. A.; Brito, F. A.; Luna, G. C.; Passos, E.; Spinelly, J.
2015-11-01
In this paper we consider the generalized uncertainty principle in the tunneling formalism via Hamilton-Jacobi method to determine the quantum-corrected Hawking temperature and entropy for 2 + 1-dimensional noncommutative acoustic black holes. In our results we obtain an area entropy, a correction logarithmic in leading order, a correction term in subleading order proportional to the radiation temperature associated with the noncommutative acoustic black holes and an extra term that depends on a conserved charge. Thus, as in the gravitational case, there is no need to introduce the ultraviolet cut-off and divergences are eliminated.
Generalized Uncertainty Relation in the Non-commutative Quantum Mechanics
NASA Astrophysics Data System (ADS)
Chung, Won Sang
2016-06-01
In this paper the non-commutative quantum mechanics (NCQM) with the generalized uncertainty relations {Δ } x1 {Δ } x2 ≥ {θ}/{2}, {Δ} p1 {Δ } p2 ≥ {bar{θ}}/{2}, {Δ } xi {Δ } pi ≥ {hbar _{eff}}/{2} is discussed. Four each uncertainty relation, wave functions saturating each uncertainty relation are explicitly constructed. The unitary operators relating the non-commutative position and momentum operators to the commutative position and momentum operators are also investigated. We also discuss the uncertainty relation related to the harmonic oscillator.
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.
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.
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2010-12-10
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Self-Assembly of Structures with Addressable Complexity.
Jacobs, William M; Frenkel, Daan
2016-03-01
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. PMID:26862684
From structure to function via complex supramolecular dendrimer systems.
Sun, Hao-Jan; Zhang, Shaodong; Percec, Virgil
2015-06-21
This tutorial review summarizes strategies elaborated for the discovery and prediction of programmed primary structures derived from quasi-equivalent constitutional isomeric libraries of self-assembling dendrons, dendrimers and dendronized polymers. These libraries demonstrate an 82% predictability, defined as the percentage of similar primary structures resulting in at least one conserved supramolecular shape with internal order. A combination of structural and retrostructural analysis that employs methodologies transplanted from structural biology, adapted to giant supramolecular assemblies was used for this process. A periodic table database of programmed primary structures was elaborated and used to facilitate the emergence of a diversity of functions in complex dendrimer systems via first principles. Assemblies generated by supramolecular and covalent polymer backbones were critically compared. Although by definition complex functional systems cannot be designed, this tutorial hints to a methodology based on database analysis principles to facilitate design principles that may help to mediate an accelerated emergence of chemical, physical and most probably also societal, political and economic complex systems on a shorter time scale and lower cost than by the current methods. This tutorial review is limited to the simplest, synthetically most accessible self-assembling minidendrons, minidendrimers and polymers dendronized with minidendrons that are best analyzed and elucidated at molecular, supramolecular and theoretical levels, and most used in other laboratories. These structures are all interrelated, and their principles expand in a simple way to their higher generations. PMID:25325787
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
One Single Static Measurement Predicts Wave Localization in Complex Structures
NASA Astrophysics Data System (ADS)
Lefebvre, Gautier; Gondel, Alexane; Dubois, Marc; Atlan, Michael; Feppon, Florian; Labbé, Aimé; Gillot, Camille; Garelli, Alix; Ernoult, Maxence; Mayboroda, Svitlana; Filoche, Marcel; Sebbah, Patrick
2016-08-01
A recent theoretical breakthrough has brought a new tool, called the localization landscape, for predicting the localization regions of vibration modes in complex or disordered systems. Here, we report on the first experiment which measures the localization landscape and demonstrates its predictive power. Holographic measurement of the static deformation under uniform load of a thin plate with complex geometry provides direct access to the landscape function. When put in vibration, this system shows modes precisely confined within the subregions delineated by the landscape function. Also the maxima of this function match the measured eigenfrequencies, while the minima of the valley network gives the frequencies at which modes become extended. This approach fully characterizes the low frequency spectrum of a complex structure from a single static measurement. It paves the way for controlling and engineering eigenmodes in any vibratory system, especially where a structural or microscopic description is not accessible.
Analyzing Complex and Structured Data via Unsupervised Learning Techniques
NASA Astrophysics Data System (ADS)
Polsterer, Kai Lars; Gieseke, Fabian; Gianniotis, Nikos; Kügler, Dennis
2015-08-01
In the last decades more and more dedicated all-sky-surveys created an enormous amount of data which is publicly available on the internet. The resulting datasets contain spatial, spectral, and temporal information which exhibit complex structures in the respective domain. The capability to deal with morphological features, spectral signatures, and complex time series data has become very important but is still a challenging task. A common approach when processing this kind of structured data is to extract representative features and use those for a further analysis. We present unsupervised learning approaches that help to visualize / cluster these complex data sets by e.g. deriving rotation / translation invariant prototypes or capturing the latent dynamics of time series without employing features and using echo-state-networks instead.
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. PMID:27563967
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 organisational model…
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…
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.
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…
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
2010-08-16
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 {center_dot} Nup145C {center_dot} Nup84 complex, the centerpiece of the heptamer, at 3.2-{angstrom} resolution. Nup84 forms a U-shaped {alpha}-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 {center_dot} 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.
Purple Bacterial Light-harvesting Complexes: From Dreams to Structures.
Cogdell, Richard J; Hashimoto, Hideki; Gardiner, Alastair T
2004-01-01
This paper describes the main stages involved in the research efforts designed to try and understand the structure and function of purple bacterial antenna complexes. Wherever possible the work has been illustrated by pictures of the major people who carried it out.
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
Quantum groups, non-commutative differential geometry and applications
Schupp, P
1993-12-09
The topic of this thesis is the development of a versatile and geometrically motivated differential calculus on non-commutative or quantum spaces, providing powerful but easy-to-use mathematical tools for applications in physics and related sciences. A generalization of unitary time evolution is proposed and studied for a simple 2-level system, leading to non-conservation of microscopic entropy, a phenomenon new to quantum mechanics. A Cartan calculus that combines functions, forms, Lie derivatives and inner derivations along general vector fields into one big algebra is constructed for quantum groups and then extended to quantum planes. The construction of a tangent bundle on a quantum group manifold and an BRST type approach to quantum group gauge theory are given as further examples of applications. The material is organized in two parts: Part I studies vector fields on quantum groups, emphasizing Hopf algebraic structures, but also introducing a ``quantum geometric`` construction. Using a generalized semi-direct product construction we combine the dual Hopf algebras A of functions and U of left-invariant vector fields into one fully bicovariant algebra of differential operators. The pure braid group is introduced as the commutant of {Delta}(U). It provides invariant maps A {yields} U and thereby bicovariant vector fields, casimirs and metrics. This construction allows the translation of undeformed matrix expressions into their less obvious quantum algebraic counter parts. We study this in detail for quasitriangular Hopf algebras, giving the determinant and orthogonality relation for the ``reflection`` matrix. Part II considers the additional structures of differential forms and finitely generated quantum Lie algebras -- it is devoted to the construction of the Cartan calculus, based on an undeformed Cartan identity.
Dynamic modeling of structures from measured complex modes
NASA Technical Reports Server (NTRS)
Ibrahim, s. R.
1982-01-01
A technique is presented to use a set of identified complex modes together with an analytical mathematical model of a structure under test to compute improved mass, stiffness and damping matrices. A set of identified normal modes, computed from the measured complex modes, is used in the mass orthogonality equation to compute an improved mass matrix. This eliminates possible errors that may result from using approximated complex modes as normal modes. The improved mass matrix, the measured complex modes and the higher analytical modes are then used to compute the improved stiffness and damping matrices. The number of degrees-of-freedom of the improved model is limited to equal the number of elements in the measured modal vectors. A simulated experiment shows considerable improvements, in the system's analytical dynamic model, over the frequency range of the given measured modal information.
Structure and Abundance of Nitrous Oxide Complexes in Earth's Atmosphere.
Salmon, Steven R; de Lange, Katrina M; Lane, Joseph R
2016-04-01
We have investigated the lowest energy structures and binding energies of a series of atmospherically relevant nitrous oxide (N2O) complexes using explicitly correlated coupled cluster theory. Specifically, we have considered complexes with nitrogen (N2-N2O), oxygen (O2-N2O), argon (Ar-N2O), and water (H2O-N2O). We have calculated rotational constants and harmonic vibrational frequencies for the complexes and the constituent monomers. Statistical mechanics was used to determine the thermodynamic parameters for complex formation as a function of temperature and pressure. These results, in combination with relevant atmospheric data, were used to estimate the abundance of N2O complexes in Earth's atmosphere as a function of altitude. We find that the abundance of N2O complexes in Earth's atmosphere is small but non-negligible, and we suggest that N2O complexes may contribute to absorption of terrestrial radiation and be relevant for understanding the atmospheric fate of N2O.
On complexity of trellis structure of linear block codes
NASA Technical Reports Server (NTRS)
Lin, Shu
1990-01-01
The trellis structure of linear block codes (LBCs) is discussed. The state and branch complexities of a trellis diagram (TD) for a LBC is investigated. The TD with the minimum number of states is said to be minimal. The branch complexity of a minimal TD for a LBC is expressed in terms of the dimensions of specific subcodes of the given code. Then upper and lower bounds are derived on the number of states of a minimal TD for a LBC, and it is shown that a cyclic (or shortened cyclic) code is the worst in terms of the state complexity among the LBCs of the same length and dimension. Furthermore, it is shown that the structural complexity of a minimal TD for a LBC depends on the order of its bit positions. This fact suggests that an appropriate permutation of the bit positions of a code may result in an equivalent code with a much simpler minimal TD. Boolean polynomial representation of codewords of a LBC is also considered. This representation helps in study of the trellis structure of the code. Boolean polynomial representation of a code is applied to construct its minimal TD. Particularly, the construction of minimal trellises for Reed-Muller codes and the extended and permuted binary primitive BCH codes which contain Reed-Muller as subcodes is emphasized. Finally, the structural complexity of minimal trellises for the extended and permuted, and double-error-correcting BCH codes is analyzed and presented. It is shown that these codes have relatively simple trellis structure and hence can be decoded with the Viterbi decoding algorithm.
2. 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
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
Solution structure of the Legionella pneumophila Mip-rapamycin complex
Ceymann, Andreas; Horstmann, Martin; Ehses, Philipp; Schweimer, Kristian; Paschke, Anne-Katrin; Steinert, Michael; Faber, Cornelius
2008-01-01
Background Legionella pneumphila is the causative agent of Legionnaires' disease. A major virulence factor of the pathogen is the homodimeric surface protein Mip. It shows peptidyl-prolyl cis/trans isomerase activty and is a receptor of FK506 and rapamycin, which both inhibit its enzymatic function. Insight into the binding process may be used for the design of novel Mip inhibitors as potential drugs against Legionnaires' disease. Results We have solved the solution structure of free Mip77–213 and the Mip77–213-rapamycin complex by NMR spectroscopy. Mip77–213 showed the typical FKBP-fold and only minor rearrangements upon binding of rapamycin. Apart from the configuration of a flexible hairpin loop, which is partly stabilized upon binding, the solution structure confirms the crystal structure. Comparisons to the structures of free FKBP12 and the FKBP12-rapamycin complex suggested an identical binding mode for both proteins. Conclusion The structural similarity of the Mip-rapamycin and FKBP12-rapamycin complexes suggests that FKBP12 ligands may be promising starting points for the design of novel Mip inhibitors. The search for a novel drug against Legionnaires' disease may therefore benefit from the large variety of known FKBP12 inhibitors. PMID:18366641
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
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
Geometric and electronic structures of potassium-adsorbed rubrene complexes
NASA Astrophysics Data System (ADS)
Li, Tsung-Lung; Lu, Wen-Cai
2015-06-01
The geometric and electronic structures of potassium-adsorbed rubrene complexes are studied in this article. It is found that the potassium-rubrene (K1RUB) complexes inherit the main symmetry characteristics from their pristine counterparts and are thus classified into D2- and C2h-like complexes according to the relative orientations of the four phenyl side groups. The geometric structures of K1RUB are governed by two general effects on the total energy: Deformation of the carbon frame of the pristine rubrene increases the total energy, while proximity of the potassium ion to the phenyl ligands decreases the energy. Under these general rules, the structures of D2- and C2h-like K1RUB, however, exhibit their respective peculiarities. These peculiarities can be illustrated by their energy profiles of equilibrium structures. For the potassium adsorption-sites, the D2-like complexes show minimum-energy basins, whereas the C2h-like ones have single-point minimum-energies. If the potassium atom ever has the energy to diffuse from the minimum-energy site, the potassium diffusion path on the D2-like complexes is most likely along the backbone in contrast to the C2h-like ones. Although the electronic structures of the minimum-energy structures of D2- and C2h-like K1RUB are very alike, decompositions of their total spectra reveal insights into the electronic structures. First, the spectral shapes are mainly determined by the facts that, in comparison with the backbone carbons, the phenyl carbons have more uniform chemical environments and far less contributions to the electronic structures around the valence-band edge. Second, the electron dissociated from the potassium atom mainly remains on the backbone and has little effects on the electronic structures of the phenyl groups. Third, the two phenyls on the same side of the backbone as the potassium atom have more similar chemical environments than the other two on the opposite side, which leads to the largely enhanced
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 (K1RUB) complexes inherit the main symmetry characteristics from their pristine counterparts and are thus classified into D2- and C2h-like complexes according to the relative orientations of the four phenyl side groups. The geometric structures of K1RUB are governed by two general effects on the total energy: Deformation of the carbon frame of the pristine rubrene increases the total energy, while proximity of the potassium ion to the phenyl ligands decreases the energy. Under these general rules, the structures of D2- and C2h-like K1RUB, however, exhibit their respective peculiarities. These peculiarities can be illustrated by their energy profiles of equilibrium structures. For the potassium adsorption-sites, the D2-like complexes show minimum-energy basins, whereas the C2h-like ones have single-point minimum-energies. If the potassium atom ever has the energy to diffuse from the minimum-energy site, the potassium diffusion path on the D2-like complexes is most likely along the backbone in contrast to the C2h-like ones. Although the electronic structures of the minimum-energy structures of D2- and C2h-like K1RUB are very alike, decompositions of their total spectra reveal insights into the electronic structures. First, the spectral shapes are mainly determined by the facts that, in comparison with the backbone carbons, the phenyl carbons have more uniform chemical environments and far less contributions to the electronic structures around the valence-band edge. Second, the electron dissociated from the potassium atom mainly remains on the backbone and has little effects on the electronic structures of the phenyl groups. Third, the two phenyls on the same side of the backbone as the potassium atom have more similar chemical environments than the other two on the opposite side, which leads to the largely enhanced
Curved noncommutative tori as Leibniz quantum compact metric spaces
NASA Astrophysics Data System (ADS)
Latrémolière, Frédéric
2015-12-01
We prove that curved noncommutative tori are Leibniz quantum compact metric spaces and that they form a continuous family over the group of invertible matrices with entries in the image of the quantum tori for the conjugation by modular conjugation operator in the regular representation, when this group is endowed with a natural length function.
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.
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.
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.
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.
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 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.
Effects of twisted noncommutativity in multi-particle Hamiltonians
NASA Astrophysics Data System (ADS)
Kuznetsova, Zhanna; Toppan, Francesco
2013-07-01
The non-commutativity induced by a Drinfel'd twist produces Bopp-shift-like transformations for deformed operators. In a single-particle setting the Drinfel'd twist allows to recover the non-commutativity obtained from various methods which are not based on Hopf algebras. In multi-particle sector, on the other hand, the Drinfel'd twist implies novel features. In conventional approaches to non-commutativity, deformed primitive operators are postulated to act additively. A Drinfel'd twist implies non-additive effects which are controlled by the coproduct. We stress that in our framework, the central element denoted as ħ is associated to an additive operator whose physical interpretation is that of the Particle Number operator. We illustrate all these features for a class of (abelian twist-deformed) 2D Hamiltonians. Suitable choices of the parameters lead to the Hamiltonian of the non-commutative Quantum Hall Effect, the harmonic oscillator, the quantization of the configuration space. The non-additive effects in the multi-particle sector, leading to results departing from the existing literature, are pointed out.
A comparison of remnants in noncommutative Bardeen black holes
NASA Astrophysics Data System (ADS)
Mehdipour, S. Hamid; Ahmadi, M. H.
2016-09-01
We derive the mass term of the Bardeen metric in the presence of a noncommutative geometry induced minimal length. In this setup, the proposal of a stable black hole remnant as a candidate to store information is confirmed. We consider the possibility of having an extremal configuration with one degenerate event horizon and compare different sizes of black hole remnants. As a result, once the magnetic charge g of the noncommutative Bardeen solution becomes larger, both the minimal nonzero mass M0 and the minimal nonzero horizon radius r0 get larger. This means, subsequently, under the condition of an adequate amount of g, the three parameters g, M0, and r0 are in a connection with each other linearly. According to our results, a noncommutative Bardeen black hole is colder than the noncommutative Schwarzschild black hole and its remnant is bigger, so the minimum required energy for the formation of such a black hole at particle colliders will be larger. We also find a closely similar result for the Hayward solution.
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.
3D quantum gravity and effective noncommutative quantum field theory.
Freidel, Laurent; Livine, Etera R
2006-06-01
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.
Structure and stability of complex coacervate core micelles with lysozyme.
Lindhoud, Saskia; Vries, Renko de; Norde, Willem; Stuart, Martien A Cohen
2007-07-01
Encapsulation of enzymes by polymers is a promising method to influence their activity and stability. Here, we explore the use of complex coacervate core micelles for encapsulation of enzymes. The core of the micelles consists of negatively charged blocks of the diblock copolymer PAA42PAAm417 and the positively charged homopolymer PDMAEMA150. For encapsulation, part of the positively charged homopolymer was replaced by the positively charged globular protein lysozyme. We have studied the formation, structure, and stability of the resulting micelles for three different mixing ratios of homopolymer and lysozyme: a system predominantly consisting of homopolymer, a system predominantly consisting of lysozyme, and a system where the molar ratio between the two positively charged molecules was almost one. We also studied complexes made of only lysozyme and PAA42PAAm417. Complex formation and the salt-induced disintegration of the complexes were studied using dynamic light-scattering titrations. Small-angle neutron scattering was used to investigate the structures of the cores. We found that micelles predominantly consisting of homopolymer are spherical but that complex coacervate core micelles predominantly consisting of lysozyme are nonspherical. The stability of the micelles containing a larger fraction of lysozyme is lower.
Structural Preferences in Phosphanylthiolato Platinum(II) Complexes.
Duran, Josep; Polo, Alfonso; Real, Julio; Benet-Buchholz, Jordi; Solà, Miquel; Poater, Albert
2016-02-01
The transition-metal complexes of heterotopic phosphanylthiolato ligands are useful in various reactions which depend on the stereochemistry of the complexes. Bis-chelate complex [Pt(SCH2CH2PPh2-κ(2) P,S)2] (1) was obtained in good yields by direct base-free substitution reaction of the corresponding phosphanylthiol (HSCH2CH2PPh2) with K2PtCl4 or by oxidative addition of the same phosphanylthiol to Pt(PPh3)4. In agreement with the antisymbiosis rule, complex 1 shows a cis-P,P arrangement in solid state crystallizing in the monoclinic system (C2/c). Density functional theory (DFT) calculations on 1 reveal the right characteristics for the preferred cis-P,P arrangement, rationalizing its formation. Direct base-free reaction of [PtCl2(1,5-cyclooctadiene)] with one equivalent of the same phosphanylthiol produce the trinuclear complex [PtCl(μ-SCH2CH2PPh2-κ(2) P,S)]3 (2) instead of the binuclear structure common in palladium and nickel derivatives. Crystals of 2 are triclinic (P 1‾ ) showing a sulfur-bridging edge-sharing cyclic trinuclear complex with square-planar coordination geometry around the platinum atoms and a Pt3S3 cycle in skew-boat conformation. This preference for the trinuclear structure was rationalized mechanistically and through conceptual DFT. PMID:27308212
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.
Structural Preferences in Phosphanylthiolato Platinum(II) Complexes
Duran, Josep; Real, Julio; Benet‐Buchholz, Jordi; Solà, Miquel
2015-01-01
Abstract The transition‐metal complexes of heterotopic phosphanylthiolato ligands are useful in various reactions which depend on the stereochemistry of the complexes. Bis‐chelate complex [Pt(SCH2CH2PPh2‐κ2 P,S)2] (1) was obtained in good yields by direct base‐free substitution reaction of the corresponding phosphanylthiol (HSCH2CH2PPh2) with K2PtCl4 or by oxidative addition of the same phosphanylthiol to Pt(PPh3)4. In agreement with the antisymbiosis rule, complex 1 shows a cis‐P,P arrangement in solid state crystallizing in the monoclinic system (C2/c). Density functional theory (DFT) calculations on 1 reveal the right characteristics for the preferred cis‐P,P arrangement, rationalizing its formation. Direct base‐free reaction of [PtCl2(1,5‐cyclooctadiene)] with one equivalent of the same phosphanylthiol produce the trinuclear complex [PtCl(μ‐SCH2CH2PPh2‐κ2 P,S)]3 (2) instead of the binuclear structure common in palladium and nickel derivatives. Crystals of 2 are triclinic (P 1‾ ) showing a sulfur‐bridging edge‐sharing cyclic trinuclear complex with square‐planar coordination geometry around the platinum atoms and a Pt3S3 cycle in skew‐boat conformation. This preference for the trinuclear structure was rationalized mechanistically and through conceptual DFT. PMID:27308212
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, spectra and stability of a tetrafluoromethane-water complex.
Mierzwicki, Krzysztof; Mielke, Zofia; Sałdyka, Magdalena; Coussan, Stephane; Roubin, Pascale
2008-03-01
The complex formed between water and tetrafluoromethane has been studied by infrared matrix isolation spectroscopy and ab initio calculations. The geometries of the CF4-H2O complexes were optimized in two steps at the MP2/aug-cc-pVTZ level of theory. The structure found at this level was reoptimized on the CP-corrected potential energy surface. The interaction energy was partitioned according to the SAPT scheme and the topological analysis of the electron density was performed. The optimized structure corresponds to the nonhydrogen bonded complex with an oxygen atom of water oriented toward the carbon atom of CF4. The infrared spectra of CF4-H2O /Ne(Ar) matrices demonstrate the presence of a well defined CF4-H2O structure in accord with theoretical prediction. Two complex vibrations were identified in the spectra of neon matrices and four vibrations were observed in the spectra of argon matrices. The available experimental data are in accord with the CP-corrected calculated data.
Latent Hierarchical Model of Temporal Structure for Complex Activity Classification.
Wang, Limin; Qiao, Yu; Tang, Xiaoou
2014-02-01
Modeling the temporal structure of sub-activities is an important yet challenging problem in complex activity classification. This paper proposes a latent hierarchical model (LHM) to describe the decomposition of complex activity into sub-activities in a hierarchical way. The LHM has a tree-structure, where each node corresponds to a video segment (sub-activity) at certain temporal scale. The starting and ending time points of each sub-activity are represented by two latent variables, which are automatically determined during the inference process. We formulate the training problem of the LHM in a latent kernelized SVM framework and develop an efficient cascade inference method to speed up classification. The advantages of our methods come from: 1) LHM models the complex activity with a deep structure, which is decomposed into sub-activities in a coarse-to-fine manner and 2) the starting and ending time points of each segment are adaptively determined to deal with the temporal displacement and duration variation of sub-activity. We conduct experiments on three datasets: 1) the KTH; 2) the Hollywood2; and 3) the Olympic Sports. The experimental results show the effectiveness of the LHM in complex activity classification. With dense features, our LHM achieves the state-of-the-art performance on the Hollywood2 dataset and the Olympic Sports dataset.
Structural mechanisms of DREAM complex assembly and regulation.
Guiley, Keelan Z; Liban, Tyler J; Felthousen, Jessica G; Ramanan, Parameshwaran; Litovchick, Larisa; Rubin, Seth M
2015-05-01
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
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
Synthetic and Structural Studies of Titanium Aminotroponiminate Complexes.
Steinhuebel, Dietrich P.; Lippard, Stephen J.
1999-12-27
The synthesis and characterization of a series of Ti(III) and Ti(IV) aminotroponiminate complexes are described. Six-coordinate [TiMe(2)(Me(2)ATI)(2)] and [TiPh(2)(Me(2)ATI)(2)] were synthesized and structurally characterized, where Me(2)ATI is N,N'-dimethylaminotroponiminate. The mono-alkyl complexes [TiClR(Me(2)ATI)(2)], R = Me, CH(2)SiMe(3), were prepared, and treatment of the former, generated in situ, with PhMgCl yielded the alkyl-aryl complex [TiMePh(Me(2)ATI)(2)]. The solid state structures of most of these complexes were determined and reveal slightly distorted, trigonal-prismatic coordination geometries. Attempts to prepare alkyl complexes containing beta-hydrogen atoms resulted instead in the isolation of [Ti(Me(2)ATI)(3)] or [Ti(2)Cl(2)(Me(2)ATI)(4)], depending on the alkyl reagent and stoichiometry. Because of the modest steric requirements of the {Ti(Me(2)ATI)(2)}(2+) fragment, five-coordinate Ti(IV) complexes were only generated with a bulky sigma-2pi donor ligand, [Ti(N-(2,6)-i-Pr(2)C(6)H(3))(Me(2)ATI)(2)] being a specific example. Attempts to prepare the isoelectronic oxo analogue afforded only dimeric [Ti(2)O(2)(Me(2)ATI)(4)]. Comparison of the metrical parameters for these complexes with those in the literature containing aryloxide and benzamidinate ligands indicate that the {Ti(Me(2)ATI)(2)}(2+) fragment is quite electron releasing. PMID:11671337
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.
Structure of the 4-aminobenzonitrile/water complexes
NASA Astrophysics Data System (ADS)
Alejandro, Estela; Fernández, José A.; Castaño, Fernando
2002-02-01
The 4-aminobenzonitrile chromophore (ABN), has two active sites for solvation with water and the ABN(H 2O) 1 complex a number of isomers of similar stability, as revealed by ab initio calculations conducted by DFT and MP2 methods. Hole burning and two-colour mass-resolved spectroscopies provide evidence on the presence of two isomers in the ABN(H 2O) complex. The identification of the observed isomers to calculated structures has been carried out by comparison between the appropriate spectra and the ab initio calculated ionization energies (IEs) and the experimental and simulated rotational contours. Stability arguments are useless owing to the close isomer dissociation energies.
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
Microwave structure for the propiolic acid-formic acid complex.
Kukolich, Stephen G; Mitchell, Erik G; Carey, Spencer J; Sun, Ming; Sargus, Bryan A
2013-10-01
New microwave spectra were measured to obtain rotational constants and centrifugal distortion constants for the DCCCOOH···HOOCH and HCCCOOD···DOOCH isotopologues. Rotational transitions were measured in the frequency range of 4.9-15.4 GHz, providing accurate rotational constants, which, combined with previous rotational constants, allowed an improved structural fit for the propiolic acid-formic acid complex. The new structural fit yields reasonably accurate orientations for both the propiolic and formic acid monomers in the complex and more accurate structural parameters describing the hydrogen bonding. The structure is planar, with a positive inertial defect of Δ = 1.33 amu Å(2). The experimental structure exhibits a greater asymmetry for the two hydrogen bond lengths than was obtained from the ab initio mp2 calculations. The best-fit hydrogen bond lengths have an r(O1-H1···O4) of 1.64 Å and an r(O3-H2···O2) of 1.87 Å. The average of the two hydrogen bond lengths is r(av)(exp) = 1.76 Å, in good agreement with r(av)(theory) = 1.72 Å. The center of mass separation of the monomers is R(CM) = 3.864 Å. Other structural parameters from the least-squares fit using the experimental rotational constants are compared with theoretical values. The spectra were obtained using two different pulsed beam Fourier transform microwave spectrometers.
Electronic Structure and Reactivity of Three-Coordinate Iron Complexes
Holland, Patrick L.
2008-01-01
Conspectus The identity and oxidation state of the metal in a coordination compound are typically thought to be the most important determinants of its reactivity. However, the coordination number (the number of bonds to the metal) can be equally influential. This Account describes iron complexes with a coordination number of only three, which differ greatly from iron complexes with octahedral (six-coordinate) geometries with respect to their magnetism, electronic structure, preference for ligands, and reactivity. Three-coordinate complexes with a trigonal-planar geometry are accessible using bulky, anionic, bidentate ligands (β-diketiminates) that steer a monodentate ligand into the plane of their two nitrogen donors. This strategy has led to a variety of three-coordinate iron complexes in which iron is in the +1, +2, and +3 oxidation states. Systematic studies on the electronic structures of these complexes have been useful in interpreting their properties. The iron ions are generally high spin, with singly occupied orbitals available for π interactions with ligands. Trends in σ-bonding show that iron(II) complexes favor electronegative ligands (O, N donors) over electropositive ligands (hydride). The combination of electrostatic σ-bonding and the availability of π-interactions stabilizes iron(II) fluoride and oxo complexes. The same factors destabilize iron(II) hydride complexes, which are reactive enough to add the hydrogen atom to unsaturated organic molecules and to take part in radical reactions. Iron(I) complexes use strong π-backbonding to transfer charge from iron into coordinated alkynes and N2, whereas iron(III) accepts charge from a π-donating imido ligand. Though the imidoiron(III) complex is stabilized by π-bonding in the trigonal-planar geometry, addition of pyridine as a fourth donor weakens the π-bonding, which enables abstraction of H atoms from hydrocarbons. The unusual bonding and reactivity patterns of three-coordinate iron compounds
NASA Astrophysics Data System (ADS)
Ghoneim, M. M.; El-Sonbati, A. Z.; El-Bindary, A. A.; Diab, M. A.; Serag, L. S.
2015-04-01
A number of novel polymer complexes of various anions of copper(II), cobalt(II), nickel(II) and uranyl(II) with N(4-(acrylamido)-2-hydroxy benzoic acid) (ABH) have been synthesized and characterized by elemental analysis, IR, 1H NMR, magnetic susceptibility measurements, electronic spin resonance, vibrational spectra and thermal analysis. The molecular structures of the ligand are optimized theoretically and the quantum chemical parameters are calculated. Tentative structures for the polymeric metal complexes due to their potential application are also suggested. The IR data exhibit the coordination of ONO2/OAc/SO4 with the metal ions in the polymeric metal complex. Vibrational spectra indicate coordination of carboxylate oxygen and phenolic OH of the ligand giving a MO4 square planar chromophore. Ligand field ESR spectra support square planar geometry around Cu(II). The thermal decomposition of the polymer complexes were discussed in relation to structure, and the thermodynamic parameters of the decomposition stages were evaluated applying Coast-Redfern and Horowitz-Metzger methods.
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.
STRIPAK Complexes: structure, biological function, and involvement in human diseases
Hwang, Juyeon; Pallas, David C.
2014-01-01
The mammalian striatin family consists of three proteins, striatin, S/G2 nuclear autoantigen, and zinedin. Striatin family members have no intrinsic catalytic activity, but rather function as scaffolding proteins. Remarkably, they organize multiple diverse, large signaling complexes that participate in a variety of cellular processes. Moreover, they appear to be regulatory/targeting subunits for the major eukaryotic serine/threonine protein phosphatase 2A. In addition, striatin family members associate with germinal center kinase III kinases as well as other novel components, earning these assemblies the name striatin-interacting phosphatase and kinase (STRIPAK) complexes. Recently, there has been a great increase in functional and mechanistic studies aimed at identifying and understanding the roles of STRIPAK–like complexes in cellular processes of multiple organisms. These studies have identified novel STRIPAK or STRIPAK-like complexes and have explored their roles in specific signaling pathways. Together, the results of these studies have sparked increased interest in striatin family complexes because they have revealed roles in signaling, cell cycle control, apoptosis, vesicular trafficking, Golgi assembly, cell polarity, cell migration, neural and vascular development, and cardiac function. Moreover, STRIPAK complexes have been connected to clinical conditions, including cardiac disease, diabetes, autism, and cerebral cavernous malformation. In this review, we discuss the expression, localization, and protein domain structure of striatin family members. Then we consider the diverse complexes these proteins and their homologs form in various organisms, emphasizing what is known regarding function and regulation. Finally, we will explore possible roles of striatin family complexes in disease, especially cerebral cavernous malformation. PMID:24333164
Electronic structure of acceptor-donor complexes in silicon
NASA Astrophysics Data System (ADS)
Atoro, E.; Ohama, Y.; Hayafuji, Y.
2003-10-01
The electronic structure of trimer acceptor-donor complexes in silicon Si clusters is studied using the ab initio discrete variational-Xα molecular-orbital (MO) method. The trimer complexes In2D (D=phosphorus P, arsenic As, antimony Sb, or bismuth Bi) consist of two indium In acceptor elements and a centered donor element D from the group V elements. Calculations are performed under the assumption that the three atoms are arranged in the nearest neighbor substitutional trimer configuration. Results indicate that the trimer complexes act as shallower acceptors having smaller ionization activation energies than In acceptor. The potential of In2D as an acceptor in Si is then discussed and In2D is proposed as a promising acceptor for the formation of channels and source/drains in ultralarge scaled integration.
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
2015-05-01
The five macromolecular complexes that jointly mediate oxidative phosphorylation (OXPHOS) in mitochondria consist of many more subunits than those of bacteria, yet, it remains unclear by which evolutionary mechanism(s) these novel subunits were recruited. Even less well understood is the structural evolution of mitochondrial ribosomes (mitoribosomes): while it was long thought that their exceptionally high protein content would physically compensate for their uniquely low amount of ribosomal RNA (rRNA), this hypothesis has been refuted by structural studies. Here, we present a cryo-electron microscopy structure of the 73S mitoribosome from Neurospora crassa, together with genomic and proteomic analyses of mitoribosome composition across the eukaryotic domain. Surprisingly, our findings reveal that both structurally and compositionally, mitoribosomes have evolved very similarly to mitochondrial OXPHOS complexes via two distinct phases: A constructive phase that mainly acted early in eukaryote evolution, resulting in the recruitment of altogether approximately 75 novel subunits, and a reductive phase that acted during metazoan evolution, resulting in gradual length-reduction of mitochondrially encoded rRNAs and OXPHOS proteins. Both phases can be well explained by the accumulation of (slightly) deleterious mutations and deletions, respectively, in mitochondrially encoded rRNAs and OXPHOS proteins. We argue that the main role of the newly recruited (nuclear encoded) ribosomal- and OXPHOS proteins is to provide structural compensation to the mutationally destabilized mitochondrially encoded components. While the newly recruited proteins probably provide a selective advantage owing to their compensatory nature, and while their presence may have opened evolutionary pathways toward novel mitochondrion-specific functions, we emphasize that the initial events that resulted in their recruitment was nonadaptive in nature. Our framework is supported by population genetic
Structural insights into neuronal K+ channel–calmodulin complexes
Mruk, Karen; Shandilya, Shiven M.D.; Blaustein, Robert O.; Schiffer, Celia A.; Kobertz, William R.
2012-01-01
Calmodulin (CaM) is a ubiquitous intracellular calcium sensor that directly binds to and modulates a wide variety of ion channels. Despite the large repository of high-resolution structures of CaM bound to peptide fragments derived from ion channels, there is no structural information about CaM bound to a fully folded ion channel at the plasma membrane. To determine the location of CaM docked to a functioning KCNQ K+ channel, we developed an intracellular tethered blocker approach to measure distances between CaM residues and the ion-conducting pathway. Combining these distance restraints with structural bioinformatics, we generated an archetypal quaternary structural model of an ion channel–CaM complex in the open state. These models place CaM close to the cytoplasmic gate, where it is well positioned to modulate channel function. PMID:22869708
Structure and dynamics of complex liquid water: Molecular dynamics simulation
NASA Astrophysics Data System (ADS)
S, Indrajith V.; Natesan, Baskaran
2015-06-01
We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.
The Analysis of Complex Structure for China Education Network
NASA Astrophysics Data System (ADS)
Deng, Zhu-Jun; Zhang, Ning
We collected the data of the documents and their links of China Education and Research Network’s which construct the complex directed network China Education Network (CEN) with large amount of documents with their edges (URLs). This paper analyzes some statistical properties, including degree distributions, average path length, clustering coefficient, and the community structure of China Education Network basing on the practical data. By analyzing the practical data, we found that the in-degree and out-degree distribution of the CEN has power-law tail and the network displays both properties of small world and scale free. The CEN has a considerably small average path length and its clustering coefficient is in the mediate. As a large scale complex network, China Education Network clearly present its community structure in which the colleges in a school constitute communities generally with a large modularity.
Chelation-Induced Polymer Structural Hierarchy/Complexity in Water.
Han, Jie; Zhou, Kaiyi; Zhu, Xuechao; Yu, Qiuping; Ding, Yi; Lu, Xinhua; Cai, Yuanli
2016-08-01
Understanding nanoscale structural hierarchy/complexity of hydrophilic flexible polymers is imperative because it can be viewed as an analogue to protein-alike superstructures. However, current understanding is still in infancy. Herein the first demonstration of nanoscale structural hierarchy/complexity via copper chelation-induced self-assembly (CCISA) is presented. Hierarchically-ordered colloidal networks and disks can be achieved by deliberate control of spacer length and solution pH. Dynamic light scattering, transmission electron microscopy, and atomic force microscopy demonstrate that CCISA underwent supramolecular-to-supracolloidal stepwise-growth mechanism, and underline amazing prospects to the hierarchically-ordered superstructures of hydrophilic flexible polymers in water. PMID:27219860
Lithium, sodium and potassium picolyl complexes: syntheses, structures and bonding.
Kennedy, Alan R; Mulvey, Robert E; Urquhart, Robert I; Robertson, Stuart D
2014-10-14
Synthetically important for introducing a picolyl scaffold into a molecular construction, alkali metallated picoline (methylpyridine) complexes are also interesting in their own right for the diversity of their ligand-metal bonding possibilities. Here the syntheses of seven new such complexes are reported: namely three 4-picoline derivatives 4-picLi·Me6TREN, 1, 4-picNa·Me6TREN, 2, and [4-picK·2(4-picH)]∞, 3; and four 2-picoline derivatives, 2-picLi·Me6TREN, 4, 2-picLi·PMDETA, 4', 2-picNa·Me6TREN, 5, and [2-picK·PMDETA]2, 6' [where pic = NC5H4(CH2); Me6TREN = tris(N,N-dimethyl-2-aminoethyl)amine, (Me2NCH2CH2)3N; PMDETA = N,N,N',N'',N''-pentamethyldiethylenetriamine, (Me2NCH2CH2)2NMe]. X-ray crystallographic studies establish that the lighter alkali metal complexes 1, 2, 4' and 5 adopt monomeric structures in contrast to the polymeric and dimeric arrangements adopted by potassium complexes 3 and 6' respectively. All complexes have also been characterized by solution NMR spectroscopy ((1)H, (13)C, and where relevant (7)Li). This study represents the first example of sodium and potassium picolyl complexes to be isolated and characterized. DOSY (Diffusion-Ordered Spectroscopy) experiments performed on 4 and 4' suggest both compounds retain their monomeric constitutions in C6D6 solution. Discussion focuses on the influence of the metal and neutral donor molecule on the structures and the nature of the ligand-metal (enamido versus aza-allylic) interactions. PMID:24770550
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. PMID:21987109
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.
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.
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
Structural properties of complex plasmas in a homogeneous dc discharge.
Mitic, S; Klumov, B A; Konopka, U; Thoma, M H; Morfill, G E
2008-09-19
We report on the first three-dimensional (3D) complex plasma structure analysis for an experiment that was performed in an elongated discharge tube in the absence of striations. The low frequency discharge was established with 1 kHz alternating dc current through a cylindrical glass tube filled with neon at 30 Pa. The injected particle cloud consisted of monodisperse microparticles. A scanning laser sheet and a camera were used to determine the particle position in 3D. The observed cylindrical-shaped particle cloud showed an ordered structure with a distinct outer particle shell. The observations are in agreement with performed molecular dynamics simulations.
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.
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, 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. PMID:6519248
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 complex networks requires both structure and dynamics
Gates, Alexander J.; Rocha, Luis M.
2016-01-01
The study of network structure has uncovered signatures of the organization of complex systems. However, there is also a need to understand how to control them; for example, identifying strategies to revert a diseased cell to a healthy state, or a mature cell to a pluripotent state. Two recent methodologies suggest that the controllability of complex systems can be predicted solely from the graph of interactions between variables, without considering their dynamics: structural controllability and minimum dominating sets. We demonstrate that such structure-only methods fail to characterize controllability when dynamics are introduced. We study Boolean network ensembles of network motifs as well as three models of biochemical regulation: the segment polarity network in Drosophila melanogaster, the cell cycle of budding yeast Saccharomyces cerevisiae, and the floral organ arrangement in Arabidopsis thaliana. We demonstrate that structure-only methods both undershoot and overshoot the number and which sets of critical variables best control the dynamics of these models, highlighting the importance of the actual system dynamics in determining control. Our analysis further shows that the logic of automata transition functions, namely how canalizing they are, plays an important role in the extent to which structure predicts dynamics. PMID:27087469
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. PMID:18413719
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.
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.
Hierarchical structure formation of cylindrical brush polymer-surfactant complexes.
Cong, Yang; Gunari, Nikhil; Zhang, Bin; Janshoff, Andreas; Schmidt, Manfred
2009-06-01
The complex formation of cylindrical brush polymers with poly(l-lysine) side chains (PLL) and sodium dodecyl sulfate (SDS) can induce a helical conformation of the cylindrical brush polymer in aqueous solution (Gunari, N.; Cong, Y.; Zhang, B.; Fischer, K.; Janshoff, A.; Schmidt, M. Macromol. Rapid Commun. 2008, 29, 821-825). Herein, we have systematically investigated the influence of surfactant, salt, and pH on the supramolecular structure formation. The cylindrical brush polymers and their complexes with surfactants were directly visualized by atomic force microscopy in air and in aqueous solution. The alkyl chain length (measured by the carbon number, n) of the surfactant plays a key role. While helical structures were formed with n=10, 11, and 12, no helices were observed with n<10 and n>13. Addition of salt destroys the helical structures as do pH conditions below 4 and above 6, most probably because the polymer-surfactant complexes start to disintegrate. Circular dichroism was utilized to monitor the PLL side chain conformation and clearly revealed that beta-sheet formation of the side chains induces the helical conformation of the atactic main chain. PMID:19326944
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
The structure of the β-barrel assembly machinery complex
Bakelar, Jeremy; Buchanan, Susan K.; Noinaj, Nicholas
2016-01-01
β-barrel outer membrane proteins (OMPs) are found within the outer membranes (OM) of Gram-negative bacteria and are essential for nutrient import, signaling, and adhesion. While the exact mechanism is unknown, a 200 kDa five component complex called the β-barrel assembly machinery (BAM) complex has been implicated in the biogenesis of OMPs. Here, we report the structure of the BAM complex from E. coli, revealing that binding of the accessory proteins BamCDE modulates the conformation of BamA, the central component of the complex, which may regulate the function of the BAM complex. The periplasmic domain of BamA was found in a closed state that prevents access to the barrel lumen from the periplasm, indicating substrate OMPs likely do not enter the barrel during biogenesis. Further, the first eight strands of the β-barrel domain undergo an unprecedented conformational shift leading to opening of the exit pore and rearrangement at the lateral gate. PMID:26744406
Structure and function of the Mitochondrial Calcium Uniporter complex
De Stefani, Diego; Patron, Maria; Rizzuto, Rosario
2015-01-01
The Mitochondrial Calcium Uniporter (MCU) is the critical protein of the inner mitochondrial membrane mediating the electrophoretic Ca2+ uptake into the matrix. It plays a fundamental role in the shaping of global calcium signaling and in the control of aerobic metabolism as well as apoptosis. Two features of mitochondrial calcium signaling have been known for a long time: i) mitochondrial Ca2+ uptake widely varies among cells and tissues, and ii) channel opening strongly relies on the extramitochondrial Ca2+ concentration, with low activity at resting [Ca2+] and high capacity as soon as calcium signaling is activated. Such complexity requires a specialized molecular machinery, with several primary components can be variably gathered together in order to match energy demands and protect from toxic stimuli. In line with this, MCU is now recognized to be part of a macromolecular complex known as the MCU complex. Our understanding of the structure and function of the MCU complex is now growing promptly, revealing an unexpected complexity that highlights the pleiotropic role of mitochondrial Ca2+ signals. PMID:25896525
Structure and function of the mitochondrial calcium uniporter complex.
De Stefani, Diego; Patron, Maria; Rizzuto, Rosario
2015-09-01
The mitochondrial calcium uniporter (MCU) is the critical protein of the inner mitochondrial membrane mediating the electrophoretic Ca²⁺ uptake into the matrix. It plays a fundamental role in the shaping of global calcium signaling and in the control of aerobic metabolism as well as apoptosis. Two features of mitochondrial calcium signaling have been known for a long time: i) mitochondrial Ca²⁺ uptake widely varies among cells and tissues, and ii) channel opening strongly relies on the extramitochondrial Ca²⁺ concentration, with low activity at resting [Ca²⁺] and high capacity as soon as calcium signaling is activated. Such complexity requires a specialized molecular machinery, with several primary components can be variably gathered together in order to match energy demands and protect from toxic stimuli. In line with this, MCU is now recognized to be part of a macromolecular complex known as the MCU complex. Our understanding of the structure and function of the MCU complex is now growing promptly, revealing an unexpected complexity that highlights the pleiotropic role of mitochondrial Ca²⁺ signals. This article is part of a Special Issue entitled: 13th European Symposium on Calcium.
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.
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. PMID:26369172
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
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. PMID:26686054
Crystal structure of a nuclear actin ternary complex.
Cao, Tingting; Sun, Lingfei; Jiang, Yuxiang; Huang, Shanjin; Wang, Jiawei; Chen, Zhucheng
2016-08-01
Actin polymerizes and forms filamentous structures (F-actin) in the cytoplasm of eukaryotic cells. It also exists in the nucleus and regulates various nucleic acid transactions, particularly through its incorporation into multiple chromatin-remodeling complexes. However, the specific structure of actin and the mechanisms that regulate its polymeric nature inside the nucleus remain unknown. Here, we report the crystal structure of nuclear actin (N-actin) complexed with actin-related protein 4 (Arp4) and the helicase-SANT-associated (HSA) domain of the chromatin remodeler Swr1. The inner face and barbed end of N-actin are sequestered by interactions with Arp4 and the HSA domain, respectively, which prevents N-actin from polymerization and binding to many actin regulators. The two major domains of N-actin are more twisted than those of globular actin (G-actin), and its nucleotide-binding pocket is occluded, freeing N-actin from binding to and regulation by ATP. These findings revealed the salient structural features of N-actin that distinguish it from its cytoplasmic counterpart and provide a rational basis for its functions and regulation inside the nucleus. PMID:27457955
Modelling polymersomes: a prototype for complex cellular structures
NASA Astrophysics Data System (ADS)
Sevink, G. J. A.; Fraaije, J. G. E. M.
2004-04-01
Self-organisation of small amphiphilic molecules is a key technique in many applications of modern nanotechnology. Thin polymer films have been extensively studied theoretically and experimentally because of their rich phase behaviour and use as templates in lithographic processes, optical devices and surfaces with molecular recognition capabilities. Encapsulating polymeric vesicles or polymersomes can be applied in very diverse applications ranging from drug delivery, templates for heterogeneous catalysts, aerosols and personal care products. Moreover, there is some understanding that polymersomes with internal structures can serve as a scaffold for the understanding of complex biological structures, such as the mitochondrium and other (sub-)cellular stuctures. The experimental technique of making polymersomes is relatively new, and the kinetics of their formation delicate, and often not well understood. As a result, the internal and external structures of experimental polymersomes are very diverse, and often highly depend on the method of preparation. Here we report the results of field-theoretic computer simulations of remarkable structures in dispersed droplets of a polymer surfactant. The preparation method is that of quenching a homogenous droplet of polymer surfactant in an aqueous bath. In the discussion part we shortly discuss the road ahead: the use of our method as a tool for understanding complex biological systems.
Yukawa terms in noncommutative SO(10) and E{sub 6} GUTs
Martin, C. P.
2010-10-15
We propose a method for constructing Yukawa terms for noncommutative SO(10) and E{sub 6} GUTs when these GUTs are formulated within the enveloping-algebra formalism. The most general noncommutative Yukawa term that we propose contains, at first order in {theta}{sup {mu}{nu},} the most general Becchi-Rouet-Stora invariant Yukawa contribution whose only dimensionful parameter is the noncommutativity parameter. This noncommutative Yukawa interaction is thus renormalizable at first order in {theta}{sup {mu}{nu}}.
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. PMID:19113767
Equivalence of curvature and noncommutativity in a physical space: Harmonic oscillator on sphere
NASA Astrophysics Data System (ADS)
Ghorashi, S. A. A.; Mahdifar, A.; Roknizadeh, R.
2014-06-01
We study the two-dimensional harmonic oscillator on a noncommutative plane. We show that by introducing appropriate Bopp shifts, one can obtain the Hamiltonian of a two-dimensional harmonic oscillator on a sphere according to the Higgs model. By calculating the commutation relations, we show that this noncommutativity is strictly dependent on the curvature of the background space. In other words, we introduce a kind of duality between noncommutativity and curvature by introducing noncommutativity parameters as functions of curvature. Also, it is shown that the physical realization of such model is a charged harmonic oscillator in the presence of electromagnetic field.
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.
The interplay between microscopic and mesoscopic structures in complex networks.
Reichardt, Jörg; Alamino, Roberto; Saad, David
2011-01-01
Understanding a complex network's structure holds the key to understanding its function. The physics community has contributed a multitude of methods and analyses to this cross-disciplinary endeavor. Structural features exist on both the microscopic level, resulting from differences between single node properties, and the mesoscopic level resulting from properties shared by groups of nodes. Disentangling the determinants of network structure on these different scales has remained a major, and so far unsolved, challenge. Here we show how multiscale generative probabilistic exponential random graph models combined with efficient, distributive message-passing inference techniques can be used to achieve this separation of scales, leading to improved detection accuracy of latent classes as demonstrated on benchmark problems. It sheds new light on the statistical significance of motif-distributions in neural networks and improves the link-prediction accuracy as exemplified for gene-disease associations in the highly consequential Online Mendelian Inheritance in Man database.
Structure of isochorismate synthase in complex with magnesium
Parsons, James F.; Shi, Katherine M.; Ladner, Jane E.
2008-01-01
The electron carrier menaquinone is one of many important bacterial metabolites that are derived from the key intermediate chorismic acid. MenF, the first enzyme in the menaquinone pathway, catalyzes the isomerization of chorismate to isochorismate. Here, an improved structure of MenF in a new crystal form is presented. The structure, solved at 2.0 Å resolution in complex with magnesium, reveals a well defined closed active site. Existing evidence suggests that the mechanism of the reaction catalyzed by MenF involves nucleophilic attack of a water molecule on the chorismate ring. The structure reveals a well defined water molecule located in an appropriate position for activation by Lys190 and attack on the substrate. PMID:18453696
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.
Random field Ising model and community structure in complex networks
NASA Astrophysics Data System (ADS)
Son, S.-W.; Jeong, H.; Noh, J. D.
2006-04-01
We propose a method to determine the community structure of a complex network. In this method the ground state problem of a ferromagnetic random field Ising model is considered on the network with the magnetic field Bs = +∞, Bt = -∞, and Bi≠s,t=0 for a node pair s and t. The ground state problem is equivalent to the so-called maximum flow problem, which can be solved exactly numerically with the help of a combinatorial optimization algorithm. The community structure is then identified from the ground state Ising spin domains for all pairs of s and t. Our method provides a criterion for the existence of the community structure, and is applicable equally well to unweighted and weighted networks. We demonstrate the performance of the method by applying it to the Barabási-Albert network, Zachary karate club network, the scientific collaboration network, and the stock price correlation network. (Ising, Potts, etc.)
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.
Landscape structure controls on biogeochemical fluxes in complex terrain (Invited)
NASA Astrophysics Data System (ADS)
McGlynn, B. L.; Riveros-Iregui, D.; Emanuel, R. E.; Pacific, V. J.; Epstein, H. E.; Welsch, D. L.
2010-12-01
Complex topography, topology, and strong environmental gradients in mountainous terrain impart fundamental controls on the distribution and redistribution of water, energy, and nutrients across the landscape. Many of these variables exhibit spatial patterns influenced by landscape structure and hydrologically mediated redistribution processes. Landscape structure therefore can lead to organized heterogeneity of ecosystem dynamics because of the interplay between abiotic and biotic processes. Mountainous terrain can also experience large diel, seasonal and interannual fluctuations in hydrometeorology. These temporal fluctuations will manifest differently across the landscape due to strong biophysical gradients and redistribution processes less influential in more homogenous terrain. Investigation in complex terrain therefore can provide insight into processes and feedbacks among nutrients, water, and climate. Here we examine space-time variability in ecosystem processes at the catchment scale with focus on carbon cycle science. We highlight controls on soil respiration and stream DOC export from plots to watershed scales based on high spatial and temporal resolution observation, empirical and numerical modeling, and eddy covariance approaches. We suggest complex terrain imparts organization on observed heterogeneity that can be used to gain new understanding of fundamental controls on ecosystem processes.
Structural chemistry of complex carbides and related compounds
NASA Astrophysics Data System (ADS)
Nowotny, Hans; Rogl, Peter; Schuster, Julius C.
1982-08-01
Complex carbides formed in ternary systems of a transition element ( M), a B-group element ( M'), and carbon and having a formula M2M'C (H-phase) or M3M'C (perovskite carbide) occur frequently. This reflects the simple geometry of the atomic arrangement of the metals and the filling mode by an interstitial stabilizer such as carbon or nitrogen. The phase relationship of the ternary combinations {Ti, Zr, Hf, V, Nb, Ta, Cr, Mn, and Ni}-aluminum-carbon was investigated. New complex carbides were found with the corresponding zirconium, hafnium, and tantalum combinations. The crystal structures in the case of Zr- and Hf-containing complex carbides can be characterized by a twelve-metal-layer sequence and by a ten-metal-layer sequence with carbon atoms again filling octahedral voids. The transition of structure types from TiC, Ti 2AlC, Ti 3SiC 2, ZrAlC 2, Zr 2Al 3C 5, to Al 4C 3 is also discussed.
Complex band structure of topological insulator Bi2Se3.
Betancourt, J; Li, S; Dang, X; Burton, J D; Tsymbal, E Y; Velev, J P
2016-10-01
Topological insulators are very interesting from a fundamental point of view, and their unique properties may be useful for electronic and spintronic device applications. From the point of view of applications it is important to understand the decay behavior of carriers injected in the band gap of the topological insulator, which is determined by its complex band structure (CBS). Using first-principles calculations, we investigate the dispersion and symmetry of the complex bands of Bi2Se3 family of three-dimensional topological insulators. We compare the CBS of a band insulator and a topological insulator and follow the CBS evolution in both when the spin-orbit interaction is turned on. We find significant differences in the CBS linked to the topological band structure. In particular, our results demonstrate that the evanescent states in Bi2Se3 are non-trivially complex, i.e. contain both the real and imaginary contributions. This explains quantitatively the oscillatory behavior of the band gap obtained from Bi2Se3 (0 0 0 1) slab calculations. PMID:27485021
Complex band structure of topological insulator Bi2Se3
NASA Astrophysics Data System (ADS)
Betancourt, J.; Li, S.; Dang, X.; Burton, J. D.; Tsymbal, E. Y.; Velev, J. P.
2016-10-01
Topological insulators are very interesting from a fundamental point of view, and their unique properties may be useful for electronic and spintronic device applications. From the point of view of applications it is important to understand the decay behavior of carriers injected in the band gap of the topological insulator, which is determined by its complex band structure (CBS). Using first-principles calculations, we investigate the dispersion and symmetry of the complex bands of Bi2Se3 family of three-dimensional topological insulators. We compare the CBS of a band insulator and a topological insulator and follow the CBS evolution in both when the spin-orbit interaction is turned on. We find significant differences in the CBS linked to the topological band structure. In particular, our results demonstrate that the evanescent states in Bi2Se3 are non-trivially complex, i.e. contain both the real and imaginary contributions. This explains quantitatively the oscillatory behavior of the band gap obtained from Bi2Se3 (0 0 0 1) slab calculations.
Structural and Biochemical Insights into MLL1 Core Complex Assembly
Avdic, Vanja; Zhang, Pamela; Lanouette, Sylvain; Groulx, Adam; Tremblay, Véronique; Brunzelle, Joseph; Couture, Jean-François
2012-05-02
Histone H3 Lys-4 methylation is predominantly catalyzed by a family of methyltransferases whose enzymatic activity depends on their interaction with a three-subunit complex composed of WDR5, RbBP5, and Ash2L. Here, we report that a segment of 50 residues of RbBP5 bridges the Ash2L C-terminal domain to WDR5. The crystal structure of WDR5 in ternary complex with RbBP5 and MLL1 reveals that both proteins binds peptide-binding clefts located on opposite sides of WDR5s {beta}-propeller domain. RbBP5 engages in several hydrogen bonds and van der Waals contacts within a V-shaped cleft formed by the junction of two blades on WDR5. Mutational analyses of both the WDR5 V-shaped cleft and RbBP5 residues reveal that the interactions between RbBP5 and WDR5 are important for the stimulation of MLL1 methyltransferase activity. Overall, this study provides the structural basis underlying the formation of the WDR5-RbBP5 subcomplex and further highlight the crucial role of WDR5 in scaffolding the MLL1 core complex.
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 Principles of CRISPR-Cas Surveillance and Effector Complexes.
Tsui, Tsz Kin Martin; Li, Hong
2015-01-01
The pathway of CRISPR-Cas immunity redefines the roles of RNA in the flow of genetic information and ignites excitement for next-generation gene therapy tools. CRISPR-Cas machineries offer a fascinating set of new enzyme assemblies from which one can learn principles of molecular interactions and chemical activities. The interference step of the CRISPR-Cas immunity pathway congregates proteins, RNA, and DNA into a single molecular entity that selectively destroys invading nucleic acids. Although much remains to be discovered, a picture of how the interference process takes place is emerging. This review focuses on the current structural data for the three known types of RNA-guided nucleic acid interference mechanisms. In it, we describe key features of individual complexes and we emphasize comparisons across types and along functional stages. We aim to provide readers with a set of core principles learned from the three types of interference complexes and a deep appreciation of the diversity among them.
Brain structural correlates of complex sentence comprehension in children
Fengler, Anja; Meyer, Lars; Friederici, Angela D.
2015-01-01
Prior structural imaging studies found initial evidence for the link between structural gray matter changes and the development of language performance in children. However, previous studies generally only focused on sentence comprehension. Therefore, little is known about the relationship between structural properties of brain regions relevant to sentence processing and more specific cognitive abilities underlying complex sentence comprehension. In this study, whole-brain magnetic resonance images from 59 children between 5 and 8 years were assessed. Scores on a standardized sentence comprehension test determined grammatical proficiency of our participants. A confirmatory factory analysis corroborated a grammar-relevant and a verbal working memory-relevant factor underlying the measured performance. Voxel-based morphometry of gray matter revealed that while children's ability to assign thematic roles is positively correlated with gray matter probability (GMP) in the left inferior temporal gyrus and the left inferior frontal gyrus, verbal working memory-related performance is positively correlated with GMP in the left parietal operculum extending into the posterior superior temporal gyrus. Since these areas are known to be differentially engaged in adults’ complex sentence processing, our data suggest a specific correspondence between children's GMP in language-relevant brain regions and differential cognitive abilities that guide their sentence comprehension. PMID:26468613
Changes in protein structure at the interface accompanying complex formation.
Chakravarty, Devlina; Janin, Joël; Robert, Charles H; Chakrabarti, Pinak
2015-11-01
Protein interactions are essential in all biological processes. The changes brought about in the structure when a free component forms a complex with another molecule need to be characterized for a proper understanding of molecular recognition as well as for the successful implementation of docking algorithms. Here, unbound (U) and bound (B) forms of protein structures from the Protein-Protein Interaction Affinity Database are compared in order to enumerate the changes that occur at the interface atoms/residues in terms of the solvent-accessible surface area (ASA), secondary structure, temperature factors (B factors) and disorder-to-order transitions. It is found that the interface atoms optimize contacts with the atoms in the partner protein, which leads to an increase in their ASA in the bound interface in the majority (69%) of the proteins when compared with the unbound interface, and this is independent of the root-mean-square deviation between the U and B forms. Changes in secondary structure during the transition indicate a likely extension of helices and strands at the expense of turns and coils. A reduction in flexibility during complex formation is reflected in the decrease in B factors of the interface residues on going from the U form to the B form. There is, however, no distinction in flexibility between the interface and the surface in the monomeric structure, thereby highlighting the potential problem of using B factors for the prediction of binding sites in the unbound form for docking another protein. 16% of the proteins have missing (disordered) residues in the U form which are observed (ordered) in the B form, mostly with an irregular conformation; the data set also shows differences in the composition of interface and non-interface residues in the disordered polypeptide segments as well as differences in their surface burial.
Quantum geometry and quantization on U(u(2)) background. Noncommutative Dirac monopole
NASA Astrophysics Data System (ADS)
Gurevich, Dimitri; Saponov, Pavel
2016-08-01
In our previous publications we introduced differential calculus on the enveloping algebras U(gl(m)) similar to the usual calculus on the commutative algebra Sym (gl(m)) . The main ingredients of our calculus are quantum partial derivatives which turn into the usual partial derivatives in the classical limit. In the particular case m = 2 we prolonged this calculus on a central extension A of the algebra U(gl(2)) . In the present paper we consider the problem of a further extension of the quantum partial derivatives on the skew-field of the algebra A and define the corresponding de Rham complex. As an application of the differential calculus we suggest a method of transferring dynamical models defined on an extended Sym (u(2)) to an extended algebra U(u(2)) . We call this procedure the quantization with noncommutative configuration space. In this sense we quantize the Dirac monopole and find a solution of this model.
3-D Numerical Modeling of a Complex Salt Structure
House, L.; Larsen, S.; Bednar, J.B.
2000-02-17
Reliably processing, imaging, and interpreting seismic data from areas with complicated structures, such as sub-salt, requires a thorough understanding of elastic as well as acoustic wave propagation. Elastic numerical modeling is an essential tool to develop that understanding. While 2-D elastic modeling is in common use, 3-D elastic modeling has been too computationally intensive to be used routinely. Recent advances in computing hardware, including commodity-based hardware, have substantially reduced computing costs. These advances are making 3-D elastic numerical modeling more feasible. A series of example 3-D elastic calculations were performed using a complicated structure, the SEG/EAGE salt structure. The synthetic traces show that the effects of shear wave propagation can be important for imaging and interpretation of images, and also for AVO and other applications that rely on trace amplitudes. Additional calculations are needed to better identify and understand the complex wave propagation effects produced in complicated structures, such as the SEG/EAGE salt structure.
Chirality Quantum Phase Transition in Noncommutative Dirac Oscillator
NASA Astrophysics Data System (ADS)
Wang, Shao-Hua; Hou, Yu-Long; Wang, Qing; Long, Zheng-Wen; Jing, Jian
2014-12-01
The charged Dirac oscillator on a noncommutative plane coupling to a uniform perpendicular magnetic held is studied in this paper. We map the noncommutative plane to a commutative one by means of Bopp shift and study this problem on the commutative plane. We find that this model can be mapped onto a quantum optics model which contains Anti—Jaynes—Cummings (AJC) or Jaynes—Cummings (JC) interactions when a dimensionless parameter ζ (which is the function of the intensity of the magnetic held) takes values in different regimes. Furthermore, this model behaves as experiencing a chirality quantum phase transition when the dimensionless parameter ζ approaches the critical point. Several evidences of the chirality quantum phase transition are presented. We also study the non-relativistic limit of this model and find that a similar chirality quantum phase transition takes place in its non-relativistic limit.
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.
Long tailed cage amines: Synthesis, metal complexation, and structure
Dittrich, Birger; Harrowfield, Jack M.; Koutsantonis, George A.; Nealon, Gareth L.; Skelton, Brian W.
2011-12-09
The generation of amphiphiles derived from macrobicyclic hexamines of the 'sarcophagine' class can be prepared through efficient and selective reactions involving the reductive alkylation, using long-chain aldehydes, of amino-functionalized sarcophagines when bound to Cu(II) or Mg(II). The Mg(II) pathway is particularly convenient for the ultimate isolation of the free ligands, which can then be used to form metalloamphiphiles with a variety of metal ions. Structural studies have been made of one of the free (protonated) ligands and some of their complexes.
Structural and Electronic Investigations of Complex Intermetallic Compounds
Ko, Hyunjin
2008-01-01
In solid state chemistry, numerous investigations have been attempted to address the relationships between chemical structure and physical properties. Such questions include: (1) How can we understand the driving forces of the atomic arrangements in complex solids that exhibit interesting chemical and physical properties? (2) How do different elements distribute themselves in a solid-state structure? (3) Can we develop a chemical understanding to predict the effects of valence electron concentration on the structures and magnetic ordering of systems by both experimental and theoretical means? Although these issues are relevant to various compound classes, intermetallic compounds are especially interesting and well suited for a joint experimental and theoretical effort. For intermetallic compounds, the questions listed above are difficult to answer since many of the constituent atoms simply do not crystallize in the same manner as in their separate, elemental structures. Also, theoretical studies suggest that the energy differences between various structural alternatives are small. For example, Al and Ga both belong in the same group on the Periodic Table of Elements and share many similar chemical properties. Al crystallizes in the fcc lattice with 4 atoms per unit cell and Ga crystallizes in an orthorhombic unit cell lattice with 8 atoms per unit cell, which are both fairly simple structures (Figure 1). However, when combined with Mn, which itself has a very complex cubic crystal structure with 58 atoms per unit cell, the resulting intermetallic compounds crystallize in a completely different fashion. At the 1:1 stoichiometry, MnAl forms a very simple tetragonal lattice with two atoms per primitive unit cell, while MnGa crystallizes in a complicated rhombohedral unit cell with 26 atoms within the primitive unit cell. The mechanisms influencing the arrangements of atoms in numerous crystal structures have been studied theoretically by calculating electronic
Quantum Groups, Non-Commutative Differential Geometry and Applications
NASA Astrophysics Data System (ADS)
Schupp, Peter
The topic of this thesis is the development of a versatile and geometrically motivated differential calculus on non-commutative or quantum spaces, providing powerful but easy-to-use mathematical tools for applications in physics and related sciences. A generalization of unitary time evolution is proposed and studied for a simple 2-level system, leading to non-conservation of microscopic entropy, a phenomenon new to quantum mechanics. A Cartan calculus that combines functions, forms, Lie derivatives and inner derivations along general vector fields into one big algebra is constructed for quantum groups and then extended to quantum planes. The construction of a tangent bundle on a quantum group manifold and an BRST type approach to quantum group gauge theory are given as further examples of applications. The material is organized in two parts: Part I studies vector fields on quantum groups, emphasizing Hopf algebraic structures, but also introducing a 'quantum geometric' construction. Using a generalized semi-direct product construction we combine the dual Hopf algebras {cal A} of functions and {cal U} of left-invariant vector fields into one fully bicovariant algebra of differential operators. The pure braid group is introduced as the commutant of Delta({cal U}). It provides invariant maps {cal A} to{cal U} and thereby bicovariant vector fields, casimirs and metrics. This construction allows the translation of undeformed matrix expressions into their less obvious quantum algebraic counter parts. We study this in detail for quasitriangular Hopf algebras, giving the determinant and orthogonality relation for the 'reflection' matrix. Part II considers the additional structures of differential forms and finitely generated quantum Lie algebras--it is devoted to the construction of the Cartan calculus, based on an undeformed Cartan identity. We attempt a classification of various types of quantum Lie algebras and present a fairly general example for their construction
Renormalization and Induced Gauge Action on a Noncommutative Space
NASA Astrophysics Data System (ADS)
Grosse, H.; Wohlgenannt, M.
Field theories on deformed spaces suffer from the IR/UV mxing and renormalization is generically spoiled. In work with R.~Wulkenhaar, one of us realized a way to cure this desease by adding one more marginal operator. We review these ideas, show the application to φ^3 models and use heat kernel expansion methods for a scalar field theory coupled to an external gauge field on a θ-deformed space and derive noncommutative gauge actions.
Semiclassical and quantum motions on the non-commutative plane
NASA Astrophysics Data System (ADS)
Baldiotti, M. C.; Gazeau, J. P.; Gitman, D. M.
2009-10-01
We study the canonical and the coherent state quantizations of a particle moving in a magnetic field on the non-commutative plane. Using a θ-modified action, we perform the canonical quantization and analyze the gauge dependence of the theory. We compare coherent states quantizations obtained through Malkin-Man'ko states and circular squeezed states. The relation between these states and the “classical” trajectories is investigated, and we present numerical explorations of some semiclassical quantities.
Structure of Block Copolymer Hydrogel Formed by Complex Coacervate Process
NASA Astrophysics Data System (ADS)
Choi, Soohyung; Ortony, Julia; Krogstad, Daniel; Spruell, Jason; Lynd, Nathaniel; Han, Songi; Kramer, Edward
2012-02-01
Complex coacervation occurs when oppositely charged polyelectrolytes associate in solution, forming dense micron-sized droplets. Hydrogels with coacervate block domains were formed by mixing two ABA and A'BA' triblock copolymer solutions in water where the A and A' blocks are oppositely charged. Small-angle neutron scattering (SANS) was used to investigate the structure of hydrogels formed by ABA triblock copolymers (A block: poly(allyl glycidyl ether) functionalized with guanidinium (A) or sulfonate (A'), B block: poly(ethylene oxide)). By using an appropriate fitting model, structural information such as coacervate core block radius and water volume fraction w can be extracted from SANS data. The results reveal that w in the coacervate core block was significantly higher than in conventional triblock copolymer hydrogels where microphase separation is driven by the hydrophobicity of the core-forming blocks.
Contaminant Organic Complexes: Their Structure and Energetics in Surface Decontamination
Samuel Traina; Shankar Sharma
2005-07-12
The Department of Energy has a goal of decontaminating an estimated 180,000 metric tons of metal wastes in various surplus facilities. Uranium (U) and other radioactive actinides and lanthanides are embedded within the mixed oxide structures of the passivity layers of corroded iron and steel. These toxic metals can be dissolved out of the surface layers by a naturally occurring bacterial siderophore called Desferrioxamine B (DFB). DFB is a trihydroxamate ligand with one amine and three hydroxamate groups, which chelates with metals through hydroxamate coordination. Complexation of DFB with U can be utilized in decontamination strategy of the passivity layers. Therefore, we have been studying reactions of uranyl U(VI) with zerovalent iron (Fe0) followed by dissolution by DFB. The objectives were to determine the structure and speciation of solution and solid phases of U and to assess the effectiveness of DVB in U dissolution.
Structural permeability of complex networks to control signals
NASA Astrophysics Data System (ADS)
Lo Iudice, Francesco; Garofalo, Franco; Sorrentino, Francesco
2015-09-01
Many biological, social and technological systems can be described as complex networks. The goal of affecting their behaviour has motivated recent work focusing on the relationship between the network structure and its propensity to be controlled. While this work has provided insight into several relevant problems, a comprehensive approach to address partial and complete controllability of networks is still lacking. Here, we bridge this gap by developing a framework to maximize the diffusion of the control signals through a network, while taking into account physical and economic constraints that inevitably arise in applications. This approach allows us to introduce the network permeability, a unified metric of the propensity of a network to be controllable. The analysis of the permeability of several synthetic and real networks enables us to extract some structural features that deepen our quantitative understanding of the ease with which specific controllability requirements can be met.
Structural complexities in the active layers of organic electronics.
Lee, Stephanie S; Loo, Yueh-Lin
2010-01-01
The field of organic electronics has progressed rapidly in recent years. However, understanding the direct structure-function relationships between the morphology in electrically active layers and the performance of devices composed of these materials has proven difficult. The morphology of active layers in organic electronics is inherently complex, with heterogeneities existing across multiple length scales, from subnanometer to micron and millimeter range. A major challenge still facing the organic electronics community is understanding how the morphology across all of the length scales in active layers collectively determines the device performance of organic electronics. In this review we highlight experiments that have contributed to the elucidation of structure-function relationships in organic electronics and also point to areas in which knowledge of such relationships is still lacking. Such knowledge will lead to the ability to select active materials on the basis of their inherent properties for the fabrication of devices with prespecified characteristics.
Frequency and Complexity of De Novo Structural Mutation in Autism
Brandler, William M.; Antaki, Danny; Gujral, Madhusudan; Noor, Amina; Rosanio, Gabriel; Chapman, Timothy R.; Barrera, Daniel J.; Lin, Guan Ning; Malhotra, Dheeraj; Watts, Amanda C.; Wong, Lawrence C.; Estabillo, Jasper A.; Gadomski, Therese E.; Hong, Oanh; Fajardo, Karin V. Fuentes; Bhandari, Abhishek; Owen, Renius; Baughn, Michael; Yuan, Jeffrey; Solomon, Terry; Moyzis, Alexandra G.; Maile, Michelle S.; Sanders, Stephan J.; Reiner, Gail E.; Vaux, Keith K.; Strom, Charles M.; Zhang, Kang; Muotri, Alysson R.; Akshoomoff, Natacha; Leal, Suzanne M.; Pierce, Karen; Courchesne, Eric; Iakoucheva, Lilia M.; Corsello, Christina; Sebat, Jonathan
2016-01-01
Genetic studies of autism spectrum disorder (ASD) have established that de novo duplications and deletions contribute to risk. However, ascertainment of structural variants (SVs) has been restricted by the coarse resolution of current approaches. By applying a custom pipeline for SV discovery, genotyping, and de novo assembly to genome sequencing of 235 subjects (71 affected individuals, 26 healthy siblings, and their parents), we compiled an atlas of 29,719 SV loci (5,213/genome), comprising 11 different classes. We found a high diversity of de novo mutations, the majority of which were undetectable by previous methods. In addition, we observed complex mutation clusters where combinations of de novo SVs, nucleotide substitutions, and indels occurred as a single event. We estimate a high rate of structural mutation in humans (20%) and propose that genetic risk for ASD is attributable to an elevated frequency of gene-disrupting de novo SVs, but not an elevated rate of genome rearrangement. PMID:27018473
Noncommutativity in weakly curved background by canonical methods
Davidovic, Lj.; Sazdovic, B.
2011-03-15
Using the canonical method, we investigate the Dp-brane world-volume noncommutativity in a weakly curved background. The term 'weakly curved' means that, in the leading order, the source of nonflatness is an infinitesimally small Kalb-Ramond field B{sub {mu}{nu}}, linear in coordinate, while the Ricci tensor does not contribute, being an infinitesimal of the second order. On the solution of boundary conditions, we find a simple expression for the space-time coordinates in terms of the effective coordinates and momenta. This basic relation helped us to prove that noncommutativity appears only on the world sheet boundary. The noncommutativity parameter has a standard form, but with the infinitesimally small and coordinate-dependent antisymmetric tensor B{sub {mu}{nu}}. This result coincides with that obtained on the group manifolds in the limit of the large level n of the current algebra. After quantization, the algebra of the functions on the Dp-brane world volume is represented with the Kontsevich star product instead of the Moyal one in the flat background.
Bosonized noncommutative bi-fundamental fermion and S-duality
NASA Astrophysics Data System (ADS)
Blas, Harold
2005-06-01
We perform the path-integral bosonization of the recently proposed noncommutative massive Thirring model (NCMT1) [JHEP 0503 (2005) 037]. This model presents two types of current-current interaction terms related to the bi-fundamental representation of the group U(1). Firstly, we address the bosonization of a bi-fundamental free Dirac fermion defined on a noncommutative (NC) euclidean plane Bbb Rθ2. In this case we show that the fermion system is dual to two copies of the NC Wess-Zumino-Novikov-Witten model. Next, we apply the bosonization prescription to the NCMT1 model living on Bbb Rθ2 and show that this model is equivalent to two-copies of the WZNW model and a two-field potential defined for scalar fields corresponding to the global U(1) × U(1) symmetry plus additional bosonized terms for the four fermion interactions. The bosonic sector resembles to the one proposed by Lechtenfeld et al. [Nucl. Phys. B 705 (2005) 477] as the noncommutative sine-Gordon for a pair of scalar fields. The bosonic and fermionic couplings are related by a strong-weak duality. We show that the couplings of the both sectors for some representations satisfy similar relationships up to relevant re-scalings, thus the NC bi-fundamental couplings are two times the corresponding ones of the NC fundamental (anti-fundamental) and eight times the couplings of the ordinary massive Thirring and sine-Gordon models.
On second quantization on noncommutative spaces with twisted symmetries
NASA Astrophysics Data System (ADS)
Fiore, Gaetano
2010-04-01
By the application of the general twist-induced sstarf-deformation procedure we translate second quantization of a system of bosons/fermions on a symmetric spacetime into a noncommutative language. The procedure deforms, in a coordinated way, the spacetime algebra and its symmetries, the wave-mechanical description of a system of n bosons/fermions, the algebra of creation and annihilation operators and also the commutation relations of the latter with functions of spacetime; our key requirement is the mode-decomposition independence of the quantum field. In a minimalistic view, the use of noncommutative coordinates can be seen just as a way to better express non-local interactions of a special kind. In a non-conservative one, we obtain a closed, covariant framework for quantum field theory (QFT) on the corresponding noncommutative spacetime consistent with quantum mechanical axioms and Bose-Fermi statistics. One distinguishing feature is that the field commutation relations remain of the type 'field (anti)commutator=a distribution'. We illustrate the results by choosing as examples interacting non-relativistic and free relativistic QFT on Moyal space(time)s.
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.
Structural Basis of Clostridium perfringens Toxin Complex Formation
Adams,J.; Gregg, K.; Bayer, E.; Boraston, A.; Smith, S.
2008-01-01
The virulent properties of the common human and livestock pathogen Clostridium perfringens are attributable to a formidable battery of toxins. Among these are a number of large and highly modular carbohydrate-active enzymes, including the {mu}-toxin and sialidases, whose catalytic properties are consistent with degradation of the mucosal layer of the human gut, glycosaminoglycans, and other cellular glycans found throughout the body. The conservation of noncatalytic ancillary modules among these enzymes suggests they make significant contributions to the overall functionality of the toxins. Here, we describe the structural basis of an ultra-tight interaction (Ka = 1.44 x 1011 M-1) between the X82 and dockerin modules, which are found throughout numerous C. perfringens carbohydrate-active enzymes. Extensive hydrogen-bonding and van der Waals contacts between the X82 and dockerin modules give rise to the observed high affinity. The {mu}-toxin dockerin module in this complex is positioned {approx}180 relative to the orientation of the dockerin modules on the cohesin module surface within cellulolytic complexes. These observations represent a unique property of these clostridial toxins whereby they can associate into large, noncovalent multitoxin complexes that allow potentiation of the activities of the individual toxins by combining complementary toxin specificities.
Structural and Operational Complexity of the Geobacter Sulfurreducens Genome
Qiu, Yu; Cho, Byung-Kwan; Park, Young S.; Lovley, Derek R.; Palsson, Bernhard O.; Zengler, Karsten
2010-06-30
Prokaryotic genomes can be annotated based on their structural, operational, and functional properties. These annotations provide the pivotal scaffold for understanding cellular functions on a genome-scale, such as metabolism and transcriptional regulation. Here, we describe a systems approach to simultaneously determine the structural and operational annotation of the Geobacter sulfurreducens genome. Integration of proteomics, transcriptomics, RNA polymerase, and sigma factor-binding information with deep-sequencing-based analysis of primary 59-end transcripts allowed for a most precise annotation. The structural annotation is comprised of numerous previously undetected genes, noncoding RNAs, prevalent leaderless mRNA transcripts, and antisense transcripts. When compared with other prokaryotes, we found that the number of antisense transcripts reversely correlated with genome size. The operational annotation consists of 1453 operons, 22% of which have multiple transcription start sites that use different RNA polymerase holoenzymes. Several operons with multiple transcription start sites encoded genes with essential functions, giving insight into the regulatory complexity of the genome. The experimentally determined structural and operational annotations can be combined with functional annotation, yielding a new three-level annotation that greatly expands our understanding of prokaryotic genomes.
Structural and operational complexity of the Geobacter sulfurreducens genome
Qiu, Yu; Cho, Byung-Kwan; Park, Young Seoub; Lovley, Derek; Palsson, Bernhard Ø.; Zengler, Karsten
2010-01-01
Prokaryotic genomes can be annotated based on their structural, operational, and functional properties. These annotations provide the pivotal scaffold for understanding cellular functions on a genome-scale, such as metabolism and transcriptional regulation. Here, we describe a systems approach to simultaneously determine the structural and operational annotation of the Geobacter sulfurreducens genome. Integration of proteomics, transcriptomics, RNA polymerase, and sigma factor-binding information with deep-sequencing-based analysis of primary 5′-end transcripts allowed for a most precise annotation. The structural annotation is comprised of numerous previously undetected genes, noncoding RNAs, prevalent leaderless mRNA transcripts, and antisense transcripts. When compared with other prokaryotes, we found that the number of antisense transcripts reversely correlated with genome size. The operational annotation consists of 1453 operons, 22% of which have multiple transcription start sites that use different RNA polymerase holoenzymes. Several operons with multiple transcription start sites encoded genes with essential functions, giving insight into the regulatory complexity of the genome. The experimentally determined structural and operational annotations can be combined with functional annotation, yielding a new three-level annotation that greatly expands our understanding of prokaryotic genomes. PMID:20592237
Crystal Structure of Baculovirus RNA Triphosphatase Complexed with Phosphate
Changela, Anita; Martin, Alexandra; Shuman, Stewart; Mondragon, Alfonso
2010-03-05
Baculovirus RNA 5'-triphosphatase (BVP) exemplifies a family of RNA-specific cysteine phosphatases that includes the RNA triphosphatase domains of metazoan and plant mRNA capping enzymes. Here we report the crystal structure of BVP in a phosphate-bound state at 1.5 {angstrom} resolution. BVP adopts the characteristic cysteine-phosphatase {alpha}/{beta} fold and binds two phosphate ions in the active site region, one of which is proposed to mimic the phosphate of the product complex after hydrolysis of the covalent phosphoenzyme intermediate. The crystal structure highlights the role of backbone amides and side chains of the P-loop motif {sup 118}HCTHGXNRT{sup 126} in binding the cleavable phosphate and stabilizing the transition state. Comparison of the BVP structure to the apoenzyme of mammalian RNA triphosphatase reveals a concerted movement of the Arg-125 side chain (to engage the phosphate directly) and closure of an associated surface loop over the phosphate in the active site. The structure highlights a direct catalytic role of Asn-124, which is the signature P-loop residue of the RNA triphosphatase family and a likely determinant of the specificity of BVP for hydrolysis of phosphoanhydride linkages.
Structure of a bacterial RNA polymerase holoenzyme open promoter complex
Bae, Brian; Feklistov, Andrey; Lass-Napiorkowska, Agnieszka; Landick, Robert; Darst, Seth A.
2015-09-08
Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 Å-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the -10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstreammore » of the -10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Additionally a RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and σA dissociation.« less
Structure of a bacterial RNA polymerase holoenzyme open promoter complex
Bae, Brian; Feklistov, Andrey; Lass-Napiorkowska, Agnieszka; Landick, Robert; Darst, Seth A.
2015-09-08
Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 Å-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the -10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstream of the -10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Additionally a RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and σ^{A} dissociation.
Epidemic fronts in complex networks with metapopulation structure
NASA Astrophysics Data System (ADS)
Hindes, Jason; Singh, Sarabjeet; Myers, Christopher R.; Schneider, David J.
2013-07-01
Infection dynamics have been studied extensively on complex networks, yielding insight into the effects of heterogeneity in contact patterns on disease spread. Somewhat separately, metapopulations have provided a paradigm for modeling systems with spatially extended and “patchy” organization. In this paper we expand on the use of multitype networks for combining these paradigms, such that simple contagion models can include complexity in the agent interactions and multiscale structure. Using a generalization of the Miller-Volz mean-field approximation for susceptible-infected-recovered (SIR) dynamics on multitype networks, we study the special case of epidemic fronts propagating on a one-dimensional lattice of interconnected networks—representing a simple chain of coupled population centers—as a necessary first step in understanding how macroscale disease spread depends on microscale topology. Applying the formalism of front propagation into unstable states, we derive the effective transport coefficients of the linear spreading: asymptotic speed, characteristic wavelength, and diffusion coefficient for the leading edge of the pulled fronts, and analyze their dependence on the underlying graph structure. We also derive the epidemic threshold for the system and study the front profile for various network configurations.
Structural insights into anaphase-promoting complex function and mechanism
Barford, David
2011-01-01
The anaphase-promoting complex or cyclosome (APC/C) controls sister chromatid segregation and the exit from mitosis by catalysing the ubiquitylation of cyclins and other cell cycle regulatory proteins. This unusually large E3 RING-cullin ubiquitin ligase is assembled from 13 different proteins. Selection of APC/C targets is controlled through recognition of short destruction motifs, predominantly the D box and KEN box. APC/C-mediated coordination of cell cycle progression is achieved through the temporal regulation of APC/C activity and substrate specificity, exerted through a combination of co-activator subunits, reversible phosphorylation and inhibitory proteins and complexes. Recent structural and biochemical studies of the APC/C are beginning to reveal an understanding of the roles of individual APC/C subunits and co-activators and how they mutually interact to mediate APC/C functions. This review focuses on the findings showing how information on the structural organization of the APC/C provides insights into the role of co-activators and core APC/C subunits in mediating substrate recognition. Mechanisms of regulating and modulating substrate recognition are discussed in the context of controlling the binding of the co-activator to the APC/C, and the accessibility and conformation of the co-activator when bound to the APC/C. PMID:22084387
Emergence of complex behaviour from simple circuit structures.
Kaufman, Marcelle; Thomas, René
2003-02-01
The set of (feedback) circuits of a complex system is the machinery that allows the system to be aware of the levels of its crucial constituents. Circuits can be identified without ambiguity from the elements of the Jacobian matrix of the system. There are two types of circuits: positive if they comprise an even number of negative interactions, negative if this number is odd. The two types of circuits play deeply different roles: negative circuits are required for homeostasis, with or without oscillations, positive circuits are required for multistationarity, and hence, in biology, for differentiation and memory. In non-linear systems, a circuit can positive or negative (an 'ambiguous circuit', depending on the location in phase space. Full circuits are those circuits (or unions of disjoint circuits) that imply all the variables of the system. There is a tight relation between circuits and steady states. Each full circuit, if isolated, generates steady state(s) whose nature (eigenvalues) is determined by the structure of the circuit. Multistationarity requires the presence of at least two full circuits of opposite Eisenfeld signs, or else, an ambiguous circuit. We show how a significant part of the dynamical behaviour of a system can be predicted by a mere examination of its Jacobian matrix. We also show how extremely complex dynamics can be generated by such simple logical structures as a single (full and ambiguous) circuit.
A new Cu–cysteamine complex: structure and optical properties
Ma, Lun; Chen, Wei; Schatte, Gabriele; Wang, Wei; Joly, Alan G.; Huang, Yining; Sammynaiken, Ramaswami; Hossu, Marius
2014-06-07
Here we report the structure and optical properties of a new Cu–cysteamine complex (Cu–Cy) with a formula of Cu3Cl(SR)2 (R ¼ CH2CH2NH2). This Cu–Cy has a different structure from a previous Cu–Cy complex, in which both thio and amine groups from cysteamine bond with copper ions. Single-crystal X-ray diffraction and solid-state nuclear magnetic resonance results show that the oxidation state of copper in Cu3Cl(SR)2 is +1 rather than +2. Further, Cu3Cl(SR)2 has been observed to show intense photoluminescence and X-ray excited luminescence. More interesting is that Cu3Cl(SR)2 particles can produce singlet oxygen under irradiation by light or X-ray. This indicates that Cu3Cl(SR)2 is a new photosensitizer that can be used for deep cancer treatment as X-ray can penetrate soft tissues. All these findings mean that Cu3Cl(SR)2 is a new material with potential applications for lighting, radiation detection and cancer treatment.
Complexation thermodynamics of modified cyclodextrins: extended cavities and distorted structures.
Schönbeck, Christian; Westh, Peter; Holm, René
2014-08-28
Inclusion complexes between two bile salts and a range of differently methylated β-cyclodextrins were studied in an attempt to rationalize the complexation thermodynamics of modified cyclodextrins. Calorimetric titrations at a range of temperatures provided precise values of the enthalpies (ΔH°), entropies (ΔS°), and heat capacities (ΔCp) of complexation, while molecular dynamics simulations assisted the interpretation of the obtained thermodynamic parameters. As previously observed for several types of modified cyclodextrins, the substituents at the rims of the cyclodextrin induced large changes in ΔH° and ΔS°, but due to enthalpy-entropy compensation the changes in Gibbs free energy, and the binding constant, were much smaller. For the methylated β-cyclodextrins, the substituent-induced increments in ΔH° and ΔS° were nonmonotonic with an initial strong increase in both ΔH° and ΔS° and then a strong decrease when the degree of substitution exceeded some threshold. Exactly the same trend was observed for ΔCp. The dehydration of nonpolar surface, as quantified by the simulations, can to a large extent explain the variation in the thermodynamic parameters. The methyl substituents form additional hydrophobic contacts with the bile salt, but at high degrees of methylation they also cause significant distortion of the otherwise circular cyclodextrin structure. These two opposing contributions to the dehydration are the major causes for the observed variations in the thermodynamic functions. The structural effects are not expected to be specific for methylated cyclodextrins but should be observed for most modified cyclodextrins. An even more general conclusion is that variations in the extent of hydration are an important underlying reason for the commonly observed phenomenon termed enthalpy-entropy compensation and also for the less frequent reports of entropy convergence around 110 °C.
On the dimension of complex responses in nonlinear structural vibrations
NASA Astrophysics Data System (ADS)
Wiebe, R.; Spottswood, S. M.
2016-07-01
The ability to accurately model engineering systems under extreme dynamic loads would prove a major breakthrough in many aspects of aerospace, mechanical, and civil engineering. Extreme loads frequently induce both nonlinearities and coupling which increase the complexity of the response and the computational cost of finite element models. Dimension reduction has recently gained traction and promises the ability to distill dynamic responses down to a minimal dimension without sacrificing accuracy. In this context, the dimensionality of a response is related to the number of modes needed in a reduced order model to accurately simulate the response. Thus, an important step is characterizing the dimensionality of complex nonlinear responses of structures. In this work, the dimensionality of the nonlinear response of a post-buckled beam is investigated. Significant detail is dedicated to carefully introducing the experiment, the verification of a finite element model, and the dimensionality estimation algorithm as it is hoped that this system may help serve as a benchmark test case. It is shown that with minor modifications, the method of false nearest neighbors can quantitatively distinguish between the response dimension of various snap-through, non-snap-through, random, and deterministic loads. The state-space dimension of the nonlinear system in question increased from 2-to-10 as the system response moved from simple, low-level harmonic to chaotic snap-through. Beyond the problem studied herein, the techniques developed will serve as a prescriptive guide in developing fast and accurate dimensionally reduced models of nonlinear systems, and eventually as a tool for adaptive dimension-reduction in numerical modeling. The results are especially relevant in the aerospace industry for the design of thin structures such as beams, panels, and shells, which are all capable of spatio-temporally complex dynamic responses that are difficult and computationally expensive to
Crystal structures of ASK1-inhibtor complexes provide a platform for structure-based drug design
Singh, Onkar; Shillings, Anthony; Craggs, Peter; Wall, Ian; Rowland, Paul; Skarzynski, Tadeusz; Hobbs, Clare I; Hardwick, Phil; Tanner, Rob; Blunt, Michelle; Witty, David R; Smith, Kathrine J
2013-01-01
ASK1, a member of the MAPK Kinase Kinase family of proteins has been shown to play a key role in cancer, neurodegeneration and cardiovascular diseases and is emerging as a possible drug target. Here we describe a ‘replacement-soaking’ method that has enabled the high-throughput X-ray structure determination of ASK1/ligand complexes. Comparison of the X-ray structures of five ASK1/ligand complexes from 3 different chemotypes illustrates that the ASK1 ATP binding site is able to accommodate a range of chemical diversity and different binding modes. The replacement-soaking system is also able to tolerate some protein flexibility. This crystal system provides a robust platform for ASK1/ligand structure determination and future structure based drug design. PMID:23776076
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.
Non-commutative holomorphic functions in elements of a Lie algebra and the absolute basis problem
NASA Astrophysics Data System (ADS)
Dosi, Anar A.
2009-12-01
We study the absolute basis problem in algebras of holomorphic functions in non-commuting variables generating a finite-dimensional nilpotent Lie algebra \\mathfrak{g}. This is motivated by J. L. Taylor's programme of non-commutative holomorphic functional calculus in the Lie algebra framework.
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.
From structure of the complex to understanding of the biology
Rossmann, Michael G.; Arisaka, Fumio; Battisti, Anthony J.; Bowman, Valorie D.; Chipman, Paul R.; Fokine, Andrei; Hafenstein, Susan; Kanamaru, Shuji; Kostyuchenko, Victor A.; Mesyanzhinov, Vadim V.; Shneider, Mikhail M.; Palermo, Laura M.; Parrish, Colin R.; Xiao, Chuan
2007-01-01
The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy single-particle reconstructions. This paper concerns itself with the study of the macromolecular complexes that constitute viruses, using structural hybrid techniques. The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy (cryo-EM) single-particle reconstructions. Both techniques lean heavily on imposing icosahedral symmetry, thereby obscuring any deviation from the assumed symmetry. However, tailed bacteriophages have icosahedral or prolate icosahedral heads that have one obvious unique vertex where the genome can enter for DNA packaging and exit when infecting a host cell. The presence of the tail allows cryo-EM reconstructions in which the special vertex is used to orient the head in a unique manner. Some very large dsDNA icosahedral viruses also develop special vertices thought to be required for infecting host cells. Similarly, preliminary cryo-EM data for the small ssDNA canine parvovirus complexed with receptor suggests that these viruses, previously considered to be accurately icosahedral, might have some asymmetric properties that generate one preferred receptor-binding site on the viral surface. Comparisons are made between rhinoviruses that bind receptor molecules uniformly to all 60 equivalent binding sites, canine parvovirus, which appears to have a preferred receptor-binding site, and bacteriophage T4, which gains major biological advantages on account of its unique vertex and tail organelle.
Unprecedented Alkene Complex of Zinc(II): Structures and Bonding of Divinylzinc Complexes
Wooten, Alfred; Carroll, Patrick J.; Maestri, Aaron G.
2008-01-01
This report describes the solid state structures of a series of divinylzinc complexes, one of which represents the only structurally characterized zinc(II) π-complex. Vinylzinc reagents, Zn[C(Me)=CH2]2 (1) and Zn[C(H)=CMe2]2 (2), have been synthesized and isolated as white crystalline solids in 66% and 72% yield, respectively. Each compound exhibits an infinite polymeric architecture in the solid state via a series of zinc-π (1) and zinc-σ-bonded (2) bridging interactions. Addition of chelating ligands to these divinylzinc compounds allowed isolation of the monomeric adducts (bipy)Zn[C(Me)=CH2]2 (1·bipy), (tmeda)Zn[C(Me)=CH2]2 (1·tmeda), (bipy)Zn[C(H)=CMe2]2 (2·bipy), and (tmeda)Zn[C(H)=CMe2]2 (2·tmeda), of which (1·bipy), (2·bipy), and (2·tmeda) have been characterized crystallography. PMID:16594699
Light transport and lasing in complex photonic structures
NASA Astrophysics Data System (ADS)
Liew, Seng Fatt
Complex photonic structures refer to composite optical materials with dielectric constant varying on length scales comparable to optical wavelengths. Light propagation in such heterogeneous composites is greatly different from homogeneous media due to scattering of light in all directions. Interference of these scattered light waves gives rise to many fascinating phenomena and it has been a fast growing research area, both for its fundamental physics and for its practical applications. In this thesis, we have investigated the optical properties of photonic structures with different degree of order, ranging from periodic to random. The first part of this thesis consists of numerical studies of the photonic band gap (PBG) effect in structures from 1D to 3D. From these studies, we have observed that PBG effect in a 1D photonic crystal is robust against uncorrelated disorder due to preservation of long-range positional order. However, in higher dimensions, the short-range positional order alone is sufficient to form PBGs in 2D and 3D photonic amorphous structures (PASS). We have identified several parameters including dielectric filling fraction and degree of order that can be tuned to create a broad isotropic PBG. The largest PBG is produced by the dielectric networks due to local uniformity in their dielectric constant distribution. In addition, we also show that deterministic aperiodic structures (DASs) such as the golden-angle spiral and topological defect structures can support a wide PBG and their optical resonances contain unexpected features compared to those in photonic crystals. Another growing research field based on complex photonic structures is the study of structural color in animals and plants. Previous studies have shown that non-iridescent color can be generated from PASs via single or double scatterings. For better understanding of the coloration mechanisms, we have measured the wavelength-dependent scattering length from the biomimetic samples. Our
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.
Structural basis of complement membrane attack complex formation
NASA Astrophysics Data System (ADS)
Serna, Marina; Giles, Joanna L.; Morgan, B. Paul; Bubeck, Doryen
2016-02-01
In response to complement activation, the membrane attack complex (MAC) assembles from fluid-phase proteins to form pores in lipid bilayers. MAC directly lyses pathogens by a `multi-hit' mechanism; however, sublytic MAC pores on host cells activate signalling pathways. Previous studies have described the structures of individual MAC components and subcomplexes; however, the molecular details of its assembly and mechanism of action remain unresolved. Here we report the electron cryo-microscopy structure of human MAC at subnanometre resolution. Structural analyses define the stoichiometry of the complete pore and identify a network of interaction interfaces that determine its assembly mechanism. MAC adopts a `split-washer' configuration, in contrast to the predicted closed ring observed for perforin and cholesterol-dependent cytolysins. Assembly precursors partially penetrate the lipid bilayer, resulting in an irregular β-barrel pore. Our results demonstrate how differences in symmetric and asymmetric components of the MAC underpin a molecular basis for pore formation and suggest a mechanism of action that extends beyond membrane penetration.
Cryo-Electron Tomography for Structural Characterization of Macromolecular Complexes
Cope, Julia; Heumann, John; Hoenger, Andreas
2011-01-01
Cryo-electron tomography (cryo-ET) is an emerging 3-D reconstruction technology that combines the principles of tomographic 3-D reconstruction with the unmatched structural preservation of biological material embedded in vitreous ice. Cryo-ET is particularly suited to investigating cell-biological samples and large macromolecular structures that are too polymorphic to be reconstructed by classical averaging-based 3-D reconstruction procedures. This unit aims to make cryo-ET accessible to newcomers and discusses the specialized equipment required, as well as the relevant advantages and hurdles associated with sample preparation by vitrification and cryo-ET. Protocols describe specimen preparation, data recording and 3-D data reconstruction for cryo-ET, with a special focus on macromolecular complexes. A step-by-step procedure for specimen vitrification by plunge freezing is provided, followed by the general practicalities of tilt-series acquisition for cryo-ET, including advice on how to select an area appropriate for acquiring a tilt series. A brief introduction to the underlying computational reconstruction principles applied in tomography is described, along with instructions for reconstructing a tomogram from cryo-tilt series data. Finally, a method is detailed for extracting small subvolumes containing identical macromolecular structures from tomograms for alignment and averaging as a means to increase the signal-to-noise ratio and eliminate missing wedge effects inherent in tomographic reconstructions. PMID:21842467
Cryo-electron tomography for structural characterization of macromolecular complexes.
Cope, Julia; Heumann, John; Hoenger, Andreas
2011-08-01
Cryo-electron tomography (cryo-ET) is an emerging 3-D reconstruction technology that combines the principles of tomographic 3-D reconstruction with the unmatched structural preservation of biological matter embedded in vitreous ice. Cryo-ET is particularly suited to investigating cell-biological samples and large macromolecular structures that are too polymorphic to be reconstructed by classical averaging-based 3-D reconstruction procedures. This unit aims to make cryo-ET accessible to newcomers and discusses the specialized equipment required, as well as relevant advantages and hurdles associated with sample preparation by vitrification and cryo-ET. Protocols describe specimen preparation, data recording and 3-D data reconstruction for cryo-ET, with a special focus on macromolecular complexes. A step-by-step procedure for specimen vitrification by plunge freezing is provided, followed by the general practicalities of tilt-series acquisition for cryo-ET, including advice on how to select an area appropriate for acquiring a tilt series. A brief introduction to the underlying computational reconstruction principles applied in tomography is described, along with instructions for reconstructing a tomogram from cryo-tilt series data. Finally, a method is detailed for extracting small subvolumes containing identical macromolecular structures from tomograms for alignment and averaging as a means to increase the signal-to-noise ratio and eliminate missing wedge effects inherent in tomographic reconstructions.
Structural development of the western Makran Accretionary Complex, Offshore Iran
NASA Astrophysics Data System (ADS)
Burberry, C. M.; Jackson, C. A.
2013-12-01
The Makran Accretionary Complex (MAC), which straddles the southern offshore regions of Iran and Pakistan, is a fold-thrust system bound by the Murray Ridge and Ornach Nal Fault to the east, and the Minab Fault System (MFS) to the west. It is c. 1000 km wide and the frontal c. 125 km of the system is submerged beneath the Gulf of Oman. Relatively little is known about this system, despite the fact that constitutes a large portion of the Central Tethyan Orogen and is one of the largest accretionary complexes in the world. We use offshore 2D seismic reflection data to investigate the structural style and evolution of the Iranian segment of the MAC. The MAC is divided into two morphologically distinct domains: (i) a northern domain (Domain 1), which is located landward of a prominant break-in-slope on the seabed and is characterised by a series of normal fault-bound sub-basins that are approximately 50 km wide, and which contain numerous, unconformity-bound seismic units; and (ii) a southern domain (Domain 2), which is located basinward of the prominent seabed slope break, and is characterised by alternating ridges and troughs. Seismic data indicate that these structures are laterally continuous (over 100 km long) north-dipping thrust faults, which are overlain by south-verging, non-cylindrical, fault-propagation folds. Towards the western end of the study area, immediately offshore of the prominent onshore trace of the MFS, there is no single structure that can be reliably interpreted as the offshore extension of the MFS. Instead, a series of oblique-slip faults with thrust and strike-slip components are identified, spanning a zone that is c. 40 km wide. In the north and close to the coastline, the faults are dominantly strike-slip, whereas further south, closer to the deformation front, the thrust-sense component is more important. Irrespective of their slip sense, faults in this zone have a similar N-S strike to the onshore trace of the MFS. In addition, the basin
The γ-secretase complex: from structure to function
Zhang, Xian; Li, Yanfang; Xu, Huaxi; Zhang, Yun-wu
2014-01-01
One of the most critical pathological features of Alzheimer’s disease (AD) is the accumulation of β-amyloid (Aβ) peptides that form extracellular senile plaques in the brain. Aβ is derived from β-amyloid precursor protein (APP) through sequential cleavage by β- and γ-secretases. γ-secretase is a high molecular weight complex minimally composed of four components: presenilins (PS), nicastrin, anterior pharynx defective 1 (APH-1), and presenilin enhancer 2 (PEN-2). In addition to APP, γ-secretase also cleaves many other type I transmembrane (TM) protein substrates. As a crucial enzyme for Aβ production, γ-secretase is an appealing therapeutic target for AD. Here, we summarize current knowledge on the structure and function of γ-secretase, as well as recent progress in developing γ-secretase targeting drugs for AD treatment. PMID:25565961
Complex dental structure and wear biomechanics in hadrosaurid dinosaurs.
Erickson, Gregory M; Krick, Brandon A; Hamilton, Matthew; Bourne, Gerald R; Norell, Mark A; Lilleodden, Erica; Sawyer, W Gregory
2012-10-01
Mammalian grinding dentitions are composed of four major tissues that wear differentially, creating coarse surfaces for pulverizing tough plants and liberating nutrients. Although such dentition evolved repeatedly in mammals (such as horses, bison, and elephants), a similar innovation occurred much earlier (~85 million years ago) within the duck-billed dinosaur group Hadrosauridae, fueling their 35-million-year occupation of Laurasian megaherbivorous niches. How this complexity was achieved is unknown, as reptilian teeth are generally two-tissue structures presumably lacking biomechanical attributes for grinding. Here we show that hadrosaurids broke from the primitive reptilian archetype and evolved a six-tissue dental composition that is among the most sophisticated known. Three-dimensional wear models incorporating fossilized wear properties reveal how these tissues interacted for grinding and ecological specialization.
The Importance of Complex Electronic Structures in Thermoelectric Materials
NASA Astrophysics Data System (ADS)
Singh, David
2015-03-01
Thermoelectric performance as characterized by the figure of merit, ZT, is a counter-indicated property of matter, meaning that high ZT depends on a combination of transport properties that do not generally occur together. A particularly important conundrum in thermoelectrics is the requirements for simultaneously having high electrical conductivity and high thermopower. I will argue that the resolution of this conundrum is through complex band structures and discuss how these arise in various known and predicted high performance thermoelectric materials. This work was done in collaboration with David Parker, Mao-Hua Du, Xin Chen and Hongliang Shi. We are grateful for support from the Department of Energy, through the Office of Basic Energy Sciences, S3TEC Energy Frontier Research Center and the Materials. Done...processed 9069 records...10:49:50
Diffraction computed tomography reveals the inner structure of complex biominerals
NASA Astrophysics Data System (ADS)
Leemreize, Hanna; Birkbak, Mie; Frølich, Simon; Kenesei, Peter; Almer, Jonathan D.; Stock, Stuart R.; Birkedal, Henrik
2014-09-01
Biological materials are complex and their investigation demands advanced characterization tools capable of elucidating their structure in three dimensions without the need for complicated sample preparation. Herein, we discuss our implementation of diffraction/scattering computed tomography (DSCT). DSCT is based on the use of diffraction information for tomographic reconstructions rather than linear attenuation as in regular μ-CT. This provides much additional information on the material under investigation. We illustrate the use of DSCT by discussion of data on a biomineralized attachment organ from a marine mussel. DSCT allowed mapping the spatial distribution of calcium carbonate polymorphs aragonite and calcite even though they were indistinguishable in absorption tomography. Detailed analysis of reconstructed diffraction patterns may provide additional insights as exemplified in the present case by mapping of the degree of chemical substitution in calcite.
Cryo electron microscopy to determine the structure of macromolecular complexes.
Carroni, Marta; Saibil, Helen R
2016-02-15
Cryo-electron microscopy (cryo-EM) is a structural molecular and cellular biology technique that has experienced major advances in recent years. Technological developments in image recording as well as in processing software make it possible to obtain three-dimensional reconstructions of macromolecular assemblies at near-atomic resolution that were formerly obtained only by X-ray crystallography or NMR spectroscopy. In parallel, cryo-electron tomography has also benefitted from these technological advances, so that visualization of irregular complexes, organelles or whole cells with their molecular machines in situ has reached subnanometre resolution. Cryo-EM can therefore address a broad range of biological questions. The aim of this review is to provide a brief overview of the principles and current state of the cryo-EM field.
Electrical resistance of complex two-dimensional structures of loops
NASA Astrophysics Data System (ADS)
Gomes, M. A. F.; Hora, R. R.; Brito, V. P.
2011-06-01
This work presents a study of the dc electrical resistance of a recently discovered hierarchical two-dimensional system which has a complex topology consisting of a distribution of disordered macroscopic loops with no characteristic size and a distribution of several types of contacts between loops. In addition to its intrinsic interest in the important context of low-dimensional systems and crumpled systems, the structures under study are of relevance in a number of areas including soft condensed matter and packing of DNA in viral capsids. In the particular case discussed here, the loops are made of layers of graphite with a height of tens of nanometers deposited on a substrate of cellulose. Experiments with these systems indicate an anomalous electrical resistance of sub-diffusive type. The results reported here are explained with scaling arguments and computer simulation. A comparison with the dc electrical properties of percolation clusters is made, and some other experimental issues as future prospects are commented.
Encoding techniques for complex information structures in connectionist systems
NASA Technical Reports Server (NTRS)
Barnden, John; Srinivas, Kankanahalli
1990-01-01
Two general information encoding techniques called relative position encoding and pattern similarity association are presented. They are claimed to be a convenient basis for the connectionist implementation of complex, short term information processing of the sort needed in common sense reasoning, semantic/pragmatic interpretation of natural language utterances, and other types of high level cognitive processing. The relationships of the techniques to other connectionist information-structuring methods, and also to methods used in computers, are discussed in detail. The rich inter-relationships of these other connectionist and computer methods are also clarified. The particular, simple forms are discussed that the relative position encoding and pattern similarity association techniques take in the author's own connectionist system, called Conposit, in order to clarify some issues and to provide evidence that the techniques are indeed useful in practice.
Structures of Large RNAs and RNA-Protein Complexes: Toward Structure Determination of Riboswitches.
Grigg, Jason C; Ke, Ailong
2015-01-01
Riboswitches are widespread and important regulatory elements. They are typically present in the mRNA of the gene under their regulation, where they form complex three-dimensional structures that can bind an effector and regulate either transcription or translation of the mRNA. Structural biology has been essential to our understanding of their ligand recognition and conformational switching mechanisms, but riboswitch determination presents several important complications. Overcoming these challenges requires a synergistic approach using rational design of the constructs and supporting methods to biochemically validate the designs and resulting structures. PMID:26068743
Biological pattern formation: from basic mechanisms to complex structures
NASA Astrophysics Data System (ADS)
Koch, A. J.; Meinhardt, H.
1994-10-01
The reliable development of highly complex organisms is an intriguing and fascinating problem. The genetic material is, as a rule, the same in each cell of an organism. How then do cells, under the influence of their common genes, produce spatial patterns? Simple models are discussed that describe the generation of patterns out of an initially nearly homogeneous state. They are based on nonlinear interactions of at least two chemicals and on their diffusion. The concepts of local autocatalysis and of long-range inhibition play a fundamental role. Numerical simulations show that the models account for many basic biological observations such as the regeneration of a pattern after excision of tissue or the production of regular (or nearly regular) arrays of organs during (or after) completion of growth. Very complex patterns can be generated in a reproducible way by hierarchical coupling of several such elementary reactions. Applications to animal coats and to the generation of polygonally shaped patterns are provided. It is further shown how to generate a strictly periodic pattern of units that themselves exhibit a complex and polar fine structure. This is illustrated by two examples: the assembly of photoreceptor cells in the eye of Drosophila and the positioning of leaves and axillary buds in a growing shoot. In both cases, the substructures have to achieve an internal polarity under the influence of some primary pattern-forming system existing in the fly's eye or in the plant. The fact that similar models can describe essential steps in organisms as distantly related as animals and plants suggests that they reveal some universal mechanisms.
Biological pattern formation: from basic mechanisms to complex structures
Koch, A.J.; Meinhardt, H. )
1994-10-01
The reliable development of highly complex organisms is an intriguing and fascinating problem. The genetic material is, as a rule, the same in each cell of an organism. How then do cells, under the influence of their common genes, produce spatial patterns Simple models are discussed that describe the generation of patterns out of an initially nearly homogeneous state. They are based on nonlinear interactions of at least two chemicals and on their diffusion. The concepts of local autocatalysis and of long-range inhibition play a fundamental role. Numerical simulations show that the models account for many basic biological observations such as the regeneration of a pattern after excision of tissue or the production of regular (or nearly regular) arrays of organs during (or after) completion of growth. Very complex patterns can be generated in a reproducible way by hierarchical coupling of several such elementary reactions. Applications to animal coats and to the generation of polygonally shaped patterns are provided. It is further shown how to generate a strictly periodic pattern of units that themselves exhibit a complex and polar fine structure. This is illustrated by two examples: the assembly of photoreceptor cells in the eye of [ital Drosophila] and the positioning of leaves and axillary buds in a growing shoot. In both cases, the substructures have to achieve an internal polarity under the influence of some primary pattern-forming system existing in the fly's eye or in the plant. The fact that similar models can describe essential steps in organisms as distantly related as animals and plants suggests that they reveal some universal mechanisms.
Hybrid Direct Write Lithographic Strategies for Complex Hierarchical Structures
NASA Astrophysics Data System (ADS)
Singer, Jonathan P.
With the number of alternative lithographic techniques for high resolution and 3D patterning rapidly increasing, there is a need to identify a set of scalable techniques which balances the ability to arbitrarily control every detail of a target pattern and to produce these complex patterns at a high rate. It is in this way that metamaterial devices put forward on a lab scale for applications such as phononics, photonics, and plasmonics can be realized in the industrial scale. This thesis, in approaching this challenge, utilizes combinations of patterning techniques, leveraging the ability for "large" scale alternative lithographic techniques, such as interference lithography or self-assembly, to create the same nanostructured morphology over a large area combined with laser direct write. The process of drawing a single line or isolated voxel can result in a hierarchical pattern defined by the latent motif of the larger-scale technique. The net resuh is to shift the burden of high resolution patterning from the direct write to the large scale technique, effectively decoupling the correlation between the level of detail and the patterning speed and control. More specifically, the following combinations with laser direct writing were investigated: (1) proximity field nanopatterning for the predefinition of diffraction-order-defined 3D resonators which were applied as "stand-up" plasmodic microresonators, (2) dewetting to conduct development-free 2D patterning of isolated sub-micron lines, and, via overlap effects, nanoscale ( <1 00 nm) gratings, (3) block copolymer self-assembly to initiate the simultaneous annealing and alignment of near-equilibrium microdomains from a metastable starting morphology, and (4) interference lithography to fabricate 3D sub-micron periodic and quasiperiodic hierarchical structures with controllable positioning and tunable fill fraction that has potential for applications to microphotonics. In conjunction with the experimental components
Complex wet-environments in electronic-structure calculations
NASA Astrophysics Data System (ADS)
Fisicaro, Giuseppe; Genovese, Luigi; Andreussi, Oliviero; Marzari, Nicola; Goedecker, Stefan
The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of an applied electrochemical potentials, including complex electrostatic screening coming from the solvent. In the present work we present a solver to handle both the Generalized Poisson and the Poisson-Boltzmann equation. A preconditioned conjugate gradient (PCG) method has been implemented for the Generalized Poisson and the linear regime of the Poisson-Boltzmann, allowing to solve iteratively the minimization problem with some ten iterations. On the other hand, a self-consistent procedure enables us to solve the Poisson-Boltzmann problem. The algorithms take advantage of a preconditioning procedure based on the BigDFT Poisson solver for the standard Poisson equation. They exhibit very high accuracy and parallel efficiency, and allow different boundary conditions, including surfaces. The solver has been integrated into the BigDFT and Quantum-ESPRESSO electronic-structure packages and it will be released as a independent program, suitable for integration in other codes. We present test calculations for large proteins to demonstrate efficiency and performances. This work was done within the PASC and NCCR MARVEL projects. Computer resources were provided by the Swiss National Supercomputing Centre (CSCS) under Project ID s499. LG acknowledges also support from the EXTMOS EU project.
The Structure and Function of the Rh antigen Complex
Westhoff, Connie M.
2007-01-01
The Rh system is one of the most important and complex blood group systems because of the large number of antigens and the serious complications for the fetus of a woman sensitized by transfusion or pregnancy. Major advances in our understanding of the Rh system have occurred with the cloning of the genes and with functional evidence that the Rh blood group proteins belong to an ancient family of membrane proteins involved in ammonia transport. The arrangement and configuration of the genes at the RH locus promotes genetic exchange, generating new antigens. Importantly, RH genetic testing can now be applied to clinical transfusion medicine and prenatal practice. This includes testing for RHD zygosity, confirmation or resolution of D antigen status, and detection of altered RHD and RHCE genes in individuals at risk for producing antibodies to high incidence Rh antigens, particularly sickle cell disease patients. The Rh proteins form a core complex that is critical to the structure of the erythrocyte membrane, and may play a physiologically role in the sequestration of blood ammonia. The Rh family of proteins now includes non-erythroid Rh homologs present in many other tissues, and comparative genomics reveals Rh homologs in all domains of life. PMID:17198846
The solution structure of the copper clioquinol complex.
Pushie, M Jake; Nienaber, Kurt H; Summers, Kelly L; Cotelesage, Julien J H; Ponomarenko, Olena; Nichol, Helen K; Pickering, Ingrid J; George, Graham N
2014-04-01
Clioquinol (5-chloro-7-iodo-8-hydroxyquinoline) recently has shown promising results in the treatment of Alzheimer's disease and in cancer therapy, both of which also are thought to be due to clioquinol's ability as a lipophilic copper chelator. Previously, clioquinol was used as an anti-fungal and anti-protozoal drug that was responsible for an epidemic of subacute myelo-optic neuropathy (SMON) in Japan during the 1960s, probably a myeloneuropathy arising from a clioquinol-induced copper deficiency. Previous X-ray absorption spectroscopy of solutions of copper chelates of clioquinol suggested unusual coordination chemistry. Here we use a combination of electron paramagnetic, UV-visible and X-ray absorption spectroscopies to provide clarification of the chelation chemistry between clioquinol and copper. We find that the solution structures for the copper complexes formed with stoichiometric and excess clioquinol are conventional 8-hydroxyquinolate chelates. Thus, the promise of clioquinol in new treatments for Alzheimer's disease and in cancer therapy is not likely to be due to any novel chelation chemistry, but rather due to other factors including the high lipophilicity of the free ligand and chelate complexes.
Complexity of coherent structures computed from braids of passive particles
NASA Astrophysics Data System (ADS)
Budisic, Marko; Thiffeault, Jean-Luc
2015-11-01
Transport in fluids can be characterized by tracking passive particles advected by the fluid flow. When particles are distributed densely, as can be achieved in laboratory, the fluid velocity field can be reconstructed through Particle Tracking Velocimetry, enabling computation of Lyapunov exponents or other numerical analyses. When particles are sparse, as in drifter measurements of oceans, the velocity field cannot be reliably reconstructed. Nevertheless, the amount of entanglement of particle paths over time can be used to estimate the dynamical complexity of the flow by computing the Finite-Time Braiding Exponent (FTBE). The technique is based on braid dynamics and measures the rate at which particle motion stretches topological loops, i.e., the ``rubber bands'' enclosing subsets of particles. Allshouse and Thiffeault showed that minimally-stretching loops correspond to the structures coherent under material transport in flows. We extend their work and couple it to the FTBE calculations in order to characterize the spatial distribution of flow complexity. Analysis is demonstrated on the Hackborn rotor-oscillator model, which exhibits regions of chaotic and regular dynamics, and can be realized both numerically and experimentally. Funded by NSF CMMI-1233935.
Integrated quality assurance for assembly and testing of complex structures
NASA Astrophysics Data System (ADS)
von Kopylow, Christoph; Bothe, Thorsten; Elandaloussi, Frank; Kalms, Michael; Jüptner, Werner
2005-11-01
Modern production processes are directed by properties of the components to be manufactured. These components have different sizes, functionalities, high assembly complexity and high security requirements. The increasing requirements during the manufacturing of complex products like cars and aircrafts demand new solutions for the quality assurance - especially for the production at different places. The main focus is to find a measurement strategy that is cost effective, flexible and adaptive. That means a clear definition of the measurement problem, the measurement with adapted resolution, the data preparation and evaluation and support during measurement and utilisation of the results directly in the production. In this paper we describe flexible measurement devices on example of three different techniques: fringe projection, fringe reflection and shearography. These techniques allow the detection of surface and subsurface defects like bumps, dents and delaminations with high resolution. The defects can be optically mapped onto the object's surface. Results are demonstrated with big components taken from automotive and aircraft production. We will point out the most important adaptations of the systems to realize miniaturized, robust and mobile devices for the quality assurance in an industrial environment. Additionally the implementation into a Mobile Maintenance and Control structure is demonstrated.
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2010-10-06
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Behavioral pattern identification for structural health monitoring in complex systems
NASA Astrophysics Data System (ADS)
Gupta, Shalabh
Estimation of structural damage and quantification of structural integrity are critical for safe and reliable operation of human-engineered complex systems, such as electromechanical, thermofluid, and petrochemical systems. Damage due to fatigue crack is one of the most commonly encountered sources of structural degradation in mechanical systems. Early detection of fatigue damage is essential because the resulting structural degradation could potentially cause catastrophic failures, leading to loss of expensive equipment and human life. Therefore, for reliable operation and enhanced availability, it is necessary to develop capabilities for prognosis and estimation of impending failures, such as the onset of wide-spread fatigue crack damage in mechanical structures. This dissertation presents information-based online sensing of fatigue damage using the analytical tools of symbolic time series analysis ( STSA). Anomaly detection using STSA is a pattern recognition method that has been recently developed based upon a fixed-structure, fixed-order Markov chain. The analysis procedure is built upon the principles of Symbolic Dynamics, Information Theory and Statistical Pattern Recognition. The dissertation demonstrates real-time fatigue damage monitoring based on time series data of ultrasonic signals. Statistical pattern changes are measured using STSA to monitor the evolution of fatigue damage. Real-time anomaly detection is presented as a solution to the forward (analysis) problem and the inverse (synthesis) problem. (1) the forward problem - The primary objective of the forward problem is identification of the statistical changes in the time series data of ultrasonic signals due to gradual evolution of fatigue damage. (2) the inverse problem - The objective of the inverse problem is to infer the anomalies from the observed time series data in real time based on the statistical information generated during the forward problem. A computer-controlled special
Complex central structures suggest complex evolutionary paths for barred S0 galaxies
NASA Astrophysics Data System (ADS)
Dullo, Bililign T.; Martínez-Lombilla, Cristina; Knapen, Johan H.
2016-11-01
We investigate three barred lenticular galaxies (NGC 2681, NGC 3945 and NGC 4371), which were previously reported to have complex central structures but without a detailed structural analysis of these galaxies' high-resolution data. We have therefore performed four- to six-component (pseudo-)bulge/disc/bar/ring/point source) decompositions of the composite (Hubble Space Telescope plus ground-based) surface brightness profiles. We find that NGC 2681 hosts three bars, while NGC 3945 and NGC 4371 are double- and single-barred galaxies, respectively, in agreement with past isophotal analysis. We find that the bulges in these galaxies are compact, and have Sérsic indices of n ˜ 2.2-3.6 and stellar masses of M* ˜ 0.28 × 1010-1.1 × 1010 M⊙. NGC 3945 and NGC 4371 have intermediate-scale `pseudo-bulges' that are well described by a Sérsic model with low n ≲ 0.5 instead of an exponential (n = 1) profile as done in the past. We measure emission line fluxes enclosed within nine different elliptical apertures, finding that NGC 2681 has a low-ionization nuclear emission region (LINER)-type emission inside R ˜ 3 arcsec, but the emission line due to star formation is significant when aperture size is increased. In contrast, NGC 3945 and NGC 4371 have composite (active galactic nucleus plus star-forming)- and LINER-type emissions inside and outside R ˜ 2 arcsec, respectively. Our findings suggest that the three galaxies have experienced a complex evolutionary path. The bulges appear to be consequences of an earlier violent merging event while subsequent disc formation via gas accretion and bar-driven perturbations may account for the build-up of pseudo-bulges, bars, rings and point sources.
Analysis and representation of complex structures in separated flows
NASA Technical Reports Server (NTRS)
Helman, James; Hesselink, Lambertus
1991-01-01
We discuss our recent work on extraction and visualization of topological information in separated fluid flow data sets. As with scene analysis, an abstract representation of a large data set can greatly facilitate the understanding of complex, high-level structures. When studying flow topology, such a representation can be produced by locating and characterizing critical points in the velocity field and generating the associated stream surfaces. In 3D flows, the surface topology serves as the starting point. The 2D tangential velocity field near the surface of the body is examined for critical points. The tangential velocity field is integrated out along the principal directions of certain classes of critical points to produce curves depicting the topology of the flow near the body. The points and curves are linked to form a skeleton representing the 2D vector field topology. This skeleton provides a basis for analyzing the 3D structures associated with the flow separation. The points along the separation curves in the skeleton are used to start tangent curve integrations. Integration origins are successively refined to produce stream surfaces. The map of the global topology is completed by generating those stream surfaces associated with 3D critical points.
Structure of unsaturated rhamnogalacturonyl hydrolase complexed with substrate
Itoh, Takafumi; Ochiai, Akihito; Mikami, Bunzo; Hashimoto, Wataru; Murata, Kousaku . E-mail: kmurata@kais.kyoto-u.ac.jp
2006-09-08
Bacillus subtilis strain 168 YteR has been identified as a novel enzyme 'unsaturated rhamnogalacturonyl hydrolase' classified in glycoside hydrolase family 105. This enzyme acts specifically on unsaturated rhamnogalacturonan (RG) produced from plant cell wall RG type-I treated with RG lyases, releasing unsaturated galacturonic acid ({delta}GalA) from the substrate. The most likely candidate catalytic residue is Asp-143. Here, we show the structure of D143N in complex with unsaturated RG disaccharide (substrate) determined at 1.9 A resolution by X-ray crystallography. This structural feature directly contributes to the postulation of the enzyme reaction mechanism. YteR triggers the hydration of vinyl ether group in {delta}GalA, but not of glycoside bond, by using Asp-143 as a general acid and base catalyst. Asp-143 donates proton to the double bond of {delta}GalA as an acid catalyst and also deprotonates a water molecule as a base catalyst. Deprotonated water molecule attacks the C5 atom of {delta}GalA.
SIR Fronts in Complex Networks with Metapopulation Structure
NASA Astrophysics Data System (ADS)
Hindes, Jason; Singh, Sarabjeet; Myers, Chris; Schneider, Dave; Analytical FrameworksInfectious Disease Dynamics Collaboration
2013-03-01
SIR dynamics has been studied extensively on complex networks, yielding insight into the effects of heterogeneity in contact patterns on the spread of infectious diseases. Separately, metapopulations have provided a paradigm for modeling systems with extended and ``patchy'' organization. In this paper we demonstrate how multi-type networks can be used to combine these paradigms such that simple disease dynamics models can include heterogeneity in connectivity and multi-scale structure. We first present a multi-type generalization of the Volz-Miller mean-field approximation for SIR dynamics on multi-type random graphs. We then use this technique to study the propagation of epidemic fronts in a simple metapopulation model with population centers composed of configuration model networks coupled on a one-dimensional lattice. Using the formalism of front propagation into unstable states, we derive the effective transport coefficients of the linear spreading: asymptotic speed, characteristic perturbation size, and diffusion coefficient for the pulled fronts, and explore their dependence on the underlying graph structure. We also derive the average steady-state incidence, the equilibrium spectrum, and the threshold for invasion.
Thermal properties of composite materials with a complex fractal structure
NASA Astrophysics Data System (ADS)
Cervantes-Álvarez, F.; Reyes-Salgado, J. J.; Dossetti, V.; Carrillo, J. L.
2014-06-01
In this work, we report the thermal characterization of platelike composite samples made of polyester resin and magnetite inclusions. By means of photoacoustic spectroscopy and thermal relaxation, the thermal diffusivity, conductivity and volumetric heat capacity of the samples were experimentally measured. The volume fraction of the inclusions was systematically varied in order to study the changes in the effective thermal conductivity of the composites. For some samples, a static magnetic field was applied during the polymerization process, resulting in anisotropic inclusion distributions. Our results show a decrease in the thermal conductivity of some of the anisotropic samples, compared to the isotropic randomly distributed ones. Our analysis indicates that the development of elongated inclusion structures leads to the formation of magnetite and resin domains, causing this effect. We correlate the complexity of the inclusion structure with the observed thermal response through a multifractal and lacunarity analysis. All the experimental data are contrasted with the well known Maxwell-Garnett effective media approximation for composite materials.
Motif structure and cooperation in real-world complex networks
NASA Astrophysics Data System (ADS)
Salehi, Mostafa; Rabiee, Hamid R.; Jalili, Mahdi
2010-12-01
Networks of dynamical nodes serve as generic models for real-world systems in many branches of science ranging from mathematics to physics, technology, sociology and biology. Collective behavior of agents interacting over complex networks is important in many applications. The cooperation between selfish individuals is one of the most interesting collective phenomena. In this paper we address the interplay between the motifs’ cooperation properties and their abundance in a number of real-world networks including yeast protein-protein interaction, human brain, protein structure, email communication, dolphins’ social interaction, Zachary karate club and Net-science coauthorship networks. First, the amount of cooperativity for all possible undirected subgraphs with three to six nodes is calculated. To this end, the evolutionary dynamics of the Prisoner’s Dilemma game is considered and the cooperativity of each subgraph is calculated as the percentage of cooperating agents at the end of the simulation time. Then, the three- to six-node motifs are extracted for each network. The significance of the abundance of a motif, represented by a Z-value, is obtained by comparing them with some properly randomized versions of the original network. We found that there is always a group of motifs showing a significant inverse correlation between their cooperativity amount and Z-value, i.e. the more the Z-value the less the amount of cooperativity. This suggests that networks composed of well-structured units do not have good cooperativity properties.
Structure of the F–actin–tropomyosin complex
von der Ecken, Julian; Müller, Mirco; Lehman, William; Manstein, Dietmar J.; Penczek, Pawel A.; Raunser, Stefan
2015-01-01
Filamentous actin (F-actin) is the major protein of muscle thin filaments, and actin microfilaments are the main component of the eukaryotic cytoskeleton. Mutations in different actin isoforms lead to early-onset autosomal dominant non-syndromic hearing loss1, familial thoracic aortic aneurysms and dissections2, and multiple variations of myopathies3. In striated muscle fibres, the binding of myosin motors to actin filaments is mainly regulated by tropomyosin and troponin4,5. Tropomyosin also binds to F-actin in smooth muscle and in non-muscle cells and stabilizes and regulates the filaments there in the absence of troponin6. Although crystal structures for monomeric actin (G-actin) are available7, a high-resolution structure of F-actin is still missing, hampering our understanding of how disease-causing mutations affect the function of thin muscle filaments and microfilaments. Here we report the three-dimensional structure of F-actin at a resolution of 3.7 ångstroms in complex with tropomyosin at a resolution of 6.5ångstroms, determined by electron cryomicroscopy. The structure reveals that the D-loop is ordered and acts as a central region for hydrophobic and electrostatic interactions that stabilize the F-actin filament. We clearly identify the density corresponding to ADP and Mg2+ and explain the possible effect of prominent disease-causing mutants. A comparison of F-actin with G-actin reveals the conformational changes during filament formation and identifies the D-loop as their key mediator. We also confirm that negatively charged tropomyosin interacts with a positively charged groove on F-actin. Comparison of the position of tropomyosin in F-actin–tropomyosin with its position in our previously determined actin–tropomyosin–myosin structure8 reveals a myosin-induced transition of tropomyosin. Our results allow us to understand the role of individual mutations in the genesis of actin- and tropomyosin-related diseases and will serve as a strong
Algebraic structures of sequences of numbers
NASA Astrophysics Data System (ADS)
Huang, I.-Chiau
2012-09-01
For certain sequences of numbers, commutative rings with a module structure over a non-commutative ring are constructed. Identities of these numbers are considered as realizations of algebraic relations.
Brain: a complex adaptive structure at multiple levels
NASA Astrophysics Data System (ADS)
Klein, Bradley G.
2001-10-01
The human brain is comprised of over 100 billion neurons organized into tracts, nuclei, circuits and systems. This provides innumerable elegant abilities that rely on the nervous system to act as a complex adaptive structure (CAS). This property is apparent with respect to overall function, the function of individual neurons and the function of sensory and motor systems. At the overall functional level, the nervous system monitors the environments and can alter that environment. Alterations such as turning on a light switch or changing the diameter of neural vasculature, can improve the performance or chance for survival of the nervous system. Individual neurons can alter the activity of their electrogenic pumps, their rate of transmitter synthesis, their neurotransmitter release and their receptor density in order to maintain optimal functioning in a circuit following changes in their micro-environment. At the systems level, the visual system adjusts the orientation of the eyes or pupillary diameter to receive the highest quality visual information. In the motor system, the myotatic reflex maintains muscle position in the face of changing load, and the gain of the muscle organ responsible for the myotatic reflex can also be automatically adjusted. Internal homeostasis, essential for optimal performance of the nervous system, can be achieved through complex behavioral actions such as feeding. The hypothalamus plays an important role in such behaviors and in the type of sensorimotor integration responsible for the CAS nature of overall nervous system function. Thinking about the CAS characteristics of the nervous system may lead to development of non-biological CAS prostheses for the brain.
Biomineralization: Some complex crystallite-oriented skeletal structures.
Sahni, Ashok
2013-12-01
The present review focuses on some specific aspects of biomineralization with regard to the evolution of the first focused visioning systems in trilobites, the formation of molluscan shell architecture, dental enamel and its biomechanical properties and the structure of the calcified amniote egg, both fossil and recent. As an interdisciplinary field, biomineralization deals with the formation, structure and mechanical strength of mineralized skeletonized tissue secreted by organisms. Mineral matter formed in this way occurs in all three domains of life and consists of several mineral varieties, of which carbonates, phosphates and opaline silica are the most common. Animals and plants need mechanical support to counteract gravitational forces on land and hydrostatic pressure in the deep ocean, which is provided by a skeletonized framework. Skeleton architecture mainly consists of basic elements represented by small usually micrometer- to nanometer-sized crystallites of calcite and aragonite for carbonate systems and apatite crystallites for phosphatic ones, and then these building blocks develop into structured more complex frameworks. As selective pressures work towards optimizing stress and response, the orientation, morphology and structural arrangement of the crystallites indicates the distribution of the stress field of the biomineralized tissue. Large animals such as the dinosaurs have to deal with large gravitational forces, but in much smaller skeletonized organism such as the coccoliths, a few micrometer in diameter made up of even smaller individual crystallites, van der Waals forces play an increasingly important role and are at present poorly understood. Skeleton formation is dependent upon many factors including ambient water chemistry, temperature and environment. Ocean chemistry has played a vital role in the origins of skeletonization, 500 to 600 million years (ma) ago with the dominance of calcium carbonate as the principal skeleton-forming tissue
Noncommuting observables in quantum detection and estimation theory
NASA Technical Reports Server (NTRS)
Helstrom, C. W.; Kennedy, R. S.
1974-01-01
Basing decisions and estimates on simultaneous approximate measurements of noncommuting observables in a quantum receiver is shown to be equivalent to measuring commuting projection operators on a large Hilbert space than that of the receiver itself. The quantum-mechanical Cramer-Rao inequalities derived from right logarithmic derivatives and symmetrized logarithmic derivatives of the density operator are compared, and it is shown that the latter give superior lower bounds on the error variances of individual unbiased estimates of arrival time and carrier frequency of a coherent signal. For a suitably weighted sum of the error variances of simultaneous estimates of these, the former yield the superior lower bound under some conditions.
On the essential spectrum of certain non-commutative oscillators
Parmeggiani, Alberto Venni, Alberto
2013-12-15
We show here that the spectrum of the family of non-commutative harmonic oscillators Q{sub (α,β)}{sup w}(x,D) for α,β∈R{sub +} in the range αβ = 1 is [0, +∞) and is entirely essential spectrum. The previous existing results concern the case αβ > 1 (case in which Q{sub (α,β)}{sup w}(x,D) is globally elliptic with a discrete spectrum whose qualitative properties are being extensively studied), and ours therefore extend the picture to the range of parameters αβ ⩾ 1.
Feynman Disentangling of Noncommuting Operators in Quantum Mechanics
Popov, V.S.
2005-11-01
Feynman's disentangling theorem is applied to noncommuting operators in the problem of quantum parametric oscillator, which is mathematically equivalent to the problem of SU(1, 1) pseudospin rotation. The number states of the oscillator correspond to unitary irreducible representations of the SU(1, 1) group. Feynman disentangling is combined with group-theoretic arguments to obtain simple analytical formulas for the matrix elements and transition probabilities between the initial and final states of the oscillator. Feynman disentangling of time evolution operators is also discussed for an atom or ion interacting with a laser field and for a model Hamiltonian possessing the 'hidden' symmetry of the hydrogen atom.
Noncommutative spectral geometry, Bogoliubov transformations and neutrino oscillations
NASA Astrophysics Data System (ADS)
Vittoria Gargiulo, Maria; Sakellariadou, Mairi; Vitiello, Giuseppe
2015-07-01
In this report we show that neutrino mixing is intrinsically contained in Connes’ noncommutatives pectral geometry construction, thanks to the introduction of the doubling of algebra, which is connected to the Bogoliubov transformation. It is known indeed that these transformations are responsible for the mixing, turning the mass vacuum state into the flavor vacuum state, in such a way that mass and flavor vacuum states are not unitary equivalent. There is thus a red thread that binds the doubling of algebra of Connes’ model to the neutrino mixing.
Cosmological perturbations of a perfect fluid and noncommutative variables
De Felice, Antonio; Gerard, Jean-Marc; Suyama, Teruaki
2010-03-15
We describe the linear cosmological perturbations of a perfect fluid at the level of an action, providing thus an alternative to the standard approach based only on the equations of motion. This action is suited not only to perfect fluids with a barotropic equation of state, but also to those for which the pressure depends on two thermodynamical variables. By quantizing the system we find that (1) some perturbation fields exhibit a noncommutativity quite analogous to the one observed for a charged particle moving in a strong magnetic field, (2) local curvature and pressure perturbations cannot be measured simultaneously, (3) ghosts appear if the null energy condition is violated.
Noncommuting observables in quantum detection and estimation theory
NASA Technical Reports Server (NTRS)
Helstrom, C. W.
1972-01-01
Basing decisions and estimates on simultaneous approximate measurements of noncommuting observables in a quantum receiver is shown to be equivalent to measuring commuting projection operators on a larger Hilbert space than that of the receiver itself. The quantum-mechanical Cramer-Rao inequalities derived from right logarithmic derivatives and symmetrized logarithmic derivatives of the density operator are compared, and it is shown that the latter give superior lower bounds on the error variances of individual unbiased estimates of arrival time and carrier frequency of a coherent signal. For a suitably weighted sum of the error variances of simultaneous estimates of these, the former yield the superior lower bound under some conditions.
Thermodynamical properties of graphene in noncommutative phase–space
Santos, Victor; Maluf, R.V.; Almeida, C.A.S.
2014-10-15
We investigated the thermodynamic properties of graphene in a noncommutative phase–space in the presence of a constant magnetic field. In particular, we determined the behaviour of the main thermodynamical functions: the Helmholtz free energy, the mean energy, the entropy and the specific heat. The high temperature limit is worked out and the thermodynamic quantities, such as mean energy and specific heat, exhibit the same features as the commutative case. Possible connections with the results already established in the literature are discussed briefly.
The complex planetary synchronization structure of the solar system
NASA Astrophysics Data System (ADS)
Scafetta, N.
2014-01-01
The complex planetary synchronization structure of the solar system, which since Pythagoras of Samos (ca. 570-495 BC) is known as the music of the spheres, is briefly reviewed from the Renaissance up to contemporary research. Copernicus' heliocentric model from 1543 suggested that the planets of our solar system form a kind of mutually ordered and quasi-synchronized system. From 1596 to 1619 Kepler formulated preliminary mathematical relations of approximate commensurabilities among the planets, which were later reformulated in the Titius-Bode rule (1766-1772), which successfully predicted the orbital position of Ceres and Uranus. Following the discovery of the ~ 11 yr sunspot cycle, in 1859 Wolf suggested that the observed solar variability could be approximately synchronized with the orbital movements of Venus, Earth, Jupiter and Saturn. Modern research has further confirmed that (1) the planetary orbital periods can be approximately deduced from a simple system of resonant frequencies; (2) the solar system oscillates with a specific set of gravitational frequencies, and many of them (e.g., within the range between 3 yr and 100 yr) can be approximately constructed as harmonics of a base period of ~ 178.38 yr; and (3) solar and climate records are also characterized by planetary harmonics from the monthly to the millennial timescales. This short review concludes with an emphasis on the contribution of the author's research on the empirical evidences and physical modeling of both solar and climate variability based on astronomical harmonics. The general conclusion is that the solar system works as a resonator characterized by a specific harmonic planetary structure that also synchronizes the Sun's activity and the Earth's climate. The special issue Pattern in solar variability, their planetary origin and terrestrial impacts (Mörner et al., 2013) further develops the ideas about the planetary-solar-terrestrial interaction with the personal contribution of 10
Structural reorganization of the interleukin-7 signaling complex
McElroy, Craig A.; Holland, Paul J.; Zhao, Peng; Lim, Jae-Min; Wells, Lance; Eisenstein, Edward; Walsh, Scott T.R.
2012-06-29
We report here an unliganded receptor structure in the common gamma-chain ({gamma}{sub c}) family of receptors and cytokines. The crystal structure of the unliganded form of the interleukin-7 alpha receptor (IL-7R{alpha}) extracellular domain (ECD) at 2.15 {angstrom} resolution reveals a homodimer forming an 'X' geometry looking down onto the cell surface with the C termini of the two chains separated by 110 {angstrom} and the dimer interface comprising residues critical for IL-7 binding. Further biophysical studies indicate a weak association of the IL-7R{alpha} ECDs but a stronger association between the {gamma}{sub c}/IL-7R{alpha} ECDs, similar to previous studies of the full-length receptors on CD4{sup +} T cells. Based on these and previous results, we propose a molecular mechanism detailing the progression from the inactive IL-7R{alpha} homodimer and IL-7R{alpha}-{gamma}{sub c} heterodimer to the active IL-7-IL-7R{alpha}-{gamma}{sub c} ternary complex whereby the two receptors undergo at least a 90{sup o} rotation away from the cell surface, moving the C termini of IL-7R{alpha} and {gamma}{sub c} from a distance of 110 {angstrom} to less than 30 {angstrom} at the cell surface. This molecular mechanism can be used to explain recently discovered IL-7- and {gamma}{sub c}-independent gain-of-function mutations in IL-7R{alpha} from B- and T-cell acute lymphoblastic leukemia patients. The mechanism may also be applicable to other {gamma}{sub c} receptors that form inactive homodimers and heterodimers independent of their cytokines.
Structure of a Proteasome Pba1-Pba2 Complex
Stadtmueller, Beth M.; Kish-Trier, Erik; Ferrell, Katherine; Petersen, Charisse N.; Robinson, Howard; Myszka, David G.; Eckert, Debra M.; Formosa, Tim; Hill, Christopher P.
2012-01-01
The 20S proteasome is an essential, 28-subunit protease that sequesters proteolytic sites within a central chamber, thereby repressing substrate degradation until proteasome activators open the entrance/exit gate. Two established activators, Blm10 and PAN/19S, induce gate opening by binding to the pockets between proteasome α-subunits using C-terminal HbYX (hydrophobic-tyrosine-any residue) motifs. Equivalent HbYX motifs have been identified in Pba1 and Pba2, which function in proteasome assembly. Here, we demonstrate that Pba1-Pba2 proteins form a stable heterodimer that utilizes its HbYX motifs to bind mature 20S proteasomes in vitro and that the Pba1-Pba2 HbYX motifs are important for a physiological function of proteasomes, the maintenance of mitochondrial function. Other factors that contribute to proteasome assembly or function also act in the maintenance of mitochondrial function and display complex genetic interactions with one another, possibly revealing an unexpected pathway of mitochondrial regulation involving the Pba1-Pba2 proteasome interaction. Our determination of a proteasome Pba1-Pba2 crystal structure reveals a Pba1 HbYX interaction that is superimposable with those of known activators, a Pba2 HbYX interaction that is different from those reported previously, and a gate structure that is disrupted but not sufficiently open to allow entry of even small peptides. These findings extend understanding of proteasome interactions with HbYX motifs and suggest multiple roles for Pba1-Pba2 interactions throughout proteasome assembly and function. PMID:22930756
Cloud structure and feedback effects in the Carina Nebula Complex
NASA Astrophysics Data System (ADS)
Roccatagliata, Veronica; Preibisch, Thomas; Gaczkowski, Benjamin; Ratzka, Thorsten
2013-07-01
The star formation process in large clusters/associations can be strongly influenced by the feedback from high mass stars. Whether the resulting net effect of the feedback is predominantly negative (cloud dispersal) or positive (triggering of star formation due to cloud compression) is still an open question. The Carina Nebula complex (CNC) represents one of the most massive star-forming regions in our Galaxy. We use our Herschel far-infrared observations to study the properties of the clouds over the entire CNC and LABOCA/APEX telescope on the central part of the CNC.Our Herschel maps resolve, for the first time, the small-scale structure of the dense clouds over the entire spatial extent of the CNC. Several particularly interesting regions, including the prominent pillars south of eta Car, are analyzed in detail. Our maps also reveal a peculiar 'wave'-like pattern in the northern part of the Carina Nebula. The total mass of the clouds seen by Herschel in the central region is about 656 000 Msun. We derive the global spectral energy distribution in the mid-infrared to mm wavelength range and derive a total mass of < 890 000 Msun. We find that the density and temperature structure of the clouds in most parts of the CNC is dominated by the strong feedback from the numerous massive stars, rather than random turbulence. Comparing the cloud mass and the star formation rate derived for the CNC to other Galactic star forming regions suggests that the CNC is forming stars very efficiently. We suggest this to be a consequence of triggered star formation by radiative cloud compression.In our LABOCA sub-mm map, we identify about 600 individual clumps. We analyze and interpret the clump initial mass function (CIMF) as signature of turbulent pre-stellar clouds or star-forming clouds.
Structuring and sampling complex conformation space: Weighted ensemble dynamics simulations.
Gong, Linchen; Zhou, Xin
2009-08-01
Based on multiple simulation trajectories, which started from dispersively selected initial conformations, the weighted ensemble dynamics method is designed to robustly and systematically explore the hierarchical structure of complex conformational space through the spectral analysis of the variance-covariance matrix of trajectory-mapped vectors. The nondegenerate ground state of the matrix directly predicts the ergodicity of simulation data. The ground state could be adopted as statistical weights of trajectories to correctly reconstruct the equilibrium properties, even though each trajectory only explores part of the conformational space. Otherwise, the degree of degeneracy simply gives the number of metastable states of the system under the time scale of individual trajectory. Manipulation on the eigenvectors leads to the classification of trajectories into nontransition ones within the states and transition ones between them. The transition states may also be predicted without a priori knowledge of the system. We demonstrate the application of the general method both to the system with a one-dimensional glassy potential and with the one of alanine dipeptide in explicit solvent.
Microstructure-based modelling of multiphase materials and complex structures
NASA Astrophysics Data System (ADS)
Werner, Ewald; Wesenjak, Robert; Fillafer, Alexander; Meier, Felix; Krempaszky, Christian
2016-09-01
Micromechanical approaches are frequently employed to monitor local and global field quantities and their evolution under varying mechanical and/or thermal loading scenarios. In this contribution, an overview on important methods is given that are currently used to gain insight into the deformational and failure behaviour of multiphase materials and complex structures. First, techniques to represent material microstructures are reviewed. It is common to either digitise images of real microstructures or generate virtual 2D or 3D microstructures using automated procedures (e.g. Voronoï tessellation) for grain generation and colouring algorithms for phase assignment. While the former method allows to capture exactly all features of the microstructure at hand with respect to its morphological and topological features, the latter method opens up the possibility for parametric studies with respect to the influence of individual microstructure features on the local and global stress and strain response. Several applications of these approaches are presented, comprising low and high strain behaviour of multiphase steels, failure and fracture behaviour of multiphase materials and the evolution of surface roughening of the aluminium top metallisation of semiconductor devices.
Structural controllability of complex networks based on preferential matching.
Zhang, Xizhe; Lv, Tianyang; Yang, XueYing; Zhang, Bin
2014-01-01
Minimum driver node sets (MDSs) play an important role in studying the structural controllability of complex networks. Recent research has shown that MDSs tend to avoid high-degree nodes. However, this observation is based on the analysis of a small number of MDSs, because enumerating all of the MDSs of a network is a #P problem. Therefore, past research has not been sufficient to arrive at a convincing conclusion. In this paper, first, we propose a preferential matching algorithm to find MDSs that have a specific degree property. Then, we show that the MDSs obtained by preferential matching can be composed of high- and medium-degree nodes. Moreover, the experimental results also show that the average degree of the MDSs of some networks tends to be greater than that of the overall network, even when the MDSs are obtained using previous research method. Further analysis shows that whether the driver nodes tend to be high-degree nodes or not is closely related to the edge direction of the network.
Structuring and sampling complex conformation space: Weighted ensemble dynamics simulations
NASA Astrophysics Data System (ADS)
Gong, Linchen; Zhou, Xin
2009-08-01
Based on multiple simulation trajectories, which started from dispersively selected initial conformations, the weighted ensemble dynamics method is designed to robustly and systematically explore the hierarchical structure of complex conformational space through the spectral analysis of the variance-covariance matrix of trajectory-mapped vectors. The nondegenerate ground state of the matrix directly predicts the ergodicity of simulation data. The ground state could be adopted as statistical weights of trajectories to correctly reconstruct the equilibrium properties, even though each trajectory only explores part of the conformational space. Otherwise, the degree of degeneracy simply gives the number of metastable states of the system under the time scale of individual trajectory. Manipulation on the eigenvectors leads to the classification of trajectories into nontransition ones within the states and transition ones between them. The transition states may also be predicted without a priori knowledge of the system. We demonstrate the application of the general method both to the system with a one-dimensional glassy potential and with the one of alanine dipeptide in explicit solvent.
Measuring the significance of community structure in complex networks
NASA Astrophysics Data System (ADS)
Hu, Yanqing; Nie, Yuchao; Yang, Hua; Cheng, Jie; Fan, Ying; di, Zengru
2010-12-01
Many complex systems can be represented as networks, and separating a network into communities could simplify functional analysis considerably. Many approaches have recently been proposed to detect communities, but a method to determine whether the detected communities are significant is still lacking. In this paper, an index to evaluate the significance of communities in networks is proposed based on perturbation of the network. In contrast to previous approaches, the network is disturbed gradually, and the index is defined by integrating all of the similarities between the community structures before and after perturbation. Moreover, by taking the null model into account, the index eliminates scale effects. Thus, it can evaluate and compare the significance of communities in different networks. The method has been tested in many artificial and real-world networks. The results show that the index is in fact independent of the size of the network and the number of communities. With this approach, clear communities are found to always exist in social networks, but significant communities cannot be found in protein interactions and metabolic networks.
Guaranteed error bounds for structured complexity reduction of biochemical networks.
Prescott, Thomas P; Papachristodoulou, Antonis
2012-07-01
Biological systems are typically modelled by nonlinear differential equations. In an effort to produce high fidelity representations of the underlying phenomena, these models are usually of high dimension and involve multiple temporal and spatial scales. However, this complexity and associated stiffness makes numerical simulation difficult and mathematical analysis impossible. In order to understand the functionality of these systems, these models are usually approximated by lower dimensional descriptions. These can be analysed and simulated more easily, and the reduced description also simplifies the parameter space of the model. This model reduction inevitably introduces error: the accuracy of the conclusions one makes about the system, based on reduced models, depends heavily on the error introduced in the reduction process. In this paper we propose a method to calculate the error associated with a model reduction algorithm, using ideas from dynamical systems. We first define an error system, whose output is the error between observables of the original and reduced systems. We then use convex optimisation techniques in order to find approximations to the error as a function of the initial conditions. In particular, we use the Sum of Squares decomposition of polynomials in order to compute an upper bound on the worst-case error between the original and reduced systems. We give biological examples to illustrate the theory, which leads us to a discussion about how these techniques can be used to model-reduce large, structured models typical of systems biology.
New images of complex structures underneath the Tibetan Plateau
NASA Astrophysics Data System (ADS)
Kumar, Mohi
2012-07-01
The Tibetan Plateau contains some of the highest mountains in the world and was formed by the collision between the Indian and Eurasian plates beginning around 55 million years ago. Curious about how such elevated terrains form, Yue et al. used data collected from a seismic experiment conducted between 2007 and 2009 to image the complex three-dimensional geometry of the crust and upper mantle in northeastern Tibet. The scientists' results detected the interaction between components of thrust and subduction, shed light on the conditions surrounding crustal loading, and located mantle discontinuities and small-scale mantle convection. Despite the thick crust of the plateau, which can reach depths of 65-75 kilometers, the authors were able to capture for the first time major vertical offsets (ranging from 10 to 20 kilometers) in the Mohorovičić discontinuity, the boundary between the crust and the mantle underlying the region. These offsets, along with the presence of other structures, bear testament to the intricate evolution of the Tibetan Plateau; the authors posit different scenarios on the history of this evolution, including the presence of buried remnant slabs of possible oceanic origin that continue to sink and create mantle eddies. (Journal of Geophysical Research-Solid Earth, doi:10.1029/2011JB008545, 2012)
Complex structure and regulation of the ABP/SHBG gene.
Joseph, D R; Sullivan, P M; Wang, Y M; Millhorn, D E; Bayliss, D M
1991-01-01
Extracellular androgen-binding proteins (ABPs) are thought to modulate the regulatory functions of androgens and the trans-acting nuclear androgen receptor. Testicular ABP and plasma sex hormone-binding globulin (SHBG), which is produced in the liver, are encoded by the same gene. We report here that the ABP/SHBG gene is also expressed in fetal rat liver and adult brain. Immunoreactive ABP was localized in the brain and fetal liver and mRNAs were identified in both tissues by northern blot hybridization. Analysis of brain and fetal liver cDNA clones revealed alternatively processed RNAs with sequence characteristics suggesting the encoded proteins could act as competitors of ABP/SHBG binding to cell surface receptors. One cDNA represented a fused transcript of the ABP/SHBG gene and the histidine decarboxylase gene that was apparently formed by a trans-splicing process. Gene sequencing experiments indicate that tissue-specific ABP/SHBG gene promoter-enhancer elements are utilized in testis, brain and fetal liver. These data demonstrate that the structure, RNA transcript processing and likely regulation of the ABP/SHBG gene are very complex. PMID:1958575
Structural basis underlying viral hijacking of a histone chaperone complex
Huang, Hongda; Deng, Zhong; Vladimirova, Olga; Wiedmer, Andreas; Lu, Fang; Lieberman, Paul M.; Patel, Dinshaw J.
2016-01-01
The histone H3.3 chaperone DAXX is implicated in formation of heterochromatin and transcription silencing, especially for newly infecting DNA virus genomes entering the nucleus. Epstein-Barr virus (EBV) can efficiently establish stable latent infection as a chromatinized episome in the nucleus of infected cells. The EBV tegument BNRF1 is a DAXX-interacting protein required for the establishment of selective viral gene expression during latency. Here we report the structure of BNRF1 DAXX-interaction domain (DID) in complex with DAXX histone-binding domain (HBD) and histones H3.3-H4. BNRF1 DID contacts DAXX HBD and histones through non-conserved loops. The BNRF1-DAXX interface is responsible for BNRF1 localization to PML-nuclear bodies typically associated with host-antiviral resistance and transcriptional repression. Paradoxically, the interface is also required for selective transcription activation of viral latent cycle genes required for driving B-cell proliferation. These findings reveal molecular details of virus reprogramming of an antiviral histone chaperone to promote viral latency and cellular immortalization. PMID:27581705
Structural Preferences in Phosphanylthiolato Platinum(II) Complexes
Duran, Josep; Real, Julio; Benet‐Buchholz, Jordi; Solà, Miquel
2016-01-01
Abstract Invited for this month's cover picture are the groups of Prof. Alfonso Polo and Dr. Albert Poater at the Universitat de Girona, as well as their collaborators from the Universitat Autònoma de Barcelona and the Institute of Chemical Research of Catalonia. The cover picture shows phosphanylthiolate ligand coordination on a platinum(II) center to give only the bischelate cis ‐P,P isomer when the ligand/Pt ratio is 2, whereas a trinuclear unexpected complex is achieved with a ligand/Pt ratio of 1. Here, the synthesis and structural determination is combined with density functional theory (DFT) calculations to rationalize the reaction mechanistically and through conceptual DFT. The exciting point of this study is that it opens the door to test new experimental pathways to monitor the preferred cis or trans arrangement of bidentate ligands to platinum. (Legend: H‐white, C‐black, P‐purple, S‐yellow, Cl‐green, Pt‐blue.) For more details, see the Full Paper on p. 51 ff. PMID:27308218
Can we image complex structures with first-arrival traveltime
Geoltrain, S.; Brac, J. . PSI Research Consortium)
1993-04-01
The authors experienced difficulties when attempting to perform seismic imaging in complex velocity fields using prestack Kirchhoff depth migration in conjunction with traveltimes computed by finite-differencing the eikonal equation. The problem arose not because of intrinsic limitations of kirchhoff migration, but rather from the failure of finite-differencing to compute traveltimes representative of the energetic part of the wavefield. Further analysis showed that the first arrival is most often associated with a marginally energetic event wherever subsequent arrivals exist. The consequence is that energetic seismic events are imaged with a kinematically incorrect operator and turn out mispositioned at depth. They therefore recommend that first-arrival traveltime fields, such as those computed by finite-differencing the eikonal equation, be used in Kirchhoff migration only with great care when the velocity field hosts multiple transmitted arrivals; such a situation is typically met where geological structure creates strong and localized velocity hetero-geneities, which partition the incident and reflected wavefields into multiple arrivals; in such an instance, imaging cannot be strictly considered a kinematic process, as it must be performed with explicit reference to the relative amplitudes of multiple arrivals.
Solution structures of stromelysin complexed to thiadiazole inhibitors.
Stockman, B. J.; Waldon, D. J.; Gates, J. A.; Scahill, T. A.; Kloosterman, D. A.; Mizsak, S. A.; Jacobsen, E. J.; Belonga, K. L.; Mitchell, M. A.; Mao, B.; Petke, J. D.; Goodman, L.; Powers, E. A.; Ledbetter, S. R.; Kaytes, P. S.; Vogeli, G.; Marshall, V. P.; Petzold, G. L.; Poorman, R. A.
1998-01-01
Unregulated or overexpressed matrix metalloproteinases (MMPs), including stromelysin, collagenase, and gelatinase. have been implicated in several pathological conditions including arthritis and cancer. Small-molecule MMP inhibitors may have therapeutic value in the treatment of these diseases. In this regard, the solution structures of two stromelysin/ inhibitor complexes have been investigated using 1H, 13C, and 15N NMR spectroscopy. Both-inhibitors are members of a novel class of matrix metalloproteinase inhibitor that contain a thiadiazole group and that interact with stromelysin in a manner distinct from other classes of inhibitors. The inhibitors coordinate the catalytic zinc atom through their exocyclic sulfur atom, with the remainder of the ligand extending into the S1-S3 side of the active site. The binding of inhibitor containing a protonated or fluorinated aromatic ring was investigated using 1H and 19F NMR spectroscopy. The fluorinated ring was found to have a reduced ring-flip rate compared to the protonated version. A strong, coplanar interaction between the fluorinated ring of the inhibitor and the aromatic ring of Tyr155 is proposed to account for the reduced ring-flip rate and for the increase in binding affinity observed for the fluorinated inhibitor compared to the protonated inhibitor. Binding interactions observed for the thiadiazole class of ligands have implications for the design of matrix metalloproteinase inhibitors. PMID:9827994
NASA Astrophysics Data System (ADS)
Guido, Daniele; Landi, Giovanni; Vassout, Stéphane
2016-07-01
This topical issue grew out of the International Conference "Noncommutative Geometry and Applications" held 16-21 June 2014 at Villa Mondragone, Frascati (Roma). The main purpose of the conference was to have a unified view of different incarnations of noncommutative geometry and its applications. The seven papers collected in the present topical issue represent a good sample of the topics covered at the workshop. The conference itself was one of the climaxes of the Franco-Italian project GREFI-GENCO, which was initiated in 2007 by CNRS and INDAM to promote and enhance collaboration and exchanges between French and Italian researchers in the area of noncommutative geometry.
Wigner function for Klein-Gordon oscillator in commutative and noncommutative spaces
NASA Astrophysics Data System (ADS)
Hassanabadi, S.; Ghominejad, M.
2016-06-01
As a quasi-probability distribution function in phase-space and a special representation of the density matrix, the Wigner function is of great significance in physics. In this work, the Wigner function for the Klein-Gordon oscillator is studied in commutative and noncommutative spaces. We first study the Wigner function for Klein-Gordon oscillator in commutative space then, by using a generalized Bopp's shift method, we obtain the corresponding Wigner function in noncommutative space. The additional terms in Wigner function on a NC space is related to the noncommutativity of space.
The Anomalous Zeeman Effect for the Hydrogen Atom in Noncommutative Space
NASA Astrophysics Data System (ADS)
Santos, Willien O.; Souza, Andre M. C.
2012-12-01
The Hamiltonian describing an anomalous Zeeman effect for the hydrogen atom on noncommutative space is studied using a Bopp's shift. Using first order perturbation theory, the correction to the energy is calculated for the case of a weak external magnetic field. We also obtained the orbital and spin g-factors in noncommutative space. We show that the experimental values for the orbital and spin g-factors put an upper bound on the magnitude of the parameter of noncommutativity of the order of, respectively, Θ≤(8 GeV)-2 and Θ≤(0.01 GeV)-2.
Collisional family structure within the Nysa-Polana complex
NASA Astrophysics Data System (ADS)
Dykhuis, Melissa J.; Greenberg, Richard
2015-05-01
The Nysa-Polana complex is a group of low-inclination asteroid families in the inner main belt, bounded in semimajor axis by the Mars-crossing region and the Jupiter 3:1 mean-motion resonance. This group is important as the most likely source region for the target of the OSIRIS-REx mission, (101955) Bennu; however, family membership in the region is complicated by the presence of several dynamically overlapping families with a range of surface reflectance properties. The large S-type structure in the region appears to be associated with the parent body (135) Hertha, and displays an (eP,aP) correlation consistent with a collision event near true anomaly of ∼180° with ejecta velocity vej ∼ 285m /s . The ejecta distribution from a collision with these orbital properties is predicted to have a maximum semimajor axis dispersion of δaej = 0.005 ± 0.008AU , which constitutes only a small fraction (7%) of the observed semimajor axis dispersion, the rest of which is attributed to the Yarkovsky effect. The age of the family is inferred from the Yarkovsky dispersion to be 300-50+60 My. Objects in a smaller cluster that overlaps the large Hertha family in proper orbital element space have reflectance properties more consistent with the X-type (135) Hertha than the surrounding S-type family. These objects form a distinct Yarkovsky "V" signature in (aP, H) space, consistent with a more recent collision, which appears to also be dynamically connected to (135) Hertha. Production of two families with different reflectance properties from a single parent could result from the partial differentiation of the parent, shock darkening effects, or other causes. The Nysa-Polana complex also contains a low-albedo family associated with (142) Polana (called "New Polana" by Walsh et al. (Walsh, K.J. et al. [2013]. Icarus 225, 283-297)), and two other low-albedo families associated with (495) Eulalia. The second Eulalia family may be a high-aP , low-eP , low-iP component of the first
Luminescence modulations of rhenium tricarbonyl complexes induced by structural variations.
Bertrand, Hélène C; Clède, Sylvain; Guillot, Régis; Lambert, François; Policar, Clotilde
2014-06-16
Octahedral d(6) low-spin Re(I) tricarbonyl complexes are of considerable interest as noninvasive imaging probes and have been deeply studied owing to their biological stability, low toxicity, large Stokes shifts, and long luminescence lifetimes. We reported recently the bimodal IR and luminescence imaging of a Re(I) tricarbonyl complex with a Pyta ligand (4-(2-pyridyl)-1,2,3-triazole) in cells and labeled such metal-carbonyl complexes SCoMPIs for single-core multimodal probes for imaging. Re(I) tricarbonyl complexes have unique photophysical properties allowing for their unequivocal detection in cells but also present some weaknesses such as a very low luminescence quantum yield in aqueous medium. Further optimizations would thus be desirable. We therefore developed new Re(I) tricarbonyl complexes prepared from different ancillary ligands. Complexes with benzothiadiazole-triazole ligands show interesting luminescent quantum yields in acetonitrile and may constitute valuable luminescent metal complexes in organic media. A series of complexes with bidentate 1-(2-quinolinyl)-1,2,3-triazole (Taquin) and 1-(2-pyridyl)-1,2,3-triazole (Tapy) ligands bearing various 4-substituted alkyl side chains has been designed and synthesized with efficient procedures. Their photophysical properties have been characterized in acetonitrile and in a H2O/DMSO (98/2) mixture and compared with those of the parent Quinta- and Pyta-based complexes. Tapy complexes bearing long alkyl chains show impressive enhancement of their luminescent properties relative to the parent Pyta complex. Theoretical calculations have been performed to further characterize this new class of rhenium tricarbonyl complexes. Preliminary cellular imaging studies in MDA-MB231 breast cancer cells reveal a strong increase in the luminescence signal in cells incubated with the Tapy complex substituted with a C12 alkyl chain. This study points out the interesting potential of the Tapy ligand in coordination chemistry
Tshuva, E Y; Goldberg, I; Kol, M; Goldschmidt, Z
2001-08-13
The coordination chemistry of titanium(IV) complexes of amine bis(phenolate) ligands was investigated by synthesizing various types of complexes and analyzing them specroscopically and structurally. Steric effects of tridentate [ONO]- and tetradentate [ONNO]-type ligands were studied by reacting the ligand precursors with titanium tetra(isopropoxide). [ONNO]-type ligands featuring an amine donor located on a pendant arm led to octahedral bis(isopropoxide) complexes, regardless of the steric bulk around the metal. Several such complexes having varying steric crowding were thus synthesized. On the other hand, steric effects were found to play a major role in determining the complex constitution when [ONO]-type ligands, featuring no side donor, were involved. Relatively sterically undemanding ligands led to octahedral bis(homoleptic) complexes, whereas increased steric bulk resulted in the formation of pentacoordinate bis(isopropoxide) complexes. These pentacoordinate complexes readily lead to bis(heteroleptic) complexes by reaction with nonsterically demanding [ONO]- and [ONNO]-type ligand precursors. In the latter case the sidearm nitrogen remains uncoordinated to the metal. The bis(isopropoxide) complexes of the [ONNO]-type ligands may also lead to bis(heteroleptic) complexes, however, these reactions are much slower. PMID:11487331
Bumba, Ladislav; Havelková-Dousová, Helena; Husák, Michal; Vácha, Frantisek
2004-07-01
The structure of photosystem II (PSII) complex isolated from thylakoid membranes of the red alga Porphyridium cruentum was investigated using electron microscopy followed by single particle image analysis. The dimeric complexes observed contain all major PSII subunits (CP47, CP43, D1 and D2 proteins) as well as the extrinsic proteins (33 kDa, 12 kDa and the cytochrome c(550)) of the oxygen-evolving complex (OEC) of PSII, encoded by the psbO, psbU and psbV genes, respectively. The single particle analysis of the top-view projections revealed the PSII complex to have maximal dimensions of 22 x 15 nm. The analysis of the side-view projections shows a maximal thickness of the PSII complex of about 9 nm including the densities on the lumenal surface that has been attributed to the proteins of the OEC complex. These results clearly demonstrate that the red algal PSII complex is structurally very similar to that of cyanobacteria and to the PSII core complex of higher plants. In addition, the arrangement of the OEC proteins on the lumenal surface of the PSII complex is consistent to that obtained by X-ray crystallography of cyanobacterial PSII.
Population Structure of the North American Cranberry Fruit Rot Complex
Technology Transfer Automated Retrieval System (TEKTRAN)
Cranberry fruit rot is caused by a complex of pathogenic fungi. Variation in the populations within this complex from region to region could delay identification of the causal agents(s) and complicate management strategies. Our objective was to assess genetic variation within the four major fruit ro...
Besenyei, Gábor; Párkányi, László; Szalontai, Gábor; Holly, Sándor; Pápai, Imre; Keresztury, Gábor; Nagy, Andrea
2004-07-01
Benzoyl azides, ArC(O)N3, 2, (Ar = phenyl or substituted phenyl), react with [Pd2Cl2(dppm)2], 1, [dppm = bis(diphenylphosphino)methane] with the formation of novel [Pd2Cl2(mu-NC(O)Ar)(dppm)2], 3, benzoylnitrene complexes that were structurally characterised by multinuclear magnetic resonance and IR spectroscopy and, in several instances, by single crystal X-ray diffraction. As shown by crystallographic studies, the C2P4Pd2 rings adopt extended twist-boat conformations with methylene groups bending towards the bridging benzoylimido moieties. X-ray diffraction studies have revealed the chiral nature of the imido complexes, the chiral element being the propeller-like C2P4Pd2 ring. Structural data accumulated on complexes 3 such as short C-N distances (1.32 A), elongated C=O bonds (1.30 A) as well as the outstandingly high barrier to internal rotation around the N-C(O) linkage (88.3 kJ mol(-1)) are in line with extensive ppi-ppi interaction between the bridging nitrogen and the carbonyl carbon atoms. Theoretical calculations indicate an electron shift from the dimer towards the apical nitrogen atom, which, in turn, facilitates the donation of electrons towards the carbonyl moiety. To elucidate the structure-reactivity relationship of benzoyl azides towards 1, crystallographic and solution IR spectroscopic studies were carried out on a series of para-substituted benzoyl azides. The reaction obeys the Hammett equation. The large positive value of the reaction constant indicates that the azides act as electrophiles in the reaction studied. The enhanced reactivity of 2-nitrobenzoyl azide has been attributed to a decreased conjugation of the phenyl and carbonyl moieties in this reagent.
Landau-like Atomic Problem on a Non-commutative Phase Space
NASA Astrophysics Data System (ADS)
Mamat, Jumakari; Dulat, Sayipjamal; Mamatabdulla, Hekim
2016-06-01
We study the motion of a neutral particle in symmetric gauge and in the framework of non-commutative Quantum Mechanics. Starting from the corresponding Hamiltonian we derive the eigenfunction and eigenvalues.
Path integral action and Chern-Simons quantum mechanics in noncommutative plane
NASA Astrophysics Data System (ADS)
Gangopadhyay, Sunandan; Scholtz, Frederik G.
2014-06-01
In this paper, the connection between the path integral representation of propagators in the coherent state basis with additional degrees of freedom (Rohwer et al 2010 J. Phys. A: Math. Theor. 43 345302) and the one without any such degrees of freedom (Gangopadhyay and Scholtz 2009 Phys. Rev. Lett. 102 241602) is established. We further demonstrate that the path integral formalism developed in the noncommutative plane using the coherent state basis leads to a quantum mechanics involving a Chern-Simons term in momentum which is of noncommutative origin. The origin of this term from the Bopp-shift point of view is also investigated. A relativistic generalization of the action derived from the path integral framework is then proposed. Finally, we construct a map from the commutative quantum Hall system to a particle in a noncommutative plane moving in a magnetic field. The value of the noncommutative parameter from this map is then computed and is found to agree with previous results.
A New Program for Detecting the Geometrical Core of a Set of Structures of Macromolecular Complexes.
Vakulenko, Yu A; Nagaev, B E; Alexeevski, A V; Karyagina, A S; Spirin, S A
2016-04-01
Comparison of structures of homological proteins often helps to understand functionally significant features of these structures. This concerns not only structures of separate protein chains, but also structures of macromolecular complexes. In particular, a comparison of complexes of homologous proteins with DNA is significant for analysis of the recognition of DNA by proteins. We present program LCore for detecting geometrical cores of a family of structures; a geometrical core is a set of amino acid residues and nucleotides that disposed similarly in all structures of the family. We describe the algorithm of the program, its web interface, and an example of its application to analysis of complexes of homeodomains with DNA.
The coquaternion algebra and complex partial differential equations
NASA Astrophysics Data System (ADS)
Dimiev, Stancho; Konstantinov, Mihail; Todorov, Vladimir
2009-11-01
In this paper we consider the problem of differentiation of coquaternionic functions. Let us recall that coquaternions are elements of an associative non-commutative real algebra with zero divisor, introduced by James Cockle (1849) under the name of split-quaternions or coquaternions. Developing two type complex representations for Cockle algebra (complex and paracomplex ones) we present the problem in a non-commutative form of the δ¯-type holomorphy. We prove that corresponding differentiable coquaternionic functions, smooth and analytic, satisfy PDE of complex, and respectively of real variables. Applications for coquaternionic polynomials are sketched.
Structure and stability of the complex formed by oligonucleotides.
Zheng, Cui; Niu, Lin; Yan, Jingjing; Liu, Jie; Luo, Ying; Liang, Dehai
2012-05-28
Polycations and cationic lipids have been widely used as non-viral vectors for the delivery of plasmid DNA, siRNA and anti-sense oligonucleotides. To demonstrate that one polycation can form a complex with several types of DNA, we conducted a comparative study on the complexation of poly(L-lysine) (PLL) with 2000 bp salmon testes DNA (dsDNA), 21 bp double-stranded oligonucleotides (ds-oligo), and 21 nt single-stranded oligonucleotides (ss-oligo) in PBS buffer. The complexes are prepared by a titration method and the process is monitored by laser light scattering. It was found that in most cases, ss-oligo and ds-oligo form complexes with higher molecular weights than the complex formed by dsDNA at the same +/- ratio immediately after mixing. More importantly, the complexes formed by oligonucleotides are not stable, the scattered intensity gradually decreases to the level of the solvent in weeks. Atomic force microscopy measurements also indicate that the freshly prepared complex is subject to environmental changes and could dissociate very quickly. The behaviour of oligonucleotides cannot be predicted by the classical polyelectrolyte theories.
Toroidal orbifolds of Z3 and Z6 symmetries of noncommutative tori
NASA Astrophysics Data System (ADS)
Walters, Sam
2015-05-01
The Hexic transform ρ of the noncommutative 2-torus Aθ is the canonical order 6 automorphism defined by ρ (U) = V, ρ (V) =e-πiθU-1 V, where U, V are the canonical unitary generators obeying the unitary Heisenberg commutation relation VU =e2πiθ UV . The Cubic transform is κ =ρ2. These are canonical analogues of the noncommutative Fourier transform, and their associated fixed point C*-algebras Aθρ, Aθκ are noncommutative Z6, Z3 toroidal orbifolds, respectively. For a large class of irrationals θ and rational approximations p / q of θ, a projection e of trace q2 θ - pq is constructed in Aθ that is invariant under the Hexic transform. Further, this projection is shown to be a matrix projection in the sense that it is approximately central, the cut down algebra eAθ e contains a Hexic invariant q × q matrix algebra M whose unit is e and such that the cut downs eUe, eVe are approximately inside M. It is also shown that these invariant matrix projections are covariant in that they arise from a continuous section E (t) of C∞-projections of the continuous field {At } 0 < t < 1 of noncommutative tori C*-algebras such that ρ (E (t)) = E (t). It turns out that the projection E (t) is the support projection of a canonical C∞-positive element that has the appearance of a noncommutative 2-dimensional Theta function. The topological invariants (or 'quantum' numbers) of E (t), e, and related projections are computed by a new and quicker method than in previous works. (They would also give topological invariants for finitely generated projective modules over noncommutative orbifolds associated to Z6 and Z3 symmetries of noncommutative tori.) We remark that these results have some bearing on research work related to noncommutative orbifolds used in string theory.
NASA Astrophysics Data System (ADS)
Basu, B.; Ghosh, Subir
2005-10-01
We have presented a quantum mechanical toy model for the study of Coulomb interactions in Quantum Hall (QH) system. Inclusion of Coulomb interaction is essential for the study of bilayer QH system and our model can simulate it, in the compound state, in a perturbative framework. We also show that in the noncommutative plane, the Coulomb interaction is modified at a higher order in the noncommutativity parameter θ, and only if θ varies from layer to layer in the QH system.
Regularization of two-dimensional supersymmetric Yang-Mills theory via non-commutative geometry
NASA Astrophysics Data System (ADS)
Valavane, K.
2000-11-01
The non-commutative geometry is a possible framework to regularize quantum field theory in a non-perturbative way. This idea is an extension of the lattice approximation by non-commutativity that allows us to preserve symmetries. The supersymmetric version is also studied and more precisely in the case of the Schwinger model on a supersphere. This paper is a generalization of this latter work to more general gauge groups.
Solution structure of the NDH-1 complex subunit CupS from Thermosynechococcus elongatus.
Korste, Annika; Wulfhorst, Hannes; Ikegami, Takahisa; Nowaczyk, Marc M; Stoll, Raphael
2015-10-01
The cyanobacterial multi-subunit membrane protein complex NDH-1 is both structurally and functionally related to Complex I of eubacteria and mitochondria. In addition to functions in respiration and cyclic electron transfer around photosystem I (PSI), the cyanobacterial NDH-1 complex is involved in a unique mechanism for inorganic carbon concentration. Although the crystal structures of the similar respiratory Complex I from Thermus thermophilus and Escherichia coli are known, atomic structural information is not available for the cyanobacterial NDH-1 complex yet. In particular, the structures of those subunits that are not homologous to Complex I will help to understand their distinct functions. The 15.7kDa protein CupS is a small soluble subunit of the complex variant NDH-1MS, which is thought to play a role in CO2 conversion. Here, we present the NMR structure of CupS from Thermosynechococcus elongatus, which is the very first structure of a specific cyanobacterial NDH-1 complex subunit. CupS shares a structural similarity with members of the Fasciclin protein superfamily. The structural comparison to Fasciclin type proteins based on known NMR structures and protein sequences of human TGFBIp, MPB70 from Mycobacterium bovis, and Fdp from Rhodobacter sphaeroides, together with a virtual docking model of CupS and NdhF3, provide first insight into the specific binding of CupS to the NDH-1MS complex at atomic resolution.
NASA Astrophysics Data System (ADS)
Blaschke, D. N.; Grosse, H.; Schweda, M.
2007-09-01
Inspired by the renormalizability of the non-commutative Φ4 model with added oscillator term, we formulate a non-commutative gauge theory, where the oscillator enters as a gauge fixing term in a BRST invariant manner. All propagators turn out to be essentially given by the Mehler kernel and the bilinear part of the action is invariant under the Langmann-Szabo duality. The model is a promising candidate for a renormalizable non-commutative U(1) gauge theory.
Li, Feng; Ge, Peng; Hui, Wong H; Atanasov, Ivo; Rogers, Kestrel; Guo, Qiang; Osato, Daren; Falick, Arnold M; Zhou, Z Hong; Simpson, Larry
2009-07-28
Uridine insertion/deletion RNA editing is a unique form of posttranscriptional RNA processing that occurs in mitochondria of kinetoplastid protists. We have carried out 3D structural analyses of the core editing complex or "L (ligase)-complex" from Leishmania tarentolae mitochondria isolated by the tandem affinity purification procedure (TAP). The purified material, sedimented at 20-25S, migrated in a blue native gel at 1 MDa and exhibited both precleaved and full-cycle gRNA-mediated U-insertion and U-deletion in vitro activities. The purified L-complex was analyzed by electron tomography to determine the extent of heterogeneity. Three-dimensional structural comparisons of individual particles in the tomograms revealed that a majority of the complexes have a similar shape of a slender triangle. An independent single-particle reconstruction, using a featureless Gaussian ball as the initial model, converged to a similar triangular structure. Another single-particle reconstruction, using the averaged tomography structure as the initial model, yielded a similar structure. The REL1 ligase was localized on the model to the base of the apex by decoration with REL1-specific IgG. This structure should prove useful for a detailed analysis of the editing reaction.
Montazerozohori, M; Mojahedi Jahromi, S; Masoudiasl, A; McArdle, P
2015-03-01
In this work, synthesis of some new five coordinated zinc halide/pseudo-halide complexes of a N3-tridentate ligand is presented. All complexes were subjected to spectroscopic and physical methods such as FT-IR, UV-visible, (1)H and (13)C NMR spectra, thermal analyses and conductivity measurements for identification. Based on spectral data, the general formula of ZnLX2 (X=Cl(-), Br(-), I(-), SCN(-) and N3(-)) was proposed for the zinc complexes. Zinc complexes have been also prepared in nano-structure sizes under ultrasonic irradiation. X-ray powder diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were applied for confirmation of nano-structure character for the complexes. Among the complexes, zinc azide complex structure was analyzed by X-ray crystallography. This complex crystallizes as a triplet in trigonal system with space group of P31. The coordination sphere around the zinc center is well shown as a distorted trigonal bipyramidal with three nitrogen atoms from Schiff base ligand and two terminal azide nitrogen atoms attached to zinc ion. Various intermolecular interactions such as NH⋯N, CH⋯N and CH⋯π hydrogen bonding interactions stabilize crystalline lattice so that they causes a three dimensional supramolecular structure for the complex. In vitro screening of the compounds for their antimicrobial activities showed that ZnLI2, ZnL(N3)2, ZnLCl2 and ZnL(NCS)2 were found as the most effective compound against bacteria of Bacillus subtilis, Staphylococcus aureus, Pseudomonas aeruginosa and Escherichia coli respectively. Also ZnLI2 and ZnLCl2 complexes were found more effective against two selected fungi than others. Finally, thermal behaviors of the zinc complexes showed that they are decomposed via 2-4 thermal steps from room temperature up to 1000°C. PMID:25528511
NASA Astrophysics Data System (ADS)
Montazerozohori, M.; Mojahedi Jahromi, S.; Masoudiasl, A.; McArdle, P.
2015-03-01
In this work, synthesis of some new five coordinated zinc halide/pseudo-halide complexes of a N3-tridentate ligand is presented. All complexes were subjected to spectroscopic and physical methods such as FT-IR, UV-visible, 1H and 13C NMR spectra, thermal analyses and conductivity measurements for identification. Based on spectral data, the general formula of ZnLX2 (X = Cl-, Br-, I-, SCN- and N3-) was proposed for the zinc complexes. Zinc complexes have been also prepared in nano-structure sizes under ultrasonic irradiation. X-ray powder diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were applied for confirmation of nano-structure character for the complexes. Among the complexes, zinc azide complex structure was analyzed by X-ray crystallography. This complex crystallizes as a triplet in trigonal system with space group of P31. The coordination sphere around the zinc center is well shown as a distorted trigonal bipyramidal with three nitrogen atoms from Schiff base ligand and two terminal azide nitrogen atoms attached to zinc ion. Various intermolecular interactions such as Nsbnd H⋯N, Csbnd H⋯N and Csbnd H⋯π hydrogen bonding interactions stabilize crystalline lattice so that they causes a three dimensional supramolecular structure for the complex. In vitro screening of the compounds for their antimicrobial activities showed that ZnLI2, ZnL(N3)2, ZnLCl2 and ZnL(NCS)2 were found as the most effective compound against bacteria of Bacillus subtilis, Staphylococcus aureus, Pseudomonas aeruginosa and Escherichia coli respectively. Also ZnLI2 and ZnLCl2 complexes were found more effective against two selected fungi than others. Finally, thermal behaviors of the zinc complexes showed that they are decomposed via 2-4 thermal steps from room temperature up to 1000 °C.
Quantization maps, algebra representation, and non-commutative Fourier transform for Lie groups
Guedes, Carlos; Oriti, Daniele; Raasakka, Matti
2013-08-15
The phase space given by the cotangent bundle of a Lie group appears in the context of several models for physical systems. A representation for the quantum system in terms of non-commutative functions on the (dual) Lie algebra, and a generalized notion of (non-commutative) Fourier transform, different from standard harmonic analysis, has been recently developed, and found several applications, especially in the quantum gravity literature. We show that this algebra representation can be defined on the sole basis of a quantization map of the classical Poisson algebra, and identify the conditions for its existence. In particular, the corresponding non-commutative star-product carried by this representation is obtained directly from the quantization map via deformation quantization. We then clarify under which conditions a unitary intertwiner between such algebra representation and the usual group representation can be constructed giving rise to the non-commutative plane waves and consequently, the non-commutative Fourier transform. The compact groups U(1) and SU(2) are considered for different choices of quantization maps, such as the symmetric and the Duflo map, and we exhibit the corresponding star-products, algebra representations, and non-commutative plane waves.
2013-01-01
Background The molecular phylogenetic relationships and population structure of the species of the Anopheles triannulatus complex: Anopheles triannulatus s.s., Anopheles halophylus and the putative species Anopheles triannulatus C were investigated. Methods The mitochondrial COI gene, the nuclear white gene and rDNA ITS2 of samples that include the known geographic distribution of these taxa were analyzed. Phylogenetic analyses were performed using Bayesian inference, Maximum parsimony and Maximum likelihood approaches. Results Each data set analyzed septely yielded a different topology but none provided evidence for the seption of An. halophylus and An. triannulatus C, consistent with the hypothesis that the two are undergoing incipient speciation. The phylogenetic analyses of the white gene found three main clades, whereas the statistical parsimony network detected only a single metapopulation of Anopheles triannulatus s.l. Seven COI lineages were detected by phylogenetic and network analysis. In contrast, the network, but not the phylogenetic analyses, strongly supported three ITS2 groups. Combined data analyses provided the best resolution of the trees, with two major clades, Amazonian (clade I) and trans-Andean + Amazon Delta (clade II). Clade I consists of multiple subclades: An. halophylus + An. triannulatus C; trans-Andean Venezuela; central Amazonia + central Bolivia; Atlantic coastal lowland; and Amazon delta. Clade II includes three subclades: Panama; cis-Andean Colombia; and cis-Venezuela. The Amazon delta specimens are in both clades, likely indicating local sympatry. Spatial and molecular variance analyses detected nine groups, corroborating some of subclades obtained in the combined data analysis. Conclusion Combination of the three molecular markers provided the best resolution for differentiation within An. triannulatus s.s. and An. halophylus and C. The latest two species seem to be very closely related and the analyses performed were
Zech, Reinhard; Kiontke, Stephan; Mueller, Uwe; Oeckinghaus, Andrea; Kümmel, Daniel
2016-09-16
Tuberous sclerosis complex (TSC) is caused by mutations in the TSC1 and TSC2 tumor suppressor genes. The gene products hamartin and tuberin form the TSC complex that acts as GTPase-activating protein for Rheb and negatively regulates the mammalian target of rapamycin complex 1 (mTORC1). Tuberin contains a RapGAP homology domain responsible for inactivation of Rheb, but functions of other protein domains remain elusive. Here we show that the TSC2 N terminus interacts with the TSC1 C terminus to mediate complex formation. The structure of the TSC2 N-terminal domain from Chaetomium thermophilum and a homology model of the human tuberin N terminus are presented. We characterize the molecular requirements for TSC1-TSC2 interactions and analyze pathological point mutations in tuberin. Many mutations are structural and produce improperly folded protein, explaining their effect in pathology, but we identify one point mutant that abrogates complex formation without affecting protein structure. We provide the first structural information on TSC2/tuberin with novel insight into the molecular function.
Epidemic spreading on complex networks with community structures
NASA Astrophysics Data System (ADS)
Stegehuis, Clara; van der Hofstad, Remco; van Leeuwaarden, Johan S. H.
2016-07-01
Many real-world networks display a community structure. We study two random graph models that create a network with similar community structure as a given network. One model preserves the exact community structure of the original network, while the other model only preserves the set of communities and the vertex degrees. These models show that community structure is an important determinant of the behavior of percolation processes on networks, such as information diffusion or virus spreading: the community structure can both enforce as well as inhibit diffusion processes. Our models further show that it is the mesoscopic set of communities that matters. The exact internal structures of communities barely influence the behavior of percolation processes across networks. This insensitivity is likely due to the relative denseness of the communities.
Inherent structure length in metallic glasses: Simplicity behind complexity
Wu, Yuan; Wang, Hui; Cheng, Yongqiang; Liu, Xiongjun; Hui, Xidong; Nieh, Taigang; Wang, Yandong; Lu, Zhaoping
2015-08-06
One of the central themes in materials science is the structure-property relationship. In conventional crystalline metals, their mechanical behaviour is often dictated by well-defined structural defects such as dislocations, impurities, and twins. However, the structure-property relationship in amorphous alloys is far from being understood, due to great difficulties in characterizing and describing the disordered atomic-level structure. Here, we report a universal, yet simple, correlation between the macroscopic mechanical properties (i.e., yield strength and shear modulus) and a unique characteristic structural length in metallic glasses (MGs). Lastly, our analysis indicates that this characteristic length can incorporate effects of both the inter-atomic distance and valence electron density in MGs, and result in the observed universal correlation. The current findings shed lights on the basic understanding of mechanical properties of MGs from their disordered atomic structures.
Inherent structure length in metallic glasses: Simplicity behind complexity
Wu, Yuan; Wang, Hui; Cheng, Yongqiang; Liu, Xiongjun; Hui, Xidong; Nieh, Taigang; Wang, Yandong; Lu, Zhaoping
2015-08-06
One of the central themes in materials science is the structure-property relationship. In conventional crystalline metals, their mechanical behaviour is often dictated by well-defined structural defects such as dislocations, impurities, and twins. However, the structure-property relationship in amorphous alloys is far from being understood, due to great difficulties in characterizing and describing the disordered atomic-level structure. Here, we report a universal, yet simple, correlation between the macroscopic mechanical properties (i.e., yield strength and shear modulus) and a unique characteristic structural length in metallic glasses (MGs). Lastly, our analysis indicates that this characteristic length can incorporate effects of both the inter-atomicmore » distance and valence electron density in MGs, and result in the observed universal correlation. The current findings shed lights on the basic understanding of mechanical properties of MGs from their disordered atomic structures.« less
Epidemic spreading on complex networks with community structures
Stegehuis, Clara; van der Hofstad, Remco; van Leeuwaarden, Johan S. H.
2016-01-01
Many real-world networks display a community structure. We study two random graph models that create a network with similar community structure as a given network. One model preserves the exact community structure of the original network, while the other model only preserves the set of communities and the vertex degrees. These models show that community structure is an important determinant of the behavior of percolation processes on networks, such as information diffusion or virus spreading: the community structure can both enforce as well as inhibit diffusion processes. Our models further show that it is the mesoscopic set of communities that matters. The exact internal structures of communities barely influence the behavior of percolation processes across networks. This insensitivity is likely due to the relative denseness of the communities. PMID:27440176
Epidemic spreading on complex networks with community structures.
Stegehuis, Clara; van der Hofstad, Remco; van Leeuwaarden, Johan S H
2016-01-01
Many real-world networks display a community structure. We study two random graph models that create a network with similar community structure as a given network. One model preserves the exact community structure of the original network, while the other model only preserves the set of communities and the vertex degrees. These models show that community structure is an important determinant of the behavior of percolation processes on networks, such as information diffusion or virus spreading: the community structure can both enforce as well as inhibit diffusion processes. Our models further show that it is the mesoscopic set of communities that matters. The exact internal structures of communities barely influence the behavior of percolation processes across networks. This insensitivity is likely due to the relative denseness of the communities. PMID:27440176
Euler polynomials and identities for non-commutative operators
NASA Astrophysics Data System (ADS)
De Angelis, Valerio; Vignat, Christophe
2015-12-01
Three kinds of identities involving non-commutating operators and Euler and Bernoulli polynomials are studied. The first identity, as given by Bender and Bettencourt [Phys. Rev. D 54(12), 7710-7723 (1996)], expresses the nested commutator of the Hamiltonian and momentum operators as the commutator of the momentum and the shifted Euler polynomial of the Hamiltonian. The second one, by Pain [J. Phys. A: Math. Theor. 46, 035304 (2013)], links the commutators and anti-commutators of the monomials of the position and momentum operators. The third appears in a work by Figuieira de Morisson and Fring [J. Phys. A: Math. Gen. 39, 9269 (2006)] in the context of non-Hermitian Hamiltonian systems. In each case, we provide several proofs and extensions of these identities that highlight the role of Euler and Bernoulli polynomials.
On gauge invariance of noncommutative Chern-Simons theories
NASA Astrophysics Data System (ADS)
Chen, Guang-Hong; Wu, Yong-Shi
2002-05-01
Motivated by possible applications to condensed matter systems, in this paper we construct U( N) noncommutative Chern-Simons (NCCS) action for a disc and for a double-layer geometry, respectively. In both cases, gauge invariance severely constrains the form of the NCCS action. In the first case, it is necessary to introduce a group-valued boson field with a nonlocal chiral boundary action, whose gauge variation cancels that of the bulk action. In the second case, the coefficient matrix K in the double U( N) NCCS action is restricted to be of the form K=k 1 1 1 1 with integer k. We suggest that this double NCCS theory with U(1) gauge group describes the so-called Halperin ( kkk) state in a double-layer quantum Hall system. Possible physical consequences are addressed.
Noncommutative-geometry model for closed bosonic strings
NASA Technical Reports Server (NTRS)
Sen, Siddhartha; Holman, R.
1987-01-01
It is shown how Witten's (1986) noncommutative geometry may be extended to describe the closed bosonic string. For closed strings, an explicit representation is provided of the integral operator needed to construct an action and of an associative product on string fields. The proper choice of the action of the integral operator and the associative product in order to give rise to a reasonable theory is explained, and the consequences of such a choice are discussed. It is shown that the ghost numbers of the operator and associative product can be chosen arbitrarily for both open and closed strings, and that this construct can be used as an action for interacting closed bosonic strings.
Measurement of noncommuting spin components using spin-orbit interaction
Sokolovski, D.; Sherman, E. Ya.
2011-09-15
We propose a possible experiment aimed at a joint measurement of two noncommuting spin-1/2 components and analyze its physical meaning. We demonstrate that switching of a strong spin-orbit interaction, e.g., in a solid-state or a cold-atom system, for a short time interval simulates a simultaneous von Neumann measurement of the operators {sigma}{sub x} and {sigma}{sub y}. With the spin dynamics mapped onto the quantum coordinate-space motion, such an experiment determines averages of {sigma}{sub x} and {sigma}{sub y} over the duration of the measurement, however short the latter may be. These time averages, unlike the instantaneous values of {sigma}{sub x} and {sigma}{sub y}, may be evaluated simultaneously to an arbitrary accuracy.
Relativistic differential-difference momentum operators and noncommutative differential calculus
Mir-Kasimov, R. M.
2013-09-15
The relativistic kinetic momentum operators are introduced in the framework of the Quantum Mechanics (QM) in the Relativistic Configuration Space (RCS). These operators correspond to the half of the non-Euclidean distance in the Lobachevsky momentum space. In terms of kinetic momentum operators the relativistic kinetic energy is separated as the independent term of the total Hamiltonian. This relativistic kinetic energy term is not distinguishing in form from its nonrelativistic counterpart. The role of the plane wave (wave function of the motion with definite value of momentum and energy) plays the generating function for the matrix elements of the unitary irreps of Lorentz group (generalized Jacobi polynomials). The kinetic momentum operators are the interior derivatives in the framework of the noncommutative differential calculus over the commutative algebra generated by the coordinate functions over the RCS.
Constraining the noncommutative spectral action via astrophysical observations.
Nelson, William; Ochoa, Joseph; Sakellariadou, Mairi
2010-09-01
The noncommutative spectral action extends our familiar notion of commutative spaces, using the data encoded in a spectral triple on an almost commutative space. Varying a rather simple action, one can derive all of the standard model of particle physics in this setting, in addition to a modified version of Einstein-Hilbert gravity. In this Letter we use observations of pulsar timings, assuming that no deviation from general relativity has been observed, to constrain the gravitational sector of this theory. While the bounds on the coupling constants remain rather weak, they are comparable to existing bounds on deviations from general relativity in other settings and are likely to be further constrained by future observations.
Triple neutral gauge boson couplings in noncommutative Standard Model
NASA Astrophysics Data System (ADS)
Deshpande, N. G.; He, Xiao-Gang
2002-05-01
It has been shown recently that the triple neutral gauge boson couplings are not uniquely determined in noncommutative extension of the Standard Model (NCSM). Depending on specific schemes used, the couplings are different and may even be zero. To distinguish different realizations of the NCSM, additional information either from theoretical or experimental considerations is needed. In this Letter we show that these couplings can be uniquely determined from considerations of unification of electroweak and strong interactions. Using SU(5) as the underlying theory and integrating out the heavy degrees of freedom, we obtain unique non-zero new triple γγγ, γγZ, γZZ, ZZZ, γGG, ZGG and GGG couplings at the leading order in the NCSM. We also briefly discuss experimental implications.
NASA Astrophysics Data System (ADS)
Courtney, Owen T.; Bianconi, Ginestra
2016-06-01
Simplicial complexes are generalized network structures able to encode interactions occurring between more than two nodes. Simplicial complexes describe a large variety of complex interacting systems ranging from brain networks to social and collaboration networks. Here we characterize the structure of simplicial complexes using their generalized degrees that capture fundamental properties of one, two, three, or more linked nodes. Moreover, we introduce the configuration model and the canonical ensemble of simplicial complexes, enforcing, respectively, the sequence of generalized degrees of the nodes and the sequence of the expected generalized degrees of the nodes. We evaluate the entropy of these ensembles, finding the asymptotic expression for the number of simplicial complexes in the configuration model. We provide the algorithms for the construction of simplicial complexes belonging to the configuration model and the canonical ensemble of simplicial complexes. We give an expression for the structural cutoff of simplicial complexes that for simplicial complexes of dimension d =1 reduces to the structural cutoff of simple networks. Finally, we provide a numerical analysis of the natural correlations emerging in the configuration model of simplicial complexes without structural cutoff.
Social scale and structural complexity in human languages
Nettle, Daniel
2012-01-01
The complexity of different components of the grammars of human languages can be quantified. For example, languages vary greatly in the size of their phonological inventories, and in the degree to which they make use of inflectional morphology. Recent studies have shown that there are relationships between these types of grammatical complexity and the number of speakers a language has. Languages spoken by large populations have been found to have larger phonological inventories, but simpler morphology, than languages spoken by small populations. The results require further investigation, and, most importantly, the mechanism whereby the social context of learning and use affects the grammatical evolution of a language needs elucidation. PMID:22641821
Coulomb problem in non-commutative quantum mechanics
Galikova, Veronika; Presnajder, Peter
2013-05-15
The aim of this paper is to find out how it would be possible for space non-commutativity (NC) to alter the quantum mechanics (QM) solution of the Coulomb problem. The NC parameter {lambda} is to be regarded as a measure of the non-commutativity - setting {lambda}= 0 which means a return to the standard quantum mechanics. As the very first step a rotationally invariant NC space R{sub {lambda}}{sup 3}, an analog of the Coulomb problem configuration space (R{sup 3} with the origin excluded) is introduced. R{sub {lambda}}{sup 3} is generated by NC coordinates realized as operators acting in an auxiliary (Fock) space F. The properly weighted Hilbert-Schmidt operators in F form H{sub {lambda}}, a NC analog of the Hilbert space of the wave functions. We will refer to them as 'wave functions' also in the NC case. The definition of a NC analog of the hamiltonian as a hermitian operator in H{sub {lambda}} is one of the key parts of this paper. The resulting problem is exactly solvable. The full solution is provided, including formulas for the bound states for E < 0 and low-energy scattering for E > 0 (both containing NC corrections analytic in {lambda}) and also formulas for high-energy scattering and unexpected bound states at ultra-high energy (both containing NC corrections singular in {lambda}). All the NC contributions to the known QM solutions either vanish or disappear in the limit {lambda}{yields} 0.
Improved wax mold technique forms complex passages in solid structures
NASA Technical Reports Server (NTRS)
Hellbaum, R. F.; Page, A. D.; Phillips, A. R.
1971-01-01
Low-cost fabricating technique produces minute, complex air passages in fluidic devices. Air jet interactions in these function as electronic and electromechanical control systems. Wax cores are fabricated without distortion by two-wax process using nonsoluble pattern-wax and water-soluble wax. Significant steps in fabrication process are discussed.
Using Plants to Explore the Nature & Structural Complexity of Life
ERIC Educational Resources Information Center
Howard, Ava R.
2014-01-01
Use of real specimens brings the study of biology to life. This activity brings easily acquired plant specimens into the classroom to tackle common alternative conceptions regarding life, size, complexity, the nature of science, and plants as multicellular organisms. The activity occurs after a discussion of the characteristics of life and engages…
Cationic Dihydrogen/Dihydride Complexes of Osmium: Structure and Dynamics
Egbert, Jonathan D.; Bullock, R. Morris; Heinekey, D. M.
2007-03-22
Reaction of Cp*Os(CO)2Cl with (Et3Si )(BArF4) under hydrogen gas affords the cationic hydrogen complex [Cp*Os(CO)2(H2)][BArF4] (1), (Cp* = C5Me5; ArF = C6F5). When this reaction is carried out with HD gas, complex 1-d1 results, with JHD = 24.5 Hz. When solutions of complex 1 are monitored by 1H NMR spectroscopy over several days, the gradual formation of a trans dihydride species is observed. Similarly, reaction of CpOs(dppm)Br with NaBArF*4 (ArF* = 3,5-(CF3)2C6H3) under hydrogen affords the cationic dihydride complex [CpOs(dppm)H2]BArF*4 (2). At 295 K, complex 2 exists as a 10:1 mixture of cis and trans isomers. The 1H NMR spectrum of the cis form in the hydride region exhibits a triplet with JHP = 6.5 Hz, due to rapid exchange of the hydrogen atoms. At low temperature, static spectra of the HH'PP' spin system can be obtained, revealing quantum mechanical exchange coupling between the two hydride ligands. The observed JHH' is temperature dependent, varying from 133 Hz at 141 K to 176 Hz at 198 K. This is the first report of detectable exchange coupling between pairs of chemically equivalent hydrogen atoms. Research at the University of Washington was supported by the National Science Foundation. Research at Brookhaven National Laboratory was carried out under contract DE-AC02-98CH10886 with the U.S. Department of Energy and was supported by its Division of Chemical Sciences, Office of Basic Energy Sciences. Research at Pacific Northwest National Laboratory (PNNL) was funded by LDRD funds. PNNL is operated by Battelle for the US Department of Energy.
Double bi-material cantilever structures for complex surface plasmon modulation.
Song, Eui-Young; Cho, Jaebum; Kim, Hwi; Choi, Woo Young; Lee, Byoungho
2015-03-01
A complex modulation structure of surface plasmon polaritons using double bi-material cantilevers is proposed. It is shown with numerical analysis that the thermally controlled mechanical actuation of double bi-material cantilevers can modulate the amplitude and phase of surface plasmon polaritons across a full complex modulation range independently and simultaneously. The complex modulation structures designed for visible wavelengths are presented and their multi-wavelength integration is discussed.
Structure of local interactions in complex financial dynamics
Jiang, X. F.; Chen, T. T.; Zheng, B.
2014-01-01
With the network methods and random matrix theory, we investigate the interaction structure of communities in financial markets. In particular, based on the random matrix decomposition, we clarify that the local interactions between the business sectors (subsectors) are mainly contained in the sector mode. In the sector mode, the average correlation inside the sectors is positive, while that between the sectors is negative. Further, we explore the time evolution of the interaction structure of the business sectors, and observe that the local interaction structure changes dramatically during a financial bubble or crisis. PMID:24936906
Rethinking Connes' approach to the standard model of particle physics via non-commutative geometry
NASA Astrophysics Data System (ADS)
Boyle, Latham; Farnsworth, Shane
2015-04-01
Connes' non-commutative geometry (NCG) is a generalization of Riemannian geometry that is particularly apt for expressing the standard model of particle physics coupled to Einstein gravity. Recently, we suggested a reformulation of this framework that is: (i) simpler and more unified in its axioms, and (ii) allows the Lagrangian for the standard model of particle physics (coupled to Einstein gravity) to be specified in a way that is tighter and more explanatory than the traditional algorithm based on effective field theory. Here we explain how this same reformulation yields a new perspective on the symmetries of a given NCG. Applying this perspective to the NCG traditionally used to describe the standard model we find, instead, an extension of the standard model by an extra U(1) B - L gauge symmetry, and a single extra complex scalar field σ, which is a singlet under SU(3)C × SU(2)L × U(1)Y , but has B - L = 2 . This field has cosmological implications, and offers a new solution to the discrepancy between the observed Higgs mass and the NCG prediction. We acknowledge support from an NSERC Discovery Grant.
Rethinking Connes’ Approach to the Standard Model of Particle Physics Via Non-Commutative Geometry
NASA Astrophysics Data System (ADS)
Farnsworth, Shane; Boyle, Latham
2015-02-01
Connes’ non-commutative geometry (NCG) is a generalization of Riemannian geometry that is particularly apt for expressing the standard model of particle physics coupled to Einstein gravity. In a previous paper, we suggested a reformulation of this framework that is: (i) simpler and more unified in its axioms, and (ii) allows the Lagrangian for the standard model of particle physics (coupled to Einstein gravity) to be specified in a way that is tighter and more explanatory than the traditional algorithm based on effective field theory. Here we explain how this same reformulation yields a new perspective on the symmetries of a given NCG. Applying this perspective to the NCG traditionally used to describe the standard model we find, instead, an extension of the standard model by an extra U{{(1)}B-L} gauge symmetry, and a single extra complex scalar field σ, which is a singlet under SU{{(3)}C}× SU{{(2)}L}× U{{(1)}Y}, but has B-L=2. This field has cosmological implications, and offers a new solution to the discrepancy between the observed Higgs mass and the NCG prediction.
Martins, R. A.
2007-08-15
The recent extension of the standard model to include massive neutrinos in the framework of noncommutative geometry and the spectral action principle involves new scalar fields and their interactions with the usual complex scalar doublet. After ensuring that they bring no unphysical consequences, we address the question of how these fields affect the physics predicted in the Weinberg-Salam theory, particularly in the context of the electroweak phase transition. Applying the Dolan-Jackiw procedure, we calculate the finite temperature corrections, and find that the phase transition is first order. The new scalar interactions significantly improve the stability of the electroweak Z string, through the 'bag' phenomenon described by Vachaspati and Watkins ['Bound states can stabilize electroweak strings', Phys. Lett. B 318, 163-168 (1993)]. (Recently, cosmic strings have climbed back into interest due to a new evidence.) Sourced by static embedded strings, an internal space analogy of Cartan's torsion is drawn, and a possible Higgs-force-like 'gravitational' effect of this nonpropagating torsion on the fermion masses is described. We also check that the field generating the Majorana mass for the {nu}{sub R} is nonzero in the physical vacuum.
Kim, Hidong; Lipscomb, W.N. )
1990-06-12
O-(((1R)-((N-(Phenylmethoxycarbonyl)-L-alanyl)amino)ethyl)hydroxyphosphinyl)-L-3-phenyllacetate (ZZA{sup P}(O)F), an analogue of (benzyloxycarbonyl)-Ala-Ala-Phe or (benzyloxycarbonyl)-Ala-Ala-phenyllactate, binds to carboxypeptidase A with great affinity. Similar phosphonates have been shown to be transition-state analogues of the CPA-catalyzed hydrolysis. In the present study, the structure of the complex of phosphonate with carboxypeptidase A has been determined by X-ray crystallography to a resolution of 2.0 {angstrom}. The structure of the complex was solved by molecular replacement. Refinement of the structure against 20,776 unique reflections between 10.0 and 2.0 {angstrom} yields a crystallographic residual of 0.193, including 140 water molecules. The two phosphinyl oxygens of the inhibitor bind to the active-site zinc at 2.2 {angstrom} on the electrophilic (Arg-127) side and 3.1 {angstrom} on the nucleophilic (Glu-270) side. Various features of the binding mode of this phosphonate inhibitor are consistent with the hypothesis that carboxypeptidase A catalyzed hydrolysis proceeds through a general-base mechanism in which the carbonyl carbon of the substrate is attached by Zn-hydroxyl (or Zn-water). This complex structure is compared with previous structures of carboxypeptidase A, including the complexes with the potato inhibitor, a hydrated keto methylene substrate analogue, and a phosphonamidate inhibitor. Comparisons are also made with the complexes of thermolysin with some phosphonamidate inhibitors.
Embracing proteins: structural themes in aptamer-protein complexes.
Gelinas, Amy D; Davies, Douglas R; Janjic, Nebojsa
2016-02-01
Understanding the structural rules that govern specific, high-affinity binding characteristic of aptamer-protein interactions is important in view of the increasing use of aptamers across many applications. From the modest number of 16 aptamer-protein structures currently available, trends are emerging. The flexible phosphodiester backbone allows folding into precise three-dimensional structures using known nucleic acid motifs as scaffolds that orient specific functional groups for target recognition. Still, completely novel motifs essential for structure and function are found in modified aptamers with diversity-enhancing side chains. Aptamers and antibodies, two classes of macromolecules used as affinity reagents with entirely different backbones and composition, recognize protein epitopes of similar size and with comparably high shape complementarity. PMID:26919170
Stage structure alters how complexity affects stability of ecological networks
Rudolf, V.H.W.; Lafferty, Kevin D.
2011-01-01
Resolving how complexity affects stability of natural communities is of key importance for predicting the consequences of biodiversity loss. Central to previous stability analysis has been the assumption that the resources of a consumer are substitutable. However, during their development, most species change diets; for instance, adults often use different resources than larvae or juveniles. Here, we show that such ontogenetic niche shifts are common in real ecological networks and that consideration of these shifts can alter which species are predicted to be at risk of extinction. Furthermore, niche shifts reduce and can even reverse the otherwise stabilizing effect of complexity. This pattern arises because species with several specialized life stages appear to be generalists at the species level but act as sequential specialists that are hypersensitive to resource loss. These results suggest that natural communities are more vulnerable to biodiversity loss than indicated by previous analyses.
Structural limits for evolutive capacities in complex molecular systems.
Bergareche, A M; Ostolaza, J F
1990-01-01
The possibilities of evolution for a system with and without a code of translation from nucleic acids into proteins are evaluated. Our interest is mainly centred on the enzymatic RNA case since this molecule has, at the same time, reproductive and functional properties. After scanning the evolutive capacities of the enzymatic RNAs, including the possibility to play the role of "synthetase" which would match nucleic acids with amino acids as a transition step towards a code, we will try to show that due to their own functional limitative factors, the matching system (code) is necessary. This would be the only way to transform the formal complexity--complexity which has not entered into action before the translation process--into functional information to drive the instructive self-reproductive process. Once this stage is reached, the system could evolve without a limit.
Direct structural damping identification method using complex FRFs
NASA Astrophysics Data System (ADS)
Arora, Vikas
2015-03-01
Most of the identification methods are based only on the viscous damping model and uses modal data. In this paper, a new FRF-based direct structural damping identification method is proposed. The proposed method is a direct method and identifies structural damping matrix explicitly. As the new method is a FRF-based method, it overcomes the problem of closely spaced modes for damping identification. The accuracy of identified structural damping matrix depends upon the accuracy of finite element model. In this paper, FRF-based model updating method is used to obtain accurate mass and stiffness matrices. Thus, the procedure to obtain accurate structural damping matrix is a two-step procedure. In the first step, mass and stiffness matrices are updated and in the second step, structural damping matrix is identified using updated mass and stiffness matrices, which are obtained in the previous step. The effectiveness of the new method is demonstrated by three numerical examples and one experimental example. The numerical studies of lumped mass system, fixed-fixed beam and L-shaped frame structure are carried out. The effects of coordinate incompleteness, ill-conditioning and robustness of method under presence of noise are investigated. The proposed method is able to predict FRFs accurately for the frequency range covering the modes considered. However, beyond the considered modes, the predicted FRFs do not match the experimental FRFs. It is suggested in this work that ill-conditioning problem should be dealt by considering all the modes in the frequency range of interest. The performance of the proposed method is investigated for cases of light, medium and heavily damped structures. The numerical studies are followed by experimental case study of cantilever beam structure. The effectiveness of the proposed method is evaluated by comparing the predicted and the experimental FRFs. The results have shown that the proposed method is able to predict accurately the
Multilamellar structures of DNA complexes with cationic liposomes.
Dan, N
1997-10-01
Studies of DNA complexes with cationic liposomes are prompted by the search for nonviral DNA carriers for gene therapy. Recent experiments have identified a stable multilamellar phase in which ordered smectic layers of DNA alternate with cationic bilayers. In this paper we identify the forces governing DNA adsorption on cationic lamellae, including a membrane-induced attraction between the adsorbed DNA. Calculating the DNA interhelical spacing as a function of system composition, the model successfully explains recent surprising observations.
A graph theoretical approach for assessing bio-macromolecular complex structural stability.
Del Carpio, Carlos Adriel; Iulian Florea, Mihai; Suzuki, Ai; Tsuboi, Hideyuki; Hatakeyama, Nozomu; Endou, Akira; Takaba, Hiromitsu; Ichiishi, Eiichiro; Miyamoto, Akira
2009-11-01
Fast and proper assessment of bio macro-molecular complex structural rigidity as a measure of structural stability can be useful in systematic studies to predict molecular function, and can also enable the design of rapid scoring functions to rank automatically generated bio-molecular complexes. Based on the graph theoretical approach of Jacobs et al. [Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF (2001) Protein flexibility predictions using graph theory. Proteins: Struct Funct Genet 44:150-165] for expressing molecular flexibility, we propose a new scheme to analyze the structural stability of bio-molecular complexes. This analysis is performed in terms of the identification in interacting subunits of clusters of flappy amino acids (those constituting regions of potential internal motion) that undergo an increase in rigidity at complex formation. Gains in structural rigidity of the interacting subunits upon bio-molecular complex formation can be evaluated by expansion of the network of intra-molecular inter-atomic interactions to include inter-molecular inter-atomic interaction terms. We propose two indices for quantifying this change: one local, which can express localized (at the amino acid level) structural rigidity, the other global to express overall structural stability for the complex. The new system is validated with a series of protein complex structures reported in the protein data bank. Finally, the indices are used as scoring coefficients to rank automatically generated protein complex decoys.
Assembly and solution structure of the core retromer protein complex.
Norwood, Suzanne J; Shaw, Daniel J; Cowieson, Nathan P; Owen, David J; Teasdale, Rohan D; Collins, Brett M
2011-01-01
Retromer is a peripheral membrane protein complex that has pleiotropic roles in endosomal membrane trafficking. The core of retromer possesses three subunits, VPS35, VPS29 and VPS26, that play different roles in binding to cargo, regulatory proteins and complex stabilization. We have performed an investigation of the thermodynamics of core retromer assembly using isothermal titration calorimetry (ITC) demonstrating that VPS35 acts as the central subunit to which VPS29 and VPS26 bind independently. Furthermore, we confirm that the conserved PRLYL motif of the large VPS35 subunit is critical for direct VPS26 interaction. Heat capacity measurements of VPS29 and VPS26 binding to VPS35 indicate extensive binding interfaces and suggest conformational alterations in VPS29 or VPS35 upon complex formation. Solution studies of the retromer core using small-angle X-ray scattering allow us to propose a model whereby VPS35 forms an extended platform with VPS29 and VPS26 bound at distal ends, with the potential for forming dimeric assemblies. PMID:20875039
Actinide-specific complexing agents: their structural and solution chemistry
Raymond, K.N.; Freeman, G.E.; Kappel, M.J.
1983-07-01
The synthesis of a series of tetracatecholate ligands designed to be specific for Pu(IV) and other actinide(IV) ions has been achieved. Although these compounds are very effective as in vivo plutonium removal agents, potentiometric and voltammetric data indicate that at neutral pH full complexation of the Pu(IV) ion by all four catecholate groups does not occur. Spectroscopic results indicate that the tetracatecholates, 3,4,3-LICAMS and 3,4,3-LICAMC, complex Am(III). The Am(IV)/(III)-catecholate couple (where catecholate = 3,4,3-LICAMS or 3,4,3-LICAMC) is not observed, but may not be observable due to the large currents associated with ligand oxidation. However, within the potential range where ligand oxidation does not occur, these experiments indicate that the reduction potential of free Am(IV)/(III) is probably greater than or equal to + 2.6 V vs NHE or higher. Proof of the complexation of americium in the trivalent oxidation state by 3,4,3-LICAMS and 3,4,3-LICAMC elimates the possibility of tetracatholates stabilizing Am(IV) in vivo.
Time-dependent Aharonov-Bohm effect on the noncommutative space
NASA Astrophysics Data System (ADS)
Ma, Kai; Wang, Jian-Hua; Yang, Huan-Xiong
2016-08-01
We study the time-dependent Aharonov-Bohm effect on the noncommutative space. Because there is no net Aharonov-Bohm phase shift in the time-dependent case on the commutative space, therefore, a tiny deviation from zero indicates new physics. Based on the Seiberg-Witten map we obtain the gauge invariant and Lorentz covariant Aharonov-Bohm phase shift in general case on noncommutative space. We find there are two kinds of contribution: momentum-dependent and momentum-independent corrections. For the momentum-dependent correction, there is a cancellation between the magnetic and electric phase shifts, just like the case on the commutative space. However, there is a non-trivial contribution in the momentum-independent correction. This is true for both the time-independent and time-dependent Aharonov-Bohm effects on the noncommutative space. However, for the time-dependent Aharonov-Bohm effect, there is no overwhelming background which exists in the time-independent Aharonov-Bohm effect on both commutative and noncommutative space. Therefore, the time-dependent Aharonov-Bohm can be sensitive to the spatial noncommutativity. The net correction is proportional to the product of the magnetic fluxes through the fundamental area represented by the noncommutative parameter θ, and through the surface enclosed by the trajectory of charged particle. More interestingly, there is an anti-collinear relation between the logarithms of the magnetic field B and the averaged flux Φ / N (N is the number of fringes shifted). This nontrivial relation can also provide a way to test the spatial noncommutativity. For BΦ / N ∼ 1, our estimation on the experimental sensitivity shows that it can reach the 10 GeV scale. This sensitivity can be enhanced by using stronger magnetic field strength, larger magnetic flux, as well as higher experimental precision on the phase shift.
Octameric structure of Staphylococcus aureus enolase in complex with phosphoenolpyruvate
Wu, Yunfei; Wang, Chengliang; Lin, Shenglong; Wu, Minhao; Han, Lu; Tian, Changlin; Zhang, Xuan; Zang, Jianye
2015-01-01
Staphylococcus aureus is a Gram-positive bacterium with strong pathogenicity that causes a wide range of infections and diseases. Enolase is an evolutionarily conserved enzyme that plays a key role in energy production through glycolysis. Additionally, enolase is located on the surface of S. aureus and is involved in processes leading to infection. Here, crystal structures of Sa_enolase with and without bound phosphoenolpyruvate (PEP) are presented at 1.6 and 2.45 Å resolution, respectively. The structure reveals an octameric arrangement; however, both dimeric and octameric conformations were observed in solution. Furthermore, enzyme-activity assays show that only the octameric variant is catalytically active. Biochemical and structural studies indicate that the octameric form of Sa_enolase is enzymatically active in vitro and likely also in vivo, while the dimeric form is catalytically inactive and may be involved in other biological processes. PMID:26627653
Complex modular structure of large-scale brain networks
NASA Astrophysics Data System (ADS)
Valencia, M.; Pastor, M. A.; Fernández-Seara, M. A.; Artieda, J.; Martinerie, J.; Chavez, M.
2009-06-01
Modular structure is ubiquitous among real-world networks from related proteins to social groups. Here we analyze the modular organization of brain networks at a large scale (voxel level) extracted from functional magnetic resonance imaging signals. By using a random-walk-based method, we unveil the modularity of brain webs and show modules with a spatial distribution that matches anatomical structures with functional significance. The functional role of each node in the network is studied by analyzing its patterns of inter- and intramodular connections. Results suggest that the modular architecture constitutes the structural basis for the coexistence of functional integration of distant and specialized brain areas during normal brain activities at rest.
Tuning structure of oppositely charged nanoparticle and protein complexes
Kumar, Sugam Aswal, V. K.; Callow, P.
2014-04-24
Small-angle neutron scattering (SANS) has been used to probe the structures of anionic silica nanoparticles (LS30) and cationic lyszyme protein (M.W. 14.7kD, I.P. ∼ 11.4) by tuning their interaction through the pH variation. The protein adsorption on nanoparticles is found to be increasing with pH and determined by the electrostatic attraction between two components as well as repulsion between protein molecules. We show the strong electrostatic attraction between nanoparticles and protein molecules leads to protein-mediated aggregation of nanoparticles which are characterized by fractal structures. At pH 5, the protein adsorption gives rise to nanoparticle aggregation having surface fractal morphology with close packing of nanoparticles. The surface fractals transform to open structures of mass fractal morphology at higher pH (7 and 9) on approaching isoelectric point (I.P.)
T-shaped platinum boryl complexes: synthesis and structure.
Braunschweig, Holger; Radacki, Krzysztof; Uttinger, Katharina
2008-01-01
A series of cationic T-shaped 14-electron boryl complexes of the type trans-[(Cy3P)2Pt(B(X)X')]+ (X=Br; X'=ortho-tolyl, tBu, NMe2, piperidyl, Br; XX'=(NMe2)2, catecholato) were synthesized by halide abstraction from trans-[(Cy3P)2Pt(Br)(B(X)X')] (Cy=cyclohexyl) with Na[BArf 4] (Arf=3,5-(CF3)2C6H3), K[B(C6F5)4], or Na[BPh4]. X-ray diffraction studies were performed on all compounds, revealing a subtle correlation between the trans-influence of the boryl moiety and the Pt-H and Pt-C separations. However, no notable agostic C-H interaction with the platinum center was detected. trans-[(Cy3P)2Pt(BCat)]+ (Cat=catecholato), the complex with the shortest Pt-H and Pt-C distances, was treated with Lewis bases (L), forming compounds of the type trans-[(Cy3P)2Pt(L)(BCat)]+, thus proving a decisive influence of the degree of trans-influence exerted by the boryl ligands on the chemical reactivity of the title complexes. Another point that was investigated and clarified is the different behavior of trans-[(Cy3P)2Pt(Br)(B(Br)Mes)] (Mes=mesityl) towards K[B(C6F5)4] with formation of the borylene species trans-[(Cy3P)2Pt(Br)(BMes)]+. PMID:18663715
Structural complexity and the time course of grammatical development.
Frank, R
1998-06-01
One traditional view of the time course of language acquisition holds that a child's difficulties in learning her language are due to general processing, memory or conceptual limitations. As the child's cognitive capacities expand, so do her abilities to use her already-acquired grammar or to recognize additional properties of her soon-to-be native language. Recent work in the study of child language, however, has discovered the existence of a number of characteristic stages, transitions between which are best described in the terms of linguistic theory proper. These stages are surprising under a view of language acquisition according to which developmental delay derives from general cognitive limitations, which cannot characterize difficulties explicable only in language-specific terms. At the same time, current linguistic theories so severely restrict the variation among possible human grammars that there remains little reason why there should be any learning problem at all or characteristic developmental stages. In this paper, I propose that these two views can be reconciled. I show that children's difficulties with a wide range of syntactic constructions, which are indeed best defined in linguistic terms, should nonetheless be derived from limitations on the child's ability to deal with processing load and formal representational complexity. I suggest however that this can be done only in the context of a particular view of syntactic representation, one which is articulated in the terms of the formal system of tree adjoining grammar (TAG). I demonstrate how precisely those difficulties that children experience in the acquisition of relative clauses, adjectival modification, control constructions, raising, wh-questions and the obligatoriness of finite inflection can be traced to the complexity associated with one of the TAG combinatory operations, adjoining. This proposal relates this apparently disparate set of constructions in a novel way and provides us with
Reduced complexity structural modeling for automated airframe synthesis
NASA Technical Reports Server (NTRS)
Hajela, Prabhat
1987-01-01
A procedure is developed for the optimum sizing of wing structures based on representing the built-up finite element assembly of the structure by equivalent beam models. The reduced-order beam models are computationally less demanding in an optimum design environment which dictates repetitive analysis of several trial designs. The design procedure is implemented in a computer program requiring geometry and loading information to create the wing finite element model and its equivalent beam model, and providing a rapid estimate of the optimum weight obtained from a fully stressed design approach applied to the beam. The synthesis procedure is demonstrated for representative conventional-cantilever and joined wing configurations.
Pinning controllability of complex networks with community structure.
Miao, Qingying; Tang, Yang; Kurths, Jürgen; Fang, Jian-an; Wong, W K
2013-09-01
In this paper, we study the controllability of networks with different numbers of communities and various strengths of community structure. By means of simulations, we show that the degree descending pinning scheme performs best among several considered pinning schemes under a small number of pinned nodes, while the degree ascending pinning scheme is becoming more powerful by increasing the number of pinned nodes. It is found that increasing the number of communities or reducing the strength of community structure is beneficial for the enhancement of the controllability. Moreover, it is revealed that the pinning scheme with evenly distributed pinned nodes among communities outperforms other kinds of considered pinning schemes. PMID:24089950
Liao, D.-I.; Basarab, G.S.; Gatenby, A.A.; Valent, B.; Jordan, D.B.
2010-03-08
Trihydroxynaphthalene reductase catalyzes two intermediate steps in the fungal melanin biosynthetic pathway. The enzyme, a typical short-chain dehydrogenase, is the biochemical target of three commercial fungicides. The fungicides bind preferentially to the NADPH form of the enzyme. Three X-ray structures of the Magnaporthe grisea enzyme complexed with NADPH and two commercial and one experimental fungicide were determined at 1.7 {angstrom} (pyroquilon), 2.0 {angstrom} (2,3-dihydro-4-nitro-1H-inden-1-one, 1), and 2.1 {angstrom} (phthalide) resolutions. The chemically distinct inhibitors occupy similar space within the enzyme's active site. The three inhibitors share hydrogen bonds with the side chain hydroxyls of Ser-164 and Tyr-178 via a carbonyl oxygen (pyroquilon and 1) or via a carbonyl oxygen and a ring oxygen (phthalide). Active site residues occupy similar positions among the three structures. A buried water molecule that is hydrogen bonded to the NZ nitrogen of Lys-182 in each of the three structures likely serves to stabilize the cationic form of the residue for participation in catalysis. The pro S hydrogen of NADPH (which is transferred as a hydride to the enzyme's naphthol substrates) is directed toward the carbonyl carbon of the inhibitors that mimic an intermediate along the reaction coordinate. Modeling tetrahydroxynaphthalene and trihydroxynaphthalene in the active site shows steric and electrostatic repulsion between the extra hydroxyl oxygen of the former substrate and the sulfur atom of Met-283 (the C-terminal residue), which accounts, in part, for the 4-fold greater substrate specificity for trihydroxynaphthalene over tetrahydroxynaphthalene.
1990-01-01
Nuclear pore complexes (NPCs) prepared from Xenopus laevis oocyte nuclear envelopes were studied in "intact" form (i.e., unexposed to detergent) and after detergent treatment by a combination of conventional transmission electron microscopy (CTEM) and quantitative scanning transmission electron microscopy (STEM). In correlation- averaged CTEM pictures of negatively stained intact NPCs and of distinct NPC components (i.e., "rings," "spoke" complexes, and "plug- spoke" complexes), several fine structural features arranged with octagonal symmetry about a central axis could reproducibly be identified. STEM micrographs of unstained/freeze-dried intact NPCs as well as of their components yielded comparable but less distinct features. Mass determination by STEM revealed the following molecular masses: intact NPC with plug, 124 +/- 11 MD; intact NPC without plug, 112 +/- 11 MD; heavy ring, 32 +/- 5 MD; light ring, 21 +/- 4 MD; plug- spoke complex, 66 +/- 8 MD; and spoke complex, 52 +/- 3 MD. Based on these combined CTEM and STEM data, a three-dimensional model of the NPC exhibiting eightfold centrosymmetry about an axis perpendicular to the plane of the nuclear envelope but asymmetric along this axis is proposed. This structural polarity of the NPC across the nuclear envelope is in accord with its well-documented functional polarity facilitating mediated nucleocytoplasmic exchange of molecules and particles. PMID:2324201
Mousso structure: A deeply eroded, medium-sized, complex impact crater in northern Chad?
NASA Astrophysics Data System (ADS)
Buchner, Elmar; Schmieder, Martin
2007-10-01
The Mousso structure, a complex, ˜3.8 km circular structure centred on 17°58' N/19°53' E and located near the Mousso oasis, Borkou-Ennedi-Tibesti, northern Chad, displays structural features typical for complex impact structures: a circular rim with concentric faults, an annular basin, and a central peak. Remote sensing investigations based on Landsat-7 Enhanced Thematic Mapper Plus (ETM+) and Shuttle Radar Topographic Mission (SRTM) data reveal a specific morphological-structural resemblance of the complex central peak of the Mousso structure to the central uplift of the Spider impact structure, Western Australia, and, to some degree, to the central uplifts of the Upheaval Dome, Sierra Madera, and Gosses Bluff impact structures. This is consistent with the layered sedimentary rocks associated with all of these structures. No endogenic geological processes such as magmatism, diapirism, karst dissolution, and glacial or fluvial erosion can conclusively explain the formation of the Mousso structure within a large area of flat-lying early Paleozoic sandstones. Thus, this paper proposes that the Mousso structure might represent a deeply eroded, medium-sized, complex impact structure. As field investigations are currently impossible due to the civil war in Chad, the search for shock-metamorphic effects in rocks of the Mousso structure remains outstanding.
Cascading failures in complex networks with community structure
NASA Astrophysics Data System (ADS)
Lin, Guoqiang; di, Zengru; Fan, Ying
2014-12-01
Much empirical evidence shows that when attacked with cascading failures, scale-free or even random networks tend to collapse more extensively when the initially deleted node has higher betweenness. Meanwhile, in networks with strong community structure, high-betweenness nodes tend to be bridge nodes that link different communities, and the removal of such nodes will reduce only the connections among communities, leaving the networks fairly stable. Understanding what will affect cascading failures and how to protect or attack networks with strong community structure is therefore of interest. In this paper, we have constructed scale-free Community Networks (SFCN) and Random Community Networks (RCN). We applied these networks, along with the Lancichinett-Fortunato-Radicchi (LFR) benchmark, to the cascading-failure scenario to explore their vulnerability to attack and the relationship between cascading failures and the degree distribution and community structure of a network. The numerical results show that when the networks are of a power-law distribution, a stronger community structure will result in the failure of fewer nodes. In addition, the initial removal of the node with the highest betweenness will not lead to the worst cascading, i.e. the largest avalanche size. The Betweenness Overflow (BOF), an index that we developed, is an effective indicator of this tendency. The RCN, however, display a different result. In addition, the avalanche size of each node can be adopted as an index to evaluate the importance of the node.
Structural Investigations of Complex Oxides using Synchrotron Radiation
Hans-Conrad zur Loye
2007-03-24
The work is a collaborative effort between Prof. Hanno zur Loye at the University of South Carolina and Dr. Tom Vogt at Brookhaven National Laboratory. The collaborative research focuses on the synthesis and the structural characterization of perovskites and perovskite related oxides and will target new oxide systems where we have demonstrated expertise in synthesis, yet lack the experimental capabilities to answer important structural issues. Synthetically, we will focus on two subgroups of perovskite structures, the double and triple perovskites, and the 2H-perovskite related oxides belonging to the A3n+3mA’nB3m+nO9m+6n family. In the first part of the proposal, our goal of synthesizing and structurally characterizing new ruthenium, iridium, rhodium and ruthenium containing double and triple perovskites, with the emphasis on exercising control over the oxidation state(s) of the metals, is described. These oxides will be of interest for their electronic and magnetic properties that will be investigated as well.
Complex nanoprecipitate structures induced by irradiation in immiscible alloy systems
NASA Astrophysics Data System (ADS)
Shu, Shipeng; Bellon, P.; Averback, R. S.
2013-04-01
We investigate the fundamentals of compositional patterning induced by energetic particle irradiation in model A-B substitutional binary alloys using kinetic Monte Carlo simulations. The study focuses on a type of nanostructure that was recently observed in dilute Cu-Fe and Cu-V alloys, where precipitates form within precipitates, a morphology that we term “cherry-pit” structures. The simulations show that the domain of stability of these cherry-pit structures depends on the thermodynamic and kinetic asymmetry between the A and B elements. In particular, both lower solubilities and diffusivities of A in B compared to those of B in A favor the stabilization of these cherry-pit structures for A-rich average compositions. The simulation results are rationalized by extending the analytic model introduced by Frost and Russell for irradiation-induced compositional patterning so as to include the possible formation of pits within precipitates. The simulations indicate also that the pits are dynamical structures that undergo nearly periodic cycles of nucleation, growth, and absorption by the matrix.
Temperature Sensitive Nanocapsule of Complex Structural Form for Methane Storage
2010-01-01
The processes of methane adsorption, storage and desorption by the nanocapsule are investigated with molecular-dynamic modeling method. The specific nanocapsule shape defines its functioning uniqueness: methane is adsorbed under 40 MPa and at normal temperature with further blocking of methane molecules the K@C601+ endohedral complex in the nanocapsule by external electric field, the storage is performed under normal external conditions, and methane desorption is performed at 350 K. The methane content in the nanocapsule during storage reaches 11.09 mass%. The nanocapsule consists of tree parts: storage chamber, junction and blocking chamber. The storage chamber comprises the nanotube (20,20). The blocking chamber is a short nanotube (20,20) with three holes. The junction consists of the nanotube (10,10) and nanotube (8,8); moreover, the nanotube (8,8) is connected with the storage chamber and nanotube (10,10) with the blocking chamber. The blocking chamber is opened and closed by the transfer of the K@C601+ endohedral complex under electrostatic field action. PMID:20652146
Solution structures of europium(III) complexes of ethylenediaminetetraacetic acid
Latva, M.; Kankara, J.; Haapakka, K.
1996-04-01
Coordination of ethylenediaminetetraacetic acid (EDTA) with europium(III) has been studied at different concentrations in solution using {sup 7}F{sub 0}{yields}{sup 5}D{sub 0} excitation spectroscopy and excited-state lifetime measurements. EDTA forms with Eu(III) ion three different species in equimolar solutions at room temperature. At low pH values EuEDTAH is formed and at higher pH values than 1.5 two EuEDTA{sup -} complexes, which differ from each other with one water molecule in the first coordination sphere of the Eu(III) ion, total coordination number and coordination geometry, are also formed. When the concentration of EDTA is higher than the concentration of Eu(III), an EuEDTA(EDTAH){sup 4-} species where the second EDTA is weakly coordinated to EuEDTA{sup -}, is formed. If the concentration of Eu(III) ion is higher than EDTA, the extra Eu(III) ions associate with EuEDTA{sup -} and link to one of the carboxylate groups of EDTA thus causing a shortening of the excited-state lifetime of the EuEDTA{sup -} complex.
Local structure analysis of some Cu(II) theophylline complexes
NASA Astrophysics Data System (ADS)
David, L.; Cozar, O.; Forizs, E.; Cr ăciun, C.; Ristoiu, D.; B ălan, C.
1999-10-01
The CuT 2L 2·2H 2O complexes [T=Theophylline (1,3-dimethylxanthine); L=NH 3, n-propylamine (npa), 2-aminoethanol (ae)] were prepared and investigated by ESR spectroscopy. Powder ESR spectrum of CuT 2(NH 3) 2·2H 2O is axial ( g||=2.255, g⊥=2.059). ESR spectrum of CuT 2(npa) 2·2H 2O with ( g||=2.299, g⊥=2.081) is a superposition of one axial ( g||=2.299, g⊥=2.073) and one isotropic component ( g0≈2.089), in the same amount. The axial spectra of the former complexes are due to a static Jahn-Teller effect ( EJT≈2880 cm -1). ESR spectrum of CuT 2(ae) 2·2H 2O is orthorhombic ( g1c=2.199, g2c=2.095, g3c=2.037). The local symmetries around the Cu(II) ions remain unchanged by DMF solvating, by adsorbing these solutions on NaY zeolite or by lowering the temperature.
Observation of two different fractal structures in nanoparticle, protein and surfactant complexes
NASA Astrophysics Data System (ADS)
Mehan, Sumit; Kumar, Sugam; Aswal, V. K.
2014-04-01
Small angle neutron scattering has been carried out from a complex of nanoparticle, protein and surfactant. Although all the components are similarly (anionic) charged, we have observed strong interactions in their complex formation. It is characterized by the coexistence of two different mass fractal structures. The first fractal structure is originated from the protein and surfactant interaction and second from the depletion effect of first fractal structure leading the nanoparticle aggregation. The fractal structure of protein-surfactant complex represents to bead necklace structure of micelle-like clusters of surfactant formed along the unfolded protein chain. Its fractal dimension depends on the surfactant to protein ratio (r) and decreases with the increase in r. However, fractal dimension of nanoparticle aggregates in nanoparticle-protein complex is found to be independent of protein concentration and governed by the diffusion limited aggregation like morphology.
Observation of two different fractal structures in nanoparticle, protein and surfactant complexes
Mehan, Sumit Kumar, Sugam Aswal, V. K.
2014-04-24
Small angle neutron scattering has been carried out from a complex of nanoparticle, protein and surfactant. Although all the components are similarly (anionic) charged, we have observed strong interactions in their complex formation. It is characterized by the coexistence of two different mass fractal structures. The first fractal structure is originated from the protein and surfactant interaction and second from the depletion effect of first fractal structure leading the nanoparticle aggregation. The fractal structure of protein-surfactant complex represents to bead necklace structure of micelle-like clusters of surfactant formed along the unfolded protein chain. Its fractal dimension depends on the surfactant to protein ratio (r) and decreases with the increase in r. However, fractal dimension of nanoparticle aggregates in nanoparticle-protein complex is found to be independent of protein concentration and governed by the diffusion limited aggregation like morphology.
Entropic force approach in a noncommutative charged black hole and the equivalence principle
NASA Astrophysics Data System (ADS)
Mehdipour, S. Hamid; Keshavarz, Arash
2012-04-01
Recently, Verlinde has suggested a novel model of duality between thermodynamics and gravity which leads to an emergent phenomenon for the origin of gravity and general relativity. In this paper, we investigate some features of this model in the presence of noncommutative charged black hole by performing the method of coordinate coherent states representing smeared structures. We derive several quantities, e.g., temperature, energy and entropic force. Our approach clearly exhibits that the entropic force on a smallest fundamental cell of holographic surface with radius r0 is halted. Accordingly, we can conclude that the black-hole remnants are absolutely inert without gravitational interactions. So, the equivalence principle of general relativity is contravened due to the fact that it is now possible to find a difference between the gravitational and inertial mass. In other words, the gravitational mass in the remnant size does not emit any gravitational field, therefore it is experienced to be zero, contrary to the inertial mass. This phenomenon illustrates a good example for a feasible experimental confirmation to the entropic picture of Newton's Second law in very short distances.
Interface Structure and Transport of Complex Oxide Junctions
Nelson-Cheeseman, B. B.; Wong, F.; Chopdekar, R. V.; Chi, M.; Arenholz, E.; Browning, N. D.; Suzuki, Y.
2008-02-01
The interface structure and magnetism of hybrid magnetic tunnel junction-spin filter devices have been investigated and correlated with the transport behavior exhibited. Magnetic tunnel junctions made of theoretically predicted half-metallic electrodes (perovskite La0.7Sr0.3MnO3 and spinel Fe3O4) sandwiching a spinel NiMn2O4 tunnel barrier exhibit very high crystalline quality as observed by transmission electron microscopy. Structurally abrupt interfaces allow for the distinct magnetic switching of the electrodes as well as large junction magnetoresistance. The change in the magnetic anisotropy observed at the spinel-spinel interface supports the presence of limited interdiffusion and the creation of a magnetically soft interfacial layer, whose strong exchange coupling to the Fe3O4 electrode likely accounts for the low background magnetoresistance observed in these junctions, and the successful spin filtering when the barrier layer is ferrimagnetic.
Interface Structure and Transport of Complex Oxide Junctions
Nelson-Cheeseman, B.B.; Wong, F.; Chopdekar, R.V.; Chi, M.; Arenholz, E.; Browning, N.D; Suzuki, Y.
2008-11-05
The interface structure and magnetism of hybrid magnetic tunnel junction-spin filter devices have been investigated and correlated with their transport properties. Magnetic tunnel junctions made of a spinel NiMn2O4 tunnel barrier sandwiched by theoretically predicted half-metallic electrodes, perovskite La0.7Sr0.3MnO3 and spinel Fe3O4, exhibit very high crystalline quality as observed by transmission electron microscopy. Structurally abrupt interfaces allow for the distinct magnetic switching of the electrodes as well as large junction magnetoresistance. The change in the magnetic anisotropy observed at the spinel-spinel interface is indicative of a thin interdiffused magnetically soft interfacial layer. The strong exchange coupling at this interface allows for low background magnetoresistance, and a spin-filter effect with when the barrier is ferrimagnetic.
Semantic Annotation of Complex Text Structures in Problem Reports
NASA Technical Reports Server (NTRS)
Malin, Jane T.; Throop, David R.; Fleming, Land D.
2011-01-01
Text analysis is important for effective information retrieval from databases where the critical information is embedded in text fields. Aerospace safety depends on effective retrieval of relevant and related problem reports for the purpose of trend analysis. The complex text syntax in problem descriptions has limited statistical text mining of problem reports. The presentation describes an intelligent tagging approach that applies syntactic and then semantic analysis to overcome this problem. The tags identify types of problems and equipment that are embedded in the text descriptions. The power of these tags is illustrated in a faceted searching and browsing interface for problem report trending that combines automatically generated tags with database code fields and temporal information.
Electrocyclization of oxatrienes in the construction of structurally complex pyranopyridones.
Fotiadou, Anna D; Zografos, Alexandros L
2012-11-16
Application of a tandem Knoevenagel/6π-electrocyclization sequence is able to produce highly substituted pyranopyridones from moderate to high yields in a one-step reaction. High diasteroselectivity is observed in some cases and was rationalized on the basis of the thermodynamic control of the evidenced reversibility of a 6π-electrocyclization reaction. Numerous examples are provided establishing a novel entry in natural product-like structures of pyranopyridone alkaloids.
Comparison and validation of community structures in complex networks
NASA Astrophysics Data System (ADS)
Gustafsson, Mika; Hörnquist, Michael; Lombardi, Anna
2006-07-01
The issue of partitioning a network into communities has attracted a great deal of attention recently. Most authors seem to equate this issue with the one of finding the maximum value of the modularity, as defined by Newman. Since the problem formulated this way is believed to be NP-hard, most effort has gone into the construction of search algorithms, and less to the question of other measures of community structures, similarities between various partitionings and the validation with respect to external information. Here we concentrate on a class of computer generated networks and on three well-studied real networks which constitute a bench-mark for network studies; the karate club, the US college football teams and a gene network of yeast. We utilize some standard ways of clustering data (originally not designed for finding community structures in networks) and show that these classical methods sometimes outperform the newer ones. We discuss various measures of the strength of the modular structure, and show by examples features and drawbacks. Further, we compare different partitions by applying some graph-theoretic concepts of distance, which indicate that one of the quality measures of the degree of modularity corresponds quite well with the distance from the true partition. Finally, we introduce a way to validate the partitionings with respect to external data when the nodes are classified but the network structure is unknown. This is here possible since we know everything of the computer generated networks, as well as the historical answer to how the karate club and the football teams are partitioned in reality. The partitioning of the gene network is validated by use of the Gene Ontology database, where we show that a community in general corresponds to a biological process.
Calculation of electrostatic fields in periodic structures of complex shape
NASA Technical Reports Server (NTRS)
Kravchenko, V. F.
1978-01-01
A universal algorithm is presented for calculating electrostatic fields in an infinite periodic structure consisting of electrodes of arbitrary shape which are located in mirror-symmetrical manner along the axis of electron-beam propagation. The method is based on the theory of R-functions, and the differential operators which are derived on the basis of the functions. Numerical results are presented and the accuracy of the results is examined.
Complex transition to cooperative behavior in a structured population model.
Miranda, Luciano; de Souza, Adauto J F; Ferreira, Fernando F; Campos, Paulo R A
2012-01-01
Cooperation plays an important role in the evolution of species and human societies. The understanding of the emergence and persistence of cooperation in those systems is a fascinating and fundamental question. Many mechanisms were extensively studied and proposed as supporting cooperation. The current work addresses the role of migration for the maintenance of cooperation in structured populations. This problem is investigated in an evolutionary perspective through the prisoner's dilemma game paradigm. It is found that migration and structure play an essential role in the evolution of the cooperative behavior. The possible outcomes of the model are extinction of the entire population, dominance of the cooperative strategy and coexistence between cooperators and defectors. The coexistence phase is obtained in the range of large migration rates. It is also verified the existence of a critical level of structuring beyond that cooperation is always likely. In resume, we conclude that the increase in the number of demes as well as in the migration rate favor the fixation of the cooperative behavior.