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Sample records for 2d network structure

  1. 2D networks of rhombic-shaped fused dehydrobenzo[12]annulenes: structural variations under concentration control.

    PubMed

    Tahara, Kazukuni; Okuhata, Satoshi; Adisoejoso, Jinne; Lei, Shengbin; Fujita, Takumi; De Feyter, Steven; Tobe, Yoshito

    2009-12-01

    A series of alkyl- and alkoxy-substituted rhombic-shaped bisDBA derivatives 1a-d, 2a, and 2b were synthesized for the purpose of the formation of porous networks at the 1,2,4-trichlorobenzene (TCB)/graphite interface. Depending on the alkyl-chain length and the solute concentration, bisDBAs exhibit five network structures, three porous structures (porous A, B, and C), and two nonporous structures (nonporous D and E), which are attributed to their rhombic core shape and the position of the substituents. BisDBAs 1a and 1b with the shorter alkyl chains favorably form a porous structure, whereas bisDBAs 1c and 1d with the longer alkyl chains are prone to form nonporous structures. However, upon dilution, nonporous structures are typically transformed into porous ones, a trend that can be understood by the effect of surface coverage, molecular density, and intermolecular interactions on the system's enthalpy. Furthermore, porous structures are stabilized by the coadsorption of solvent molecules. The most intriguing porous structure, the Kagome pattern, was formed for all compounds at least to some extent, and the size of its triangular and hexagonal pores could be tuned by the alkyl-chain length. The present study proves that the concentration control is a powerful and general tool for the construction of porous networks at the liquid-solid interface.

  2. Geometric Bioinspired Networks for Recognition of 2-D and 3-D Low-Level Structures and Transformations.

    PubMed

    Bayro-Corrochano, Eduardo; Vazquez-Santacruz, Eduardo; Moya-Sanchez, Eduardo; Castillo-Munis, Efrain

    2016-10-01

    This paper presents the design of radial basis function geometric bioinspired networks and their applications. Until now, the design of neural networks has been inspired by the biological models of neural networks but mostly using vector calculus and linear algebra. However, these designs have never shown the role of geometric computing. The question is how biological neural networks handle complex geometric representations involving Lie group operations like rotations. Even though the actual artificial neural networks are biologically inspired, they are just models which cannot reproduce a plausible biological process. Until now researchers have not shown how, using these models, one can incorporate them into the processing of geometric computing. Here, for the first time in the artificial neural networks domain, we address this issue by designing a kind of geometric RBF using the geometric algebra framework. As a result, using our artificial networks, we show how geometric computing can be carried out by the artificial neural networks. Such geometric neural networks have a great potential in robot vision. This is the most important aspect of this contribution to propose artificial geometric neural networks for challenging tasks in perception and action. In our experimental analysis, we show the applicability of our geometric designs, and present interesting experiments using 2-D data of real images and 3-D screw axis data. In general, our models should be used to process different types of inputs, such as visual cues, touch (texture, elasticity, temperature), taste, and sound. One important task of a perception-action system is to fuse a variety of cues coming from the environment and relate them via a sensor-motor manifold with motor modules to carry out diverse reasoned actions. PMID:26340785

  3. Geometric Bioinspired Networks for Recognition of 2-D and 3-D Low-Level Structures and Transformations.

    PubMed

    Bayro-Corrochano, Eduardo; Vazquez-Santacruz, Eduardo; Moya-Sanchez, Eduardo; Castillo-Munis, Efrain

    2016-10-01

    This paper presents the design of radial basis function geometric bioinspired networks and their applications. Until now, the design of neural networks has been inspired by the biological models of neural networks but mostly using vector calculus and linear algebra. However, these designs have never shown the role of geometric computing. The question is how biological neural networks handle complex geometric representations involving Lie group operations like rotations. Even though the actual artificial neural networks are biologically inspired, they are just models which cannot reproduce a plausible biological process. Until now researchers have not shown how, using these models, one can incorporate them into the processing of geometric computing. Here, for the first time in the artificial neural networks domain, we address this issue by designing a kind of geometric RBF using the geometric algebra framework. As a result, using our artificial networks, we show how geometric computing can be carried out by the artificial neural networks. Such geometric neural networks have a great potential in robot vision. This is the most important aspect of this contribution to propose artificial geometric neural networks for challenging tasks in perception and action. In our experimental analysis, we show the applicability of our geometric designs, and present interesting experiments using 2-D data of real images and 3-D screw axis data. In general, our models should be used to process different types of inputs, such as visual cues, touch (texture, elasticity, temperature), taste, and sound. One important task of a perception-action system is to fuse a variety of cues coming from the environment and relate them via a sensor-motor manifold with motor modules to carry out diverse reasoned actions.

  4. Modeling and Analysis of Granite Matrix Pore Structure and Hydraulic Characteristics in 2D and 3D Networks

    NASA Astrophysics Data System (ADS)

    Gvozdik, L.; Polak, M.; Zaruba, J.; Vanecek, M.

    2010-12-01

    A geological environment labeled as a Granite massif represents in terms of groundwater flow and transport a distinct hydrogeological environment from that of sedimentary basins, the characterisation of which is generally more complex and uncertain. Massifs are composed of hard crystalline rocks with the very low effective porosity. Due to their rheological properties such rocks are predisposed to brittle deformation resulting from changes in stress conditions. Our specific research project (Research on the influence of intergrangular porosity on deep geological disposal: geological formations, methodology and the development of measurement apparatus) is focussed on the problem of permeable zones within apparently undisturbed granitic rock matrix. The project including the both laboratory and in-situ tracer tests study migration along and through mineral grains in fresh and altered granite. The objective of the project is to assess whether intergranular porosity is a general characteristic of the granitic rock matrix or subject to significant evolution resulting from geochemical and/or hydrogeochemical processes, geotechnical and/or mechanical processes. Moreover, the research is focussed on evaluating methods quantifying intergranular porosity by both physical testing and mathematical modelling using verified standard hydrological software tools. Groundwater flow in microfractures and intergranular pores in granite rock matrix were simulated in three standard hydrogeological modeling programs with completely different conceptual approaches: MODFLOW (Equivalent Continuum concept), FEFLOW (Discrete Fracture and Equivalent Continuum concepts) and NAPSAC (Discrete Fracture Network concept). Specialized random fracture generators were used for creation of several 2D and 3D models in each of the chosen program. Percolation characteristics of these models were tested and analyzed. Several scenarios of laboratory tests of the rock samples permeability made in triaxial

  5. CYP2D6: novel genomic structures and alleles

    PubMed Central

    Kramer, Whitney E.; Walker, Denise L.; O’Kane, Dennis J.; Mrazek, David A.; Fisher, Pamela K.; Dukek, Brian A.; Bruflat, Jamie K.; Black, John L.

    2010-01-01

    Objective CYP2D6 is a polymorphic gene. It has been observed to be deleted, to be duplicated and to undergo recombination events involving the CYP2D7 pseudogene and surrounding sequences. The objective of this study was to discover the genomic structure of CYP2D6 recombinants that interfere with clinical genotyping platforms that are available today. Methods Clinical samples containing rare homozygous CYP2D6 alleles, ambiguous readouts, and those with duplication signals and two different alleles were analyzed by long-range PCR amplification of individual genes, PCR fragment analysis, allele-specific primer extension assay, and DNA sequencing to characterize alleles and genomic structure. Results Novel alleles, genomic structures, and the DNA sequence of these structures are described. Interestingly, in 49 of 50 DNA samples that had CYP2D6 gene duplications or multiplications where two alleles were detected, the chromosome containing the duplication or multiplication had identical tandem alleles. Conclusion Several new CYP2D6 alleles and genomic structures are described which will be useful for CYP2D6 genotyping. The findings suggest that the recombination events responsible for CYP2D6 duplications and multiplications are because of mechanisms other than interchromosomal crossover during meiosis. PMID:19741566

  6. Nonlinear Heat Transfer 2d Structure

    1987-09-01

    DOT-BPMD is a general-purpose, finite-element, heat-transfer program used to predict thermal environments. The code considers linear and nonlinear transient or steady-state heat conduction in two-dimensional planar or axisymmetric representations of structures. Capabilities are provided for modeling anisotropic heterogeneous materials with temperature-dependent thermal properties and time-dependent temperature, heat flux, convection and radiation boundary conditions, together with time-dependent internal heat generation. DOT-BPMD may be used in the evaluation of steady-state geothermal gradients as well as in themore » transient heat conduction analysis of repository and waste package subsystems. Strengths of DOT-BPMD include its ability to account for a wide range of possible boundary conditions, nonlinear material properties, and its efficient equation solution algorithm. Limitations include the lack of a three-dimensional analysis capability, no radiative or convective internal heat transfer, and the need to maintain a constant time-step in each program execution.« less

  7. Duality Between Spin Networks and the 2D Ising Model

    NASA Astrophysics Data System (ADS)

    Bonzom, Valentin; Costantino, Francesco; Livine, Etera R.

    2016-06-01

    The goal of this paper is to exhibit a deep relation between the partition function of the Ising model on a planar trivalent graph and the generating series of the spin network evaluations on the same graph. We provide respectively a fermionic and a bosonic Gaussian integral formulation for each of these functions and we show that they are the inverse of each other (up to some explicit constants) by exhibiting a supersymmetry relating the two formulations. We investigate three aspects and applications of this duality. First, we propose higher order supersymmetric theories that couple the geometry of the spin networks to the Ising model and for which supersymmetric localization still holds. Secondly, after interpreting the generating function of spin network evaluations as the projection of a coherent state of loop quantum gravity onto the flat connection state, we find the probability distribution induced by that coherent state on the edge spins and study its stationary phase approximation. It is found that the stationary points correspond to the critical values of the couplings of the 2D Ising model, at least for isoradial graphs. Third, we analyze the mapping of the correlations of the Ising model to spin network observables, and describe the phase transition on those observables on the hexagonal lattice. This opens the door to many new possibilities, especially for the study of the coarse-graining and continuum limit of spin networks in the context of quantum gravity.

  8. 2D pattern evolution constrained by complex network dynamics

    NASA Astrophysics Data System (ADS)

    da Rocha, L. E. C.; Costa, L. da F.

    2007-03-01

    Complex networks have established themselves in recent years as being particularly suitable and flexible for representing and modelling several complex natural and artificial systems. In the same time in which the structural intricacies of such networks are being revealed and understood, efforts have also been directed at investigating how such connectivity properties define and constrain the dynamics of systems unfolding on such structures. However, less attention has been focused on hybrid systems, i.e. involving more than one type of network and/or dynamics. Several real systems present such an organization, e.g. the dynamics of a disease coexisting with the dynamics of the immune system. The current paper investigates a specific system involving diffusive (linear and nonlinear) dynamics taking place in a regular network while interacting with a complex network of defensive agents following Erdös Rényi (ER) and Barabási Albert (BA) graph models with moveable nodes. More specifically, the complex network is expected to control, and if possible, to extinguish the diffusion of some given unwanted process (e.g. fire, oil spilling, pest dissemination, and virus or bacteria reproduction during an infection). Two types of pattern evolution are considered: Fick and Gray Scott. The nodes of the defensive network then interact with the diffusing patterns and communicate between themselves in order to control the diffusion. The main findings include the identification of higher efficiency for the BA control networks and the presence of relapses in the case of the ER model.

  9. 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.

  10. Temperature dependent structural variation from 2D supramolecular network to 3D interpenetrated metal–organic framework: In situ cleavage of S–S and C–S bonds

    SciTech Connect

    Ugale, Bharat; Singh, Divyendu; Nagaraja, C.M.

    2015-03-15

    Two new Zn(II)–organic compounds, [Zn(muco)(dbds){sub 2}(H{sub 2}O){sub 2}] (1) and [Zn(muco)(dbs)] (2) (where, muco=trans, trans-muconate dianion, dbds=4,4′-dipyridyldisulfide and dbs=4,4′-dipyridylsulfide) have been synthesized from same precursors but at two different temperatures. Both the compounds have been characterized by single-crystal X-ray diffraction, powder X-ray diffraction, elemental analysis, IR spectroscopy, thermal analysis and photoluminescence studies. Compound 1 prepared at room temperature possesses a molecular structure extended to 2D supramolecular network through (H–O…H) hydrogen-bonding interactions. Compound 2, obtained at high temperature (100 °C) shows a 3-fold interpenetrating 3D framework constituted by an in situ generated dbs linker by the cleavage of S–S and C–S bonds of dbds linker. Thus, the influence of reaction temperature on the formation of two structural phases has been demonstrated. Both 1 and 2 exhibit ligand based luminescence emission owing to n→π⁎ and π→π⁎ transitions and also high thermal stabilities. - Graphical abstract: The influence of temperature on the formation of two structural phases, a 2D supramolecular network and a 3D 3-fold interpenetrating framework has been demonstrated and their luminescence emission is measured. - Highlights: • Two new Zn(II)–organic compounds were synthesized by tuning reaction temperatures. • Temperature induced in situ generation of dbs linker has been observed. • The compounds exhibit high thermal stability and luminescence emission properties. • The effect of temperature on structure, dimension and topology has been presented.

  11. 2D ice from first principles: structures and phase transitions

    NASA Astrophysics Data System (ADS)

    Chen, Ji; Schusteritsch, Georg; Pickard, Chris J.; Salzmann, Christoph G.; Michaelides, Angelos

    Despite relevance to disparate areas such as cloud microphysics and tribology, major gaps in the understanding of the structures and phase transitions of low-dimensional water ice remain. Here we report a first principles study of confined 2D ice as a function of pressure. We find that at ambient pressure hexagonal and pentagonal monolayer structures are the two lowest enthalpy phases identified. Upon mild compression the pentagonal structure becomes the most stable and persists up to ca. 2 GPa at which point square and rhombic phases are stable. The square phase agrees with recent experimental observations of square ice confined within graphene sheets. We also find a double layer AA stacked square ice phase, which clarifies the difference between experimental observations and earlier force field simulations. This work provides a fresh perspective on 2D confined ice, highlighting the sensitivity of the structures observed to both the confining pressure and width.

  12. Synchronization of semiconductor laser arrays with 2D Bragg structures

    NASA Astrophysics Data System (ADS)

    Baryshev, V. R.; Ginzburg, N. S.

    2016-08-01

    A model of a planar semiconductor multi-channel laser is developed. In this model two-dimensional (2D) Bragg mirror structures are used for synchronizing radiation of multiple laser channels. Coupling of longitudinal and transverse waves can be mentioned as the distinguishing feature of these structures. Synchronization of 20 laser channels is demonstrated with a semi-classical approach based on Maxwell-Bloch equations.

  13. Adaptation algorithms for 2-D feedforward neural networks.

    PubMed

    Kaczorek, T

    1995-01-01

    The generalized weight adaptation algorithms presented by J.G. Kuschewski et al. (1993) and by S.H. Zak and H.J. Sira-Ramirez (1990) are extended for 2-D madaline and 2-D two-layer feedforward neural nets (FNNs).

  14. The NH2D hyperfine structure revealed by astrophysical observations

    NASA Astrophysics Data System (ADS)

    Daniel, F.; Coudert, L. H.; Punanova, A.; Harju, J.; Faure, A.; Roueff, E.; Sipilä, O.; Caselli, P.; Güsten, R.; Pon, A.; Pineda, J. E.

    2016-02-01

    Context. The 111-101 lines of ortho- and para-NH2D (o/p-NH2D) at 86 and 110 GHz, respectively, are commonly observed to provide constraints on the deuterium fractionation in the interstellar medium. In cold regions, the hyperfine structure that is due to the nitrogen (14N) nucleus is resolved. To date, this splitting is the only one that is taken into account in the NH2D column density estimates. Aims: We investigate how including the hyperfine splitting caused by the deuterium (D) nucleus affects the analysis of the rotational lines of NH2D. Methods: We present 30 m IRAM observations of the above mentioned lines and APEX o/p-NH2D observations of the 101-000 lines at 333 GHz. The hyperfine patterns of the observed lines were calculated taking into account the splitting induced by the D nucleus. The analysis then relies on line lists that either neglect or include the splitting induced by the D nucleus. Results: The hyperfine spectra are first analyzed with a line list that only includes the hyperfine splitting that is due to the 14N nucleus. We find inconsistencies between the line widths of the 101-000 and 111-101 lines, the latter being larger by a factor of ~1.6 ± 0.3. Such a large difference is unexpected because the two sets of lines probably originate from the same region. We next employed a newly computed line list for the o/p-NH2D transitions where the hyperfine structure induced by both nitrogen and deuterium nuclei was included. With this new line list, the analysis of the previous spectra leads to compatible line widths. Conclusions: Neglecting the hyperfine structure caused by D leads to overestimating the line widths of the o/p-NH2D lines at 3 mm. The error for a cold molecular core is about 50%. This error propagates directly to the column density estimate. We therefore recommend to take the hyperfine splittings caused by both the 14N and D nuclei into account in any analysis that relies on these lines. Based on observations carried out with the IRAM

  15. 2D Four-Channel Perfect Reconstruction Filter Bank Realized with the 2D Lattice Filter Structure

    NASA Astrophysics Data System (ADS)

    Sezen, S.; Ertüzün, A.

    2006-12-01

    A novel orthogonal 2D lattice structure is incorporated into the design of a nonseparable 2D four-channel perfect reconstruction filter bank. The proposed filter bank is obtained by using the polyphase decomposition technique which requires the design of an orthogonal 2D lattice filter. Due to constraint of perfect reconstruction, each stage of this lattice filter bank is simply parameterized by two coefficients. The perfect reconstruction property is satisfied regardless of the actual values of these parameters and of the number of the lattice stages. It is also shown that a separable 2D four-channel perfect reconstruction lattice filter bank can be constructed from the 1D lattice filter and that this is a special case of the proposed 2D lattice filter bank under certain conditions. The perfect reconstruction property of the proposed 2D lattice filter approach is verified by computer simulations.

  16. In-Cell Protein Structures from 2D NMR Experiments.

    PubMed

    Müntener, Thomas; Häussinger, Daniel; Selenko, Philipp; Theillet, Francois-Xavier

    2016-07-21

    In-cell NMR spectroscopy provides atomic resolution insights into the structural properties of proteins in cells, but it is rarely used to solve entire protein structures de novo. Here, we introduce a paramagnetic lanthanide-tag to simultaneously measure protein pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs) to be used as input for structure calculation routines within the Rosetta program. We employ this approach to determine the structure of the protein G B1 domain (GB1) in intact Xenopus laevis oocytes from a single set of 2D in-cell NMR experiments. Specifically, we derive well-defined GB1 ensembles from low concentration in-cell NMR samples (∼50 μM) measured at moderate magnetic field strengths (600 MHz), thus offering an easily accessible alternative for determining intracellular protein structures. PMID:27379949

  17. Confinement properties of 2D porous molecular networks on metal surfaces.

    PubMed

    Müller, Kathrin; Enache, Mihaela; Stöhr, Meike

    2016-04-20

    Quantum effects that arise from confinement of electronic states have been extensively studied for the surface states of noble metals. Utilizing small artificial structures for confinement allows tailoring of the surface properties and offers unique opportunities for applications. So far, examples of surface state confinement include thin films, artificial nanoscale structures, vacancy and adatom islands, self-assembled 1D chains, vicinal surfaces, quantum dots and quantum corrals. In this review we summarize recent achievements in changing the electronic structure of surfaces by adsorption of nanoporous networks whose design principles are based on the concepts of supramolecular chemistry. Already in 1993, it was shown that quantum corrals made from Fe atoms on a Cu(1 1 1) surface using single atom manipulation with a scanning tunnelling microscope confine the Shockley surface state. However, since the atom manipulation technique for the construction of corral structures is a relatively time consuming process, the fabrication of periodic two-dimensional (2D) corral structures is practically impossible. On the other side, by using molecular self-assembly extended 2D porous structures can be achieved in a parallel process, i.e. all pores are formed at the same time. The molecular building blocks are usually held together by non-covalent interactions like hydrogen bonding, metal coordination or dipolar coupling. Due to the reversibility of the bond formation defect-free and long-range ordered networks can be achieved. However, recently also examples of porous networks formed by covalent coupling on the surface have been reported. By the choice of the molecular building blocks, the dimensions of the network (pore size and pore to pore distance) can be controlled. In this way, the confinement properties of the individual pores can be tuned. In addition, the effect of the confined state on the hosting properties of the pores will be discussed in this review article

  18. Confinement properties of 2D porous molecular networks on metal surfaces

    NASA Astrophysics Data System (ADS)

    Müller, Kathrin; Enache, Mihaela; Stöhr, Meike

    2016-04-01

    Quantum effects that arise from confinement of electronic states have been extensively studied for the surface states of noble metals. Utilizing small artificial structures for confinement allows tailoring of the surface properties and offers unique opportunities for applications. So far, examples of surface state confinement include thin films, artificial nanoscale structures, vacancy and adatom islands, self-assembled 1D chains, vicinal surfaces, quantum dots and quantum corrals. In this review we summarize recent achievements in changing the electronic structure of surfaces by adsorption of nanoporous networks whose design principles are based on the concepts of supramolecular chemistry. Already in 1993, it was shown that quantum corrals made from Fe atoms on a Cu(1 1 1) surface using single atom manipulation with a scanning tunnelling microscope confine the Shockley surface state. However, since the atom manipulation technique for the construction of corral structures is a relatively time consuming process, the fabrication of periodic two-dimensional (2D) corral structures is practically impossible. On the other side, by using molecular self-assembly extended 2D porous structures can be achieved in a parallel process, i.e. all pores are formed at the same time. The molecular building blocks are usually held together by non-covalent interactions like hydrogen bonding, metal coordination or dipolar coupling. Due to the reversibility of the bond formation defect-free and long-range ordered networks can be achieved. However, recently also examples of porous networks formed by covalent coupling on the surface have been reported. By the choice of the molecular building blocks, the dimensions of the network (pore size and pore to pore distance) can be controlled. In this way, the confinement properties of the individual pores can be tuned. In addition, the effect of the confined state on the hosting properties of the pores will be discussed in this review article.

  19. Magnetic anisotropy of metal functionalized phthalocyanine 2D networks

    NASA Astrophysics Data System (ADS)

    Zhu, Guojun; Zhang, Yun; Xiao, Huaping; Cao, Juexian

    2016-06-01

    The magnetic anisotropy of metal including Cr, Mn, Fe, Co, Mo, Tc, Ru, Rh, W, Re, Os, Ir atoms functionalized phthalocyanine networks have been investigated with first-principles calculations. The magnetic moments can be expressed as 8-n μB with n the electronic number of outmost d shell in the transition metals. The huge magnetocrystalline anisotropy energy (MAE) is obtained by torque method. Especially, the MAE of Re functionalized phthalocyanine network is about 20 meV with an easy axis perpendicular to the plane of phthalocyanine network. The MAE is further manipulated by applying the external biaxial strain. It is found that the MAE is linear increasing with the external strain in the range of -2% to 2%. Our results indicate an effective approach to modulate the MAE for practical application.

  20. Active transport and cluster formation on 2D networks.

    PubMed

    Greulich, P; Santen, L

    2010-06-01

    We introduce a model for active transport on inhomogeneous networks embedded in a diffusive environment which is motivated by vesicular transport on actin filaments. In the presence of a hard-core interaction, particle clusters are observed that exhibit an algebraically decaying distribution in a large parameter regime, indicating the existence of clusters on all scales. The scale-free behavior can be understood by a mechanism promoting preferential attachment of particles to large clusters. The results are compared with a diffusion-limited aggregation model and active transport on a regular network. For both models we observe aggregation of particles to clusters which are characterized by a finite size scale if the relevant time scales and particle densities are considered. PMID:20556462

  1. Designing 2D arrays for SHM of planar structures: a review

    NASA Astrophysics Data System (ADS)

    Stepinski, Tadeusz; Ambrozinski, Lukasz; Uhl, Tadeusz

    2013-04-01

    Monitoring structural integrity of large planar structures that aims at detecting and localizing impact or damage at any point of the structure requires normally a relatively dense network of uniformly distributed ultrasonic sensors. 2-D ultrasonic phased arrays, due to their beam-steering capability and all azimuth angle coverage are a very promising tool for structural health monitoring (SHM) of plate-like structures using Lamb waves (LW). Linear phased arrays that have been proposed for that purpose, produce mirrored image characterized by azimuth dependent resolution, which prevents unequivocal damage localization. 2D arrays do not have this drawback and they are even capable of mode selectivity when generating and receiving LWs. Performance of 2D arrays depends on their topology as well as the number of elements (transducers) used and their spacing in terms of wavelength. In this paper we propose a consistent methodology for three-step: theoretical, numerical and experimental investigation of a diversity of 2D array topologies in SHM applications. In the first step, the theoretical evaluation is performed using frequency-dependent structure transfer function (STF). STF that defines linear propagation of different LWs modes through the dispersive medium enables theoretical investigation of the particular array performance for a predefined tone-burst excitation signal. A dedicated software tool has been developed for the numerical evaluation of 2D array directional characteristics (beampattern) in a specific structure. The simulations are performed using local interaction simulation approach (LISA), implemented using NVIDIA CUDA graphical computation unit (GPU), which enables time-efficient 3D simulations of LWs propagation. Beampatterns of a 2D array can be to some extend evaluated analytically and using numerical simulations; in most cases, however, they require experimental verification. Using scanning laser vibrometer is proposed for that purpose, in a setup

  2. Construction and repair of highly ordered 2D covalent networks by chemical equilibrium regulation.

    PubMed

    Guan, Cui-Zhong; Wang, Dong; Wan, Li-Jun

    2012-03-21

    The construction of well-ordered 2D covalent networks via the dehydration of di-borate aromatic molecules was successfully realized through introducing a small amount of water into a closed reaction system to regulate the chemical equilibrium.

  3. Properties of interacting 2D chiral tensor network states

    NASA Astrophysics Data System (ADS)

    Bradlyn, Barry; Dubail, Jerome; Read, Nicholas

    2015-03-01

    In a recent paper, Dubail and Read gave a construction for free fermion tensor network states(TNSs) in the chiral p + ip and ν = 1 Chern insulator topological phases in two dimensions, and gave a generalization to Laughlin-like states. However, on general principles these free fermion states must be ground states of gapless local Hamiltonians. In this talk, we address the issue of the energy gap in the interacting states, with a particular focus on the ν = 1 / 2 bosonic Laughlin-like TNS. Through a combination of analytic and numerical arguments, we will show that these states too have gapless local parent Hamiltonians. Nevertheless, we will explore to what degree they can be used as numerical approximations to gapped phases.

  4. Properties of 2D Chiral Tensor Network States

    NASA Astrophysics Data System (ADS)

    Bradlyn, Barry; Dubail, Jerome; Read, Nicholas

    2014-03-01

    States that can be represented as a sum over local auxiliary degress of freedom are known as tensor network states (TNSs). In a recent paper, Dubail and Read gave a construction for free fermion TNSs in the chiral p + ip and ν = 1 Chern insulator topological phases in two dimensions, and gave a generalization to Laughlin-like states. However, on general principles these free fermion states must be ground states of gapless local Hamiltonians. In this talk, we address the issue of what topological properties persist in these gapless states. We show analytically that the DC Hall conductivity for the ν = 1 Chern insulator TNS is quantized, although the conductivity tensor at finite frequency suffers from non-analytic corrections. Additionally, we investigate the issue of the energy gap for the interacting ν = 1 / 2 Laughlin-like TNS through Monte Carlo simulations.

  5. Photo-electroactive ternary chalcogenido-indate-stannates with a unique 2-D porous structure.

    PubMed

    Wu, Jing; Pu, Ya-Yang; Zhao, Xiao-Wei; Qian, Li-Wen; Bian, Guo-Qing; Zhu, Qin-Yu; Dai, Jie

    2015-03-14

    A lot of ternary In-Sb-Q (Q = S, Se) chalcogenido-metalates with amines or complex cations have been recently reported for their diverse structures, however, such a type of In-Sn-Q chalcogenido-metalate has been rarely announced. Herein, we report a series of 2-D In-Sn-Q compounds prepared using a metal-phenanthroline cationic template, [M(Phen)3](In2Sn2Q8)·(amine)·nH2O (M = Ni(II), Fe(II) or Co(II); amine = cyclohexylamine (Cha) or 1,6-diaminohexane (Dah); Q = S or Se). Their anions are isostructural and a 2-D porous network with large 16-tetrahedron-rings. The 2-D network joint of In-Sn-Q is a (In/Sn)3Q3 six-membered ring, which is different from the Sn3Q4 pseudosemicube of most 2-D Sn-Q binary compounds. The materials exhibit photocurrent response properties measured using a photo-electrochemical cell. The result shows that (1) the selenides exhibit more intense photocurrents than the sulfides and (2) the current intensity is related to the metal-phenanthroline cations. PMID:25653182

  6. 2D-CELL: image processing software for extraction and analysis of 2-dimensional cellular structures

    NASA Astrophysics Data System (ADS)

    Righetti, F.; Telley, H.; Leibling, Th. M.; Mocellin, A.

    1992-01-01

    2D-CELL is a software package for the processing and analyzing of photographic images of cellular structures in a largely interactive way. Starting from a binary digitized image, the programs extract the line network (skeleton) of the structure and determine the graph representation that best models it. Provision is made for manually correcting defects such as incorrect node positions or dangling bonds. Then a suitable algorithm retrieves polygonal contours which define individual cells — local boundary curvatures are neglected for simplicity. Using elementary analytical geometry relations, a range of metric and topological parameters describing the population are then computed, organized into statistical distributions and graphically displayed.

  7. Optimal design of 2D digital filters based on neural networks

    NASA Astrophysics Data System (ADS)

    Wang, Xiao-hua; He, Yi-gang; Zheng, Zhe-zhao; Zhang, Xu-hong

    2005-02-01

    Two-dimensional (2-D) digital filters are widely useful in image processing and other 2-D digital signal processing fields,but designing 2-D filters is much more difficult than designing one-dimensional (1-D) ones.In this paper, a new design approach for designing linear-phase 2-D digital filters is described,which is based on a new neural networks algorithm (NNA).By using the symmetry of the given 2-D magnitude specification,a compact express for the magnitude response of a linear-phase 2-D finite impulse response (FIR) filter is derived.Consequently,the optimal problem of designing linear-phase 2-D FIR digital filters is turned to approximate the desired 2-D magnitude response by using the compact express.To solve the problem,a new NNA is presented based on minimizing the mean-squared error,and the convergence theorem is presented and proved to ensure the designed 2-D filter stable.Three design examples are also given to illustrate the effectiveness of the NNA-based design approach.

  8. 2D image classification for 3D anatomy localization: employing deep convolutional neural networks

    NASA Astrophysics Data System (ADS)

    de Vos, Bob D.; Wolterink, Jelmer M.; de Jong, Pim A.; Viergever, Max A.; Išgum, Ivana

    2016-03-01

    Localization of anatomical regions of interest (ROIs) is a preprocessing step in many medical image analysis tasks. While trivial for humans, it is complex for automatic methods. Classic machine learning approaches require the challenge of hand crafting features to describe differences between ROIs and background. Deep convolutional neural networks (CNNs) alleviate this by automatically finding hierarchical feature representations from raw images. We employ this trait to detect anatomical ROIs in 2D image slices in order to localize them in 3D. In 100 low-dose non-contrast enhanced non-ECG synchronized screening chest CT scans, a reference standard was defined by manually delineating rectangular bounding boxes around three anatomical ROIs -- heart, aortic arch, and descending aorta. Every anatomical ROI was automatically identified using a combination of three CNNs, each analyzing one orthogonal image plane. While single CNNs predicted presence or absence of a specific ROI in the given plane, the combination of their results provided a 3D bounding box around it. Classification performance of each CNN, expressed in area under the receiver operating characteristic curve, was >=0.988. Additionally, the performance of ROI localization was evaluated. Median Dice scores for automatically determined bounding boxes around the heart, aortic arch, and descending aorta were 0.89, 0.70, and 0.85 respectively. The results demonstrate that accurate automatic 3D localization of anatomical structures by CNN-based 2D image classification is feasible.

  9. Inversion of 2-D DC resistivity data using rapid optimization and minimal complexity neural network

    NASA Astrophysics Data System (ADS)

    Singh, U. K.; Tiwari, R. K.; Singh, S. B.

    2010-02-01

    The backpropagation (BP) artificial neural network (ANN) technique of optimization based on steepest descent algorithm is known to be inept for its poor performance and does not ensure global convergence. Nonlinear and complex DC resistivity data require efficient ANN model and more intensive optimization procedures for better results and interpretations. Improvements in the computational ANN modeling process are described with the goals of enhancing the optimization process and reducing ANN model complexity. Well-established optimization methods, such as Radial basis algorithm (RBA) and Levenberg-Marquardt algorithms (LMA) have frequently been used to deal with complexity and nonlinearity in such complex geophysical records. We examined here the efficiency of trained LMA and RB networks by using 2-D synthetic resistivity data and then finally applied to the actual field vertical electrical resistivity sounding (VES) data collected from the Puga Valley, Jammu and Kashmir, India. The resulting ANN reconstruction resistivity results are compared with the result of existing inversion approaches, which are in good agreement. The depths and resistivity structures obtained by the ANN methods also correlate well with the known drilling results and geologic boundaries. The application of the above ANN algorithms proves to be robust and could be used for fast estimation of resistive structures for other complex earth model also.

  10. Dispersive dielectric and conductive effects in 2D resistor--capacitor networks

    SciTech Connect

    Hamou, R F F; Macdonald, Ross J.; Tuncer, Enis

    2009-01-01

    How to predict and better understand the effective properties of disordered material mixtures has been a long-standing problem in different research fields, especially in condensed matter physics. In order to address this subject and achieve a better understanding of the frequency-dependent properties of these systems, a large 2D L x L square structure of resistors and capacitors was used to calculate the immittance response of a network formed by random filling of binary conductor/insulator phases with 1000 O resistors and 10 nF capacitors. The effects of percolating clusters on the immittance response were studied statistically through the generation of 10 000 different random network samples at the percolation threshold. The scattering of the imaginary part of the immittance near the dc limit shows a clear separation between the responses of percolating and non-percolating samples, with the gap between their distributions dependent on both network size and applied frequency. These results could be used to monitor connectivity in composite materials. The effects of the content and structure of the percolating path on the nature of the observed dispersion were investigated, with special attention paid to the geometrical fractal concept of the backbone and its influence on the behavior of relaxation-time distributions. For three different resistor-capacitor proportions, the appropriateness of many fitting models was investigated for modeling and analyzing individual resistor-capacitor network dispersed frequency responses using complex-nonlinear-least-squares fitting. Several remarkable new features were identified, including a useful duality relationship and the need for composite fitting models rather than either a simple power law or a single Davidson-Cole one. Good fits of data for fully percolating random networks required two dispersive fitting models in parallel or series, with a cutoff at short times of the distribution of relaxation times of one of them

  11. Higher-Order Neural Networks Applied to 2D and 3D Object Recognition

    NASA Technical Reports Server (NTRS)

    Spirkovska, Lilly; Reid, Max B.

    1994-01-01

    A Higher-Order Neural Network (HONN) can be designed to be invariant to geometric transformations such as scale, translation, and in-plane rotation. Invariances are built directly into the architecture of a HONN and do not need to be learned. Thus, for 2D object recognition, the network needs to be trained on just one view of each object class, not numerous scaled, translated, and rotated views. Because the 2D object recognition task is a component of the 3D object recognition task, built-in 2D invariance also decreases the size of the training set required for 3D object recognition. We present results for 2D object recognition both in simulation and within a robotic vision experiment and for 3D object recognition in simulation. We also compare our method to other approaches and show that HONNs have distinct advantages for position, scale, and rotation-invariant object recognition. The major drawback of HONNs is that the size of the input field is limited due to the memory required for the large number of interconnections in a fully connected network. We present partial connectivity strategies and a coarse-coding technique for overcoming this limitation and increasing the input field to that required by practical object recognition problems.

  12. Two 2D silver(I) coordination polymers derived from mixed ligands: Syntheses, structures, photoluminescent and thermal properties

    NASA Astrophysics Data System (ADS)

    Liu, Fu-Jing; Sun, Di; Li, Yun-Hua; Hao, Hong-Jun; Huang, Rong-Bin; Zheng, Lan-Sun

    2011-07-01

    Two isomers of the aminobenzonitrile were reacted with Ag 2O and phthalic acid under ultrasonic condition, yielding two coordination polymers (CPs) of the formula [Ag 2( o-abn)(pa)] n ( 1) and [Ag 4( m-abn)(pa) 2] n ( 2). They have been characterized by elemental analysis, IR spectrum and single crystal X-ray diffraction. Both complexes 1 and 2 are 2D sheet structures which contain two different Ag(I) aggregates, 1D silver helical chain and 2D silver sheet for 1 and 2, respectively. The o-abn in 1 adopts a rare tridentate μ 3- N, N' N' mode to bridge the neighboring 1D silver chains to form a 2D coordination network, while the m-abn ligand just acts as a monodentate N-donor in 2 and does not contribute to the extension of the 2D silver sheet to the higher dimensionality. As the change of the relative position of amino and cyano groups of the aminobenzonitrile ligand, the dimensionality of the Ag(I) aggregates in 1 and 2 increases from 1D to 2D, which indicates that the relative positions of amino and cyano groups of aminobenzonitrile play an important role in the formation of the diverse Ag(I) aggregates, as a consequence, different 2D coordination networks are produced. Additionally, results about emissive behaviors and thermal stabilities of them are discussed.

  13. Scaling analysis of 2D fractal cellular structures

    NASA Astrophysics Data System (ADS)

    Schliecker, Gudrun

    2001-01-01

    The correlations between topological and metric properties of fractal tessellations are analysed. To this end, Sierpinski cellular structures are constructed for different geometries related to Sierpinski gaskets and to the Apollonian packing of discs. For these geometries, the properties of the distribution of the cells' areas and topologies can be derived analytically. In all cases, an algebraic increase of the cell's average area with its number of neighbours is obtained. This property, unknown from natural cellular structures, confirms previous observations in numerical studies of Voronoi tessellations generated by fractal point sets. In addition, a simple rigorous scaling resp. multiscaling properties relating the shapes and the sizes of the cells are found.

  14. Design of 2D chitosan scaffolds via electrochemical structuring

    PubMed Central

    Altomare, Lina; Guglielmo, Elena; Varoni, Elena Maria; Bertoldi, Serena; Cochis, Andrea; Rimondini, Lia; De Nardo, Luigi

    2014-01-01

    Chitosan (CS) is a versatile biopolymer whose morphological and chemico-physical properties can be designed for a variety of biomedical applications. Taking advantage of its electrolytic nature, cathodic polarization allows CS deposition on electrically conductive substrates, resulting in thin porous structures with tunable morphology. Here we propose an easy method to obtain CS membranes with highly oriented micro-channels for tissue engineering applications, relying on simple control of process parameters and cathodic substrate geometry.   Cathodic deposition was performed on two different aluminum grids in galvanostatic conditions at 6.25 mA cm−2 from CS solution [1g L−1] in acetic acid (pH 3.5). Self-standing thin scaffolds were cross linked either with genipin or epichlorohydrin, weighted, and observed by optical and electron microscopy. Swelling properties at pH 5 and pH 7.4 have been also investigated and tensile tests performed on swollen samples at room temperature. Finally, direct and indirect assays have been performed to evaluate the cytotoxicity at 24 and 72 h. Thin scaffolds with two different oriented porosities (1000µm and 500µm) have been successfully fabricated by electrochemical techniques. Both cross-linking agents did not affected the mechanical properties and cytocompatibility of the resulting structures. Depending on the pH, these structures show interesting swelling properties that can be exploited for drug delivery systems. Moreover, thanks to the possibility of controlling the porosity and the micro-channel orientation, they should be used for the regeneration of tissues requiring a preferential cells orientation, e.g., cardiac patches or ligament regeneration. PMID:25093705

  15. Electronic structure study on 2D hydrogenated Icosagens nitride nanosheets

    NASA Astrophysics Data System (ADS)

    Ramesh, S.; Marutheeswaran, S.; Ramaclus, Jerald V.; Paul, Dolon Chapa

    2014-12-01

    Metal nitride nanosheets has attracted remarkable importance in surface catalysis due to its characteristic ionic nature. In this paper, using density functional theory, we investigate geometric stability and electronic properties of hydrogenated Icosagen nitride nanosheets. Binding energy of the sheets reveals hydrogenation is providing more stability. Band structure of the hydrogenated sheets is found to be n-type semiconductor. Partial density of states shows metals (B, Al, Ga and In) and its hydrogens dominating in the Fermi region. Mulliken charge analysis indications that hydrogenated nanosheets are partially hydridic surface nature except boron nitride.

  16. Adaptive reorganization of 2D molecular nanoporous network induced by coadsorbed guest molecule.

    PubMed

    Zheng, Qing-Na; Wang, Lei; Zhong, Yu-Wu; Liu, Xuan-He; Chen, Ting; Yan, Hui-Juan; Wang, Dong; Yao, Jian-Nian; Wan, Li-Jun

    2014-03-25

    The ordered array of nanovoids in nanoporous networks, such as honeycomb, Kagome, and square, provides a molecular template for the accommodation of "guest molecules". Compared with the commonly studied guest molecules featuring high symmetry evenly incorporated into the template, guest molecules featuring lower symmetry are rare to report. Herein, we report the formation of a distinct patterned superlattice of guest molecules by selective trapping of guest molecules into the honeycomb network of trimesic acid (TMA). Two distinct surface patterns have been achieved by the guest inclusion induced adaptive reconstruction of a 2D molecular nanoporous network. The honeycomb networks can synergetically tune the arrangement upon inclusion of the guest molecules with different core size but similar peripherals groups, resulting in a trihexagonal Kagome or triangular patterns.

  17. Speckle lithography for fabricating Gaussian, quasi-random 2D structures and black silicon structures.

    PubMed

    Bingi, Jayachandra; Murukeshan, Vadakke Matham

    2015-01-01

    Laser speckle pattern is a granular structure formed due to random coherent wavelet interference and generally considered as noise in optical systems including photolithography. Contrary to this, in this paper, we use the speckle pattern to generate predictable and controlled Gaussian random structures and quasi-random structures photo-lithographically. The random structures made using this proposed speckle lithography technique are quantified based on speckle statistics, radial distribution function (RDF) and fast Fourier transform (FFT). The control over the speckle size, density and speckle clustering facilitates the successful fabrication of black silicon with different surface structures. The controllability and tunability of randomness makes this technique a robust method for fabricating predictable 2D Gaussian random structures and black silicon structures. These structures can enhance the light trapping significantly in solar cells and hence enable improved energy harvesting. Further, this technique can enable efficient fabrication of disordered photonic structures and random media based devices.

  18. Speckle lithography for fabricating Gaussian, quasi-random 2D structures and black silicon structures

    PubMed Central

    Bingi, Jayachandra; Murukeshan, Vadakke Matham

    2015-01-01

    Laser speckle pattern is a granular structure formed due to random coherent wavelet interference and generally considered as noise in optical systems including photolithography. Contrary to this, in this paper, we use the speckle pattern to generate predictable and controlled Gaussian random structures and quasi-random structures photo-lithographically. The random structures made using this proposed speckle lithography technique are quantified based on speckle statistics, radial distribution function (RDF) and fast Fourier transform (FFT). The control over the speckle size, density and speckle clustering facilitates the successful fabrication of black silicon with different surface structures. The controllability and tunability of randomness makes this technique a robust method for fabricating predictable 2D Gaussian random structures and black silicon structures. These structures can enhance the light trapping significantly in solar cells and hence enable improved energy harvesting. Further, this technique can enable efficient fabrication of disordered photonic structures and random media based devices. PMID:26679513

  19. Topologic connection between 2-D layered structures and 3-D diamond structures for conventional semiconductors

    PubMed Central

    Wang, Jianwei; Zhang, Yong

    2016-01-01

    When coming to identify new 2D materials, our intuition would suggest us to look from layered instead of 3D materials. However, since graphite can be hypothetically derived from diamond by stretching it along its [111] axis, many 3D materials can also potentially be explored as new candidates for 2D materials. Using a density functional theory, we perform a systematic study over the common Group IV, III–V, and II–VI semiconductors along different deformation paths to reveal new structures that are topologically connected to but distinctly different from the 3D parent structure. Specifically, we explore two major phase transition paths, originating respectively from wurtzite and NiAs structure, by applying compressive and tensile strain along the symmetry axis, and calculating the total energy changes to search for potential metastable states, as well as phonon spectra to examine the structural stability. Each path is found to further split into two branches under tensile strain–low buckled and high buckled structures, which respectively lead to a low and high buckled monolayer structure. Most promising new layered or planar structures identified include BeO, GaN, and ZnO on the tensile strain side, Ge, Si, and GaP on the compressive strain side. PMID:27090430

  20. Topologic connection between 2-D layered structures and 3-D diamond structures for conventional semiconductors.

    PubMed

    Wang, Jianwei; Zhang, Yong

    2016-01-01

    When coming to identify new 2D materials, our intuition would suggest us to look from layered instead of 3D materials. However, since graphite can be hypothetically derived from diamond by stretching it along its [111] axis, many 3D materials can also potentially be explored as new candidates for 2D materials. Using a density functional theory, we perform a systematic study over the common Group IV, III-V, and II-VI semiconductors along different deformation paths to reveal new structures that are topologically connected to but distinctly different from the 3D parent structure. Specifically, we explore two major phase transition paths, originating respectively from wurtzite and NiAs structure, by applying compressive and tensile strain along the symmetry axis, and calculating the total energy changes to search for potential metastable states, as well as phonon spectra to examine the structural stability. Each path is found to further split into two branches under tensile strain-low buckled and high buckled structures, which respectively lead to a low and high buckled monolayer structure. Most promising new layered or planar structures identified include BeO, GaN, and ZnO on the tensile strain side, Ge, Si, and GaP on the compressive strain side. PMID:27090430

  1. Topologic connection between 2-D layered structures and 3-D diamond structures for conventional semiconductors

    NASA Astrophysics Data System (ADS)

    Wang, Jianwei; Zhang, Yong

    2016-04-01

    When coming to identify new 2D materials, our intuition would suggest us to look from layered instead of 3D materials. However, since graphite can be hypothetically derived from diamond by stretching it along its [111] axis, many 3D materials can also potentially be explored as new candidates for 2D materials. Using a density functional theory, we perform a systematic study over the common Group IV, III–V, and II–VI semiconductors along different deformation paths to reveal new structures that are topologically connected to but distinctly different from the 3D parent structure. Specifically, we explore two major phase transition paths, originating respectively from wurtzite and NiAs structure, by applying compressive and tensile strain along the symmetry axis, and calculating the total energy changes to search for potential metastable states, as well as phonon spectra to examine the structural stability. Each path is found to further split into two branches under tensile strain–low buckled and high buckled structures, which respectively lead to a low and high buckled monolayer structure. Most promising new layered or planar structures identified include BeO, GaN, and ZnO on the tensile strain side, Ge, Si, and GaP on the compressive strain side.

  2. Dehydration induced 2D-to-3D crystal-to-crystal network re-assembly and ferromagnetism tuning within two chiral copper(II)-tartrate coordination polymers.

    PubMed

    Liu, Yen-Hsiang; Lee, Szu-Hsuan; Chiang, Jung-Chun; Chen, Po-Chen; Chien, Po-Hsiu; Yang, Chen-I

    2013-12-28

    The synthesis of two homochiral l-tartrate-copper(II) coordination polymers, [Cu2(C4H4O6)2(H2O)2·xH2O]n (1), and [Cu(C4H4O6)]n (2), under hydrothermal conditions, is reported. Compound 1 adopts a 2D layered network structure with a space group of P21, while compound 2 features a 3D network structure with a space group P21212. Interestingly, the 2D layered structure of compound 1 can undergo a crystal-to-crystal network reassembly, with the formation of the 3D network structure of compound 2 under dehydration conditions. Variable temperature and field magnetic studies reveal the existence of a distinct ferromagnetic interaction between Cu(2+) ions as the result of distinct syn-anti carboxylate bridging coordination modes.

  3. Simulation and analysis of solute transport in 2D fracture/pipe networks: the SOLFRAC program.

    PubMed

    Bodin, Jacques; Porel, Gilles; Delay, Fred; Ubertosi, Fabrice; Bernard, Stéphane; de Dreuzy, Jean-Raynald

    2007-01-01

    The Time Domain Random Walk (TDRW) method has been recently developed by Delay and Bodin [Delay, F. and Bodin, J., 2001. Time domain random walk method to simulate transport by advection-dispersion and matrix diffusion in fracture networks. Geophys. Res. Lett., 28(21): 4051-4054.] and Bodin et al. [Bodin, J., Porel, G. and Delay, F., 2003c. Simulation of solute transport in discrete fracture networks using the time domain random walk method. Earth Planet. Sci. Lett., 6566: 1-8.] for simulating solute transport in discrete fracture networks. It is assumed that the fracture network can reasonably be represented by a network of interconnected one-dimensional pipes (i.e. flow channels). Processes accounted for are: (1) advection and hydrodynamic dispersion in the channels, (2) matrix diffusion, (3) diffusion into stagnant zones within the fracture planes, (4) sorption reactions onto the fracture walls and in the matrix, (5) linear decay, and (6) mass sharing at fracture intersections. The TDRW method is handy and very efficient in terms of computation costs since it allows for the one-step calculation of the particle residence time in each bond of the network. This method has been programmed in C++, and efforts have been made to develop an efficient and user-friendly software, called SOLFRAC. This program is freely downloadable at the URL (labo.univ-poitiers.fr/hydrasa/intranet/telechargement.htm). It calculates solute transport into 2D pipe networks, while considering different types of injections and different concepts of local dispersion within each flow channel. Post-simulation analyses are also available, such as the mean velocity or the macroscopic dispersion at the scale of the entire network. The program may be used to evaluate how a given transport mechanism influences the macroscopic transport behaviour of fracture networks. It may also be used, as is the case, e.g., with analytical solutions, to interpret laboratory or field tracer test experiments performed

  4. Protein structure validation and identification from unassigned residual dipolar coupling data using 2D-PDPA.

    PubMed

    Fahim, Arjang; Mukhopadhyay, Rishi; Yandle, Ryan; Prestegard, James H; Valafar, Homayoun

    2013-08-22

    More than 90% of protein structures submitted to the PDB each year are homologous to some previously characterized protein structure. The extensive resources that are required for structural characterization of proteins can be justified for the 10% of the novel structures, but not for the remaining 90%. This report presents the 2D-PDPA method, which utilizes unassigned residual dipolar coupling in order to address the economics of structure determination of routine proteins by reducing the data acquisition and processing time. 2D-PDPA has been demonstrated to successfully identify the correct structure of an array of proteins that range from 46 to 445 residues in size from a library of 619 decoy structures by using unassigned simulated RDC data. When using experimental data, 2D-PDPA successfully identified the correct NMR structures from the same library of decoy structures. In addition, the most homologous X-ray structure was also identified as the second best structural candidate. Finally, success of 2D-PDPA in identifying and evaluating the most appropriate structure from a set of computationally predicted structures in the case of a previously uncharacterized protein Pf2048.1 has been demonstrated. This protein exhibits less than 20% sequence identity to any protein with known structure and therefore presents a compelling and practical application of our proposed work.

  5. Protein structure validation and identification from unassigned residual dipolar coupling data using 2D-PDPA.

    PubMed

    Fahim, Arjang; Mukhopadhyay, Rishi; Yandle, Ryan; Prestegard, James H; Valafar, Homayoun

    2013-01-01

    More than 90% of protein structures submitted to the PDB each year are homologous to some previously characterized protein structure. The extensive resources that are required for structural characterization of proteins can be justified for the 10% of the novel structures, but not for the remaining 90%. This report presents the 2D-PDPA method, which utilizes unassigned residual dipolar coupling in order to address the economics of structure determination of routine proteins by reducing the data acquisition and processing time. 2D-PDPA has been demonstrated to successfully identify the correct structure of an array of proteins that range from 46 to 445 residues in size from a library of 619 decoy structures by using unassigned simulated RDC data. When using experimental data, 2D-PDPA successfully identified the correct NMR structures from the same library of decoy structures. In addition, the most homologous X-ray structure was also identified as the second best structural candidate. Finally, success of 2D-PDPA in identifying and evaluating the most appropriate structure from a set of computationally predicted structures in the case of a previously uncharacterized protein Pf2048.1 has been demonstrated. This protein exhibits less than 20% sequence identity to any protein with known structure and therefore presents a compelling and practical application of our proposed work. PMID:23973992

  6. Protein Structure Validation and Identification from Unassigned Residual Dipolar Coupling Data Using 2D-PDPA

    PubMed Central

    Fahim, Arjang; Mukhopadhyay, Rishi; Yandle, Ryan; Prestegard, James H.; Valafar, Homayoun

    2014-01-01

    More than 90% of protein structures submitted to the PDB each year are homologous to some previously characterized protein structure. The extensive resources that are required for structural characterization of proteins can be justified for the 10% of the novel structures, but not for the remaining 90%. This report presents the 2D-PDPA method, which utilizes unassigned residual dipolar coupling in order to address the economics of structure determination of routine proteins by reducing the data acquisition and processing time. 2D-PDPA has been demonstrated to successfully identify the correct structure of an array of proteins that range from 46 to 445 residues in size from a library of 619 decoy structures by using unassigned simulated RDC data. When using experimental data, 2D-PDPA successfully identified the correct NMR structures from the same library of decoy structures. In addition, the most homologous X-ray structure was also identified as the second best structural candidate. Finally, success of 2D-PDPA in identifying and evaluating the most appropriate structure from a set of computationally predicted structures in the case of a previously uncharacterized protein Pf2048.1 has been demonstrated. This protein exhibits less than 20% sequence identity to any protein with known structure and therefore presents a compelling and practical application of our proposed work. PMID:23973992

  7. Topological evolutionary computing in the optimal design of 2D and 3D structures

    NASA Astrophysics Data System (ADS)

    Burczynski, T.; Poteralski, A.; Szczepanik, M.

    2007-10-01

    An application of evolutionary algorithms and the finite-element method to the topology optimization of 2D structures (plane stress, bending plates, and shells) and 3D structures is described. The basis of the topological evolutionary optimization is the direct control of the density material distribution (or thickness for 2D structures) by the evolutionary algorithm. The structures are optimized for stress, mass, and compliance criteria. The numerical examples demonstrate that this method is an effective technique for solving problems in computer-aided optimal design.

  8. Laser fabrication of 2D and 3D metal nanoparticle structures and arrays.

    PubMed

    Kuznetsov, A I; Kiyan, R; Chichkov, B N

    2010-09-27

    A novel method for fabrication of 2D and 3D metal nanoparticle structures and arrays is proposed. This technique is based on laser-induced transfer of molten metal nanodroplets from thin metal films. Metal nanoparticles are produced by solidification of these nanodroplets. The size of the transferred nanoparticles can be controllably changed in the range from 180 nm to 1500 nm. Several examples of complex 2D and 3D microstructures generated form gold nanoparticles are demonstrated. PMID:20941016

  9. A series of 2D metal-quinolone complexes: Syntheses, structures, and physical properties

    SciTech Connect

    He, Jiang-Hong; Xiao, Dong-Rong; Chen, Hai-Yan; Sun, Dian-Zhen; Yan, Shi-Wei; Wang, Xin; Ye, Zhong-Li; Luo, Qun-Li; Wang, En-Bo

    2013-02-15

    Six novel 2D metal-quinolone complexes, namely [Cd(cfH)(bpdc)]{center_dot}H{sub 2}O (1), [M(norfH)(bpdc)]{center_dot}H{sub 2}O (M=Cd (2) and Mn (3)), [Mn{sub 2}(cfH)(odpa)(H{sub 2}O){sub 3}]{center_dot}0.5H{sub 2}O (4), [Co{sub 2}(norfH)(bpta)({mu}{sub 2}-H{sub 2}O)(H{sub 2}O){sub 2}]{center_dot}H{sub 2}O (5) and [Co{sub 3}(saraH){sub 2}(Hbpta){sub 2}(H{sub 2}O){sub 4}]{center_dot}9H{sub 2}O (6) (cfH=ciprofloxacin, norfH=norfloxacin, saraH=sarafloxacin, bpdc=4,4 Prime -biphenyldicarboxylate, odpa=4,4 Prime -oxydiphthalate, bpta=3,3 Prime ,4,4 Prime -biphenyltetracarboxylate) have been synthesized and characterized. Compounds 1-3 consist of 2D arm-shaped layers based on the 1D {l_brace}M(COO){r_brace}{sub n}{sup n+} chains. Compounds 4 and 5 display 2D structures based on tetranuclear manganese or cobalt clusters with (3,6)-connected kgd topology. Compound 6 exhibits a 2D bilayer structure, which represents the first example of metal-quinolone complexes with 2D bilayer structure. By inspection of the structures of 1-6, it is believed that the long aromatic polycarboxylate ligands are important for the formation of 2D metal-quinolone complexes. The magnetic properties of compounds 3-6 was studied, indicating the existence of antiferromagnetic interactions. Furthermore, the luminescent properties of compounds 1-2 are discussed. - Graphical abstract: Six novel 2D metal-quinolone complexes have been prepared by self-assemblies of the quinolones and metal salts in the presence of long aromatic polycarboxylates. Highlights: Black-Right-Pointing-Pointer Compounds 1-3 consist of novel 2D arm-shaped layers based on the 1D {l_brace}M(COO){r_brace}{sub n}{sup n+} chains. Black-Right-Pointing-Pointer Compounds 4 and 5 are two novel 2D layers based on tetranuclear Mn or Co clusters with kgd topology. Black-Right-Pointing-Pointer Compound 6 is the first example of metal-quinolone complexes with 2D bilayer structure. Black-Right-Pointing-Pointer Compounds 1-6 represent six unusual

  10. Hydrothermal Synthesis, Crystal Structure and Electrochemical Behavior of 2d Hybrid Coordination Polymer

    NASA Astrophysics Data System (ADS)

    Fan, Weiqiang; Zhu, Lin; Shi, Weidong; Chen, Fuxiao; Bai, Hongye; Song, Shuyan; Yan, Yongsheng

    2013-06-01

    A novel metal-organic coordination polymer [Cu(phen)(L)0.5(H2O)]n (H4L = (N,N‧-5,5‧-bis(isophthalic acid)-p-xylylenediamine, and phen = 1,10-phenanthroline) has been hydrothermally synthesized and characterized by elemental analysis, IR, TGA, and single-crystal X-ray diffraction. The crystallographic data show that the title compound crystallizes in monoclinic space group P21/n with a = 10.682(2), b = 15.682(3), c = 11.909(2) Å, β = 91.39(3)°, V = 1994.3(7) Å3, C24H17CuN3O5, Mr = 490.95, Dc = 1.635 g/cm3, F(000) = 1004, Z = 4, μ(MoKα) = 1.141 mm-1, the final R = 0.0418 and wR = 0.0983 for 3578 observed reflections (I > 2σ(I)). The structural analyses reveal that the title compound exhibits shows a 2D layer structure, which are further linked by hydrogen bonding interactions to form a three-dimensional supramolecular network. In addition, the thermal stability and electrochemical behavior of title compound has been studied. CCDC: 900413.

  11. Bernstein copula approach to model direction-length dependency for 2D discrete fracture network simulation

    NASA Astrophysics Data System (ADS)

    Mendoza-Torres, F.; Diaz-Viera, M. A.

    2015-12-01

    In many natural fractured porous media, such as aquifers, soils, oil and geothermal reservoirs, fractures play a crucial role in their flow and transport properties. An approach that has recently gained popularity for modeling fracture systems is the Discrete Fracture Network (DFN) model. This approach consists in applying a stochastic boolean simulation method, also known as object simulation method, where fractures are represented as simplified geometric objects (line segments in 2D and polygons in 3D). One of the shortcomings of this approach is that it usually does not consider the dependency relationships that may exist between the geometric properties of fractures (direction, length, aperture, etc), that is, each property is simulated independently. In this work a method for modeling such dependencies by copula theory is introduced. In particular, a nonparametric model using Bernstein copulas for direction-length fracture dependency in 2D is presented. The application of this method is illustrated in a case study for a fractured rock sample from a carbonate reservoir outcrop.

  12. Some tensor-network diagnostics for a class of 2D SPT states with internal symmetry

    NASA Astrophysics Data System (ADS)

    Prakash, Abhishodh; Wei, Tzu-Chieh

    We demonstrate some diagnostic techniques to characterize certain 2D tensor network states with internal symmetries that are classified by the third group cohomology of the symmetry group. We use the discussions of Else et al. [Phys. Rev. B 90, 235137 (2014)] to extract data that determines the phase of matter from the tensors that make up a specific class of wave functions. This is possible because the symmetry transformation at the `physical' level, which is of product form, translates to a symmetry in the `virtual' level which may no longer be of product form. An appropriate analysis of the virtual-space symmetry helps us obtain the topological information (the 3-cocycle twist) that places the wave function in the classification scheme. This reproduces the results of Chen et al. [Phys. Rev. B 87,155114 (2013)] without using projection operators in merging two 'Matrix Product Operators' of the symmetry representation of two group actions.

  13. Toward IMRT 2D dose modeling using artificial neural networks: A feasibility study

    SciTech Connect

    Kalantzis, Georgios; Vasquez-Quino, Luis A.; Zalman, Travis; Pratx, Guillem; Lei, Yu

    2011-10-15

    Purpose: To investigate the feasibility of artificial neural networks (ANN) to reconstruct dose maps for intensity modulated radiation treatment (IMRT) fields compared with those of the treatment planning system (TPS). Methods: An artificial feed forward neural network and the back-propagation learning algorithm have been used to replicate dose calculations of IMRT fields obtained from PINNACLE{sup 3} v9.0. The ANN was trained with fluence and dose maps of IMRT fields for 6 MV x-rays, which were obtained from the amorphous silicon (a-Si) electronic portal imaging device of Novalis TX. Those fluence distributions were imported to the TPS and the dose maps were calculated on the horizontal midpoint plane of a water equivalent homogeneous cylindrical virtual phantom. Each exported 2D dose distribution from the TPS was classified into two clusters of high and low dose regions, respectively, based on the K-means algorithm and the Euclidian metric in the fluence-dose domain. The data of each cluster were divided into two sets for the training and validation phase of the ANN, respectively. After the completion of the ANN training phase, 2D dose maps were reconstructed by the ANN and isodose distributions were created. The dose maps reconstructed by ANN were evaluated and compared with the TPS, where the mean absolute deviation of the dose and the {gamma}-index were used. Results: A good agreement between the doses calculated from the TPS and the trained ANN was achieved. In particular, an average relative dosimetric difference of 4.6% and an average {gamma}-index passing rate of 93% were obtained for low dose regions, and a dosimetric difference of 2.3% and an average {gamma}-index passing rate of 97% for high dose region. Conclusions: An artificial neural network has been developed to convert fluence maps to corresponding dose maps. The feasibility and potential of an artificial neural network to replicate complex convolution kernels in the TPS for IMRT dose calculations

  14. A 2D zinc-organic network being easily exfoliated into isolated sheets

    NASA Astrophysics Data System (ADS)

    Yu, Guihong; Li, Ruiqing; Leng, Zhihua; Gan, Shucai

    2016-08-01

    A metal-organic aggregate, namely {Zn2Cl2(BBC)}n (BBC = 4,4‧,4‧‧-(benzene-1,3,5-triyl-tris(benzene-4,1-diyl))tribenzoate) was obtained by solvothermal synthesis. Its structure is featured with the Zn2(COO)3 paddle-wheels with two chloride anions on axial positions and hexagonal pores in the layers. The exclusion of water in the precursor and the solvent plays a crucial role in the formation of target compound. This compound can be easily dissolved in alkaline solution and exfoliated into isolated sheets, which shows a novel way for the preparation of 2D materials.

  15. Energy-filtered Electron Transport Structures for Low-power Low-noise 2-D Electronics

    PubMed Central

    Pan, Xuan; Qiu, Wanzhi; Skafidas, Efstratios

    2016-01-01

    In addition to cryogenic techniques, energy filtering has the potential to achieve high-performance low-noise 2-D electronic systems. Assemblies based on graphene quantum dots (GQDs) have been demonstrated to exhibit interesting transport properties, including resonant tunnelling. In this paper, we investigate GQDs based structures with the goal of producing energy filters for next generation lower-power lower-noise 2-D electronic systems. We evaluate the electron transport properties of the proposed GQD device structures to demonstrate electron energy filtering and the ability to control the position and magnitude of the energy passband by appropriate device dimensioning. We also show that the signal-to-thermal noise ratio performance of the proposed nanoscale device can be modified according to device geometry. The tunability of two-dimensional GQD structures indicates a promising route for the design of electron energy filters to produce low-power and low-noise electronics. PMID:27796343

  16. Facial Sketch Synthesis Using 2D Direct Combined Model-Based Face-Specific Markov Network.

    PubMed

    Tu, Ching-Ting; Chan, Yu-Hsien; Chen, Yi-Chung

    2016-08-01

    A facial sketch synthesis system is proposed, featuring a 2D direct combined model (2DDCM)-based face-specific Markov network. In contrast to the existing facial sketch synthesis systems, the proposed scheme aims to synthesize sketches, which reproduce the unique drawing style of a particular artist, where this drawing style is learned from a data set consisting of a large number of image/sketch pairwise training samples. The synthesis system comprises three modules, namely, a global module, a local module, and an enhancement module. The global module applies a 2DDCM approach to synthesize the global facial geometry and texture of the input image. The detailed texture is then added to the synthesized sketch in a local patch-based manner using a parametric 2DDCM model and a non-parametric Markov random field (MRF) network. Notably, the MRF approach gives the synthesized results an appearance more consistent with the drawing style of the training samples, while the 2DDCM approach enables the synthesis of outcomes with a more derivative style. As a result, the similarity between the synthesized sketches and the input images is greatly improved. Finally, a post-processing operation is performed to enhance the shadowed regions of the synthesized image by adding strong lines or curves to emphasize the lighting conditions. The experimental results confirm that the synthesized facial images are in good qualitative and quantitative agreement with the input images as well as the ground-truth sketches provided by the same artist. The representing power of the proposed framework is demonstrated by synthesizing facial sketches from input images with a wide variety of facial poses, lighting conditions, and races even when such images are not included in the training data set. Moreover, the practical applicability of the proposed framework is demonstrated by means of automatic facial recognition tests. PMID:27244737

  17. Amide I'-II' 2D IR spectroscopy provides enhanced protein secondary structural sensitivity.

    PubMed

    Deflores, Lauren P; Ganim, Ziad; Nicodemus, Rebecca A; Tokmakoff, Andrei

    2009-03-11

    We demonstrate how multimode 2D IR spectroscopy of the protein amide I' and II' vibrations can be used to distinguish protein secondary structure. Polarization-dependent amide I'-II' 2D IR experiments on poly-l-lysine in the beta-sheet, alpha-helix, and random coil conformations show that a combination of amide I' and II' diagonal and cross peaks can effectively distinguish between secondary structural content, where amide I' infrared spectroscopy alone cannot. The enhanced sensitivity arises from frequency and amplitude correlations between amide II' and amide I' spectra that reflect the symmetry of secondary structures. 2D IR surfaces are used to parametrize an excitonic model for the amide I'-II' manifold suitable to predict protein amide I'-II' spectra. This model reveals that the dominant vibrational interaction contributing to this sensitivity is a combination of negative amide II'-II' through-bond coupling and amide I'-II' coupling within the peptide unit. The empirically determined amide II'-II' couplings do not significantly vary with secondary structure: -8.5 cm(-1) for the beta sheet, -8.7 cm(-1) for the alpha helix, and -5 cm(-1) for the coil.

  18. A deformed shape monitoring model for building structures based on a 2D laser scanner.

    PubMed

    Choi, Se Woon; Kim, Bub Ryur; Lee, Hong Min; Kim, Yousok; Park, Hyo Seon

    2013-01-01

    High-rise buildings subjected to lateral loads such as wind and earthquake loads must be checked not to exceed the limits on the maximum lateral displacement or the maximum inter-story drift ratios. In this paper, a sensing model for deformed shapes of a building structure in motion is presented. The deformed shape sensing model based on a 2D scanner consists of five modules: (1) module for acquiring coordinate information of a point in a building; (2) module for coordinate transformation and data arrangement for generation of time history of the point; (3) module for smoothing by adjacent averaging technique; (4) module for generation of the displacement history for each story and deformed shape of a building, and (5) module for evaluation of the serviceability of a building. The feasibility of the sensing model based on a 2D laser scanner is tested through free vibration tests of a three-story steel frame structure with a relatively high slenderness ratio of 5.0. Free vibration responses measured from both laser displacement sensors and a 2D laser scanner are compared. In the experimentation, the deformed shapes were obtained from three different methods: the model based on the 2D laser scanner, the direct measurement based on laser displacement sensors, and the numerical method using acceleration data and the displacements from GPS. As a result, it is confirmed that the deformed shape measurement model based on a 2D laser scanner can be a promising alternative for high-rise buildings where installation of laser displacement sensors is impossible.

  19. The influence of pressure on the structure of a 2D uranium(VI) carboxyphosphonoate compound

    SciTech Connect

    Spencer, Elinor C.; Ross, Nancy L.; Surbella, Robert G.; Cahill, Christopher L.

    2014-10-15

    We report the first quantitative analysis of the structural evolution of a uranyl bearing coordination polymer in response to pressure. The material that is central to this study, (UO{sub 2})(O{sub 3}PCH{sub 2}CO{sub 2}H) (1), is constructed from rigid 2D inorganic layers comprising edge sharing UO{sub 7} pentagonal bipyramids cross-linked by [PO{sub 3}(COOH)]{sup 2−} anions. Strong hydrogen bonding interactions exist between the pendent carboxylic acid groups on adjacent layers. Under pressure, 1 exhibits compressional behaviour primarily in the direction perpendicular to the inorganic layers, which is aided by a reduction in the interlayer distance and shifting of the layers with respect to each other. The bulk modulus for the 2D compound 1 is unexpectedly high [18.1(1) GPa] and is within the range reported for 3D CPs assembled from Zn{sup II} cations and inflexible imidazolate anions, and is at the lower end of the range of moduli observed for aluminosilicate zeolites (19–59 GPa). - Graphical Abstract: The compression mechanism and elastic constants for a 2D Uranium(VI) carboxyphosphonoate compound are reported. - Highlights: • The response to pressure of a uranium carboxyphosphonoate compound has been studied. • High-pressure single-crystal XRD data for this 2D uranium compound were collected. • Elastic constants for this material have been determined. • The compression mechanism for the compound has been elucidated.

  20. Free-standing silicene obtained by cooling from 2D liquid Si: structure and thermodynamic properties

    NASA Astrophysics Data System (ADS)

    Van Hoang, Vo; Thi Cam Mi, Huynh

    2014-12-01

    The structure and various thermodynamic properties of free-standing silicene have been studied by computer simulation. Models are obtained by cooling from buckling two-dimensional (2D) liquid Si via molecular dynamics (MD) simulation with Stillinger-Weber interatomic potential. The temperature dependence of total energy, heat capacity, mean ring size and mean coordination number shows that silicenization of 2D liquid Si exhibits a first-order-like behavior. The evolution of radial distribution function upon cooling from the melt also shows that solidification occurs in the system. The final configuration of silicene is analyzed via coordination, bond-angle, interatomic distance and ring distributions or distribution of buckling in the system. 2D visualization of atomic configurations clearly demonstrated that silicene obtained ‘naturally’ by cooling from the melt exhibits various structural previously unreported behaviors. We find the formation of polycrystalline silicene with clear grain boundaries containing various defects including various vacancies, Stone-Wales defects or skew rings and multimembered rings unlike those proposed in the literature. However, atoms in the obtained silicene are mostly involved in six-fold rings, forming a buckling honeycomb structure like that found in practice. We find that buckling is not unique for all atoms in the models although the majority of atoms reveal buckling of the most stable low-buckling silicene found in the literature. The buckling distribution is broad and symmetric. Our comprehensive MD simulation of a relatively large silicene model containing 104 atoms and obtained ‘naturally’ by cooling from the melt provides original insights into the structure and thermodynamics of this important 2D material.

  1. Hydrogen-bond-assisted "gold cold fusion" for fabrication of 2D web structures.

    PubMed

    Mandal, Saikat; Shundo, Atsuomi; Acharya, Somobrata; Hill, Jonathan P; Ji, Qingmin; Ariga, Katsuhiko

    2009-07-01

    Keeping their cool: Fabrication of a 2D weblike nanonetwork of gold was successfully demonstrated through a two-step procedure including complexation of gold precursors to a weblike supramolecular assembly of surfactant followed by in situ reduction of the precursors to gold. Molecular assemblies stabilized by hydrogen bonding provided a sound template, leading to the highly integrated structure of gold through room-temperature (cold) nanostructure fusion.

  2. Membrane proteins: functional and structural studies using reconstituted proteoliposomes and 2-D crystals.

    PubMed

    Rigaud, J-L

    2002-07-01

    Reconstitution of membrane proteins into lipid bilayers is a powerful tool to analyze functional as well as structural areas of membrane protein research. First, the proper incorporation of a purified membrane protein into closed lipid vesicles, to produce proteoliposomes, allows the investigation of transport and/or catalytic properties of any membrane protein without interference by other membrane components. Second, the incorporation of a large amount of membrane proteins into lipid bilayers to grow crystals confined to two dimensions has recently opened a new way to solve their structure at high resolution using electron crystallography. However, reconstitution of membrane proteins into functional proteoliposomes or 2-D crystallization has been an empirical domain, which has been viewed for a long time more like "black magic" than science. Nevertheless, in the last ten years, important progress has been made in acquiring knowledge of lipid-protein-detergent interactions and has permitted to build upon a set of basic principles that has limited the empirical approach of reconstitution experiments. Reconstitution strategies have been improved and new strategies have been developed, facilitating the success rate of proteoliposome formation and 2-D crystallization. This review deals with the various strategies available to obtain proteoliposomes and 2-D crystals from detergent-solubilized proteins. It gives an overview of the methods that have been applied, which may be of help for reconstituting more proteins into lipid bilayers in a form suitable for functional studies at the molecular level and for high-resolution structural analysis.

  3. Formats and Network Protocols for Browser Access to 2D Raster Data

    NASA Astrophysics Data System (ADS)

    Plesea, L.

    2015-12-01

    Tiled web maps in browsers are a major success story, forming the foundation of many current web applications. Enabling tiled data access is the next logical step, and is likely to meet with similar success. Many ad-hoc approaches have already started to appear, and something similar is explored within the Open Geospatial Consortium. One of the main obstacles in making browser data access a reality is the lack of a well-known data format. This obstacle also represents an opportunity to analyze the requirements and possible candidates, applying lessons learned from web tiled image services and protocols. Similar to the image counterpart, a web tile raster data format needs to have good intrinsic compression and be able to handle high byte count data types including floating point. An overview of a possible solution to the format problem, a 2D data raster compression algorithm called Limited Error Raster Compression (LERC) will be presented. In addition to the format, best practices for high request rate HTTP services also need to be followed. In particular, content delivery network (CDN) caching suitability needs to be part of any design, not an after-thought. Last but not least, HTML 5 browsers will certainly be part of any solution since they provide improved access to binary data, as well as more powerful ways to view and interact with the data in the browser. In a simple but relevant application, digital elevation model (DEM) raster data is served as LERC compressed data tiles which are used to generate terrain by a HTML5 scene viewer.

  4. Locally adaptive 2D-3D registration using vascular structure model for liver catheterization.

    PubMed

    Kim, Jihye; Lee, Jeongjin; Chung, Jin Wook; Shin, Yeong-Gil

    2016-03-01

    Two-dimensional-three-dimensional (2D-3D) registration between intra-operative 2D digital subtraction angiography (DSA) and pre-operative 3D computed tomography angiography (CTA) can be used for roadmapping purposes. However, through the projection of 3D vessels, incorrect intersections and overlaps between vessels are produced because of the complex vascular structure, which makes it difficult to obtain the correct solution of 2D-3D registration. To overcome these problems, we propose a registration method that selects a suitable part of a 3D vascular structure for a given DSA image and finds the optimized solution to the partial 3D structure. The proposed algorithm can reduce the registration errors because it restricts the range of the 3D vascular structure for the registration by using only the relevant 3D vessels with the given DSA. To search for the appropriate 3D partial structure, we first construct a tree model of the 3D vascular structure and divide it into several subtrees in accordance with the connectivity. Then, the best matched subtree with the given DSA image is selected using the results from the coarse registration between each subtree and the vessels in the DSA image. Finally, a fine registration is conducted to minimize the difference between the selected subtree and the vessels of the DSA image. In experimental results obtained using 10 clinical datasets, the average distance errors in the case of the proposed method were 2.34±1.94mm. The proposed algorithm converges faster and produces more correct results than the conventional method in evaluations on patient datasets.

  5. Locally adaptive 2D-3D registration using vascular structure model for liver catheterization.

    PubMed

    Kim, Jihye; Lee, Jeongjin; Chung, Jin Wook; Shin, Yeong-Gil

    2016-03-01

    Two-dimensional-three-dimensional (2D-3D) registration between intra-operative 2D digital subtraction angiography (DSA) and pre-operative 3D computed tomography angiography (CTA) can be used for roadmapping purposes. However, through the projection of 3D vessels, incorrect intersections and overlaps between vessels are produced because of the complex vascular structure, which makes it difficult to obtain the correct solution of 2D-3D registration. To overcome these problems, we propose a registration method that selects a suitable part of a 3D vascular structure for a given DSA image and finds the optimized solution to the partial 3D structure. The proposed algorithm can reduce the registration errors because it restricts the range of the 3D vascular structure for the registration by using only the relevant 3D vessels with the given DSA. To search for the appropriate 3D partial structure, we first construct a tree model of the 3D vascular structure and divide it into several subtrees in accordance with the connectivity. Then, the best matched subtree with the given DSA image is selected using the results from the coarse registration between each subtree and the vessels in the DSA image. Finally, a fine registration is conducted to minimize the difference between the selected subtree and the vessels of the DSA image. In experimental results obtained using 10 clinical datasets, the average distance errors in the case of the proposed method were 2.34±1.94mm. The proposed algorithm converges faster and produces more correct results than the conventional method in evaluations on patient datasets. PMID:26824922

  6. Bonding-restricted structure search for novel 2D materials with dispersed C2 dimers.

    PubMed

    Zhang, Cunzhi; Zhang, Shunhong; Wang, Qian

    2016-01-01

    Currently, the available algorithms for unbiased structure searches are primarily atom-based, where atoms are manipulated as the elementary units, and energy is used as the target function without any restrictions on the bonding of atoms. In fact, in many cases such as nanostructure-assembled materials, the structural units are nanoclusters. We report a study of a bonding-restricted structure search method based on the particle swarm optimization (PSO) for finding the stable structures of two-dimensional (2D) materials containing dispersed C2 dimers rather than individual C atoms. The C2 dimer can be considered as a prototype of nanoclusters. Taking Si-C, B-C and Ti-C systems as test cases, our method combined with density functional theory and phonon calculations uncover new ground state geometrical structures for SiC2, Si2C2, BC2, B2C2, TiC2, and Ti2C2 sheets and their low-lying energy allotropes, as well as their electronic structures. Equally important, this method can be applied to other complex systems even containing f elements and other molecular dimers such as S2, N2, B2 and Si2, where the complex orbital orientations require extensive search for finding the optimal orientations to maximize the bonding with the dimers, predicting new 2D materials beyond MXenes (a family of transition metal carbides or nitrides) and dichalcogenide monolayers. PMID:27403589

  7. Bonding-restricted structure search for novel 2D materials with dispersed C2 dimers

    PubMed Central

    Zhang, Cunzhi; Zhang, Shunhong; Wang, Qian

    2016-01-01

    Currently, the available algorithms for unbiased structure searches are primarily atom-based, where atoms are manipulated as the elementary units, and energy is used as the target function without any restrictions on the bonding of atoms. In fact, in many cases such as nanostructure-assembled materials, the structural units are nanoclusters. We report a study of a bonding-restricted structure search method based on the particle swarm optimization (PSO) for finding the stable structures of two-dimensional (2D) materials containing dispersed C2 dimers rather than individual C atoms. The C2 dimer can be considered as a prototype of nanoclusters. Taking Si-C, B-C and Ti-C systems as test cases, our method combined with density functional theory and phonon calculations uncover new ground state geometrical structures for SiC2, Si2C2, BC2, B2C2, TiC2, and Ti2C2 sheets and their low-lying energy allotropes, as well as their electronic structures. Equally important, this method can be applied to other complex systems even containing f elements and other molecular dimers such as S2, N2, B2 and Si2, where the complex orbital orientations require extensive search for finding the optimal orientations to maximize the bonding with the dimers, predicting new 2D materials beyond MXenes (a family of transition metal carbides or nitrides) and dichalcogenide monolayers. PMID:27403589

  8. Bonding-restricted structure search for novel 2D materials with dispersed C2 dimers.

    PubMed

    Zhang, Cunzhi; Zhang, Shunhong; Wang, Qian

    2016-07-12

    Currently, the available algorithms for unbiased structure searches are primarily atom-based, where atoms are manipulated as the elementary units, and energy is used as the target function without any restrictions on the bonding of atoms. In fact, in many cases such as nanostructure-assembled materials, the structural units are nanoclusters. We report a study of a bonding-restricted structure search method based on the particle swarm optimization (PSO) for finding the stable structures of two-dimensional (2D) materials containing dispersed C2 dimers rather than individual C atoms. The C2 dimer can be considered as a prototype of nanoclusters. Taking Si-C, B-C and Ti-C systems as test cases, our method combined with density functional theory and phonon calculations uncover new ground state geometrical structures for SiC2, Si2C2, BC2, B2C2, TiC2, and Ti2C2 sheets and their low-lying energy allotropes, as well as their electronic structures. Equally important, this method can be applied to other complex systems even containing f elements and other molecular dimers such as S2, N2, B2 and Si2, where the complex orbital orientations require extensive search for finding the optimal orientations to maximize the bonding with the dimers, predicting new 2D materials beyond MXenes (a family of transition metal carbides or nitrides) and dichalcogenide monolayers.

  9. Bonding-restricted structure search for novel 2D materials with dispersed C2 dimers

    NASA Astrophysics Data System (ADS)

    Zhang, Cunzhi; Zhang, Shunhong; Wang, Qian

    2016-07-01

    Currently, the available algorithms for unbiased structure searches are primarily atom-based, where atoms are manipulated as the elementary units, and energy is used as the target function without any restrictions on the bonding of atoms. In fact, in many cases such as nanostructure-assembled materials, the structural units are nanoclusters. We report a study of a bonding-restricted structure search method based on the particle swarm optimization (PSO) for finding the stable structures of two-dimensional (2D) materials containing dispersed C2 dimers rather than individual C atoms. The C2 dimer can be considered as a prototype of nanoclusters. Taking Si-C, B-C and Ti-C systems as test cases, our method combined with density functional theory and phonon calculations uncover new ground state geometrical structures for SiC2, Si2C2, BC2, B2C2, TiC2, and Ti2C2 sheets and their low-lying energy allotropes, as well as their electronic structures. Equally important, this method can be applied to other complex systems even containing f elements and other molecular dimers such as S2, N2, B2 and Si2, where the complex orbital orientations require extensive search for finding the optimal orientations to maximize the bonding with the dimers, predicting new 2D materials beyond MXenes (a family of transition metal carbides or nitrides) and dichalcogenide monolayers.

  10. Imaging Meso-Scale Structures in TEXTOR with 2D-ECE

    NASA Astrophysics Data System (ADS)

    Classen, I. G. J.; Jaspers, R. J. E.; Park, H. K.; Spakman, G. W.; van der Pol, M. J.; Domier, C. W.; Donne, A. J. H.; Luhmann, N. C., Jr.; Westerhof, E.; Jakubowski, M. W.; TEXTOR Team

    The detection and control of instabilities in a tokamak is one of the exciting challenges in fusion research on the way to a reactor. Thanks to a combination of an innovative 2D temperature imaging technique (ECEI), a versatile ECRH/ECCD system and a unique possibility to externally induce tearing modes in the plasma, TEXTOR is able to make pioneering contributions in this field. This paper focuses on two meso-scale phenomena in tokamaks: m = 2 tearing modes and magnetic structures in the stochastic boundary. In these cases the 2D-ECEI diagnostic can resolve features not attainable before. In addition the possibility to use the diagnostic for fluctuation measurements is addressed.

  11. pH-induced structural changes of ovalbumin studied by 2D correlation IR spectroscopy

    NASA Astrophysics Data System (ADS)

    Kang, Daehoon; Ryu, Soo Ryeon; Park, Yeonju; Czarnik-Matusewicz, Bogusława; Jung, Young Mee

    2014-07-01

    The secondary structural changes of pH-induced ovalbumin during the transition from native state into intermediate state were studied with the use of 2D correlation spectroscopy and principal component analysis. 2D correlation spectra constructed from the pH-dependent IR spectra of ovalbumin solution revealed the following scenario of the intensity changes with pH decrease. When pH decreased from 5.5 and 3.6 intensity of components attributed to the β-turns, the α-helical elements, and native β-sheets increased. It was caused by protonation induced changes in environment of these elements. When the protonation of the acidic groups were finalized the system adopted the intermediate structure. It was accompanied by weak structural changes that mainly included the β-turns and the α-helices. In extreme acidic conditions at pH below pH 2 the intermediate structure was no longer stable and oligomers rich in the β-sheet structure were formed.

  12. LOCA hydroloads calculations with multidimensional nonlinear fluid/structure interaction. Volume 2: STEALTH 2D/WHAMSE 2D single-phse fluid and elastic structure studies. Final report. [PWR

    SciTech Connect

    Chang, F.H.; Santee, G.E. Jr.; Mortensen, G.A.; Brockett, G.F.; Gross, M.B.; Silling, S.A.; Belytschko, T.

    1981-03-01

    This report, the second in a series of reports for RP-1065, describes the second step in the stepwise approach for developing the three-dimensional, nonlinear, fluid/structure interaction methodology to assess the hydroloads on a large PWR during the subcooled portions of a hypothetical LOCA. The second step in the methodology considers enhancements and special modifications to the 2D STEALTH-HYDRO computer program and the 2D WHAMSE computer program. The 2D STEALTH-HYDRO enhancements consist of a fluid-fluid coupling control-volume model and an orifice control-volume model. The enhancements to 2D WHAMSE include elimination of the implicit integration routines, material models, and structural elements not required for the hydroloads application. In addition the logic for coupling the 2D STEALTH-HYDRO computer program to the 2D WHAMSE computer program is discussed.

  13. Allosteric pathway identification through network analysis: from molecular dynamics simulations to interactive 2D and 3D graphs.

    PubMed

    Allain, Ariane; Chauvot de Beauchêne, Isaure; Langenfeld, Florent; Guarracino, Yann; Laine, Elodie; Tchertanov, Luba

    2014-01-01

    Allostery is a universal phenomenon that couples the information induced by a local perturbation (effector) in a protein to spatially distant regulated sites. Such an event can be described in terms of a large scale transmission of information (communication) through a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. To elaborate a rational description of allosteric coupling, we propose an original approach - MOdular NETwork Analysis (MONETA) - based on the analysis of inter-residue dynamical correlations to localize the propagation of both structural and dynamical effects of a perturbation throughout a protein structure. MONETA uses inter-residue cross-correlations and commute times computed from molecular dynamics simulations and a topological description of a protein to build a modular network representation composed of clusters of residues (dynamic segments) linked together by chains of residues (communication pathways). MONETA provides a brand new direct and simple visualization of protein allosteric communication. A GEPHI module implemented in the MONETA package allows the generation of 2D graphs of the communication network. An interactive PyMOL plugin permits drawing of the communication pathways between chosen protein fragments or residues on a 3D representation. MONETA is a powerful tool for on-the-fly display of communication networks in proteins. We applied MONETA for the analysis of communication pathways (i) between the main regulatory fragments of receptors tyrosine kinases (RTKs), KIT and CSF-1R, in the native and mutated states and (ii) in proteins STAT5 (STAT5a and STAT5b) in the phosphorylated and the unphosphorylated forms. The description of the physical support for allosteric coupling by MONETA allowed a comparison of the mechanisms of (a) constitutive activation induced by equivalent mutations in two RTKs and (b) allosteric regulation in the activated and non

  14. Synthesis, structure and luminescence property of 2D lanthanide complexes with 3-fluorophthalate and oxalate

    SciTech Connect

    Cha, Yu-E; Li, Xia; Song, Shuang

    2012-12-15

    Complexes [Ln{sub 2}(fpht){sub 2}(ox)(H{sub 2}O){sub 4}]{center_dot}H{sub 2}O (Ln=Sm 1, Eu 2, Tb 3 and Dy 4; fpht=3-fluorophthalate and ox=oxalate) have been synthesized and structurally characterized by single crystal X-ray diffraction. The four complexes possess similar 2D framework structures constructed from Ln-fpht double-stranded helices and ox linkages. Complexes 2 and 3 display the characteristic emission {sup 5}D{sub 0}{yields}{sup 7}F{sub J} (J=0-4) transitions of Eu(III) ion and {sup 5}D{sub 4}{yields}{sup 7}F{sub J} (J=6-3) transitions of Tb(III) ion, respectively. The emission decay curves reveal a monoexponential behavior yielding the lifetime values of 0.266{+-}0.002 ms for 2 and 0.733{+-}0.002 ms for 3. The emission spectrum of 1 shows three weak bands corresponding to the characteristic emission {sup 4}G{sub 5/2}{yields}{sup 6}H{sub 5/2}, {sup 4}G{sub 5/2}{yields}{sup 6}H{sub 7/2} and {sup 4}G{sub 5/2}{yields}{sup 6}H{sub 9/2} transitions of Sm(III) ion. The emission spectrum of 4 displays a broad band centered at 438 nm, which comes from the {pi}{sup Low-Asterisk }-{pi} transition of the ligand. - Graphical abstract: Complexes [Ln{sub 2}(fpht){sub 2}(ox)(H{sub 2}O){sub 4}]{center_dot}H{sub 2}O (fpht=3-fluorophthalate, ox=oxalate) possess 2D structures. Sm(III), Eu(III) and Tb(III) complexes show the characteristic fluorescent emission of the Ln(III). Dy(III) complex displays ligand-based luminescent behavior. Highlights: Black-Right-Pointing-Pointer [Ln{sub 2}(fpht){sub 2}(ox)(H{sub 2}O){sub 4}]{center_dot}H{sub 2}O (fpht=3-fluorophthalate; ox=oxalate) show 2D structures. Black-Right-Pointing-Pointer The 2D structures are constructed from Ln-fpht double-stranded helices and ox linkage. Black-Right-Pointing-Pointer The Sm(III), Eu(III) and Tb(III) complexes show the characteristic emission of the Ln(III) ions. Black-Right-Pointing-Pointer Dy(III) complex displays ligand-based luminescent behavior.

  15. Estimation of 3-D pore network coordination number of rocks from watershed segmentation of a single 2-D image

    NASA Astrophysics Data System (ADS)

    Rabbani, Arash; Ayatollahi, Shahab; Kharrat, Riyaz; Dashti, Nader

    2016-08-01

    In this study, we have utilized 3-D micro-tomography images of real and synthetic rocks to introduce two mathematical correlations which estimate the distribution parameters of 3-D coordination number using a single 2-D cross-sectional image. By applying a watershed segmentation algorithm, it is found that the distribution of 3-D coordination number is acceptably predictable by statistical analysis of the network extracted from 2-D images. In this study, we have utilized 25 volumetric images of rocks in order to propose two mathematical formulas. These formulas aim to approximate the average and standard deviation of coordination number in 3-D pore networks. Then, the formulas are applied for five independent test samples to evaluate the reliability. Finally, pore network flow modeling is used to find the error of absolute permeability prediction using estimated and measured coordination numbers. Results show that the 2-D images are considerably informative about the 3-D network of the rocks and can be utilized to approximate the 3-D connectivity of the porous spaces with determination coefficient of about 0.85 that seems to be acceptable considering the variety of the studied samples.

  16. The effect of hydrazine intercalation on the structure and capacitance of 2D titanium carbide (MXene).

    PubMed

    Mashtalir, O; Lukatskaya, M R; Kolesnikov, A I; Raymundo-Piñero, E; Naguib, M; Barsoum, M W; Gogotsi, Y

    2016-04-28

    Herein we show that hydrazine intercalation into 2D titanium carbide (Ti3C2-based MXene) results in changes in its surface chemistry by decreasing the amounts of fluorine, OH surface groups and intercalated water. It also creates a pillaring effect between Ti3C2Tx layers pre-opening the structure and improving the accessability to active sites. The hydrazine treated material has demonstrated a greatly improved capacitance of 250 F g(-1) in acidic electrolytes with an excellent cycling ability for electrodes as thick as 75 μm.

  17. Nonlinear soil-structure interaction calculations simulating the SIMQUAKE experiment using STEALTH 2D

    NASA Technical Reports Server (NTRS)

    Tang, H. T.; Hofmann, R.; Yee, G.; Vaughan, D. K.

    1980-01-01

    Transient, nonlinear soil-structure interaction simulations of an Electric Power Research Institute, SIMQUAKE experiment were performed using the large strain, time domain STEALTH 2D code and a cyclic, kinematically hardening cap soil model. Results from the STEALTH simulations were compared to identical simulations performed with the TRANAL code and indicate relatively good agreement between all the STEALTH and TRANAL calculations. The differences that are seen can probably be attributed to: (1) large (STEALTH) vs. small (TRANAL) strain formulation and/or (2) grid discretization differences.

  18. The effect of hydrazine intercalation on the structure and capacitance of 2D titanium carbide (MXene)

    DOE PAGES

    Mashtalir, O.; Lukatskaya, Maria R.; Kolesnikov, Alexander I.; Raymundo-Pinero, E.; Naguib, Michael; Barsoum, M. W.; Gogotsi, Yury G.

    2016-03-25

    Herein we show that hydrazine intercalation into 2D titanium carbide (Ti3C2-based MXene) results in changes in its surface chemistry by decreasing the amounts of fluorine, OH surface groups and intercalated water. It also creates a pillaring effect between Ti3C2Tx layers pre-opening the structure and improving the accessability to active sites. Furthermore, the hydrazine treated material has demonstrated a greatly improved capacitance of 250 F g–1 in acidic electrolytes with an excellent cycling ability for electrodes as thick as 75 μm.

  19. Correlating Structural and Electronic Degrees of Freedom in 2D Transition Metal Dichalcogenides

    NASA Astrophysics Data System (ADS)

    Tung, I.-Cheng; Zhang, Z.; Seyler, K. L.; Jones, A. M.; Clark, G.; Xiao, D.; Laanait, N.; Xu, X.; Wen, H.

    We have conducted a microscopic study of the interplay between structural and electronic degrees of freedom in two-dimensional (2D) transition metal dichalcogenide (TMD) monolayers, multilayers and heterostructures. Using the recently developed full field x-ray reflection interface microscopy with the photoluminescence microscopic probe capability at the Advanced Photon Source, we demonstrated the x-ray reflection imaging of a monolayer 2D material for the first time. The structural variation across an exfoliated WSe2 monolayer is quantified by interlayer spacing relative to the crystal substrate and the smoothness of the layer. This structural information is correlated with the electronic properties of TMDs characterized by the in-situ photoluminescence measurements. This work is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-SC0012509. The use of Advanced Photon Source is supported by U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-06CH11357.

  20. Adaptive finite element modeling of direct current resistivity in 2-D generally anisotropic structures

    NASA Astrophysics Data System (ADS)

    Yan, Bo; Li, Yuguo; Liu, Ying

    2016-07-01

    In this paper, we present an adaptive finite element (FE) algorithm for direct current (DC) resistivity modeling in 2-D generally anisotropic conductivity structures. Our algorithm is implemented on an unstructured triangular mesh that readily accommodates complex structures such as topography and dipping layers and so on. We implement a self-adaptive, goal-oriented grid refinement algorithm in which the finite element analysis is performed on a sequence of refined grids. The grid refinement process is guided by an a posteriori error estimator. The problem is formulated in terms of total potentials where mixed boundary conditions are incorporated. This type of boundary condition is superior to the Dirichlet type of conditions and improves numerical accuracy considerably according to model calculations. We have verified the adaptive finite element algorithm using a two-layered earth with azimuthal anisotropy. The FE algorithm with incorporation of mixed boundary conditions achieves high accuracy. The relative error between the numerical and analytical solutions is less than 1% except in the vicinity of the current source location, where the relative error is up to 2.4%. A 2-D anisotropic model is used to demonstrate the effects of anisotropy upon the apparent resistivity in DC soundings.

  1. The effect of hydrazine intercalation on the structure and capacitance of 2D titanium carbide (MXene)

    NASA Astrophysics Data System (ADS)

    Mashtalir, O.; Lukatskaya, M. R.; Kolesnikov, A. I.; Raymundo-Piñero, E.; Naguib, M.; Barsoum, M. W.; Gogotsi, Y.

    2016-04-01

    Herein we show that hydrazine intercalation into 2D titanium carbide (Ti3C2-based MXene) results in changes in its surface chemistry by decreasing the amounts of fluorine, OH surface groups and intercalated water. It also creates a pillaring effect between Ti3C2Tx layers pre-opening the structure and improving the accessability to active sites. The hydrazine treated material has demonstrated a greatly improved capacitance of 250 F g-1 in acidic electrolytes with an excellent cycling ability for electrodes as thick as 75 μm.Herein we show that hydrazine intercalation into 2D titanium carbide (Ti3C2-based MXene) results in changes in its surface chemistry by decreasing the amounts of fluorine, OH surface groups and intercalated water. It also creates a pillaring effect between Ti3C2Tx layers pre-opening the structure and improving the accessability to active sites. The hydrazine treated material has demonstrated a greatly improved capacitance of 250 F g-1 in acidic electrolytes with an excellent cycling ability for electrodes as thick as 75 μm. Electronic supplementary information (ESI) available: Characterization methods, additional XRD patterns (Fig. S1) and INS spectra (Fig. S2-S4). See DOI: 10.1039/c6nr01462c

  2. Two 2D Cd(II) coordination polymers based on asymmetrical Schiff-base ligand: Synthesis, crystal structures and luminescent properties

    NASA Astrophysics Data System (ADS)

    Dang, Dong-Bin; Li, Meng-Meng; Bai, Yan; Zhou, Rui-Min

    2013-02-01

    Two new two-dimensional coordination polymers [Cd3L2(SCN)6]n (1) and [CdLI2]n (2) have been synthesized and characterized by IR spectroscopy, elemental analysis, TG technique, XRPD and complete single crystal structure analysis, where L is 4-(pyridine-2-yl)methyleneamino-1,2,4-trizaole. Asymmetrical Schiff-base ligand L with five- and six-membered N-containing heterocyclic rings acts as a tridentate bridging ligand to bind two Cd(II) centers through one terminal Ntriazolyl and one pyridylimine chelate unit in 1 and 2. For polymer 1, tridentate bridging ligands link Cd-(1,3-μ-SCN-) 1D inorganic chains to form a 2D layer network. The existence of Csbnd H⋯π and πsbnd π stacking interactions between 2D hybrid layers further gives rise to a 3D supramolecular network. In comparison with 1, polymer 2 shows a 2D layer network containing hexanuclear macrometallacyclic units. The 2D layers are staggered together through the combination of Csbnd H⋯π and πsbnd π stacking interactions and forming a 3D supramolecular structure. The luminescent properties of the polymers 1 and 2 were investigated in the solid state at room temperature.

  3. Modeling of 2D photonic bandgap structures using a triangular mesh finite difference method

    NASA Astrophysics Data System (ADS)

    Hadley, G. Ronald

    2001-10-01

    A numerical model is presented for computing the out-of- plane losses of a general class of row-defect waveguides formed by the superposition of a 2D photonic crystal onto a slab confinement structure. The usefulness of this model is demonstrated here by calculating the propagation loss of a single-row-defect waveguide composed of hexagonal air holes etched into two different slab structures. The results are interpreted in terms of a simple coupled-mode-theory picture in which loss is due to coupling by the waveguide corrugation between the fundamental and certain radiative slab modes. These calculations show that low-loss photonic crystal waveguides should be possible by carefully engineering the radiation modes of the slab waveguide.

  4. Local electronic structures and 2D topological phase transition of ultrathin Sb films

    NASA Astrophysics Data System (ADS)

    Kim, Sunghwan; Jin, Kyung-Hwan; Park, Joonbum; Kim, Jun Sung; Jhi, Seung-Hoon; Yeom, Han Woong

    We investigate local electronic structures of ultrathin Sb islands and their edges grown on Bi2Te2Se by scanning tunneling microscopy/spectroscopy (STM/STS) and density functional theory (DFT) calculations. The Sb islands of various thickness are grown with atomically well ordered edge structure over the 3 bilayers (BL). On the surfaces and edges of these islands, we clearly resolve edge-localized electronic states by STS measurements, which depend on the thickness. The DFT calculations identify that the strongly localized edge states of 4 and 5 BL films correspond to a quantum spin Hall (QSH) states while the edge states of 3 BL are trivial. Our experimental and theoretical results confirm the 2D topological phase transition of the ultrathin Sb films from trivial to QSH phase. Center for Artificial Low Dimensional Electronic Systems, Institute for Basic Science and Department of Physics, Pohang University of Science and Technology, Korea.

  5. A simple configuration for fabrication of 2D and 3D photonic quasicrystals with complex structures

    NASA Astrophysics Data System (ADS)

    Sun, XiaoHong; Wang, Shuai; Liu, Wei; Jiang, LiuDi

    2016-06-01

    A simple method using a single-prism common-path interferometer is presented for the fabrication of complex quasicrystals in sub-micrometer scales. Multiple types of two-dimensional (2D) and three-dimensional (3D) quasicrystalline structures are designed and their diffraction patterns are obtained by using Fourier Transform method. Multi-fold rotational symmetries are demonstrated and compared. By using this method, a wide range of quasicrystals types can be produced with arbitrary complexities and rotational symmetries. The transmittance studies of 12-fold and 18-fold structures also reveal the existence of complete photonic bandgaps, which also demonstrates increased symmetry and significantly improved characteristics of photonic band-gaps.

  6. Maintaining the genuine structure of 2D materials and catalytic nanoparticles at atomic resolution.

    PubMed

    Calderon, H A; Kisielowski, C; Specht, P; Barton, B; Godinez-Salomon, F; Solorza-Feria, O

    2015-01-01

    The recent development of atomic resolution, low dose-rate electron microscopy allows investigating 2D materials as well as catalytic nano particles without compromising their structural integrity. For graphene and a variety of nanoparticle compositions, it is shown that a critical dose rate exists of <100 e(-)/Å(2) s at 80 keV of electron acceleration that allows maintaining the genuine object structures including their surfaces and edges even if particles are only 3 nm large or smaller. Moreover, it is demonstrated that electron beam-induced phonon excitation from outside the field of view contributes to a contrast degradation in recorded images. These degradation effects can be eliminated by delivering electrons onto the imaged area, only, by using a Nilsonian illumination scheme in combination with a suitable aperture at the electron gun/monochromator assembly.

  7. The influence of pressure on the structure of a 2D uranium(VI) carboxyphosphonoate compound

    NASA Astrophysics Data System (ADS)

    Spencer, Elinor C.; Ross, Nancy L.; Surbella, Robert G.; Cahill, Christopher L.

    2014-10-01

    We report the first quantitative analysis of the structural evolution of a uranyl bearing coordination polymer in response to pressure. The material that is central to this study, (UO2)(O3PCH2CO2H) (1), is constructed from rigid 2D inorganic layers comprising edge sharing UO7 pentagonal bipyramids cross-linked by [PO3(COOH)]2- anions. Strong hydrogen bonding interactions exist between the pendent carboxylic acid groups on adjacent layers. Under pressure, 1 exhibits compressional behaviour primarily in the direction perpendicular to the inorganic layers, which is aided by a reduction in the interlayer distance and shifting of the layers with respect to each other. The bulk modulus for the 2D compound 1 is unexpectedly high [18.1(1) GPa] and is within the range reported for 3D CPs assembled from ZnII cations and inflexible imidazolate anions, and is at the lower end of the range of moduli observed for aluminosilicate zeolites (19-59 GPa).

  8. Structure and interaction in 2D assemblies of tobacco mosaic viruses

    SciTech Connect

    Yang, L.; Wang. S.; Masafumi, F.; Checco, A.; Zhongwei, N.; Wang, Q.

    2009-08-27

    We created two-dimensional (2D) assemblies of tobacco mosaic viruses (TMVs) and characterized their structures using Atomic Force Microscopy (AFM) and X-ray scattering. The TMVs were adsorbed on an oppositely charged, fluid lipid monolayer supported by a solid substrate and submerged in a buffer solution. The lipid monolayer confined the viral particles within a plane, while providing them with lateral mobility so that overall the TMV assembly behaved like a 2D liquid. We controlled the inter-particle interaction by adjusting the chemical condition in the buffer to induce ordered TMV assemblies. We found that the presence of the lipid layer was essential for forming ordered TMV assemblies. Packed TMV assemblies formed on the lipid layer, with an average inter-particle spacing of 42 nm. By introducing Ca2+ ions into the buffer solution, we were able to improve the in-plane order within the TMV assemblies and reduce the average inter-particle spacing to 20 nm, compared to the TMV diameter of 18 nm. Quantitative analysis of the X-ray scattering data shows that the structural order within the TMV assemblies prepared under a Ca{sup 2+}-free buffer solution is consistent with purely repulsive, electrostatic inter-particle interaction. In contrast, the structural order within Ca{sup 2+}-induced TMV assemblies is consistent with the behavior of a fluid of sticky rods, implying the presence of a strong attraction between TMVs. In addition to the screening of Coulomb repulsion, this behavior is likely the result of counterion-induced as well as membrane-mediated attractions.

  9. Structure and Interaction in 2D Assemblies of Tobacco Mosaic Viruses

    SciTech Connect

    Fukuto, M.; Yang, L.; Wang, S.; Fukuto, M.; Checco, A.; Niu, Z.; Wang, Q.

    2009-12-07

    We created two-dimensional (2D) assemblies of tobacco mosaic viruses (TMVs) and characterized their structures using Atomic Force Microscopy (AFM) and X-ray scattering. The TMVs were adsorbed on an oppositely charged, fluid lipid monolayer supported by a solid substrate and submerged in a buffer solution. The lipid monolayer confined the viral particles within a plane, while providing them with lateral mobility so that overall the TMV assembly behaved like a 2D liquid. We controlled the inter-particle interaction by adjusting the chemical condition in the buffer to induce ordered TMV assemblies. We found that the presence of the lipid layer was essential for forming ordered TMV assemblies. Packed TMV assemblies formed on the lipid layer, with an average inter-particle spacing of 42 nm. By introducing Ca{sup 2+} ions into the buffer solution, we were able to improve the in-plane order within the TMV assemblies and reduce the average inter-particle spacing to 20 nm, compared to the TMV diameter of 18 nm. Quantitative analysis of the X-ray scattering data shows that the structural order within the TMV assemblies prepared under a Ca{sup 2+}-free buffer solution is consistent with purely repulsive, electrostatic inter-particle interaction. In contrast, the structural order within Ca{sup 2+}-induced TMV assemblies is consistent with the behavior of a fluid of sticky rods, implying the presence of a strong attraction between TMVs. In addition to the screening of Coulomb repulsion, this behavior is likely the result of counterion-induced as well as membrane-mediated attractions.

  10. Growth of Large and Highly Ordered 2D Crystals of a K+ Channel, Structural Role of Lipidic Environment

    PubMed Central

    De Zorzi, Rita; Nicholson, William V.; Guigner, Jean-Michel; Erne-Brand, Françoise; Vénien-Bryan, Catherine

    2013-01-01

    2D crystallography has proven to be an excellent technique to determine the 3D structure of membrane proteins. Compared to 3D crystallography, it has the advantage of visualizing the protein in an environment closer to the native one. However, producing good 2D crystals is still a challenge and little statistical knowledge can be gained from literature. Here, we present a thorough screening of 2D crystallization conditions for a prokaryotic inwardly rectifying potassium channel (>130 different conditions). Key parameters leading to very large and well-organized 2D crystals are discussed. In addition, the problem of formation of multilayers during the growth of 2D crystals is also addressed. An intermediate resolution projection map of KirBac3.1 at 6 Å is presented, which sheds (to our knowledge) new light on the structure of this channel in a lipid environment. PMID:23870261

  11. Enantiomeric Excess-Tuned 2D Structural Transition: From Heterochiral to Homochiral Supramolecular Assemblies.

    PubMed

    Li, Shu-Ying; Chen, Ting; Wang, Lin; Sun, Bing; Wang, Dong; Wan, Li-Jun

    2016-07-12

    Spontaneous resolution of enantiomers is an intriguing and important phenomenon in surface chirality studies. Herein, we report on a two-dimensional (2D) structural transition from the heterochiral to homochiral assembly tuned by changing the enantiomeric excess (ee) of enantiomers in the solution phase. Enantiomers cocrystallize as racemates on the surface when the ee of the R-enantiomer (or S-enantiomer) remains below a critical value, whereas chiral segregation is achieved, and globally homochiral surfaces composed of exclusively one enantiomer are obtained as the critical ee is exceeded. The heterochiral-homochiral transition is ascribed to the formation of energetically unfavored homochiral molecular dimers under the control of the majority-rules principle at high ee values. Such results present an intriguing phenomenon in chiral ordering at surfaces, promising a new enlightenment toward understanding chiral resolution and the evolution of chirality. PMID:27287273

  12. Self assembly of sandwich-layered 2D silver(I) coordination polymers stabilized by argentophilic interactions: Synthesis, crystal structures and ab initio intramolecular energetics

    NASA Astrophysics Data System (ADS)

    Zorlu, Yunus; Can, Hatice

    2014-11-01

    Two different two-dimensional silver(I) coordination polymers, namely {[Ag2(dcpa)}n (1) and {[Ag2(ma)]}n (2), where dcpa = 4,5-dichlorophthalate; ma = maleate, were synthesized and structurally analyzed by single crystal X-ray diffraction technique. Complexes 1 and 2 represent 2D coordination polymer with metal-organic sandwich type. Two independent Ag(I) ions in both complexes are linked to constructed 2D layer by μ8-η3:η2:η2:η1 (for complex 1) and μ8-η3:η3:η2:η2 (for complex 2) carboxylate bridging fashions. The 2D layers of 1 are further extended into a three-dimensional (3D) supramolecular network by weak Cl⋯Cl interactions while 2D layers of 2 are linked by weak CH⋯O interactions into a 3D supramolecular framework. These two complexes exhibit considerable short Ag-Ag argentophilic interactions. The long-range corrected density functional theory (DFT) method was used to investigate intramolecular energetics, which are responsible for these 2D structures. Natural bond orbital (NBO) analysis with long-range corrected DFT method assists to understand these intramolecular interactions.

  13. Tuning the resonance properties of 2D carbon nanotube networks towards a mechanical resonator

    NASA Astrophysics Data System (ADS)

    Zhan, Haifei; Zhang, Guiyong; Zhang, Baocheng; Bell, John M.; Gu, Yuantong

    2015-08-01

    The capabilities of the mechanical resonator-based nanosensors in detecting ultra-small mass or force shifts have driven a continuing exploration of the palette of nanomaterials for such application purposes. Based on large-scale molecular dynamics simulations, we have assessed the applicability of a new class of carbon nanomaterials for nanoresonator usage, i.e. the single-wall carbon nanotube (SWNT) network. It is found that SWNT networks inherit excellent mechanical properties from the constituent SWNTs, possessing a high natural frequency. However, although a high quality factor is suggested from the simulation results, it is hard to obtain an unambiguous Q-factor due to the existence of vibration modes in addition to the dominant mode. The nonlinearities resulting from these extra vibration modes are found to exist uniformly under various testing conditions including different initial actuations and temperatures. Further testing shows that these modes can be effectively suppressed through the introduction of axial strain, leading to an extremely high quality factor in the order of 109 estimated from the SWNT network with 2% tensile strain. Additional studies indicate that the carbon rings connecting the SWNTs can also be used to alter the vibrational properties of the resulting network. This study suggests that the SWNT network can be a good candidate for applications as nanoresonators.

  14. Computational Study and Analysis of Structural Imperfections in 1D and 2D Photonic Crystals

    SciTech Connect

    Maskaly, Karlene Rosera

    2005-06-01

    increasing RMS roughness. Again, the homogenization approximation is able to predict these results. The problem of surface scratches on 1D photonic crystals is also addressed. Although the reflectivity decreases are lower in this study, up to a 15% change in reflectivity is observed in certain scratched photonic crystal structures. However, this reflectivity change can be significantly decreased by adding a low index protective coating to the surface of the photonic crystal. Again, application of homogenization theory to these structures confirms its predictive power for this type of imperfection as well. Additionally, the problem of a circular pores in 2D photonic crystals is investigated, showing that almost a 50% change in reflectivity can occur for some structures. Furthermore, this study reveals trends that are consistent with the 1D simulations: parameter changes that increase the absolute reflectivity of the photonic crystal will also increase its tolerance to structural imperfections. Finally, experimental reflectance spectra from roughened 1D photonic crystals are compared to the results predicted computationally in this thesis. Both the computed and experimental spectra correlate favorably, validating the findings presented herein.

  15. 2-D Finite Difference Modeling of the D'' Structure Beneath the Eastern Cocos Plate: Part I

    NASA Astrophysics Data System (ADS)

    Helmberger, D. V.; Song, T. A.; Sun, D.

    2005-12-01

    The discovery of phase transition from Perovskite (Pv) to Post-Perovskite (PPv) at depth nears the lowermost mantle has revealed a new view of the earth's D'' layer (Oganov et al. 2004; Murakami et al. 2004). Hernlund et al. (2004) recently pusposed that, depending on the geotherm at the core-mantle boundary (CMB), a double-crossing of the phase boundary by the geotherm at two different depths may also occur. To explore these new findings, we adopt 2-D finite difference scheme (Helmberger and Vidale, 1988) to model wave propagation in rapidly varying structure. We collect broadband waveform data recorded by several Passcal experiments, such as La Ristra transect and CDROM transect in the southwest US to constrain the lateral variations in D'' structure. These data provide fairly dense sampling (~ 20 km) in the lowermost mantle beneath the eastern Cocos plate. Since the source-receiver paths are mostly in the same azimuth, we make 2-D cross-sections from global tomography model (Grand, 2002) and compute finite difference synthetics. We modify the lowermost mantle below 2500 km with constraints from transverse-component waveform data at epicentral distances of 70-82 degrees in the time window between S and ScS, essentially foward modeling waveforms. Assuming a velocity jump of 3 % at D'', our preferred model shows that the D'' topography deepens from the north to the south by about 120 km over a lateral distance of 300 km. Such large topography jumps have been proposed by Thomas et al. (2004) using data recorded by TriNet. In addition, there is a negative velocity jump (-3 %) 100 km above the CMB in the south. This simple model compare favorably with results from a study by Sun, Song and Helmberger (2005), who follow Sidorin et al. (1999) approach and produce a thermodynamically consistent velocity model with Pv-PPv phase boundary. It appears that much of this complexity exists in Grand's tomographic maps with rapid variation in velocities just above the D''. We also

  16. 2D and 3D multipactor modeling in dielectric-loaded accelerator structures

    NASA Astrophysics Data System (ADS)

    Sinitsyn, Oleksandr; Nusinovich, Gregory; Antonsen, Thomas

    2010-11-01

    Multipactor (MP) is known as the avalanche growth of the number of secondary electrons emitted from a solid surface exposed to an RF electric field under vacuum conditions. MP is a severe problem in modern rf systems and, therefore, theoretical and experimental studies of MP are of great interest to the researchers working in various areas of physics and engineering. In this work we present results of MP studies in dielectric-loaded accelerator (DLA) structures. First, we show simulation results obtained with the use of the 2D self-consistent MP model (O. V. Sinitsyn, et. al., Phys. Plasmas, vol. 16, 073102 (2009)) and compare those to experimental ones obtained during recent extensive studies of DLA structures performed by Argonne National Laboratory, Naval Research Laboratory, SLAC National Accelerator Laboratory and Euclid TechLabs (C. Jing, et al., IEEE Trans. Plasma Sci., vol. 38, pp. 1354-1360 (2010)). Then we present some new results of 3D analysis of MP which include studies of particle trajectories and studies of MP development at the early stage.

  17. An interpolating 2D pixel readout structure for synchrotron X-ray diffraction in protein crystallography

    NASA Astrophysics Data System (ADS)

    Besch, H. J.; Junk, M.; Meißner, W.; Sarvestani, A.; Stiehler, R.; Walenta, A. H.

    1997-02-01

    The high rates available now at synchrotron beam lines ask for detectors allowing online measurements with good spatial resolution and a precise intensity measurement. For this purpose gaseous detectors operating in the single photon counting mode are well suited. An interpolating 2D pixel readout structure will be presented. It has been tested as backplane of a MSGC or a CAT-detector (recently developed by the group of M. Lemonnier at LURE), and it operates on the principle of resistive charge partition, allowing asynchronous readout. A resolution of 200 μm is reached. Under similar conditions the energy resolution from the signals of the readout structure presented is nearly the same as that of standard readout. In combination with a CAT an energy resolution of 20% is reached. A prototype of 64 channels with a sensitive area of 14 mm × 14 mm was tested at the synchrotron at LURE (Orsay). Diffraction patterns from a collagenase protein crystal were measured and rocking curves were obtained with an angular resolution of 1.5 × 10 -5.

  18. Identifying Key Structural Features and Spatial Relationships in Archean Microbialites Using 2D and 3D Visualization Methods

    NASA Astrophysics Data System (ADS)

    Stevens, E. W.; Sumner, D. Y.

    2009-12-01

    Microbialites in the 2521 ± 3 Ma Gamohaan Formation, South Africa, have several different end-member morphologies which show distinct growth structures and spatial relationships. We characterized several growth structures and spatial relationships in two samples (DK20 and 2_06) using a combination of 2D and 3D analytical techniques. There are two main goals in studying complicated microbialites with a combination of 2D and 3D methods. First, one can better understand microbialite growth by identifying important structures and structural relationships. Once structures are identified, the order in which the structures formed and how they are related can be inferred from observations of crosscutting relationships. Second, it is important to use both 2D and 3D methods to correlate 3D observations with those in 2D that are more common in the field. Combining analysis provides significantly more insight into the 3D morphology of microbial structures. In our studies, 2D analysis consisted of describing polished slabs and serial sections created by grinding down the rock 100 microns at a time. 3D analysis was performed on serial sections visualized in 3D using Vrui and 3DVisualizer software developed at KeckCAVES, UCD (http://keckcaves.org). Data were visualized on a laptop and in an immersive cave system. Both samples contain microbial laminae and more vertically orients microbial "walls" called supports. The relationships between these features created voids now filled with herringbone and blocky calcite crystals. DK20, a classic plumose structure, contains two types of support structures. Both are 1st order structures (1st order structures with organic inclusions and 1st without organic inclusions) interpreted as planar features based on 2D analysis. In the 2D analysis the 1st order structures show v branching relationships as well as single cuspate relationships (two 1st order structures with inclusions merging upward), and single tented relationships (three supports

  19. The development and testing of a 2D laboratory seismic modelling system for heterogeneous structure investigations

    NASA Astrophysics Data System (ADS)

    Mo, Yike; Greenhalgh, Stewart A.; Robertsson, Johan O. A.; Karaman, Hakki

    2015-05-01

    Lateral velocity variations and low velocity near-surface layers can produce strong scattered and guided waves which interfere with reflections and lead to severe imaging problems in seismic exploration. In order to investigate these specific problems by laboratory seismic modelling, a simple 2D ultrasonic model facility has been recently assembled within the Wave Propagation Lab at ETH Zurich. The simulated geological structures are constructed from 2 mm thick metal and plastic sheets, cut and bonded together. The experiments entail the use of a piezoelectric source driven by a pulse amplifier at ultrasonic frequencies to generate Lamb waves in the plate, which are detected by piezoelectric receivers and recorded digitally on a National Instruments recording system, under LabVIEW software control. The 2D models employed were constructed in-house in full recognition of the similitude relations. The first heterogeneous model features a flat uniform low velocity near-surface layer and deeper dipping and flat interfaces separating different materials. The second model is comparable but also incorporates two rectangular shaped inserts, one of low velocity, the other of high velocity. The third model is identical to the second other than it has an irregular low velocity surface layer of variable thickness. Reflection as well as transmission experiments (crosshole & vertical seismic profiling) were performed on each model. The two dominant Lamb waves recorded are the fundamental symmetric mode (non-dispersive) and the fundamental antisymmetric (flexural) dispersive mode, the latter normally being absent when the source transducer is located on a model edge but dominant when it is on the flat planar surface of the plate. Experimental group and phase velocity dispersion curves were determined and plotted for both modes in a uniform aluminium plate. For the reflection seismic data, various processing techniques were applied, as far as pre-stack Kirchhoff migration. The

  20. Power Versus Spectrum 2-D Sensing in Energy Harvesting Cognitive Radio Networks

    NASA Astrophysics Data System (ADS)

    Zhang, Yanyan; Han, Weijia; Li, Di; Zhang, Ping; Cui, Shuguang

    2015-12-01

    Energy harvester based cognitive radio is a promising solution to address the shortage of both spectrum and energy. Since the spectrum access and power consumption patterns are interdependent, and the power value harvested from certain environmental sources are spatially correlated, the new power dimension could provide additional information to enhance the spectrum sensing accuracy. In this paper, the Markovian behavior of the primary users is considered, based on which we adopt a hidden input Markov model to specify the primary vs. secondary dynamics in the system. Accordingly, we propose a 2-D spectrum and power (harvested) sensing scheme to improve the primary user detection performance, which is also capable of estimating the primary transmit power level. Theoretical and simulated results demonstrate the effectiveness of the proposed scheme, in term of the performance gain achieved by considering the new power dimension. To the best of our knowledge, this is the first work to jointly consider the spectrum and power dimensions for the cognitive primary user detection problem.

  1. Mercury (I) nitroprusside: A 2D structure supported on homometallic interactions

    SciTech Connect

    Osiry, H.; Cano, A.; Reguera, L.; Lemus-Santana, A.A.; Reguera, E.

    2015-01-15

    The pentacyanonitrosylferrate complex anion, [Fe(CN){sub 5}NO]{sup 2−}, forms an insoluble solid with Hg(I) ion, of formula unit Hg{sub 2}[Fe(CN){sub 5}NO]·2H{sub 2}O, whose crystal structure and related properties are unknown. This contribution reports the preparation of that compound by the precipitation method and its structural study from X-ray powder patterns complemented with spectroscopic information from IR, Raman, and UV–vis techniques. The crystal structure was solved ab initio and then refined using the Rietveld method. The solid crystallizes with a triclinic unit cell, in the P−1 space group, with cell parameters a=10.1202(12), b=10.1000(13), c=7.4704(11) Å; α=110.664(10), β=110.114(10), γ=104.724(8) °. Within the unit cell, two formula units are accommodated (Z=2). It adopts a layered structure related with the coordination of the equatorial CN groups at their N end to the Hg atoms while the axial CN ligand remains unlinked. Within the layers neighboring Hg{sub 2}[Fe(CN){sub 5}NO] building units remain linked through four relatively strong Hg–Hg interactions, with an interatomic distance of 2.549(3) Å. The charge donation from the equatorial CN groups through their 5σ orbitals results into an increase for the electron density on the Hg atoms, which strengths the Hg–Hg bond. In the Raman spectrum, that metal–metal bond is detected as a stretching vibration band at 167 cm{sup −1}. The available free volume between neighboring layers accommodates two water molecules, which are stabilized within the framework through hydrogen bonds with the N end of the unlinked axial CN group. The removal of these weakly bonded water molecules results in structural disorder for the material 3D framework. - Graphical abstract: Assembling of Hg{sub 2}[Fe(CN){sub 5}NO] units through Hg–Hg interactions. - Highlights: • Homometallic Hg–Hg interactions in metal nitroprusside. • 2D structure supported on metal–metal interactions. • Crystal

  2. Topological defect formation in 1D and 2D spin chains realized by network of optical parametric oscillators

    NASA Astrophysics Data System (ADS)

    Hamerly, Ryan; Inaba, Kensuke; Inagaki, Takahiro; Takesue, Hiroki; Yamamoto, Yoshihisa; Mabuchi, Hideo

    2016-09-01

    A network of optical parametric oscillators (OPOs) is used to simulate classical Ising and XY spin chains. The collective nonlinear dynamics of this network, driven by quantum noise rather than thermal fluctuations, seeks out the Ising/XY ground state as the system transitions from below to above the lasing threshold. We study the behavior of this “Ising machine” for three canonical problems: a 1D ferromagnetic spin chain, a 2D square lattice and problems where next-nearest-neighbor couplings give rise to frustration. If the pump turn-on time is finite, topological defects form (domain walls for the Ising model, winding number and vortices for XY) and their density can be predicted from a numerical model involving a linear “growth stage” and a nonlinear “saturation stage”. These predictions are compared against recent data for a 10,000-spin 1D Ising machine.

  3. Dynamic force measurement of rearrangements in a 2D network of droplets

    NASA Astrophysics Data System (ADS)

    Barkley, Solomon; Backholm, Matilda; Dalnoki-Veress, Kari

    2015-03-01

    The interaction between two liquid droplets in an immiscible liquid is well understood. However, the emulsions relevant to biological and industrial processes involve high concentrations of these droplets, and multi-body effects cannot be ignored. As droplets rearrange in response to a disturbance, the importance of individual pair-wise interactions between droplets changes with the geometry of neighbours. Here we report on an experimental setup consisting of a two- dimensional network of monodisperse droplets stabilized with a surfactant. The system is studied with micropipette deflection, which permits direct measurement of forces along with simultaneous imaging of the droplet network. One micropipette is used to apply a tensile or compressive force to the droplet cluster, while a second pipette acts as a force-transducing cantilever, deflecting in response to rearrangements of the droplets.

  4. Guided Lamb wave based 2-D spiral phased array for structural health monitoring of thin panel structures

    NASA Astrophysics Data System (ADS)

    Yoo, Byungseok

    2011-12-01

    In almost all industries of mechanical, aerospace, and civil engineering fields, structural health monitoring (SHM) technology is essentially required for providing the reliable information of structural integrity of safety-critical structures, which can help reduce the risk of unexpected and sometimes catastrophic failures, and also offer cost-effective inspection and maintenance of the structures. State of the art SHM research on structural damage diagnosis is focused on developing global and real-time technologies to identify the existence, location, extent, and type of damage. In order to detect and monitor the structural damage in plate-like structures, SHM technology based on guided Lamb wave (GLW) interrogation is becoming more attractive due to its potential benefits such as large inspection area coverage in short time, simple inspection mechanism, and sensitivity to small damage. However, the GLW method has a few critical issues such as dispersion nature, mode conversion and separation, and multiple-mode existence. Phased array technique widely used in all aspects of civil, military, science, and medical industry fields may be employed to resolve the drawbacks of the GLW method. The GLW-based phased array approach is able to effectively examine and analyze complicated structural vibration responses in thin plate structures. Because the phased sensor array operates as a spatial filter for the GLW signals, the array signal processing method can enhance a desired signal component at a specific direction while eliminating other signal components from other directions. This dissertation presents the development, the experimental validation, and the damage detection applications of an innovative signal processing algorithm based on two-dimensional (2-D) spiral phased array in conjunction with the GLW interrogation technique. It starts with general backgrounds of SHM and the associated technology including the GLW interrogation method. Then, it is focused on the

  5. Contact transfer length investigation of a 2D nanoparticle network by scanning probe microscopy.

    PubMed

    Ruiz-Vargas, Carlos S; Reissner, Patrick A; Wagner, Tino; Wyss, Roman M; Park, Hyung Gyu; Stemmer, Andreas

    2015-09-11

    Nanoparticle network devices find growing application in sensing and electronics. One recurring challenge in the design and fabrication of this class of devices is ensuring a stable interface via robust yet unobstructive electrodes. A figure of merit which dictates the minimum electrode overlap required for optimal charge injection into the network is the contact transfer length. However, we find that traditional contact characterization using the transmission line model, an indirect method which requires extrapolation, is insufficient for network devices. Instead, we apply Kelvin probe force microscopy to characterize the contact resistance by imaging the surface potential with nanometer resolution. We then use scanning probe lithography to directly investigate the contact transfer length. We have determined the transfer length in graphene contacted devices to be 200-400 nm, thus apt for further device reduction which is often necessary for on-site sensing applications. Simulations from a two-dimensional resistor model support our observations and are expected to be an important tool for further optimizing the design of nanoparticle-based devices. PMID:26291069

  6. Probing Magnetism in 2D Molecular Networks after in Situ Metalation by Transition Metal Atoms.

    PubMed

    Schouteden, K; Ivanova, Ts; Li, Z; Iancu, V; Janssens, E; Van Haesendonck, C

    2015-03-19

    Metalated molecules are the ideal building blocks for the bottom-up fabrication of, e.g., two-dimensional arrays of magnetic particles for spintronics applications. Compared to chemical synthesis, metalation after network formation by an atom beam can yield a higher degree of control and flexibility and allows for mixing of different types of magnetic atoms. We report on successful metalation of tetrapyridyl-porphyrins (TPyP) by Co and Cr atoms, as demonstrated by scanning tunneling microscopy experiments. For the metalation, large periodic networks formed by the TPyP molecules on a Ag(111) substrate are exposed in situ to an atom beam. Voltage-induced dehydrogenation experiments support the conclusion that the porphyrin macrocycle of the TPyP molecule incorporates one transition metal atom. The newly synthesized Co-TPyP and Cr-TPyP complexes exhibit striking differences in their electronic behavior, leading to a magnetic character for Cr-TPyP only as evidenced by Kondo resonance measurements.

  7. Fracture network evaluation program (FraNEP): A software for analyzing 2D fracture trace-line maps

    NASA Astrophysics Data System (ADS)

    Zeeb, Conny; Gomez-Rivas, Enrique; Bons, Paul D.; Virgo, Simon; Blum, Philipp

    2013-10-01

    Fractures, such as joints, faults and veins, strongly influence the transport of fluids through rocks by either enhancing or inhibiting flow. Techniques used for the automatic detection of lineaments from satellite images and aerial photographs, LIDAR technologies and borehole televiewers significantly enhanced data acquisition. The analysis of such data is often performed manually or with different analysis software. Here we present a novel program for the analysis of 2D fracture networks called FraNEP (Fracture Network Evaluation Program). The program was developed using Visual Basic for Applications in Microsoft Excel™ and combines features from different existing software and characterization techniques. The main novelty of FraNEP is the possibility to analyse trace-line maps of fracture networks applying the (1) scanline sampling, (2) window sampling or (3) circular scanline and window method, without the need of switching programs. Additionally, binning problems are avoided by using cumulative distributions, rather than probability density functions. FraNEP is a time-efficient tool for the characterisation of fracture network parameters, such as density, intensity and mean length. Furthermore, fracture strikes can be visualized using rose diagrams and a fitting routine evaluates the distribution of fracture lengths. As an example of its application, we use FraNEP to analyse a case study of lineament data from a satellite image of the Oman Mountains.

  8. 2D and 3D GPR imaging of structural ceilings in historic and existing constructions

    NASA Astrophysics Data System (ADS)

    Colla, Camilla

    2014-05-01

    GPR applications in civil engineering are to date quite diversified. With respect to civil constructions and monumental buildings, detection of voids, cavities, layering in structural elements, variation of geometry, of moisture content, of materials, areas of decay, defects, cracks have been reported in timber, concrete and masonry elements. Nonetheless, many more fields of investigation remain unexplored. This contribution gives an account of a variety of examples of structural ceilings investigation by GPR radar in reflection mode, either as 2D or 3D data acquisition and visualisation. Ceilings have a pre-eminent role in buildings as they contribute to a good structural behaviour of the construction. Primarily, the following functions can be listed for ceilings: a) they carry vertical dead and live loads on floors and distribute such loads to the vertical walls; b) they oppose to external horizontal forces such as wind loads and earthquakes helping to transfer such forces from the loaded element to the other walls; c) they contribute to create the box skeleton and behaviour of a building, connecting the different load bearing walls and reducing the slenderness and flexural instability of such walls. Therefore, knowing how ceilings are made in specific buildings is of paramount importance for architects and structural engineers. According to the type of building and age of construction, ceilings may present very different solutions and materials. Moreover, in existing constructions, ceilings may have been substituted, modified or strengthened due to material decay or to change of use of the building. These alterations may often go unrecorded in technical documentation or technical drawings may be unavailable. In many cases, the position, orientation and number of the load carrying elements in ceilings may be hidden or not be in sight, due for example to the presence of false ceilings or to technical plants. GPR radar can constitute a very useful tool for

  9. Detecting 2D symmetry-protected topological phases with the tensor-network method

    NASA Astrophysics Data System (ADS)

    Huang, Ching-Yu; Wei, Tzu-Chieh

    Symmetry-protected topological (SPT) phases exhibit nontrivial order if symmetry is respected but are adiabatically connected to the trivial product phase if symmetry is not respected. However, unlike the symmetry breaking phase, there is no local order parameter for SPT phases. Here we employ a tensor-network method to compute the topological invariants characterized by the simulated modular S and T matrices proposed by Hung and Wen to study a transition in a one-parameter family of wavefunctions which are Z2 symmetric. The studied wavefunctions are in some sense the SPT analog of Z2 topological states under a string tension. The numerically obtained S and T matrices are able to characterize the two different phases and identify the transition point.

  10. Structural and Functional Analysis of JMJD2D Reveals Molecular Basis for Site-Specific Demethylation among JMJD2 Demethylases

    SciTech Connect

    Krishnan, Swathi; Trievel, Raymond C.

    2013-01-08

    We found that JMJD2 lysine demethylases (KDMs) participate in diverse genomic processes. Most JMJD2 homologs display dual selectivity toward H3K9me3 and H3K36me3, with the exception of JMJD2D, which is specific for H3K9me3. Here, we report the crystal structures of the JMJD2D•2-oxoglutarate•H3K9me3 ternary complex and JMJD2D apoenzyme. Utilizing structural alignments with JMJD2A, molecular docking, and kinetic analysis with an array of histone peptide substrates, we elucidate the specific signatures that permit efficient recognition of H3K9me3 by JMJD2A and JMJD2D, and the residues in JMJD2D that occlude H3K36me3 demethylation. Surprisingly, these results reveal that JMJD2A and JMJD2D exhibit subtle yet important differences in H3K9me3 recognition, despite the overall similarity in the substrate-binding conformation. Further, we show that H3T11 phosphorylation abrogates demethylation by JMJD2 KDMs. These studies reveal the molecular basis for JMJD2 site specificity and provide a framework for structure-based design of selective inhibitors of JMJD2 KDMs implicated in disease.

  11. A Fast Parallel Algorithm for Selected Inversion of Structured Sparse Matrices with Application to 2D Electronic Structure Calculations

    SciTech Connect

    Lin, Lin; Yang, Chao; Lu, Jiangfeng; Ying, Lexing; E, Weinan

    2009-09-25

    We present an efficient parallel algorithm and its implementation for computing the diagonal of $H^-1$ where $H$ is a 2D Kohn-Sham Hamiltonian discretized on a rectangular domain using a standard second order finite difference scheme. This type of calculation can be used to obtain an accurate approximation to the diagonal of a Fermi-Dirac function of $H$ through a recently developed pole-expansion technique \\cite{LinLuYingE2009}. The diagonal elements are needed in electronic structure calculations for quantum mechanical systems \\citeHohenbergKohn1964, KohnSham 1965,DreizlerGross1990. We show how elimination tree is used to organize the parallel computation and how synchronization overhead is reduced by passing data level by level along this tree using the technique of local buffers and relative indices. We analyze the performance of our implementation by examining its load balance and communication overhead. We show that our implementation exhibits an excellent weak scaling on a large-scale high performance distributed parallel machine. When compared with standard approach for evaluating the diagonal a Fermi-Dirac function of a Kohn-Sham Hamiltonian associated a 2D electron quantum dot, the new pole-expansion technique that uses our algorithm to compute the diagonal of $(H-z_i I)^-1$ for a small number of poles $z_i$ is much faster, especially when the quantum dot contains many electrons.

  12. Metal Decoration Effects on the Gas-Sensing Properties of 2D Hybrid-Structures on Flexible Substrates

    PubMed Central

    Cho, Byungjin; Yoon, Jongwon; Lim, Sung Kwan; Kim, Ah Ra; Choi, Sun-Young; Kim, Dong-Ho; Lee, Kyu Hwan; Lee, Byoung Hun; Ko, Heung Cho; Hahm, Myung Gwan

    2015-01-01

    We have investigated the effects of metal decoration on the gas-sensing properties of a device with two-dimensional (2D) molybdenum disulfide (MoS2) flake channels and graphene electrodes. The 2D hybrid-structure device sensitively detected NO2 gas molecules (>1.2 ppm) as well as NH3 (>10 ppm). Metal nanoparticles (NPs) could tune the electronic properties of the 2D graphene/MoS2 device, increasing sensitivity to a specific gas molecule. For instance, palladium NPs accumulate hole carriers of graphene/MoS2, electronically sensitizing NH3 gas molecules. Contrarily, aluminum NPs deplete hole carriers, enhancing NO2 sensitivity. The synergistic combination of metal NPs and 2D hybrid layers could be also applied to a flexible gas sensor. There was no serious degradation in the sensing performance of metal-decorated MoS2 flexible devices before/after 5000 bending cycles. Thus, highly sensitive and endurable gas sensor could be achieved through the metal-decorated 2D hybrid-structure, offering a useful route to wearable electronic sensing platforms. PMID:26404279

  13. Electronic structure of disordered CuPd alloys by positron-annihilation 2D-ACAR

    SciTech Connect

    Smedskjaer, L.C.; Benedek, R.; Siegel, R.W.; Legnini, D.G.; Stahulak, M.D.; Bansil, A.

    1988-01-01

    We report 2D-ACAR experiments and KKR CPA calculations on alpha-phase single-crystal Cu/sub 1-x/Pd/sub x/ in the range x less than or equal to 0.25. The flattening of the Fermi surface near (110) with increasing x predicted by theory is confirmed by our experimental results. 16 refs., 2 figs.

  14. Two novel 2D lanthanide sulfate frameworks: Syntheses, structures, and luminescence properties

    NASA Astrophysics Data System (ADS)

    Li, Zhong-Yi; Zhang, Chi; Zhang, Fu-Li; Zhang, Fu-Qiang; Zhang, Xiang-Fei; Li, Su-Zhi; Cao, Guang-Xiu; Zhai, Bin

    2016-03-01

    Two novel lanthanide-sulfate compounds, [Ln2(SO4)3(H2O)8] (Ln = Tb (1) and Dy (2)), have been synthesized under hydrothermal reactions. X-ray crystal structure analyses reveal that 1 and 2 are isomorphous and crystallize in monoclinic C2/c pace group, showing a layered structure. The layers bear a rare quasi-honeycomb metal arrangement, which is fastened by μ3 = η1:η1:η1 and μ2 = η1:η1 sulfates. If assigning the μ3 = η1:η1:η1 sulfate as a 3-connected node and the Ln3+ ion as a 4-connected node, the network can be rationalized as a binodal (3,4)-connected V2O5 topology with a Schäfli symbol of (42·63·8) (42·6). In addition, the infrared, thermogravimetric analysis and luminescent properties were also studied. Complexes 1 and 2 exhibit outstanding thermal stability and characteristic terbium and dysprosium luminescence.

  15. Structure, Density and Velocity Fluctuations in Quasi-2D non-Brownian Suspensions of Spheres

    NASA Astrophysics Data System (ADS)

    Rouyer, Florence; Lhuillier, Daniel; Martin, Jérôme; Salin, Dominique

    1999-11-01

    Non-brownian sedimenting suspensions exhibit density and velocity fluctuations. We have performed experiments on a quasi-2D counter-flow stabilized suspension of 2000 spherical particles, namely a liquid-solid fluidized bed in a Hele-Shaw cell. This 2D suspension displays a uniform concentration but the particle radial distribution function and the fluctuations of the particle number in a sub-volume of the suspension suggest that the micostructure is homogeneous but not random. We have also measured the velocity fluctuations of a test-particle and the fluctuation of the mean particle velocity in a sub-volume. It happens that the relation between velocity and concentration fluctuation in a sub-volume can be deduced from a balance between buoyancy and parietal friction forces.

  16. Cyano-bridged coordination polymer hydrogel-derived Sn-Fe binary oxide nanohybrids with structural diversity: from 3D, 2D, to 2D/1D and enhanced lithium-storage performance

    NASA Astrophysics Data System (ADS)

    Zhang, Weiyu; Zhu, Xiaoshu; Chen, Xuguang; Zhou, Yiming; Tang, Yawen; Ding, Liangxin; Wu, Ping

    2016-05-01

    Metal oxide nanohybrids with uniform dimensions and controlled architectures possess unique compositional and structural superiorities, and thus harbor promising potential for a series of applications in energy, catalysis, and sensing systems. Herein, we propose a facile, general, and scalable cyano-bridged coordination polymer hydrogel-derived thermal-oxidation route for the construction of main-group metal and transition-metal heterometallic oxide nanohybrids with controlled constituents and architectures. The formation of Sn-Fe binary oxide nanohybrids has been demonstrated as an example by using cyano-bridged Sn(iv)-Fe(ii) bimetallic coordination polymer hydrogels (i.e., SnCl4-K4Fe(CN)6 cyanogels, Sn-Fe cyanogels) as precursors. The physicochemical properties of Sn-Fe cyanogels with different Sn/Fe ratios have been systematically examined, and it is found that perfect Sn-Fe cyanogels without unbridged Sn(iv) or Fe(ii) can be formed with Sn/Fe ratios from 2 : 1 to 1 : 2. More importantly, the simple adjustment of Sn/Fe ratios in the Sn-Fe cyanogel precursors can realize flexible dimensional control of the Sn-Fe binary oxide nanohybrids, and 2D/1D SnO2-Fe2O3 hierarchitectures, 2D SnO2-Fe2O3 nanosheets, and 3D SnO2-Fe2O3 networks have been synthesized using the Sn-Fe 1 : 2, Sn-Fe 1 : 1, and Sn-Fe 2 : 1 cyanogels as precursors, respectively. To demonstrate their compositional/structural superiorities and potential applications, the lithium-storage utilization of the Sn-Fe binary oxide nanohybrids has been selected as an objective application, and the nanohybrids exhibit Sn/Fe ratio-dependent lithium-storage performance. As a representative example, the 2D/1D SnO2-Fe2O3 hierarchitectures manifest markedly enhanced Li-storage performance in terms of reversible capacities and cycling stability in comparison with their constituent units, i.e., bare SnO2 nanosheets and Fe2O3 nanorods. The proposed cyanogel-derived thermal-oxidation strategy could open up new

  17. Molecular Dynamics Simulations to Investigate the Influences of Amino Acid Mutations on Protein Three-Dimensional Structures of Cytochrome P450 2D6.1, 2, 10, 14A, 51, and 62.

    PubMed

    Fukuyoshi, Shuichi; Kometani, Masaharu; Watanabe, Yurie; Hiratsuka, Masahiro; Yamaotsu, Noriyuki; Hirono, Shuichi; Manabe, Noriyoshi; Takahashi, Ohgi; Oda, Akifumi

    2016-01-01

    Many natural mutants of the drug metabolizing enzyme cytochrome P450 (CYP) 2D6 have been reported. Because the enzymatic activities of many mutants are different from that of the wild type, the genetic polymorphism of CYP2D6 plays an important role in drug metabolism. In this study, the molecular dynamics simulations of the wild type and mutants of CYP2D6, CYP2D6.1, 2, 10, 14A, 51, and 62 were performed, and the predictions of static and dynamic structures within them were conducted. In the mutant CYP2D6.10, 14A, and 61, dynamic properties of the F-G loop, which is one of the components of the active site access channel of CYP2D6, were different from that of the wild type. The F-G loop acted as the "hatch" of the channel, which was closed in those mutants. The structure of CYP2D6.51 was not converged by the simulation, which indicated that the three-dimensional structure of CYP2D6.51 was largely different from that of the wild type. In addition, the intramolecular interaction network of CYP2D6.10, 14A, and 61 was different from that of the wild type, and it is considered that these structural changes are the reason for the decrease or loss of enzymatic activities. On the other hand, the static and dynamic properties of CYP2D6.2, whose activity was normal, were not considerably different from those of the wild type.

  18. Molecular Dynamics Simulations to Investigate the Influences of Amino Acid Mutations on Protein Three-Dimensional Structures of Cytochrome P450 2D6.1, 2, 10, 14A, 51, and 62

    PubMed Central

    Watanabe, Yurie; Hiratsuka, Masahiro; Yamaotsu, Noriyuki; Hirono, Shuichi; Manabe, Noriyoshi; Takahashi, Ohgi; Oda, Akifumi

    2016-01-01

    Many natural mutants of the drug metabolizing enzyme cytochrome P450 (CYP) 2D6 have been reported. Because the enzymatic activities of many mutants are different from that of the wild type, the genetic polymorphism of CYP2D6 plays an important role in drug metabolism. In this study, the molecular dynamics simulations of the wild type and mutants of CYP2D6, CYP2D6.1, 2, 10, 14A, 51, and 62 were performed, and the predictions of static and dynamic structures within them were conducted. In the mutant CYP2D6.10, 14A, and 61, dynamic properties of the F-G loop, which is one of the components of the active site access channel of CYP2D6, were different from that of the wild type. The F-G loop acted as the “hatch” of the channel, which was closed in those mutants. The structure of CYP2D6.51 was not converged by the simulation, which indicated that the three-dimensional structure of CYP2D6.51 was largely different from that of the wild type. In addition, the intramolecular interaction network of CYP2D6.10, 14A, and 61 was different from that of the wild type, and it is considered that these structural changes are the reason for the decrease or loss of enzymatic activities. On the other hand, the static and dynamic properties of CYP2D6.2, whose activity was normal, were not considerably different from those of the wild type. PMID:27046024

  19. Epitaxial MoS2/GaN structures to enable vertical 2D/3D semiconductor heterostructure devices

    NASA Astrophysics Data System (ADS)

    Ruzmetov, D.; Zhang, K.; Stan, G.; Kalanyan, B.; Eichfeld, S.; Burke, R.; Shah, P.; O'Regan, T.; Crowne, F.; Birdwell, A. G.; Robinson, J.; Davydov, A.; Ivanov, T.

    MoS2/GaN structures are investigated as a building block for vertical 2D/3D semiconductor heterostructure devices that utilize a 3D substrate (GaN) as an active component of the semiconductor device without the need of mechanical transfer of the 2D layer. Our CVD-grown monolayer MoS2 has been shown to be epitaxially aligned to the GaN lattice which is a pre-requisite for high quality 2D/3D interfaces desired for efficient vertical transport and large area growth. The MoS2 coverage is nearly 50 % including isolated triangles and monolayer islands. The GaN template is a double-layer grown by MOCVD on sapphire and allows for measurement of transport perpendicular to the 2D layer. Photoluminescence, Raman, XPS, Kelvin force probe microscopy, and SEM analysis identified high quality monolayer MoS2. The MoS2/GaN structures electrically conduct in the out-of-plane direction and across the van der Waals gap, as measured with conducting AFM (CAFM). The CAFM current maps and I-V characteristics are analyzed to estimate the MoS2/GaN contact resistivity to be less than 4 Ω-cm2 and current spreading in the MoS2 monolayer to be approx. 1 μm in diameter. Epitaxial MoS2/GaN heterostructures present a promising platform for the design of energy-efficient, high-speed vertical devices incorporating 2D layered materials with 3D semiconductors.

  20. [Network structures in biological systems].

    PubMed

    Oleskin, A V

    2013-01-01

    Network structures (networks) that have been extensively studied in the humanities are characterized by cohesion, a lack of a central control unit, and predominantly fractal properties. They are contrasted with structures that contain a single centre (hierarchies) as well as with those whose elements predominantly compete with one another (market-type structures). As far as biological systems are concerned, their network structures can be subdivided into a number of types involving different organizational mechanisms. Network organization is characteristic of various structural levels of biological systems ranging from single cells to integrated societies. These networks can be classified into two main subgroups: (i) flat (leaderless) network structures typical of systems that are composed of uniform elements and represent modular organisms or at least possess manifest integral properties and (ii) three-dimensional, partly hierarchical structures characterized by significant individual and/or intergroup (intercaste) differences between their elements. All network structures include an element that performs structural, protective, and communication-promoting functions. By analogy to cell structures, this element is denoted as the matrix of a network structure. The matrix includes a material and an immaterial component. The material component comprises various structures that belong to the whole structure and not to any of its elements per se. The immaterial (ideal) component of the matrix includes social norms and rules regulating network elements' behavior. These behavioral rules can be described in terms of algorithms. Algorithmization enables modeling the behavior of various network structures, particularly of neuron networks and their artificial analogs.

  1. Long-range alignments of single fullerenes by site-selective inclusion into a double-cavity 2D open network.

    PubMed

    Piot, Luc; Silly, Fabien; Tortech, Ludovic; Nicolas, Yohann; Blanchard, Philippe; Roncali, Jean; Fichou, Denis

    2009-09-16

    We show by means of STM that C(60) molecules can be trapped into specific sites of a 2D double-cavity open network, thus forming long-range alignments of single molecules. Since only one of the two cavities has the right size to host C(60), the smallest cavity remains empty and is thus available to trap additional species of smaller size. This novel 2D supramolecular network opens new perspectives in the design of multicomponent guest-host architectures with electronic functionalities. PMID:19462948

  2. Low-cost chemiresistive sensor for volatile amines based on a 2D network of a zinc(II) Schiff-base complex

    NASA Astrophysics Data System (ADS)

    Mirabella, S.; Oliveri, I. P.; Ruffino, F.; Maccarrone, G.; Di Bella, S.

    2016-10-01

    A marked chemiresistive behavior is revealed in a nanostructured material obtained by spin-coating a solution of a bis(salycilaldiminato)Zn(II) Schiff-base (ZnSB) complex. The resulting submicron 2D network exhibits reversible changes in absorbance and resistance under the cycles of absorption and desorption of a volatile amine. These results are explained in terms of a Lewis donor-acceptor interaction between the ZnSB (acceptor) and the chemisorbed amine (donor). The 2D network of ZnSB was employed as a sensing element to fabricate a low-cost device for the volatile amines detection, showing promising results for food spoilage detection.

  3. Image restoration using 2D autoregressive texture model and structure curve construction

    NASA Astrophysics Data System (ADS)

    Voronin, V. V.; Marchuk, V. I.; Petrosov, S. P.; Svirin, I.; Agaian, S.; Egiazarian, K.

    2015-05-01

    In this paper an image inpainting approach based on the construction of a composite curve for the restoration of the edges of objects in an image using the concepts of parametric and geometric continuity is presented. It is shown that this approach allows to restore the curved edges and provide more flexibility for curve design in damaged image by interpolating the boundaries of objects by cubic splines. After edge restoration stage, a texture restoration using 2D autoregressive texture model is carried out. The image intensity is locally modeled by a first spatial autoregressive model with support in a strongly causal prediction region on the plane. Model parameters are estimated by Yule-Walker method. Several examples considered in this paper show the effectiveness of the proposed approach for large objects removal as well as recovery of small regions on several test images.

  4. 2D-ordered dielectric sub-micron bowls on a metal surface: a useful hybrid plasmonic-photonic structure

    NASA Astrophysics Data System (ADS)

    Lan, Yue; Wang, Shiqiang; Yin, Xianpeng; Liang, Yun; Dong, Hao; Gao, Ning; Li, Jian; Wang, Hui; Li, Guangtao

    2016-07-01

    Recently, it has been demonstrated that the combination of periodic dielectric structures with metallic structures provides an efficient means to yield a synergetic optical response or functionality in the resultant hybrid plasmonic-photonic systems. In this work, a new hybrid plasmonic-photonic structure of 2D-ordered dielectric sub-micron bowls on a flat gold surface was proposed, prepared, and theoretically and experimentally characterized. This hybrid structure supports two types of modes: surface plasmon polaritons bound at the metallic surface and waveguided mode of light confined in the cavity of bowls. Optical responses of this hybrid structure as well as the spatial electric field distribution of each mode are found to be strongly dependent on the structural parameters of this system, and thus could be widely modified on demand. Importantly, compared to the widely studied hybrid systems, namely the flat metallic surface coated with a monolayer array of latex spheres, the waveguided mode with strong field enhancement appearing in the cavities of bowls is more facilely accessible and thus suitable for practical use. For demonstration, a 2D-ordered silica sub-micron bowl array deposited on a flat gold surface was fabricated and used as a regenerable platform for fluorescence enhancement by simply accommodating emitters in bowls. All the simulation and experiment results indicate that the 2D-ordered dielectric sub-micron bowls on a metal surface should be a useful hybrid plasmonic-photonic system with great potential for applications such as sensors or tunable emitting devices if appropriate periods and materials are employed.Recently, it has been demonstrated that the combination of periodic dielectric structures with metallic structures provides an efficient means to yield a synergetic optical response or functionality in the resultant hybrid plasmonic-photonic systems. In this work, a new hybrid plasmonic-photonic structure of 2D-ordered dielectric sub

  5. 2D-ordered dielectric sub-micron bowls on a metal surface: a useful hybrid plasmonic-photonic structure.

    PubMed

    Lan, Yue; Wang, Shiqiang; Yin, Xianpeng; Liang, Yun; Dong, Hao; Gao, Ning; Li, Jian; Wang, Hui; Li, Guangtao

    2016-07-21

    Recently, it has been demonstrated that the combination of periodic dielectric structures with metallic structures provides an efficient means to yield a synergetic optical response or functionality in the resultant hybrid plasmonic-photonic systems. In this work, a new hybrid plasmonic-photonic structure of 2D-ordered dielectric sub-micron bowls on a flat gold surface was proposed, prepared, and theoretically and experimentally characterized. This hybrid structure supports two types of modes: surface plasmon polaritons bound at the metallic surface and waveguided mode of light confined in the cavity of bowls. Optical responses of this hybrid structure as well as the spatial electric field distribution of each mode are found to be strongly dependent on the structural parameters of this system, and thus could be widely modified on demand. Importantly, compared to the widely studied hybrid systems, namely the flat metallic surface coated with a monolayer array of latex spheres, the waveguided mode with strong field enhancement appearing in the cavities of bowls is more facilely accessible and thus suitable for practical use. For demonstration, a 2D-ordered silica sub-micron bowl array deposited on a flat gold surface was fabricated and used as a regenerable platform for fluorescence enhancement by simply accommodating emitters in bowls. All the simulation and experiment results indicate that the 2D-ordered dielectric sub-micron bowls on a metal surface should be a useful hybrid plasmonic-photonic system with great potential for applications such as sensors or tunable emitting devices if appropriate periods and materials are employed.

  6. The use of 2D fingerprint methods to support the assessment of structural similarity in orphan drug legislation

    PubMed Central

    2014-01-01

    Background In the European Union, medicines are authorised for some rare disease only if they are judged to be dissimilar to authorised orphan drugs for that disease. This paper describes the use of 2D fingerprints to show the extent of the relationship between computed levels of structural similarity for pairs of molecules and expert judgments of the similarities of those pairs. The resulting relationship can be used to provide input to the assessment of new active compounds for which orphan drug authorisation is being sought. Results 143 experts provided judgments of the similarity or dissimilarity of 100 pairs of drug-like molecules from the DrugBank 3.0 database. The similarities of these pairs were also computed using BCI, Daylight, ECFC4, ECFP4, MDL and Unity 2D fingerprints. Logistic regression analyses demonstrated a strong relationship between the human and computed similarity assessments, with the resulting regression models having significant predictive power in experiments using data from submissions of orphan drug medicines to the European Medicines Agency. The BCI fingerprints performed best overall on the DrugBank dataset while the BCI, Daylight, ECFP4 and Unity fingerprints performed comparably on the European Medicines Agency dataset. Conclusions Measures of structural similarity based on 2D fingerprints can provide a useful source of information for the assessment of orphan drug status by regulatory authorities. PMID:24485002

  7. Micro PIV measurements of turbulent flow over 2D structured roughness

    NASA Astrophysics Data System (ADS)

    Hartenberger, Joel; Perlin, Marc

    2015-11-01

    We investigate the turbulent boundary layer over surfaces with 2D spanwise square and triangular protrusions having nominal heights of 100 - 300 microns for Reynolds numbers ranging from Reτ ~ 1500 through Reτ ~ 4500 using a high speed, high magnification imaging system. Micro PIV analysis gives finely resolved velocity fields of the flow (on the order of 10 microns between vectors) enabling a detailed look at the inner region as well as the flow in the immediate vicinity of the roughness elements. Additionally, planar PIV with lower resolution is performed to capture the remainder of the boundary layer to the freestream flow. Varying the streamwise distance between individual roughness elements from one to ten times the nominal heights allows investigation of k-type and d-type roughness in both the transitionally rough and fully rough regimes. Preliminary results show a shift in the mean velocity profile similar to the results of previous studies. Turbulent statistics will be presented also. The authors would like to acknowledge the support of NAVSEA which funded this project through the Naval Engineering Education Center (NEEC).

  8. A methodology for linking 2D overland flow models with the sewer network model SWMM 5.1 based on dynamic link libraries.

    PubMed

    Leandro, Jorge; Martins, Ricardo

    2016-01-01

    Pluvial flooding in urban areas is characterized by a gradually varying inundation process caused by surcharge of the sewer manholes. Therefore urban flood models need to simulate the interaction between the sewer network and the overland flow in order to accurately predict the flood inundation extents. In this work we present a methodology for linking 2D overland flow models with the storm sewer model SWMM 5. SWMM 5 is a well-known free open-source code originally developed in 1971. The latest major release saw its structure re-written in C ++ allowing it to be compiled as a command line executable or through a series of calls made to function inside a dynamic link library (DLL). The methodology developed herein is written inside the same DLL in C + +, and is able to simulate the bi-directional interaction between both models during simulation. Validation is done in a real case study with an existing urban flood coupled model. The novelty herein is that the new methodology can be added to SWMM without the need for editing SWMM's original code. Furthermore, it is directly applicable to other coupled overland flow models aiming to use SWMM 5 as the sewer network model. PMID:27332848

  9. Computational design of soft materials for the capture of Cs-137 in contaminated environments: From 2D covalent cucurbituril networks to 3D supramolecular materials

    NASA Astrophysics Data System (ADS)

    Pichierri, Fabio

    2016-08-01

    Using computational quantum chemistry methods we design novel 2D and 3D soft materials made of cucurbituril macrocycles covalently connected with each other via rigid linkers. Such covalent cucurbituril networks might be useful for the capture of radioactive Cs-137 (present as Cs+) in the contaminated environment.

  10. An algorithm for computing the 2D structure of fast rotating stars

    NASA Astrophysics Data System (ADS)

    Rieutord, Michel; Espinosa Lara, Francisco; Putigny, Bertrand

    2016-08-01

    Stars may be understood as self-gravitating masses of a compressible fluid whose radiative cooling is compensated by nuclear reactions or gravitational contraction. The understanding of their time evolution requires the use of detailed models that account for a complex microphysics including that of opacities, equation of state and nuclear reactions. The present stellar models are essentially one-dimensional, namely spherically symmetric. However, the interpretation of recent data like the surface abundances of elements or the distribution of internal rotation have reached the limits of validity of one-dimensional models because of their very simplified representation of large-scale fluid flows. In this article, we describe the ESTER code, which is the first code able to compute in a consistent way a two-dimensional model of a fast rotating star including its large-scale flows. Compared to classical 1D stellar evolution codes, many numerical innovations have been introduced to deal with this complex problem. First, the spectral discretization based on spherical harmonics and Chebyshev polynomials is used to represent the 2D axisymmetric fields. A nonlinear mapping maps the spheroidal star and allows a smooth spectral representation of the fields. The properties of Picard and Newton iterations for solving the nonlinear partial differential equations of the problem are discussed. It turns out that the Picard scheme is efficient on the computation of the simple polytropic stars, but Newton algorithm is unsurpassed when stellar models include complex microphysics. Finally, we discuss the numerical efficiency of our solver of Newton iterations. This linear solver combines the iterative Conjugate Gradient Squared algorithm together with an LU-factorization serving as a preconditioner of the Jacobian matrix.

  11. Analysis of simple 2-D and 3-D metal structures subjected to fragment impact

    NASA Technical Reports Server (NTRS)

    Witmer, E. A.; Stagliano, T. R.; Spilker, R. L.; Rodal, J. J. A.

    1977-01-01

    Theoretical methods were developed for predicting the large-deflection elastic-plastic transient structural responses of metal containment or deflector (C/D) structures to cope with rotor burst fragment impact attack. For two-dimensional C/D structures both, finite element and finite difference analysis methods were employed to analyze structural response produced by either prescribed transient loads or fragment impact. For the latter category, two time-wise step-by-step analysis procedures were devised to predict the structural responses resulting from a succession of fragment impacts: the collision force method (CFM) which utilizes an approximate prediction of the force applied to the attacked structure during fragment impact, and the collision imparted velocity method (CIVM) in which the impact-induced velocity increment acquired by a region of the impacted structure near the impact point is computed. The merits and limitations of these approaches are discussed. For the analysis of 3-d responses of C/D structures, only the CIVM approach was investigated.

  12. Four divalent transition metal carboxyarylphosphonate compounds: Hydrothermal synthesis, structural chemistry and generalized 2D FTIR correlation spectroscopy studies

    NASA Astrophysics Data System (ADS)

    Lei, Ran; Chai, Xiaochuan; Mei, Hongxin; Zhang, Hanhui; Chen, Yiping; Sun, Yanqiong

    2010-07-01

    Four divalent transition metal carboxyarylphosphonates, [Ni(4,4'-bipy)H 2L 1(HL 1) 2(H 2O) 2]·2H 2O 1, [Ni 2(4,4'-bipy)(L 2)(OH)(H 2O) 2]·3H 2O 2, Mn(phen) 2(H 2L 1) 23 and Mn(phen)(HL 2) 4 (H 3L 1= p-H 2O 3PCH 2-C 6H 4-COOH, H 3L 2= m-H 2O 3PCH 2-C 6H 4-COOH, 4,4'-bipy=4,4'-bipyridine, phen=1,10-phenanthroline) were synthesized under hydrothermal conditions. 1 features 1D linear chains built from Ni(II) ions bridging 4,4'-bipy. In 2, neighboring Ni 4 cluster units are connected by pairs of H 3L 2 ligands to form 1D double-crankshaft chains, which are interconnected by pairs of 4,4'-bipy into 2D sheets. 3 exhibits 2D supramolecular layers via the R 22(8) ringed hydrogen bonding units. 4 has 1D ladderlike chains, in which the 4-membered rings are cross-linked by the organic moieties of the H 3L 2 ligands. Additionally, 2D FTIR correlation analysis is applied with thermal and magnetic perturbation to clarify the structural changes of functional groups from H 3L 1 and H 3L 2 ligands in the compounds more efficiently.

  13. 2-D Structure of the A Region of Xist RNA and Its Implication for PRC2 Association

    PubMed Central

    Maenner, Sylvain; Blaud, Magali; Fouillen, Laetitia; Savoye, Anne; Marchand, Virginie; Dubois, Agnès; Sanglier-Cianférani, Sarah; Van Dorsselaer, Alain; Clerc, Philippe; Avner, Philip; Visvikis, Athanase; Branlant, Christiane

    2010-01-01

    In placental mammals, inactivation of one of the X chromosomes in female cells ensures sex chromosome dosage compensation. The 17 kb non-coding Xist RNA is crucial to this process and accumulates on the future inactive X chromosome. The most conserved Xist RNA region, the A region, contains eight or nine repeats separated by U-rich spacers. It is implicated in the recruitment of late inactivated X genes to the silencing compartment and likely in the recruitment of complex PRC2. Little is known about the structure of the A region and more generally about Xist RNA structure. Knowledge of its structure is restricted to an NMR study of a single A repeat element. Our study is the first experimental analysis of the structure of the entire A region in solution. By the use of chemical and enzymatic probes and FRET experiments, using oligonucleotides carrying fluorescent dyes, we resolved problems linked to sequence redundancies and established a 2-D structure for the A region that contains two long stem-loop structures each including four repeats. Interactions formed between repeats and between repeats and spacers stabilize these structures. Conservation of the spacer terminal sequences allows formation of such structures in all sequenced Xist RNAs. By combination of RNP affinity chromatography, immunoprecipitation assays, mass spectrometry, and Western blot analysis, we demonstrate that the A region can associate with components of the PRC2 complex in mouse ES cell nuclear extracts. Whilst a single four-repeat motif is able to associate with components of this complex, recruitment of Suz12 is clearly more efficient when the entire A region is present. Our data with their emphasis on the importance of inter-repeat pairing change fundamentally our conception of the 2-D structure of the A region of Xist RNA and support its possible implication in recruitment of the PRC2 complex. PMID:20052282

  14. Three 2D Ag(I)-framework isomers with helical structures controlled by the chirality of camphor-10-sulfonic acid.

    PubMed

    Guo, Peng

    2011-02-28

    Three 2D Ag(I)-framework isomers were constructed from enantiopure camphor-10-sulfonic acids or racemic camphor-10-sulfonic acids, together with achiral 4-aminobenzoic acids. In complex 1, (+)-camphor-10-sulfonic acids bridge the single left-handed helices that are made up of Ag ions and 4-aminobenzoic acids, generating a homochiral 2D layer. In such a structure, the interweaving of triple left-handed homohelices was also found. It is worth noting that the helicity of complex 2 could be controlled by the handedness of the camphor-10-sulfonic acid. In complex 2, there are right-handed helical structures, including single right-handed and triple right-handed helical structures connected by (-)-camphor-10-sulfonic acids. For a comparative study, (±)-camphor-10-sulfonic acids were utilized to synthesize complex 3, in which equal numbers of right-handed or left-handed double-helical chains are created. All the complexes were characterized by single-crystal X-ray structure determination, powder X-ray diffraction, IR, TGA and element analysis. Circular dichroism spectra of complexes 1 and 2 were been studied to confirm the fact that enantiopure bridging ligands do not racemize. PMID:21264423

  15. Three 2D Ag(I)-framework isomers with helical structures controlled by the chirality of camphor-10-sulfonic acid.

    PubMed

    Guo, Peng

    2011-02-28

    Three 2D Ag(I)-framework isomers were constructed from enantiopure camphor-10-sulfonic acids or racemic camphor-10-sulfonic acids, together with achiral 4-aminobenzoic acids. In complex 1, (+)-camphor-10-sulfonic acids bridge the single left-handed helices that are made up of Ag ions and 4-aminobenzoic acids, generating a homochiral 2D layer. In such a structure, the interweaving of triple left-handed homohelices was also found. It is worth noting that the helicity of complex 2 could be controlled by the handedness of the camphor-10-sulfonic acid. In complex 2, there are right-handed helical structures, including single right-handed and triple right-handed helical structures connected by (-)-camphor-10-sulfonic acids. For a comparative study, (±)-camphor-10-sulfonic acids were utilized to synthesize complex 3, in which equal numbers of right-handed or left-handed double-helical chains are created. All the complexes were characterized by single-crystal X-ray structure determination, powder X-ray diffraction, IR, TGA and element analysis. Circular dichroism spectra of complexes 1 and 2 were been studied to confirm the fact that enantiopure bridging ligands do not racemize.

  16. Toward predicting vertical detachment energies for superhalogen anions exclusively from 2-D structures

    NASA Astrophysics Data System (ADS)

    Sikorska, Celina

    2015-04-01

    In this work, the multiple linear regression (MLR) method was applied for quantitative structure-property relationship (QSPR) modeling and predicting vertical detachment energy of superhalogen anions with descriptors calculated from the molecular structure for the first time. The square of the correlation coefficient (R2 = 0.975), the cross-validated correlation coefficient (QCV2 = 0.859), and the square of correlation coefficients of the test set (QEXT2 = 0.960) demonstrated the reliability of the model. Since the developed QSPR model does not require 3-D structure generation and thus structure optimization with extensive quantum mechanical calculations it can be further used for relatively fast designing of new superhalogen anions.

  17. 2D and 3D reconstruction and geomechanical characterization of kilometre-scale complex folded structures

    NASA Astrophysics Data System (ADS)

    Zanchi, Andrea; Agliardi, Federico; Crosta, Giovanni B.; Villa, Alberto; Bistacchi, Andrea; Iudica, Gaetano

    2015-04-01

    The geometrical, structural and geomechanical characterization of large-scale folded structures in sedimentary rocks is an important issue for different geological and geo-hazard applications (e.g. hydrocarbon and geothermal reservoir exploitation, natural rock slope stability, mining, and tunnelling). Fold geometry controls topography and the spatial distribution of rock types with different strength and permeability. Fold-related fracture systems condition the fracture intensity, degree of freedom, and overall strength of rock masses. Nevertheless, scale issues and limited accessibility or partial exposure of structures often hamper a complete characterization of these complex structures. During the last years, advances in remote survey techniques as terrestrial Lidar (TLS) allowed significant improvements in the geometrical and geological characterization of large or inaccessible outcrops. However, sound methods relating structures to rock mass geomechanical properties are yet to be developed. Here we present results obtained by integrating remote survey and field assessment techniques to characterize a folded sedimentary succession exposed in unreachable vertical rock walls. The study area is located in the frontal part of the Southern Alps near Bergamo, Italy. We analysed large-scale detachment folds developed in the Upper Triassic sedimentary cover in the Zu Limestone. Folds are parallel and disharmonic, with regular wavelengths and amplitudes of about 200-250 m. We used a Riegl VZ-1000 long-range laser scanner to obtain points clouds with nominal spacings between 5 cm and 20 cm from 9 scan positions characterized by range between 350 m and 1300 m. We fixed shadowing and occlusion effects related to fold structure exposure by filling point clouds with data collected by terrestrial digital photogrammetry (TDP). In addition, we carried out field surveys of fold-related brittle structures and their geomechanical attributes at key locations. We classified cloud

  18. New dicyano cyclometalated compounds containing Pd(II)-Tl(I) bonds as building blocks in 2D extended structures: synthesis, structure, and luminescence studies.

    PubMed

    Sicilia, Violeta; Forniés, Juan; Fuertes, Sara; Martín, Antonio

    2012-10-15

    New mixed metal complexes [PdTl(C^N)(CN)(2)] [C^N = 7,8-benzoquinolinate (bzq, 3); 2-phenylpyridinate (ppy, 4)] have been synthesized by reaction of their corresponding precursors (NBu(4))[Pd(C^N)(CN)(2)] [C^N = bzq (1), ppy (2)] with TlPF(6). Compounds 3 and 4 were studied by X-ray diffraction, showing the not-so-common Pd(II)-Tl(I) bonds. Both crystal structures exhibit 2-D extended networks fashioned by organometallic "PdTl(C^N)(CN)(2)" units, each one containing a donor-acceptor Pd(II)-Tl(I) bond, which are connected through additional Tl···N≡C contacts and weak Tl···π (bzq) contacts in the case of 3. Solid state emissions are red-shifted compared with those of the precursors and have been assigned to metal-metal'-to-ligand charge transfer (MM'LCT [d/s σ*(Pd,Tl) → π*(C^N)]) mixed with some intraligand ((3)IL[π(C^N) → π*(C^N)]) character. In diluted solution either at room temperature or 77 K, the Pd-Tl bond is no longer retained as confirmed by mass spectrometry, NMR, and UV-vis spectroscopic techniques.

  19. New dicyano cyclometalated compounds containing Pd(II)-Tl(I) bonds as building blocks in 2D extended structures: synthesis, structure, and luminescence studies.

    PubMed

    Sicilia, Violeta; Forniés, Juan; Fuertes, Sara; Martín, Antonio

    2012-10-15

    New mixed metal complexes [PdTl(C^N)(CN)(2)] [C^N = 7,8-benzoquinolinate (bzq, 3); 2-phenylpyridinate (ppy, 4)] have been synthesized by reaction of their corresponding precursors (NBu(4))[Pd(C^N)(CN)(2)] [C^N = bzq (1), ppy (2)] with TlPF(6). Compounds 3 and 4 were studied by X-ray diffraction, showing the not-so-common Pd(II)-Tl(I) bonds. Both crystal structures exhibit 2-D extended networks fashioned by organometallic "PdTl(C^N)(CN)(2)" units, each one containing a donor-acceptor Pd(II)-Tl(I) bond, which are connected through additional Tl···N≡C contacts and weak Tl···π (bzq) contacts in the case of 3. Solid state emissions are red-shifted compared with those of the precursors and have been assigned to metal-metal'-to-ligand charge transfer (MM'LCT [d/s σ*(Pd,Tl) → π*(C^N)]) mixed with some intraligand ((3)IL[π(C^N) → π*(C^N)]) character. In diluted solution either at room temperature or 77 K, the Pd-Tl bond is no longer retained as confirmed by mass spectrometry, NMR, and UV-vis spectroscopic techniques. PMID:22998590

  20. Synthesis and Crystal Structures of Zirconium Phosphate Fluorides with New 2D and 3D Structure Types

    NASA Astrophysics Data System (ADS)

    Wloka, Martin; Troyanov, Sergei I.; Kemnitz, Erhard

    2000-01-01

    Three new zirconium phosphate fluorides, [amH2]0.5 [Zr2(PO4)(HPO4)2F2]·0.5H2O (1), [amH2]1.5[Zr3(PO4)3F6]·1.5H2O (2) (am=trans-1,4-diaminocyclohexane for 1 and 2), and [amH2]0.5[Zr3(PO4)3(HPO4)F2]·1.5H2O (am=2,2-dimethyl-1,3-diaminopropane) (3), were synthesized under hydrothermal conditions and structurally characterized. Zr is octahedrally coordinated in all three structures. In 1, the octahedra consist of ZrO6 and ZrO4F2 units. Compound 2 is made exclusively of ZrO4F2. In 3, there are three different types of Zr-octahedra, namely, ZrO6, ZrO5F, and ZrO4F2. The Zr octahedra and PO4 tetrahedra are connected via non-OH oxygen atoms. In 1 and 2, all F atoms are terminal, whereas in 3, one of the two F atoms bridges between the ZrO5F and ZrO4F2 octahedra. In structures 1 and 2 with higher F/Zr ratios, two-dimensional inorganic networks exist. The inorganic sheets are connected by the protonated templates via N-H···F and in 1 additionally by O-H···F hydrogen bonds. In 3, the lower F/Zr ratio results in the formation of a three-dimensional inorganic framework with characteristic 'double' channels in which the highly disordered templates are located. The existence of several structure types in the ZrPOF-n family is discussed on the basis of different template geometry and F/Zr ratios.

  1. Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics

    NASA Astrophysics Data System (ADS)

    Reppert, Mike; Tokmakoff, Andrei

    2016-05-01

    Two-dimensional infrared spectroscopy of amide I vibrations is increasingly being used to study the structure and dynamics of proteins and peptides. Amide I, a primarily carbonyl stretching vibration of the protein backbone, provides information on secondary structures as a result of vibrational couplings and on hydrogen-bonding contacts when isotope labeling is used to isolate specific sites. In parallel with experiments, computational models of amide I spectra that use atomistic structures from molecular dynamics simulations have evolved to calculate experimental spectra. Mixed quantum-classical models use spectroscopic maps to translate the structural information into a quantum-mechanical Hamiltonian for the spectroscopically observed vibrations. This allows one to model the spectroscopy of large proteins, disordered states, and protein conformational dynamics. With improvements in amide I models, quantitative modeling of time-dependent structural ensembles and of direct feedback between experiments and simulations is possible. We review the advances in developing these models, their theoretical basis, and current and future applications.

  2. Learning the 3-D structure of objects from 2-D views depends on shape, not format

    PubMed Central

    Tian, Moqian; Yamins, Daniel; Grill-Spector, Kalanit

    2016-01-01

    Humans can learn to recognize new objects just from observing example views. However, it is unknown what structural information enables this learning. To address this question, we manipulated the amount of structural information given to subjects during unsupervised learning by varying the format of the trained views. We then tested how format affected participants' ability to discriminate similar objects across views that were rotated 90° apart. We found that, after training, participants' performance increased and generalized to new views in the same format. Surprisingly, the improvement was similar across line drawings, shape from shading, and shape from shading + stereo even though the latter two formats provide richer depth information compared to line drawings. In contrast, participants' improvement was significantly lower when training used silhouettes, suggesting that silhouettes do not have enough information to generate a robust 3-D structure. To test whether the learned object representations were format-specific or format-invariant, we examined if learning novel objects from example views transfers across formats. We found that learning objects from example line drawings transferred to shape from shading and vice versa. These results have important implications for theories of object recognition because they suggest that (a) learning the 3-D structure of objects does not require rich structural cues during training as long as shape information of internal and external features is provided and (b) learning generates shape-based object representations independent of the training format. PMID:27153196

  3. Formation of 2D nanoparticles with block structure in simultaneous electric explosion of conductors

    SciTech Connect

    Kryzhevich, Dmitrij S. E-mail: kost@ispms.ru; Zolnikov, Konstantin P. E-mail: kost@ispms.ru; Abdrashitov, Andrei V.; Lerner, Marat I.; Psakhie, Sergey G.

    2014-11-14

    A molecular dynamics simulation of nanoparticle formation in simultaneous electric explosion of conductors is performed. Interatomic interaction is described using potentials calculated in the framework of the embedded atom method. High-rate heating results in failure of the conductors with the formation of nanoparticles. The influence of the heating rate, temperature distribution over the specimen cross-section and the distance between simultaneously exploded conductors on the structure of formed nanoparticles is studied. The calculation results show that the electric explosion of conductors allows the formation of nanoparticles with block structure.

  4. Finding local community structure in networks

    NASA Astrophysics Data System (ADS)

    Clauset, Aaron

    2005-08-01

    Although the inference of global community structure in networks has recently become a topic of great interest in the physics community, all such algorithms require that the graph be completely known. Here, we define both a measure of local community structure and an algorithm that infers the hierarchy of communities that enclose a given vertex by exploring the graph one vertex at a time. This algorithm runs in time O(k2d) for general graphs when d is the mean degree and k is the number of vertices to be explored. For graphs where exploring a new vertex is time consuming, the running time is linear, O(k) . We show that on computer-generated graphs the average behavior of this technique approximates that of algorithms that require global knowledge. As an application, we use this algorithm to extract meaningful local clustering information in the large recommender network of an online retailer.

  5. Mercury (I) nitroprusside: A 2D structure supported on homometallic interactions

    NASA Astrophysics Data System (ADS)

    Osiry, H.; Cano, A.; Reguera, L.; Lemus-Santana, A. A.; Reguera, E.

    2015-01-01

    The pentacyanonitrosylferrate complex anion, [Fe(CN)5NO]2-, forms an insoluble solid with Hg(I) ion, of formula unit Hg2[Fe(CN)5NO]·2H2O, whose crystal structure and related properties are unknown. This contribution reports the preparation of that compound by the precipitation method and its structural study from X-ray powder patterns complemented with spectroscopic information from IR, Raman, and UV-vis techniques. The crystal structure was solved ab initio and then refined using the Rietveld method. The solid crystallizes with a triclinic unit cell, in the P-1 space group, with cell parameters a=10.1202(12), b=10.1000(13), c=7.4704(11) Å; α=110.664(10), β=110.114(10), γ=104.724(8) °. Within the unit cell, two formula units are accommodated (Z=2). It adopts a layered structure related with the coordination of the equatorial CN groups at their N end to the Hg atoms while the axial CN ligand remains unlinked. Within the layers neighboring Hg2[Fe(CN)5NO] building units remain linked through four relatively strong Hg-Hg interactions, with an interatomic distance of 2.549(3) Å. The charge donation from the equatorial CN groups through their 5σ orbitals results into an increase for the electron density on the Hg atoms, which strengths the Hg-Hg bond. In the Raman spectrum, that metal-metal bond is detected as a stretching vibration band at 167 cm-1. The available free volume between neighboring layers accommodates two water molecules, which are stabilized within the framework through hydrogen bonds with the N end of the unlinked axial CN group. The removal of these weakly bonded water molecules results in structural disorder for the material 3D framework.

  6. Reverse modeling of 2D and 3D diapiric salt structures

    NASA Astrophysics Data System (ADS)

    Fernandez, N.; Kaus, B.

    2013-12-01

    Mechanical forward modeling of salt diapirs formed by two different processes (differential loading and buoyancy driven) has been widely performed with numerical codes in many studies, whereas works focusing on the dynamic retro-deformation of such structures remain scarce. Buoyancy driven diapirs, in which the density difference between salt and overburden induces upward motion of salt, have been successfully retro-deformed in two and three dimensions using simple rheologies for the salt and overburden (e.g., Kaus & Podladchikov 2001). However, retro-deformation of down-building diapirs (syndepositional process in which salt structures grow while sediments are being deposited) using mechanical codes has only been done in two dimensions (e.g., Ismael-Zadeh et al. 2001), even though the importance of three-dimensionality in salt diapirism is accepted. We have used the two-dimensional visco-elasto-plastic finite element code MILAMIN_VEP to perform both forward and backward simulations and to check the validity of a reversed time step method (Kaus & Podladchikov 2001 and Ismael-Zadeh et al. 2001) for a wide range of parameters, variable sedimentation rates, and for non-linear rheologies. Forward simulations are run until the salt layer is exhausted and then a reverse time step is applied in order to retro-deform the model. Down-building process was mimicked using a fast-erosion condition at the surface, which keeps it flat and redistributes material at every time step. Initially, we have tested our method by retro-deforming salt structures that develop from an interface that is sinusoidally perturbed. More realistic simulations were performed by starting with randomly perturbed salt interface and using different rheological parameters for the salt and the overburden as well as variable sedimentation rates. Once the method has been proved successful for different parameters in two dimensions, the finite differences parallel code LaMEM has also been used to dynamically

  7. Investigation of 2D laterally dispersive photonic crystal structures : LDRD 33602 final report.

    SciTech Connect

    Subramania,Ganapathi Subramanian; Vawter, Gregory Allen; Wendt, Joel Robert; Peake, Gregory Merwin; Guo, Junpeng; Peters, David William; Hadley, G. Ronald

    2003-12-01

    Artificially structured photonic lattice materials are commonly investigated for their unique ability to block and guide light. However, an exciting aspect of photonic lattices which has received relatively little attention is the extremely high refractive index dispersion within the range of frequencies capable of propagating within the photonic lattice material. In fact, it has been proposed that a negative refractive index may be realized with the correct photonic lattice configuration. This report summarizes our investigation, both numerically and experimentally, into the design and performance of such photonic lattice materials intended to optimize the dispersion of refractive index in order to realize new classes of photonic devices.

  8. SPE-LEEM Studies on the Surface and Electronic Structure of 2-D Transition Metal Dichalcogenides

    NASA Astrophysics Data System (ADS)

    Yeh, Po-Chun; Jin, Wencan; Zaki, Nader; Zhang, Datong; Sadowski, Jerzy; Al-Mahboob, Abdullah; van de Zande, Arend; Chenet, Daniel; Dadap, Jerry; Herman, Irving; Sutter, Petter; Hone, James; Osgood, Richard

    2014-03-01

    In this work, we studied the surface and electronic structure of monolayer and few-layer exfoliated MoS2 and WSe2, as well as chemical-vapor-deposition (CVD) grown MoS2, using Spectroscopic Photoemission and Low Energy Electron Microscope (SPE-LEEM). LEEM measurements reveal that, unlike exfoliated MoS2, CVD-grown MoS2 exhibits grain-boundary alterations due to surface strain. However, LEEM and micro-probe low energy electron diffraction show that the quality of CVD-grown MoS2 is comparable to that of exfoliated MoS2. Micrometer-scale angle-resolved photoemission spectroscopy (ARPES) measurement on exfoliated MoS2 and WSe2 single-crystals provides direct evidence for the shifting of the valence band maximum from Γ to K, when the layer number is thinned down to one, as predicted by density functional theory. Our measurements of the k-space resolved electronic structure allow for further comparison with other theoretical predictions and with transport measurements. Session I and II

  9. Pore formation by antimicrobial peptides: structural tendencies in bulk and quasi-2D membrane systems

    NASA Astrophysics Data System (ADS)

    Gordon, Vernita; Yang, Lihua; Davis, Matthew; Som, A.; Tew, G.; Wong, Gerard

    2007-03-01

    Antimicrobial peptides are cationic, amphiphilic structures that are key components of innate immunity. A prototypical family of synthetic analogs are the phenylene ethynylene antimicrobial oligomers (AMOs), which have hydrophobic alkyl chains connected to cationic hydrophilic regions. Synchrotron small-angle x-ray scattering (SAXS) shows that when AMO is mixed with concentrated model membranes, initially in the form of Small Unilamellar Vesicles, the sample forms the inverted hexagonal phase. This is a 3-dimensional phase characterized by a regular array of size-defined water channels. We demonstrate how this structural tendency is expressed when AMOs interact with dilute model membranes in the form of Giant Unilamellar Vesicles (GUVs). Using confocal microscopy, we see that applying AMO to the GUVs causes small encapsulated molecules to be released while large molecules are retained, indicating that size-defined pores have been created. Examining the partial release of polydisperse intermediately-sized molecules allows a closer measurement of the pore size, and there are indications that this single-vesicle microscopy will allow elucidation of the kinetics of the pore-forming process.

  10. Crystal structure and temperature-dependent fluorescent property of a 2D cadmium (II) complex based on 3,6-dibromobenzene-1,2,4,5-tetracarboxylic acid

    NASA Astrophysics Data System (ADS)

    Zhang, Liang-Liang; Guo, Yu; Wei, Yan-Hui; Guo, Jie; Wang, Xing-Po; Sun, Dao-Feng

    2013-04-01

    A new cadmium (II) organic coordination polymers [Cd(dbtec)0.5(H2O)3]·H2O (1), has been constructed based on 3,6-dibromobenzene-1,2,4,5-tetracarboxylic acid (H4dbtec), and characterized by elemental analysis (EA), infrared spectroscopy (IR), powder X-ray diffraction (PXRD), and single crystal X-ray diffraction. In 1, μ2-η1:η1 and μ4-η2:η2 dbtec ligands link four hepta-coordinated CdII ions to form a 2D 44 topological layer structure, which is further connected into an interesting 3D network by hydrogen bond and Br⋯O halogen bond. Moreover, the thermal stabilities, solid ultraviolet spectroscopy and temperature-dependent fluorescent properties of 1 were investigated.

  11. Scaling Analysis of Ocean Surface Turbulent Heterogeneities from Satellite Remote Sensing: Use of 2D Structure Functions.

    PubMed

    Renosh, P R; Schmitt, Francois G; Loisel, Hubert

    2015-01-01

    Satellite remote sensing observations allow the ocean surface to be sampled synoptically over large spatio-temporal scales. The images provided from visible and thermal infrared satellite observations are widely used in physical, biological, and ecological oceanography. The present work proposes a method to understand the multi-scaling properties of satellite products such as the Chlorophyll-a (Chl-a), and the Sea Surface Temperature (SST), rarely studied. The specific objectives of this study are to show how the small scale heterogeneities of satellite images can be characterised using tools borrowed from the fields of turbulence. For that purpose, we show how the structure function, which is classically used in the frame of scaling time series analysis, can be used also in 2D. The main advantage of this method is that it can be applied to process images which have missing data. Based on both simulated and real images, we demonstrate that coarse-graining (CG) of a gradient modulus transform of the original image does not provide correct scaling exponents. We show, using a fractional Brownian simulation in 2D, that the structure function (SF) can be used with randomly sampled couple of points, and verify that 1 million of couple of points provides enough statistics.

  12. Scaling Analysis of Ocean Surface Turbulent Heterogeneities from Satellite Remote Sensing: Use of 2D Structure Functions

    PubMed Central

    Renosh, P. R.; Schmitt, Francois G.; Loisel, Hubert

    2015-01-01

    Satellite remote sensing observations allow the ocean surface to be sampled synoptically over large spatio-temporal scales. The images provided from visible and thermal infrared satellite observations are widely used in physical, biological, and ecological oceanography. The present work proposes a method to understand the multi-scaling properties of satellite products such as the Chlorophyll-a (Chl-a), and the Sea Surface Temperature (SST), rarely studied. The specific objectives of this study are to show how the small scale heterogeneities of satellite images can be characterised using tools borrowed from the fields of turbulence. For that purpose, we show how the structure function, which is classically used in the frame of scaling time series analysis, can be used also in 2D. The main advantage of this method is that it can be applied to process images which have missing data. Based on both simulated and real images, we demonstrate that coarse-graining (CG) of a gradient modulus transform of the original image does not provide correct scaling exponents. We show, using a fractional Brownian simulation in 2D, that the structure function (SF) can be used with randomly sampled couple of points, and verify that 1 million of couple of points provides enough statistics. PMID:26017551

  13. Electronic Structure calculations in a 2D SixGe1-x alloy under an applied electric field

    NASA Astrophysics Data System (ADS)

    Padilha, José. Eduardo; Pontes, Renato B.; Seixas, Leandro; da Silva, António J. R.; Fazzio, Adalberto

    2013-03-01

    The recent advances and promises in nanoscience and nanotechnology have been focused on hexagonal materials, mainly on carbon-based nanostructures. Recently, new candidates have been raised, where the greatest efforts are devoted to a new hexagonal and buckled material made of silicon, named Silicene. This new material presents an energy gap due to spin-orbit interaction of approximately 1.5 meV, where the measurement of quantum spin Hall effect(QSHE) can be made experimentally. Some investigations also show that the QSHE in 2D low-buckled hexagonal structures of germanium is present. Since the similarities, and at the same time the differences, between Si and Ge, over the years, have motivated a lot of investigations in these materials. In this work we performed systematic investigations on the electronic structure and band topology in both ordered and disordered SixGe1-x alloys monolayer with 2D honeycomb geometry by first-principles calculations. We show that an applied electric field can tune the gap size for both alloys. However, as a function of electric field, the disordered alloy presents a W-shaped behavior, similarly to the pure Si or Ge, whereas for the ordered alloy a V-shaped behavior is observed. This work is supported by CAPES, CNPq and FAPESP.

  14. Self-assembly of 2D-->2D interpenetrating coordination polymers showing polyrotaxane- and polycatenane-like motifs: influence of various ligands on topological structural diversity.

    PubMed

    Lan, Ya-Qian; Li, Shun-Li; Qin, Jun-Sheng; Du, Dong-Ying; Wang, Xin-Long; Su, Zhong-Min; Fu, Qiang

    2008-11-17

    A series of mixed-ligand coordination complexes, namely, [Cd 2(bimb) 2(L (1)) 2] ( 1), [Cd(bpimb) 0.5(L (2))(H 2O)] ( 2), [Zn 5(bpib) 2(L (3)) 4(OH) 2(H 2O) 2] ( 3), [Zn(bpib) 0.5(L (4))] ( 4), and [Cd(bib)(L (4))] ( 5), where bimb = 1,4-bis((1 H-imidazol-1-yl)methyl)benzene, bpimb = 1,4-bis((2-(pyridin-2-yl)-1 H-imidazol-1-yl)methyl)benzene, bpib = 1,4-bis(2-(pyridin-2-yl)-1 H-imidazol-1-yl)butane, bib = 1,4-bis(1 H-imidazol-1-yl)butane, H 2L (1) = 4-((4-(dihydroxymethyl)phenoxy)methyl)benzoic acid, H 2L (2) = 4,4'-methylenebis(oxy)dibenzoic acid, H 2L (3) = 3,3'-methylenebis(oxy)dibenzoic acid, and H 2L (4) = 4,4'-(2,2'-oxybis(ethane-2,1-diyl)bis(oxy))dibenzoic acid, have been synthesized under hydrothermal conditions. Their structures have been determined by single-crystal X-ray diffraction analyses and further characterized by elemental analyses, IR spectra, and thermogravimetric (TG) analyses. In 1, (L (1)) (2-) anions link the metal-neutral ligand subunits to generate a 2-fold parallel interpenetrating net with the 6 (3) topology. In 2- 4, neutral ligands connect the various metal-carboxylic ligand subunits to give a 2-fold parallel interpenetrating net with (4,4) topology in 2, a 2-fold parallel interpenetrating net with (3,6)-connected topology in 3, and a 3-fold parallel interpenetrating net with (4,4) topology in 4. Compounds 1- 4 display both polyrotaxane and polycatenane characters. Compound 5 is a 5-fold parallel interpenetrating net with (4,4) topology. By careful inspection of these structures, we find that different topological structures showing both polyrotaxane and polycatenane characters have been achieved with increase of the carboxylic ligand length. It is believed that various carboxylic ligands and N-donor ligands with different coordination modes and conformations are important for the formation of the different structures. In addition, the luminescent properties of these compounds are discussed.

  15. Structure elucidation of organic compounds from natural sources using 1D and 2D NMR techniques

    NASA Astrophysics Data System (ADS)

    Topcu, Gulacti; Ulubelen, Ayhan

    2007-05-01

    In our continuing studies on Lamiaceae family plants including Salvia, Teucrium, Ajuga, Sideritis, Nepeta and Lavandula growing in Anatolia, many terpenoids, consisting of over 50 distinct triterpenoids and steroids, and over 200 diterpenoids, several sesterterpenoids and sesquiterpenoids along with many flavonoids and other phenolic compounds have been isolated. For Salvia species abietanes, for Teucrium and Ajuga species neo-clerodanes for Sideritis species ent-kaurane diterpenes are characteristic while nepetalactones are specific for Nepeta species. In this review article, only some interesting and different type of skeleton having constituents, namely rearranged, nor- or rare diterpenes, isolated from these species will be presented. For structure elucidation of these natural diterpenoids intensive one- and two-dimensional NMR techniques ( 1H, 13C, APT, DEPT, NOE/NOESY, 1H- 1H COSY, HETCOR, COLOC, HMQC/HSQC, HMBC, SINEPT) were used besides mass and some other spectroscopic methods.

  16. Algorithms for the automatic generation of 2-D structured multi-block grids

    NASA Technical Reports Server (NTRS)

    Schoenfeld, Thilo; Weinerfelt, Per; Jenssen, Carl B.

    1995-01-01

    Two different approaches to the fully automatic generation of structured multi-block grids in two dimensions are presented. The work aims to simplify the user interactivity necessary for the definition of a multiple block grid topology. The first approach is based on an advancing front method commonly used for the generation of unstructured grids. The original algorithm has been modified toward the generation of large quadrilateral elements. The second method is based on the divide-and-conquer paradigm with the global domain recursively partitioned into sub-domains. For either method each of the resulting blocks is then meshed using transfinite interpolation and elliptic smoothing. The applicability of these methods to practical problems is demonstrated for typical geometries of fluid dynamics.

  17. 2D transition-metal diselenides: phase segregation, electronic structure, and magnetism.

    PubMed

    Manchanda, Priyanka; Skomski, Ralph

    2016-02-17

    Density-functional theory is used to investigate the phase-segregation behavior of two-dimensional transition-metal dichalcogenides, which are of current interest as beyond-graphene materials for optoelectronic and spintronic applications. Our focus is on the behavior of W1-x V x Se2 monolayers, whose end members are semiconducting WSe2 and ferromagnetic VSe2. The energetics favors phase segregation, but the spinodal decomposition temperature is rather low, about 420 K. The addition of V leads to a transition from a nonmagnetic semiconductor to a metallic ferromagnet, with a ferromagnetic moment of about 1.0 μ B per V atom. The transition is caused by a p-type doping mechanism, which shifts the Fermi level into the valence band. The finite-temperature structure and magnetism of the diselenide systems are discussed in terms of Onsager-type critical fluctuations and Bruggeman effective-medium behavior.

  18. 2D transition-metal diselenides: phase segregation, electronic structure, and magnetism

    NASA Astrophysics Data System (ADS)

    Manchanda, Priyanka; Skomski, Ralph

    2016-02-01

    Density-functional theory is used to investigate the phase-segregation behavior of two-dimensional transition-metal dichalcogenides, which are of current interest as beyond-graphene materials for optoelectronic and spintronic applications. Our focus is on the behavior of W1-x V x Se2 monolayers, whose end members are semiconducting WSe2 and ferromagnetic VSe2. The energetics favors phase segregation, but the spinodal decomposition temperature is rather low, about 420 K. The addition of V leads to a transition from a nonmagnetic semiconductor to a metallic ferromagnet, with a ferromagnetic moment of about 1.0 μ B per V atom. The transition is caused by a p-type doping mechanism, which shifts the Fermi level into the valence band. The finite-temperature structure and magnetism of the diselenide systems are discussed in terms of Onsager-type critical fluctuations and Bruggeman effective-medium behavior.

  19. Network structure of production

    PubMed Central

    Atalay, Enghin; Hortaçsu, Ali; Roberts, James; Syverson, Chad

    2011-01-01

    Complex social networks have received increasing attention from researchers. Recent work has focused on mechanisms that produce scale-free networks. We theoretically and empirically characterize the buyer–supplier network of the US economy and find that purely scale-free models have trouble matching key attributes of the network. We construct an alternative model that incorporates realistic features of firms’ buyer–supplier relationships and estimate the model’s parameters using microdata on firms’ self-reported customers. This alternative framework is better able to match the attributes of the actual economic network and aids in further understanding several important economic phenomena. PMID:21402924

  20. Conductance based characterization of structure and hopping site density in 2D molecule-nanoparticle arrays.

    PubMed

    McCold, Cliff E; Fu, Qiang; Howe, Jane Y; Hihath, Joshua

    2015-09-28

    Composite molecule-nanoparticle hybrid systems have recently emerged as important materials for applications ranging from chemical sensing to nanoscale electronics. However, creating reproducible and repeatable composite materials with precise properties has remained one of the primary challenges to the implementation of these technologies. Understanding the sources of variation that dominate the assembly and transport behavior is essential for the advancement of nanoparticle-array based devices. In this work, we use a combination of charge-transport measurements, electron microscopy, and optical characterization techniques to determine the role of morphology and structure on the charge transport properties of 2-dimensional monolayer arrays of molecularly-interlinked Au nanoparticles. Using these techniques we are able to determine the role of both assembly-dependent and particle-dependent defects on the conductivities of the films. These results demonstrate that assembly processes dominate the dispersion of conductance values, while nanoparticle and ligand features dictate the mean value of the conductance. By performing a systematic study of the conductance of these arrays as a function of nanoparticle size we are able to extract the carrier mobility for specific molecular ligands. We show that nanoparticle polydispersity correlates with the void density in the array, and that because of this correlation it is possible to accurately determine the void density within the array directly from conductance measurements. These results demonstrate that conductance-based measurements can be used to accurately and non-destructively determine the morphological and structural properties of these hybrid arrays, and thus provide a characterization platform that helps move 2-dimensional nanoparticle arrays toward robust and reproducible electronic systems.

  1. Four divalent transition metal carboxyarylphosphonate compounds: Hydrothermal synthesis, structural chemistry and generalized 2D FTIR correlation spectroscopy studies

    SciTech Connect

    Lei Ran; Chai Xiaochuan; Mei Hongxin; Zhang Hanhui; Chen Yiping; Sun Yanqiong

    2010-07-15

    Four divalent transition metal carboxyarylphosphonates, [Ni(4,4'-bipy)H{sub 2}L{sup 1}(HL{sup 1}){sub 2}(H{sub 2}O){sub 2}].2H{sub 2}O 1, [Ni{sub 2}(4,4'-bipy)(L{sup 2})(OH)(H{sub 2}O){sub 2}].3H{sub 2}O 2, Mn(phen){sub 2}(H{sub 2}L{sup 1}){sub 2}3 and Mn(phen)(HL{sup 2}) 4 (H{sub 3}L{sup 1}=p-H{sub 2}O{sub 3}PCH{sub 2}-C{sub 6}H{sub 4}-COOH, H{sub 3}L{sup 2}=m-H{sub 2}O{sub 3}PCH{sub 2}-C{sub 6}H{sub 4}-COOH, 4,4'-bipy=4,4'-bipyridine, phen=1,10-phenanthroline) were synthesized under hydrothermal conditions. 1 features 1D linear chains built from Ni(II) ions bridging 4,4'-bipy. In 2, neighboring Ni{sub 4} cluster units are connected by pairs of H{sub 3}L{sup 2} ligands to form 1D double-crankshaft chains, which are interconnected by pairs of 4,4'-bipy into 2D sheets. 3 exhibits 2D supramolecular layers via the R{sub 2}{sup 2}(8) ringed hydrogen bonding units. 4 has 1D ladderlike chains, in which the 4-membered rings are cross-linked by the organic moieties of the H{sub 3}L{sup 2} ligands. Additionally, 2D FTIR correlation analysis is applied with thermal and magnetic perturbation to clarify the structural changes of functional groups from H{sub 3}L{sup 1} and H{sub 3}L{sup 2} ligands in the compounds more efficiently. - Graphical abstract: A series of divalent transition metal carboxyarylphosphonate compounds were synthesized under hydrothermal conditions. The figure displays 2D sheet structure with large windows in compound 2.

  2. A novel 2-D transition metal cyanide membrane: Modeling, structural, magnetic, and functional characterization

    NASA Astrophysics Data System (ADS)

    Goss, Marcus

    A novel 2-dimensional crystalline material composed of cyanide-bridged metal nanosheets with a square planar framework has been prepared. This material, similar to Hofmann clathrates, has a variety of interesting properties. The material is crystalline and possesses characteristics that include magnetic properties, electronic properties and useful structural features. They have recently been exfoliated into individual crystalline sheets. These sheets show a strong potential for use as ion selective membranes. Performance improvements in water purification and desalination by reverse osmosis methods owing to their single atom thickness is possible. A series of dynamic molecular simulations has provided an understanding of the mechanism for water permeability and salt rejection. Energy profiles for the passage of water and ionic species through the porous areas of these nanosheets have been built and reported. Performance estimates of the efficacy of this novel material for use as an ion selective membrane such as an improved desalination RO membrane are presented. Experiments in synthesis and exfoliation of this class of cyanide-bridged transition metal complex were conducted and the results are presented. A preliminary investigation into the magnetic properties of these materials is included.

  3. Theoretical predictions on the electronic structure and charge carrier mobility in 2D Phosphorus sheets

    PubMed Central

    Xiao, Jin; Long, Mengqiu; Zhang, Xiaojiao; Ouyang, Jun; Xu, Hui; Gao, Yongli

    2015-01-01

    We have investigated the electronic structure and carrier mobility of four types of phosphorous monolayer sheet (α-P, β-P,γ-P and δ-P) using density functional theory combined with Boltzmann transport method and relaxation time approximation. It is shown that α-P, β-P and γ-P are indirect gap semiconductors, while δ-P is a direct one. All four sheets have ultrahigh carrier mobility and show anisotropy in-plane. The highest mobility value is ~3 × 105 cm2V−1s−1, which is comparable to that of graphene. Because of the huge difference between the hole and electron mobilities, α-P, γ-P and δ-P sheets can be considered as n-type semiconductors, and β-P sheet can be considered as a p-type semiconductor. Our results suggest that phosphorous monolayer sheets can be considered as a new type of two dimensional materials for applications in optoelectronics and nanoelectronic devices. PMID:26035176

  4. Structure and properties of phosphorene-like IV-VI 2D materials

    NASA Astrophysics Data System (ADS)

    Ma, Zhinan; Wang, Bo; Ou, Liangkai; Zhang, Yan; Zhang, Xu; Zhou, Zhen

    2016-10-01

    Because of the excellent physical and chemical properties of phosphorene, phosphorene and phosphorene-like materials have attracted extensive attention. Since phosphorus belongs to group V, some group IV-VI compounds could also form phosphorene-like configurations. In this work, GeO, SnO, GeS, and SnS monolayers were constructed to investigate the structural and electronic properties by employing first-principles computations. Phonon spectra suggest that these monolayers are dynamically stable and could be realized in experiments. These monolayers are all semiconductors with the band gaps of 2.26 ∼ 4.13 eV. Based on the monolayers, GeO, SnO, GeS, and SnS bilayers were also constructed. The band gaps of these bilayers are smaller than those of the corresponding monolayers. Moreover, the optical properties of these monolayers and bilayers were calculated, and the results indicate that the SnO, GeS and SnS bilayers exhibit obvious optical absorption in the visible spectrum. All the results suggest that phosphorene-like IV-VI materials are promising candidates for electronic and optical devices.

  5. Structure and properties of phosphorene-like IV-VI 2D materials.

    PubMed

    Ma, Zhinan; Wang, Bo; Ou, Liangkai; Zhang, Yan; Zhang, Xu; Zhou, Zhen

    2016-10-14

    Because of the excellent physical and chemical properties of phosphorene, phosphorene and phosphorene-like materials have attracted extensive attention. Since phosphorus belongs to group V, some group IV-VI compounds could also form phosphorene-like configurations. In this work, GeO, SnO, GeS, and SnS monolayers were constructed to investigate the structural and electronic properties by employing first-principles computations. Phonon spectra suggest that these monolayers are dynamically stable and could be realized in experiments. These monolayers are all semiconductors with the band gaps of 2.26 ∼ 4.13 eV. Based on the monolayers, GeO, SnO, GeS, and SnS bilayers were also constructed. The band gaps of these bilayers are smaller than those of the corresponding monolayers. Moreover, the optical properties of these monolayers and bilayers were calculated, and the results indicate that the SnO, GeS and SnS bilayers exhibit obvious optical absorption in the visible spectrum. All the results suggest that phosphorene-like IV-VI materials are promising candidates for electronic and optical devices.

  6. Structure and properties of phosphorene-like IV-VI 2D materials.

    PubMed

    Ma, Zhinan; Wang, Bo; Ou, Liangkai; Zhang, Yan; Zhang, Xu; Zhou, Zhen

    2016-10-14

    Because of the excellent physical and chemical properties of phosphorene, phosphorene and phosphorene-like materials have attracted extensive attention. Since phosphorus belongs to group V, some group IV-VI compounds could also form phosphorene-like configurations. In this work, GeO, SnO, GeS, and SnS monolayers were constructed to investigate the structural and electronic properties by employing first-principles computations. Phonon spectra suggest that these monolayers are dynamically stable and could be realized in experiments. These monolayers are all semiconductors with the band gaps of 2.26 ∼ 4.13 eV. Based on the monolayers, GeO, SnO, GeS, and SnS bilayers were also constructed. The band gaps of these bilayers are smaller than those of the corresponding monolayers. Moreover, the optical properties of these monolayers and bilayers were calculated, and the results indicate that the SnO, GeS and SnS bilayers exhibit obvious optical absorption in the visible spectrum. All the results suggest that phosphorene-like IV-VI materials are promising candidates for electronic and optical devices. PMID:27608201

  7. Unusual Domain Structure and Filamentary Superfluidity for 2D Hard-Core Bosons in Insulating Charge-Ordered Phase

    NASA Astrophysics Data System (ADS)

    Panov, Yu. D.; Moskvin, A. S.; Rybakov, F. N.; Borisov, A. B.

    2016-01-01

    We made use of a special algorithm for compute unified device architecture for NVIDIA graphics cards, a nonlinear conjugate-gradient method to minimize energy functional, and Monte-Carlo technique to directly observe the forming of the ground state configuration for the 2D hard-core bosons by lowering the temperature and its evolution with deviation away from half-filling. The novel technique allowed us to examine earlier implications and uncover novel features of the phase transitions, in particular, look upon the nucleation of the odd domain structure, emergence of filamentary superfluidity nucleated at the antiphase domain walls of the charge-ordered phase, and nucleation and evolution of different topological structures.

  8. Bifurcations of edge states—topologically protected and non-protected—in continuous 2D honeycomb structures

    NASA Astrophysics Data System (ADS)

    Fefferman, C. L.; Lee-Thorp, J. P.; Weinstein, M. I.

    2016-03-01

    Edge states are time-harmonic solutions to energy-conserving wave equations, which are propagating parallel to a line-defect or ‘edge’ and are localized transverse to it. This paper summarizes and extends the authors’ work on the bifurcation of topologically protected edge states in continuous two-dimensional (2D) honeycomb structures. We consider a family of Schrödinger Hamiltonians consisting of a bulk honeycomb potential and a perturbing edge potential. The edge potential interpolates between two different periodic structures via a domain wall. We begin by reviewing our recent bifurcation theory of edge states for continuous 2D honeycomb structures (http://arxiv.org/abs/1506.06111). The topologically protected edge state bifurcation is seeded by the zero-energy eigenstate of a one-dimensional Dirac operator. We contrast these protected bifurcations with (more common) non-protected bifurcations from spectral band edges, which are induced by bound states of an effective Schrödinger operator. Numerical simulations for honeycomb structures of varying contrasts and ‘rational edges’ (zigzag, armchair and others), support the following scenario: (a) for low contrast, under a sign condition on a distinguished Fourier coefficient of the bulk honeycomb potential, there exist topologically protected edge states localized transverse to zigzag edges. Otherwise, and for general edges, we expect long lived edge quasi-modes which slowly leak energy into the bulk. (b) For an arbitrary rational edge, there is a threshold in the medium-contrast (depending on the choice of edge) above which there exist topologically protected edge states. In the special case of the armchair edge, there are two families of protected edge states; for each parallel quasimomentum (the quantum number associated with translation invariance) there are edge states which propagate in opposite directions along the armchair edge.

  9. Dihydrofolate reductase: Sequential resonance assignments using 2D and 3D NMR and secondary structure determination in solution

    SciTech Connect

    Carr, M.D.; Birdsall, B.; Jimenez-Barbero, J.; Polshakov, V.I.; McCormick, J.E.; Feeney, J.; Frenkiel, T.A.; Bauer, C.J. ); Roberts, G.C.K. )

    1991-06-25

    Three-dimensional (3D) heteronuclear NMR techniques have been used to make sequential {sup 1}H and {sup 15}H resonance assignments for most of the residues of Lactobacillus casei dihydrofolate reductase (DHFR), a monomeric protein of molecular mass 18,300 Da. A uniformly {sup 15}N-labeled sample of the protein was prepared and its complex with methotrexate (MTX) studied by 3D {sup 15}N/{sup 1}H nuclear Overhauserheteronuclear multiple quantum coherence (NOESY-HMQC), Harmann-Hahn-heteronuclear multiple quantum coherence (HOHAHA-HMQC), and HMQC-NOESY-HMQC experiments. These experiments overcame most of the spectral overlap problems caused by chemical shift degeneracies in 2D spectra and allowed the {sup 1}H-{sup 1}H through-space and through-bond connectivities to be identified unambiguously, leading to the resonance assignments. The novel HMQC-NOESY-HMQC experiment allows NOE cross peaks to be detected between NH protons even when their {sup 1}H chemical shifts are degenerate as long as the amide {sup 15}N chemical shifts are nondegenerate. The 3D experiments, in combination with conventional 2D NOESY, COSY, and HOHAHA experiments on unlabelled and selectively deuterated DHFR, provide backbone assignments for 146 of the 162 residues and side-chain assignments for 104 residues of the protein. Data from the NOE-based experiments and identification of the slowly exchanging amide protons provide detailed information about the secondary structure of the binary complex of the protein with methotrexate.

  10. MIA-QSAR: a simple 2D image-based approach for quantitative structure activity relationship analysis

    NASA Astrophysics Data System (ADS)

    Freitas, Matheus P.; Brown, Steven D.; Martins, José A.

    2005-03-01

    An accessible and quite simple QSAR method, based on 2D image analysis, is reported. A case study is carried out in order to compare this model with a previously reported sophisticated methodology. A well known set of ( S)- N-[(1-ethyl-2-pyrrolidinyl)methyl]-6-methoxybenzamides, compounds with affinity to the dopamine D 2 receptor subtype, was divided in 40 calibration compounds and 18 test compounds and the descriptors were generated from pixels of 2D structures of each compound, which can be drawn with aid of any appropriate program. Bilinear (conventional) PLS was utilized as the regression method and leave-one-out cross-validation was performed using the NIPALS algorithm. The good predicted Q2 value obtained for the series of test compounds (0.58), together with the similar prediction quality obtained to other data sets (nAChR ligands, HIV protease inhibitors, COX-2 inhibitors and anxiolytic agents), suggests that the model is robust and seems to be as applicable as more complex methods.

  11. Structural inference for uncertain networks

    NASA Astrophysics Data System (ADS)

    Martin, Travis; Ball, Brian; Newman, M. E. J.

    2016-01-01

    In the study of networked systems such as biological, technological, and social networks the available data are often uncertain. Rather than knowing the structure of a network exactly, we know the connections between nodes only with a certain probability. In this paper we develop methods for the analysis of such uncertain data, focusing particularly on the problem of community detection. We give a principled maximum-likelihood method for inferring community structure and demonstrate how the results can be used to make improved estimates of the true structure of the network. Using computer-generated benchmark networks we demonstrate that our methods are able to reconstruct known communities more accurately than previous approaches based on data thresholding. We also give an example application to the detection of communities in a protein-protein interaction network.

  12. Computation of self-field hysteresis losses in conductors with helicoidal structure using a 2D finite element method

    NASA Astrophysics Data System (ADS)

    Stenvall, A.; Siahrang, M.; Grilli, F.; Sirois, F.

    2013-04-01

    It is well known that twisting current-carrying conductors helps to reduce their coupling losses. However, the impact of twisting on self-field hysteresis losses has not been as extensively investigated as that on the reduction of coupling losses. This is mostly because the reduction of coupling losses has been an important issue to tackle in the past, and it is not possible to consider twisting within the classical two-dimensional (2D) approaches for the computation of self-field hysteresis losses. Recently, numerical codes considering the effect of twisting in continuous symmetries have appeared. For general three-dimensional (3D) simulations, one issue is that no robust, widely accepted and easy to obtain model for expressing the relationship between the current density and the electric field is available. On the other hand, we can consider that in these helicoidal structures currents flow only along the helicoidal trajectories. This approach allows one to use the scalar power-law for superconductor resistivity and makes the eddy current approach to a solution of a hysteresis loss problem feasible. In this paper we use the finite element method to solve the eddy current model in helicoidal structures in 2D domains utilizing the helicoidal symmetry. The developed tool uses the full 3D geometry but allows discretization which takes advantage of the helicoidal symmetry to reduce the computational domain to a 2D one. We utilize in this tool the non-linear power law for modelling the resistivity in the superconducting regions and study how the self-field losses are influenced by the twisting of a 10-filament wire. Additionally, in the case of high aspect ratio tapes, we compare the results computed with the new tool and a one-dimensional program based on the integral equation method and developed for simulating single layer power cables made of ReBCO coated conductors. Finally, we discuss modelling issues and present open questions related to helicoidal structures

  13. A hybrid wave-mode formulation for the vibro-acoustic analysis of 2D periodic structures

    NASA Astrophysics Data System (ADS)

    Droz, C.; Zhou, C.; Ichchou, M. N.; Lainé, J.-P.

    2016-02-01

    In the framework of vibrational analysis of 2D periodic waveguides, Floquet-Bloch theorem is widely applied for the determination of wave dispersion characteristics. In this context, the Wave Finite Element Method (WFEM) combines Periodic Structure Theory (PST) with standard FE packages, enabling wave dispersion analysis of waveguides involving structurally realistic unit-cells. For such applications, the computational efficiency of the WFEM depends on the choice of the formulation and can lead to numerical issues, worsen by extensive computational cost. This paper presents a coupled wave-mode approach for the determination of wave dispersion characteristics in structurally advanced periodic structures. It combines two scales of model order reduction. At the unit-cell's scale, Component Mode Synthesis (CMS) provides the displacement field associated with local resonances of the periodic structure, while the free wave propagation is considered using a spectral problem projection on a reduced set of shape functions associated with propagating waves, thus providing considerable reduction of the computational cost. An application is provided for a bi-directionally stiffened panel and the influence of reduction parameters is discussed, as well as the robustness of the numerical results.

  14. Simultaneous image segmentation and medial structure estimation: application to 2D and 3D vessel tree extraction

    NASA Astrophysics Data System (ADS)

    Makram-Ebeid, Sherif; Stawiaski, Jean; Pizaine, Guillaume

    2011-03-01

    We propose a variational approach which combines automatic segmentation and medial structure extraction in a single computationally efficient algorithm. In this paper, we apply our approach to the analysis of vessels in 2D X-ray angiography and 3D X-ray rotational angiography of the brain. Other variational methods proposed in the literature encode the medial structure of vessel trees as a skeleton with associated vessel radii. In contrast, our method provides a dense smooth level set map which sign provides the segmentation. The ridges of this map define the segmented regions skeleton. The differential structure of the smooth map (in particular the Hessian) allows the discrimination between tubular and other structures. In 3D, both circular and non-circular tubular cross-sections and tubular branching can be handled conveniently. This algorithm allows accurate segmentation of complex vessel structures. It also provides key tools for extracting anatomically labeled vessel tree graphs and for dealing with challenging issues like kissing vessel discrimination and separation of entangled 3D vessel trees.

  15. Insights into the growth of bismuth nanoparticles on 2D structured BiOCl photocatalysts: an in situ TEM investigation.

    PubMed

    Chang, Xiaofeng; Wang, Shuangbao; Qi, Qi; Gondal, Mohammed A; Rashid, Siddique G; Gao, Si; Yang, Deyuan; Shen, Kai; Xu, Qingyu; Wang, Peng

    2015-09-28

    The synthetic techniques for novel photocatalytic crystals had evolved by a trial-and-error process that spanned more than two decades, and an insight into the photocatalytic crystal growth process is a challenging area and prerequisite for achieving an excellent photoactivity. Bismuth nanoparticle based hybrids, such as Bi/BiOCl composites, have recently been investigated as highly efficient photocatalytic systems because of the localized surface plasmon resonance (LSPR) of nanostructured bismuth. In this work, the observation towards the formation and growth of bismuth nanoparticles onto 2D structured BiOCl photocatalysts has been performed using a transmission electron microscope (TEM) directly in real time. The growth of bismuth nanoparticles on BiOCl nanosheets can be emulated and speeded up driven by the electron beam (e(-) beam) in TEM. The crystallinity, growth and the elemental evolution during the formation of bismuth nanoparticles have also been probed in this work.

  16. Exploring the Structure and Chemical Activity of 2-D Gold Islands on Graphene Moire/Ru(0001)

    SciTech Connect

    Xu, Y.; Semidey-Flecha, Lymarie; Liu, L.; Zhou, Zihao; Goodman, D. Wayne

    2011-01-01

    Au deposited on Ru(0001)-supported extended, continuous graphene moiré forms large 2-D islands at room temperature that are several nanometers in diameter but only 0.55 nm in height, in the apparent absence of typical binding sites such as defects and adsorbates. These Au islands conform to the corrugation of the underlying graphene and display commensurate moiré patterns. Several extended Au structure models on graphene/Ru(0001) are examined using density functional theory calculations. Close-packed Au overlayers are energetically more stable, but all interact weakly with the support. Preliminary tests found the Au islands/graphene/Ru(0001) surface to be active for CO oxidation at cryogenic temperature, which suggests that the Au itself is the locus of catalytic activity.

  17. Scaling Analysis of Ocean Surface Turbulent Heterogeneities from Satellite Remote Sensing: Use of 2D Structure Functions, methodology and applications

    NASA Astrophysics Data System (ADS)

    Schmitt, F. G.; Pannimpullath Remanan, R.; Loisel, H.

    2015-12-01

    Satellite remote sensing observations allow the ocean surface to be sampled over large spatio-temporal scales. The images provided from visible and thermal infrared satellite observations are widely used in physical, biological, and ecological oceanography. The present work proposes a method to understand the multi-scaling properties of satellite products such as the Chlorophyll-a (Chl-a), and the Sea Surface Temperature (SST). The specific objectives of this study are to show how the small scale heterogeneities of satellite images can be characterised using tools borrowed from the fields of turbulence. We show how the structure function, which is classically used in the frame of scaling time series analysis, can be used also in 2D. The main advantage of this method is that it can be applied to process images which have missing data. Based on both simulated and real images, we demonstrate that coarse-graining (CG) of a gradient modulus transform of the original image does not provide correct scaling exponents. We show, using a fractional Brownian simulation in 2D, that the structure function (SF) can be used with randomly sampled couple of points, and verify that 1 million of couple of points provides enough statistics. After this methodological study, some applications are presented: the nonlinear moment function ζ(q) is fitted using the lognormal model with 2 parameters, the Hurst index H and the intermittency μ. The values of H and μ are discussed for 4 different parameters (Chl-a, SST, Rrs-443 and Rrs-555) and for different locations, chosen among different contrasted regions of the ocean, characterized by high spatial heterogeneity in Chl-a and SST.

  18. A review of MBE grown 0D, 1D and 2D quantum structures in a nanowire

    NASA Astrophysics Data System (ADS)

    de la Mata, Maria; Zhou, Xiang; Furtmayr, Florian; Teubert, Jörg; Gradecak, Silvija; Eickhoff, Martin; Fontcuberta i Morral, Anna; Arbiol, Jordi

    2013-05-01

    We review different strategies to achieve a three-dimensional energy bandgap modulation in a nanowire (NW) by the introduction of self-assembled 0D, 1D and 2D quantum structures, quantum dots (QDs), quantum wires (QWRs) and quantum wells (QWs). Starting with the well-known axial, radial (coaxial/prismatic) or polytypic quantum wells in GaN/AlN, GaAs/AlAs or wurtzite/zinc-blende systems, respectively, we move to more sophisticated structures by lowering their dimensionality. New recent approaches developed for the self-assembly of GaN quantum wires and InAs or AlGaAs quantum dots on single nanowire templates are reported and discussed. Aberration corrected scanning transmission electron microcopy is presented as a powerful tool to determine the structure and morphology at the atomic scale allowing for the creation of 3D atomic models that can help us to understand the enhanced optical properties of these advanced quantum structures.

  19. Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

    PubMed Central

    Shoshan, Michal S.; Tshuva, Edit Y.; Shalev, Deborah E.

    2013-01-01

    Copper (I) binding by metallochaperone transport proteins prevents copper oxidation and release of the toxic ions that may participate in harmful redox reactions. The Cu (I) complex of the peptide model of a Cu (I) binding metallochaperone protein, which includes the sequence MTCSGCSRPG (underlined is conserved), was determined in solution under inert conditions by NMR spectroscopy. NMR is a widely accepted technique for the determination of solution structures of proteins and peptides. Due to difficulty in crystallization to provide single crystals suitable for X-ray crystallography, the NMR technique is extremely valuable, especially as it provides information on the solution state rather than the solid state. Herein we describe all steps that are required for full three-dimensional structure determinations by NMR. The protocol includes sample preparation in an NMR tube, 1D and 2D data collection and processing, peak assignment and integration, molecular mechanics calculations, and structure analysis. Importantly, the analysis was first conducted without any preset metal-ligand bonds, to assure a reliable structure determination in an unbiased manner. PMID:24378924

  20. Kohn-Sham Band Structure Benchmark Including Spin-Orbit Coupling for 2D and 3D Solids

    NASA Astrophysics Data System (ADS)

    Huhn, William; Blum, Volker

    2015-03-01

    Accurate electronic band structures serve as a primary indicator of the suitability of a material for a given application, e.g., as electronic or catalytic materials. Computed band structures, however, are subject to a host of approximations, some of which are more obvious (e.g., the treatment of the exchange-correlation of self-energy) and others less obvious (e.g., the treatment of core, semicore, or valence electrons, handling of relativistic effects, or the accuracy of the underlying basis set used). We here provide a set of accurate Kohn-Sham band structure benchmarks, using the numeric atom-centered all-electron electronic structure code FHI-aims combined with the ``traditional'' PBE functional and the hybrid HSE functional, to calculate core, valence, and low-lying conduction bands of a set of 2D and 3D materials. Benchmarks are provided with and without effects of spin-orbit coupling, using quasi-degenerate perturbation theory to predict spin-orbit splittings. This work is funded by Fritz-Haber-Institut der Max-Planck-Gesellschaft.

  1. Self-Assembly of Graphene Single Crystals with Uniform Size and Orientation: The First 2D Super-Ordered Structure.

    PubMed

    Zeng, Mengqi; Wang, Lingxiang; Liu, Jinxin; Zhang, Tao; Xue, Haifeng; Xiao, Yao; Qin, Zhihui; Fu, Lei

    2016-06-29

    The challenges facing the rapid developments of highly integrated electronics, photonics, and microelectromechanical systems suggest that effective fabrication technologies are urgently needed to produce ordered structures using components with high performance potential. Inspired by the spontaneous organization of molecular units into ordered structures by noncovalent interactions, we succeed for the first time in synthesizing a two-dimensional superordered structure (2DSOS). As demonstrated by graphene, the 2DSOS was prepared via self-assembly of high-quality graphene single crystals under mutual electrostatic force between the adjacent crystals assisted by airflow-induced hydrodynamic forces at the liquid metal surface. The as-obtained 2DSOS exhibits tunable periodicity in the crystal space and outstanding uniformity in size and orientation. Moreover, the intrinsic property of each building block is preserved. With simplicity, scalability, and continuously adjustable feature size, the presented approach may open new territory for the precise assembly of 2D atomic crystals and facilitate its application in structurally derived integrated systems. PMID:27313075

  2. Covalent Titanium(IV)-Aryloxide Network Materials: 4,4‧-Biphenoxide 3D and Polyphenolic 2D Motifs

    NASA Astrophysics Data System (ADS)

    Tanski, Joseph M.; Lobkovsky, Emil B.; Wolczanski, Peter

    2000-06-01

    The three- and two-dimensional covalent metal-organic network (CMON) compounds {[Ti(μ1,6:η2,η1-4,4‧-OC12H8O)0.5(μ1,6:η2,η1-4,4‧-OC12H8O)(OiPr)(HOiPr)]2·THF}n (1) and {[Ti(μ1,3-1,3-OC6H4O)(μ-1,3-OC6H4OH)(1,3-OC6H4OH) (HOiPr)]2}n (2) were synthesized by treatment of Ti(OiPr)4 with 4,4‧-dihydroxybiphenyl in THF and resorcinol in CS2, respectively, at 100°C. Diffraction data was collected at the Cornell High Energy Synchrotron Source (CHESS) because of the small, weakly diffracting nature of the crystals. 1 (C26H31O5.5Ti, monoclinic, P21, a=10.137(2), b=15.988(3), c=15.745(3), β=107.76(3)°, Z=4, R=0.0858) and 2 (C21H22O7Ti, monoclinic, P21/c, a=11.955(2), b=16.275(3), c=11.028(2), β=113.25(3)°, Z=4, R=0.0550) are both based upon similar edge-sharing bioctahedral dititanium building blocks, (i.e., Ti2(μ-OAr)2). Six connections per dititanium unit constrain the structural motif of 1 to be base-centered. Four μ1,3-diphenoxides per dititanium core in 2 connect to provide a rectangular net, but the regiochemistry of resorcinol ultimately restricts its dimensionality. The structures suggest design elements based on the number and geometry of connecting organic linkages.

  3. Controllability of structural brain networks

    PubMed Central

    Gu, Shi; Pasqualetti, Fabio; Cieslak, Matthew; Telesford, Qawi K.; Yu, Alfred B.; Kahn, Ari E.; Medaglia, John D.; Vettel, Jean M.; Miller, Michael B.; Grafton, Scott T.; Bassett, Danielle S.

    2015-01-01

    Cognitive function is driven by dynamic interactions between large-scale neural circuits or networks, enabling behaviour. However, fundamental principles constraining these dynamic network processes have remained elusive. Here we use tools from control and network theories to offer a mechanistic explanation for how the brain moves between cognitive states drawn from the network organization of white matter microstructure. Our results suggest that densely connected areas, particularly in the default mode system, facilitate the movement of the brain to many easily reachable states. Weakly connected areas, particularly in cognitive control systems, facilitate the movement of the brain to difficult-to-reach states. Areas located on the boundary between network communities, particularly in attentional control systems, facilitate the integration or segregation of diverse cognitive systems. Our results suggest that structural network differences between cognitive circuits dictate their distinct roles in controlling trajectories of brain network function. PMID:26423222

  4. Network Structure and City Size

    PubMed Central

    Levinson, David

    2012-01-01

    Network structure varies across cities. This variation may yield important knowledge about how the internal structure of the city affects its performance. This paper systematically compares a set of surface transportation network structure variables (connectivity, hierarchy, circuity, treeness, entropy, accessibility) across the 50 largest metropolitan areas in the United States. A set of scaling parameters are discovered to show how network size and structure vary with city size. These results suggest that larger cities are physically more inter-connected. Hypotheses are presented as to why this might obtain. This paper then consistently measures and ranks access to jobs across 50 US metropolitan areas. It uses that accessibility measure, along with network structure variables and city size to help explain journey-to-work time and auto mode share in those cities. A 1 percent increase in accessibility reduces average metropolitan commute times by about 90 seconds each way. A 1 percent increase in network connectivity reduces commute time by 0.1 percent. A 1 percent increase in accessibility results in a 0.0575 percent drop in auto mode share, while a 1 percent increase in treeness reduces auto mode share by 0.061 percent. Use of accessibility and network structure measures is important for planning and evaluating the performance of network investments and land use changes. PMID:22253764

  5. Collective network for computer structures

    DOEpatents

    Blumrich, Matthias A.; Coteus, Paul W.; Chen, Dong; Gara, Alan; Giampapa, Mark E.; Heidelberger, Philip; Hoenicke, Dirk; Takken, Todd E.; Steinmacher-Burow, Burkhard D.; Vranas, Pavlos M.

    2011-08-16

    A system and method for enabling high-speed, low-latency global collective communications among interconnected processing nodes. The global collective network optimally enables collective reduction operations to be performed during parallel algorithm operations executing in a computer structure having a plurality of the interconnected processing nodes. Router devices ate included that interconnect the nodes of the network via links to facilitate performance of low-latency global processing operations at nodes of the virtual network and class structures. The global collective network may be configured to provide global barrier and interrupt functionality in asynchronous or synchronized manner. When implemented in a massively-parallel supercomputing structure, the global collective network is physically and logically partitionable according to needs of a processing algorithm.

  6. Imaging 2D structures by the CSAMT method: application to the Pantano di S. Gregorio Magno faulted basin (Southern Italy)

    NASA Astrophysics Data System (ADS)

    Troiano, Antonio; Di Giuseppe, Maria Giulia; Petrillo, Zaccaria; Patella, Domenico

    2009-06-01

    A controlled source audiofrequency magnetotelluric (CSAMT) survey has been undertaken in the Pantano di San Gregorio Magno faulted basin, an earthquake prone area of Southern Apennines in Italy. A dataset from 11 soundings, distributed along a nearly N-S 780 m long profile, was acquired in the basin's easternmost area, where the fewest data are available as to the faulting shallow features. A preliminary skew analysis allowed a prevailing 2D nature of the dataset to be ascertained. Then, using a single-site multi-frequency approach, Dantzig's simplex algorithm was introduced for the first time to estimate the CSAMT decomposition parameters. The simplex algorithm, freely available online, proved to be fast and efficient. By this approach, the TM and TE mode field diagrams were obtained and a N35°W ± 10° 2D strike mean direction was estimated along the profile, in substantial agreement with the fault traces within the basin. A 2D inversion of the apparent resistivity and phase curves at seven almost noise-free sites distributed along the central portion of the profile was finally elaborated, reinforced by a sensitivity analysis, which allowed the best resolved portion of the model to be imaged from the first few meters of depth down to a mean depth of 300 m b.g.l. From the inverted section, the following features have been outlined: (i) a cover layer with resistivity in the range 3-30 Ω m ascribed to the Quaternary lacustrine clayey deposits filling the basin, down to an average depth of about 35 m b.g.l., underlain by a structure with resistivity over 50 Ω m up to about 600 Ω m, ascribed to the Mesozoic carbonate bedrock; (ii) a system of two normal faults within the carbonate basement, extending down to the maximum best resolved depth of the order of 300 m b.g.l.; (iii) two wedge-shaped domains separating the opposite blocks of the faults with resistivity ranging between 30 Ω m and 50 Ω m and horizontal extent of the order of some tens of metres, likely

  7. Anion-induced structural transformation of a sulfate-incorporated 2D Cd(II)-organic framework

    NASA Astrophysics Data System (ADS)

    Lee, Li-Wei; Luo, Tzuoo-Tsair; Wang, Chih-Min; Lee, Gene-Hsiang; Peng, Shie-Ming; Liu, Yen-Hsiang; Lee, Sheng-Long; Lu, Kuang-Lieh

    2016-07-01

    A Cd(II)-organic framework {[Cd2(tpim)4(SO4)(H2O)2]·(SO4)·21H2O}n (1) was synthesized by reacting CdSO4·8/3H2O and 2,4,5-tri(4-pyridyl)imidazole (tpim) under hydrothermal conditions. A structural analysis showed that compound 1 adopts a layered structure in which the [Cd(tpim)2]n chains are linked by sulfate anions. These 2D layers are further packed into a 3D supramolecular framework via π-π interactions. The structure contains two types of SO42- anions, i.e., bridging SO42- and free SO42- anions, the latter of which are included in the large channels of the framework. Compound 1 exhibits interesting anion exchange behavior. In the presence of SCN- anions, both the bridging and free SO42- anions in 1 were completely exchanged by SCN- ligands to form a 1D species [Cd(tpim)2(SCN)2] (1A), in which the SCN- moieties function as a monodentate ligand. On the other hand, when compound 1 was ion exchanged with N3- anions in aqueous solution, the bridging SO42- moieties remained intact, and only the free guest SO42- were replaced by N3- anions. The gas adsorption behavior of the activated compound 1 was also investigated.

  8. Automatic classification of pulmonary peri-fissural nodules in computed tomography using an ensemble of 2D views and a convolutional neural network out-of-the-box.

    PubMed

    Ciompi, Francesco; de Hoop, Bartjan; van Riel, Sarah J; Chung, Kaman; Scholten, Ernst Th; Oudkerk, Matthijs; de Jong, Pim A; Prokop, Mathias; van Ginneken, Bram

    2015-12-01

    In this paper, we tackle the problem of automatic classification of pulmonary peri-fissural nodules (PFNs). The classification problem is formulated as a machine learning approach, where detected nodule candidates are classified as PFNs or non-PFNs. Supervised learning is used, where a classifier is trained to label the detected nodule. The classification of the nodule in 3D is formulated as an ensemble of classifiers trained to recognize PFNs based on 2D views of the nodule. In order to describe nodule morphology in 2D views, we use the output of a pre-trained convolutional neural network known as OverFeat. We compare our approach with a recently presented descriptor of pulmonary nodule morphology, namely Bag of Frequencies, and illustrate the advantages offered by the two strategies, achieving performance of AUC = 0.868, which is close to the one of human experts. PMID:26458112

  9. Automatic classification of pulmonary peri-fissural nodules in computed tomography using an ensemble of 2D views and a convolutional neural network out-of-the-box.

    PubMed

    Ciompi, Francesco; de Hoop, Bartjan; van Riel, Sarah J; Chung, Kaman; Scholten, Ernst Th; Oudkerk, Matthijs; de Jong, Pim A; Prokop, Mathias; van Ginneken, Bram

    2015-12-01

    In this paper, we tackle the problem of automatic classification of pulmonary peri-fissural nodules (PFNs). The classification problem is formulated as a machine learning approach, where detected nodule candidates are classified as PFNs or non-PFNs. Supervised learning is used, where a classifier is trained to label the detected nodule. The classification of the nodule in 3D is formulated as an ensemble of classifiers trained to recognize PFNs based on 2D views of the nodule. In order to describe nodule morphology in 2D views, we use the output of a pre-trained convolutional neural network known as OverFeat. We compare our approach with a recently presented descriptor of pulmonary nodule morphology, namely Bag of Frequencies, and illustrate the advantages offered by the two strategies, achieving performance of AUC = 0.868, which is close to the one of human experts.

  10. Ligand-controlled assembly of Cd(II) coordination polymers based on mixed ligands of naphthalene-dicarboxylate and dipyrido[3,2-d:2',3'-f]quinoxaline: From 0D+1D cocrystal, 2D rectangular network (4,4), to 3D PtS-type architecture

    SciTech Connect

    Liu Guocheng; Chen Yongqiang; Wang Xiuli Chen Baokuan; Lin Hongyan

    2009-03-15

    Three novel Cd(II) coordination polymers, namely, [Cd(Dpq)(1,8-NDC)(H{sub 2}O){sub 2}][Cd(Dpq)(1,8-NDC)].2H{sub 2}O (1), [Cd(Dpq)(1,4-NDC)(H{sub 2}O)] (2), and [Cd(Dpq)(2,6-NDC)] (3) have been obtained from hydrothermal reactions of cadmium(II) nitrate with the mixed ligands dipyrido [3,2-d:2',3'-f]quinoxaline (Dpq) and three structurally related naphthalene-dicarboxylate ligands [1,8-naphthalene-dicarboxylic acid (1,8-H{sub 2}NDC), 1,4-naphthalene-dicarboxylic acid (1,4-H{sub 2}NDC), and 2,6-naphthalene-dicarboxylic acid (2,6-H{sub 2}NDC)]. Single-crystal X-ray diffraction analysis reveals that the three polymers exhibit novel structures due to different naphthalene-dicarboxylic acid. Compound 1 is a novel cocrystal of left- and right-handed helical chains and binuclear complexes and ultimately packed into a 3D supramolecular structure through hydrogen bonds and {pi}-{pi} stacking interactions. Compound 2 shows a 2D rectangular network (4,4) bridged by 1,4-NDC with two kinds of coordination modes and ultimately packed into a 3D supramolecular structure through inter-layer {pi}-{pi} stacking interactions. Compound 3 is a new 3D coordination polymer with distorted PtS-type network. In addition, the title compounds exhibit blue/green emission in solid state at room temperature. - Graphical abstract: Three novel Cd(II) compounds have been synthesized under hydrothermal conditions exhibiting a systematic variation of architecture by the employment of three structurally related naphthalene-dicarboxylate ligands.

  11. Collective network for computer structures

    DOEpatents

    Blumrich, Matthias A; Coteus, Paul W; Chen, Dong; Gara, Alan; Giampapa, Mark E; Heidelberger, Philip; Hoenicke, Dirk; Takken, Todd E; Steinmacher-Burow, Burkhard D; Vranas, Pavlos M

    2014-01-07

    A system and method for enabling high-speed, low-latency global collective communications among interconnected processing nodes. The global collective network optimally enables collective reduction operations to be performed during parallel algorithm operations executing in a computer structure having a plurality of the interconnected processing nodes. Router devices are included that interconnect the nodes of the network via links to facilitate performance of low-latency global processing operations at nodes of the virtual network. The global collective network may be configured to provide global barrier and interrupt functionality in asynchronous or synchronized manner. When implemented in a massively-parallel supercomputing structure, the global collective network is physically and logically partitionable according to the needs of a processing algorithm.

  12. 3D spin-flop transition in enhanced 2D layered structure single crystalline TlCo2Se2.

    PubMed

    Jin, Z; Xia, Z-C; Wei, M; Yang, J-H; Chen, B; Huang, S; Shang, C; Wu, H; Zhang, X-X; Huang, J-W; Ouyang, Z-W

    2016-10-01

    The enhanced 2D layered structure single crystalline TlCo2Se2 has been successfully fabricated, which exhibits field-induced 3D spin-flop phase transitions. In the case of the magnetic field parallel to the c-axis (B//c), the applied magnetic field induces the evolution of the noncollinear helical magnetic coupling into a ferromagnetic (FM) state with all the magnetization of the Co ion parallel to the c-axis. A striking variation of the field-induced strain within the ab-plane is noticed in the magnetic field region of 20-30 T. In the case of the magnetic field perpendicular to the c-axis (B  ⊥  c), the inter-layer helical antiferromagnetic (AFM) coupling may transform to an initial canted AFM coupling, and then part of it transforms to an intermediate metamagnetic phase with the alignment of two-up-one-down Co magnetic moments and finally to an ultimate FM coupling in higher magnetic fields. The robust noncollinear AFM magnetic coupling is completely destroyed above 30 T. In combination with the measurements of magnetization, magnetoresistance and field-induced strain, a complete magnetic phase diagram of the TlCo2Se2 single crystal has been depicted, demonstrating complex magnetic structures even though the crystal geometry itself gives no indication of the magnetic frustration. PMID:27485370

  13. Recent Advances In 2D-Band Structure Imaging By k-PEEM and Prospects For Technological Materials

    NASA Astrophysics Data System (ADS)

    Mathieu, C.; Renault, O.; Rotella, H.; Barrett, N.; Chabli, A.

    2011-11-01

    The imaging of surfaces using the PhotoElectron Emission Microscopy (PEEM) technique has recently received considerable interest, mainly thanks to the use of high brilliance synchrotron radiation which facilitates the study of surface properties and chemical selectivity. By inserting a transfer lens in the optical column of a high transmission and full energy-filtering PEEM, it is possible to image the back focal plane, named k-PEEM imaging mode. Hence, the corresponding image shows the angular distribution of the emitted photoelectrons for a given kinetic energy. By varying the kinetic energy, the complete energy filtering provides full 2D cuts of the band structure in reciprocal space. In this paper, we present the principles and the capabilities of this new imaging mode, and compare it to the standard ARPES technique. Then, we present results obtained on a model sample: Ag(100), and on a technological sample, epitaxial graphene on SiC(0001), highlighting the potential of this new imaging mode for the spatially resolved characterization of the electronic structure of monocrystalline materials in devices.

  14. 3D spin-flop transition in enhanced 2D layered structure single crystalline TlCo2Se2

    NASA Astrophysics Data System (ADS)

    Jin, Z.; Xia, Z.-C.; Wei, M.; Yang, J.-H.; Chen, B.; Huang, S.; Shang, C.; Wu, H.; Zhang, X.-X.; Huang, J.-W.; Ouyang, Z.-W.

    2016-10-01

    The enhanced 2D layered structure single crystalline TlCo2Se2 has been successfully fabricated, which exhibits field-induced 3D spin-flop phase transitions. In the case of the magnetic field parallel to the c-axis (B//c), the applied magnetic field induces the evolution of the noncollinear helical magnetic coupling into a ferromagnetic (FM) state with all the magnetization of the Co ion parallel to the c-axis. A striking variation of the field-induced strain within the ab-plane is noticed in the magnetic field region of 20-30 T. In the case of the magnetic field perpendicular to the c-axis (B  ⊥  c), the inter-layer helical antiferromagnetic (AFM) coupling may transform to an initial canted AFM coupling, and then part of it transforms to an intermediate metamagnetic phase with the alignment of two-up-one-down Co magnetic moments and finally to an ultimate FM coupling in higher magnetic fields. The robust noncollinear AFM magnetic coupling is completely destroyed above 30 T. In combination with the measurements of magnetization, magnetoresistance and field-induced strain, a complete magnetic phase diagram of the TlCo2Se2 single crystal has been depicted, demonstrating complex magnetic structures even though the crystal geometry itself gives no indication of the magnetic frustration.

  15. Large structure rearrangement of colicin ia channel domain after membrane binding from 2D 13C spin diffusion NMR.

    PubMed

    Luo, Wenbin; Yao, Xiaolan; Hong, Mei

    2005-05-01

    One of the main mechanisms of membrane protein folding is by spontaneous insertion into the lipid bilayer from the aqueous environment. The bacterial toxin, colicin Ia, is one such protein. To shed light on the conformational changes involved in this dramatic transfer from the polar to the hydrophobic milieu, we carried out 2D magic-angle spinning (13)C NMR experiments on the water-soluble and membrane-bound states of the channel-forming domain of colicin Ia. Proton-driven (13)C spin diffusion spectra of selectively (13)C-labeled protein show unequivocal attenuation of cross-peaks after membrane binding. This attenuation can be assigned to distance increases but not reduction of the diffusion coefficient. Analysis of the statistics of the interhelical and intrahelical (13)C-(13)C distances in the soluble protein structure indicates that the observed cross-peak reduction is well correlated with a high percentage of short interhelical contacts in the soluble protein. This suggests that colicin Ia channel domain becomes open and extended upon membrane binding, thus lengthening interhelical distances. In comparison, cross-peaks with similar intensities between the two states are dominated by intrahelical contacts in the soluble state. This suggests that the membrane-bound structure of colicin Ia channel domain may be described as a "molten globule", in which the helical secondary structure is retained while the tertiary structure is unfolded. This study demonstrates that (13)C spin diffusion NMR is a valuable tool for obtaining qualitative long-range distance constraints on membrane protein folding. PMID:15853348

  16. Structure of the HCMV UL16-MICB complex elucidates select binding of a viral immunoevasin to diverse NKG2D ligands.

    PubMed

    Müller, Steffen; Zocher, Georg; Steinle, Alexander; Stehle, Thilo

    2010-01-01

    The activating immunoreceptor NKG2D promotes elimination of infected or malignant cells by cytotoxic lymphocytes through engagement of stress-induced MHC class I-related ligands. The human cytomegalovirus (HCMV)-encoded immunoevasin UL16 subverts NKG2D-mediated immune responses by retaining a select group of diverse NKG2D ligands inside the cell. We report here the crystal structure of UL16 in complex with the NKG2D ligand MICB at 1.8 A resolution, revealing the molecular basis for the promiscuous, but highly selective, binding of UL16 to unrelated NKG2D ligands. The immunoglobulin-like UL16 protein utilizes a three-stranded beta-sheet to engage the alpha-helical surface of the MHC class I-like MICB platform domain. Intriguingly, residues at the center of this beta-sheet mimic a central binding motif employed by the structurally unrelated C-type lectin-like NKG2D to facilitate engagement of diverse NKG2D ligands. Using surface plasmon resonance, we find that UL16 binds MICB, ULBP1, and ULBP2 with similar affinities that lie in the nanomolar range (12-66 nM). The ability of UL16 to bind its ligands depends critically on the presence of a glutamine (MICB) or closely related glutamate (ULBP1 and ULBP2) at position 169. An arginine residue at this position however, as found for example in MICA or ULBP3, would cause steric clashes with UL16 residues. The inability of UL16 to bind MICA and ULBP3 can therefore be attributed to single substitutions at key NKG2D ligand locations. This indicates that selective pressure exerted by viral immunoevasins such as UL16 contributed to the diversification of NKG2D ligands.

  17. Structure of the HCMV UL16-MICB complex elucidates select binding of a viral immunoevasin to diverse NKG2D ligands.

    PubMed

    Müller, Steffen; Zocher, Georg; Steinle, Alexander; Stehle, Thilo

    2010-01-01

    The activating immunoreceptor NKG2D promotes elimination of infected or malignant cells by cytotoxic lymphocytes through engagement of stress-induced MHC class I-related ligands. The human cytomegalovirus (HCMV)-encoded immunoevasin UL16 subverts NKG2D-mediated immune responses by retaining a select group of diverse NKG2D ligands inside the cell. We report here the crystal structure of UL16 in complex with the NKG2D ligand MICB at 1.8 A resolution, revealing the molecular basis for the promiscuous, but highly selective, binding of UL16 to unrelated NKG2D ligands. The immunoglobulin-like UL16 protein utilizes a three-stranded beta-sheet to engage the alpha-helical surface of the MHC class I-like MICB platform domain. Intriguingly, residues at the center of this beta-sheet mimic a central binding motif employed by the structurally unrelated C-type lectin-like NKG2D to facilitate engagement of diverse NKG2D ligands. Using surface plasmon resonance, we find that UL16 binds MICB, ULBP1, and ULBP2 with similar affinities that lie in the nanomolar range (12-66 nM). The ability of UL16 to bind its ligands depends critically on the presence of a glutamine (MICB) or closely related glutamate (ULBP1 and ULBP2) at position 169. An arginine residue at this position however, as found for example in MICA or ULBP3, would cause steric clashes with UL16 residues. The inability of UL16 to bind MICA and ULBP3 can therefore be attributed to single substitutions at key NKG2D ligand locations. This indicates that selective pressure exerted by viral immunoevasins such as UL16 contributed to the diversification of NKG2D ligands. PMID:20090832

  18. Ligand-controlled assembly of Cd(II) coordination polymers based on mixed ligands of naphthalene-dicarboxylate and dipyrido[3,2-d:2‧,3‧-f]quinoxaline: From 0D+1D cocrystal, 2D rectangular network (4,4), to 3D PtS-type architecture

    NASA Astrophysics Data System (ADS)

    Liu, Guocheng; Chen, Yongqiang; Wang, Xiuli; Chen, Baokuan; Lin, Hongyan

    2009-03-01

    Three novel Cd(II) coordination polymers, namely, [Cd(Dpq)(1,8-NDC)(H 2O) 2][Cd(Dpq)(1,8-NDC)]·2H 2O ( 1), [Cd(Dpq)(1,4-NDC)(H 2O)] ( 2), and [Cd(Dpq)(2,6-NDC)] ( 3) have been obtained from hydrothermal reactions of cadmium(II) nitrate with the mixed ligands dipyrido [3,2-d:2',3'-f]quinoxaline (Dpq) and three structurally related naphthalene-dicarboxylate ligands [1,8-naphthalene-dicarboxylic acid (1,8-H 2NDC), 1,4-naphthalene-dicarboxylic acid (1,4-H 2NDC), and 2,6-naphthalene-dicarboxylic acid (2,6-H 2NDC)]. Single-crystal X-ray diffraction analysis reveals that the three polymers exhibit novel structures due to different naphthalene-dicarboxylic acid. Compound 1 is a novel cocrystal of left- and right-handed helical chains and binuclear complexes and ultimately packed into a 3D supramolecular structure through hydrogen bonds and π- π stacking interactions. Compound 2 shows a 2D rectangular network (4,4) bridged by 1,4-NDC with two kinds of coordination modes and ultimately packed into a 3D supramolecular structure through inter-layer π- π stacking interactions. Compound 3 is a new 3D coordination polymer with distorted PtS-type network. In addition, the title compounds exhibit blue/green emission in solid state at room temperature.

  19. A 2-D Pore-Network Model of the Drying of Single-Component Liquids in Porous Media

    SciTech Connect

    Yortsos, Yanic C.; Yiotis, A.G.; Stubos, A.K.; Boundovis, A.G.

    2000-01-20

    The drying of liquid-saturated porous media is typically approaching using macroscopic continuum models involving phenomenological coefficients. Insight on these coefficients can be obtained by a more fundamental study at the pore- and pore-network levels. In this report, a model based on pore-network representation of porous media that accounts for various process at the pore-scale is presented. These include mass transfer by advection and diffusion in the gas phase, viscous flow in liquid and gas phases and capillary effects at the gas-liquid menisci in the pore throats.

  20. 2D double-layer-tube-shaped structure Bi2S3/ZnS heterojunction with enhanced photocatalytic activities

    NASA Astrophysics Data System (ADS)

    Gao, Xiaoming; Wang, Zihang; Fu, Feng; Li, Xiang; Li, Wenhong

    2015-10-01

    Bi2S3/ZnS heterojunction with 2D double-layer-tube-shaped structures was prepared by the facile synthesis method. The corresponding relationship was obtained among loaded content to phase, morphology, and optical absorption property of Bi2S3/ZnS composite. The results shown that Bi2S3 loaded could evidently change the crystallinity of ZnS, enhance the optical absorption ability for visible light of ZnS, and improve the morphologies and microstructure of ZnS. The photocatalytic activities of the Bi2S3/ZnS sample were evaluated for the photodegradation of phenol and desulfurization of thiophene under visible light irradiation. The results showed that Bi2S3 loaded greatly improved the photocatalytic activity of ZnS, and the content of loaded Bi2S3 had an impact on the catalytic activity of ZnS. Moreover, the mechanism of enhanced photocatalytic activity was also investigated by analysis of relative band positions of Bi2S3 and ZnS, and photo-generated hole was main active radicals during photocatalytic oxidation process.

  1. Structural environments of carboxyl groups in natural organic molecules from terrestrial systems. Part 2: 2D NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Deshmukh, Ashish P.; Pacheco, Carlos; Hay, Michael B.; Myneni, Satish C. B.

    2007-07-01

    Carboxyl groups are abundant in natural organic molecules (NOM) and play a major role in their reactivity. The structural environments of carboxyl groups in IHSS soil and river humic samples were investigated using 2D NMR (heteronuclear and homonuclear correlation) spectroscopy. Based on the 1H- 13C heteronuclear multiple-bond correlation (HMBC) spectroscopy results, the carboxyl environments in NOM were categorized as Type I (unsubstituted and alkyl-substituted aliphatic/alicyclic), Type II (functionalized carbon substituted), Type IIIa, b (heteroatom and olefin substituted), and Type IVa, b (5-membered heterocyclic aromatic and 6-membered aromatic). The most intense signal in the HMBC spectra comes from the Type I carboxyl groups, including the 2JCH and 3JCH couplings of unsubstituted aliphatic and alicyclic acids, though this spectral region also includes the 3JCH couplings of Type II and III structures. Type II and III carboxyls have small but detectable 2JCH correlations in all NOM samples except for the Suwannee River humic acid. Signals from carboxyls bonded to 5-membered aromatic heterocyclic fragments (Type IVa) are observed in the soil HA and Suwannee River FA, while correlations to 6-membered aromatics (Type IVb) are only observed in Suwannee River HA. In general, aromatic carboxylic acids may be present at concentrations lower than previously imagined in these samples. Vibrational spectroscopy results for these NOM samples, described in an accompanying paper [Hay M. B. and Myneni S. C. B. (2007) Structural environments of carboxyl groups in natural organic molecules from terrestrial systems. Part 1: Infrared spectroscopy. Geochim. Cosmochim. Acta (in press)], suggest that Type II and Type III carboxylic acids with α substituents (e.g., -OH, -OR, or -CO 2H) constitute the majority of carboxyl structures in all humic substances examined. Furoic and salicylic acid structures (Type IV) are also feasible fragments, albeit as minor constituents. The

  2. Syntheses, crystal structures, and characterization of three 1D, 2D and 3D complexes based on mixed multidentate N- and O-donor ligands

    NASA Astrophysics Data System (ADS)

    Yang, Huai-Xia; Liang, Zhen; Hao, Bao-Lian; Meng, Xiang-Ru

    2014-10-01

    Three new 1D to 3D complexes, namely, {[Ni(btec)(Himb)2(H2O)2]·6H2O}n (1), {[Cd(btec)0.5(imb)(H2O)]·1.5H2O}n (2), and {[Zn(btec)0.5(imb)]·H2O}n (3) (H4btec=1,2,4,5-benzenetetracarboxylic acid, imb=2-(1H-imidazol-1-methyl)-1H-benzimidazole) have been synthesized by adjusting the central metal ions. Single-crystal X-ray diffraction analyses reveal that complex 1 possesses a 1D chain structure which is further extended into the 3D supramolecular architecture via hydrogen bonds. Complex 2 features a 2D network with Schla¨fli symbol (53·62·7)(52·64). Complex 3 presents a 3D framework with a point symbol of (4·64·8)(42·62·82). Moreover, their IR spectra, PXRD patterns, thermogravimetric curves, and luminescent emissions were studied at room temperature.

  3. Mesh2d

    2011-12-31

    Mesh2d is a Fortran90 program designed to generate two-dimensional structured grids of the form [x(i),y(i,j)] where [x,y] are grid coordinates identified by indices (i,j). The x(i) coordinates alone can be used to specify a one-dimensional grid. Because the x-coordinates vary only with the i index, a two-dimensional grid is composed in part of straight vertical lines. However, the nominally horizontal y(i,j0) coordinates along index i are permitted to undulate or otherwise vary. Mesh2d also assignsmore » an integer material type to each grid cell, mtyp(i,j), in a user-specified manner. The complete grid is specified through three separate input files defining the x(i), y(i,j), and mtyp(i,j) variations.« less

  4. Structural reducibility of multilayer networks

    NASA Astrophysics Data System (ADS)

    de Domenico, Manlio; Nicosia, Vincenzo; Arenas, Alexandre; Latora, Vito

    2015-04-01

    Many complex systems can be represented as networks consisting of distinct types of interactions, which can be categorized as links belonging to different layers. For example, a good description of the full protein-protein interactome requires, for some organisms, up to seven distinct network layers, accounting for different genetic and physical interactions, each containing thousands of protein-protein relationships. A fundamental open question is then how many layers are indeed necessary to accurately represent the structure of a multilayered complex system. Here we introduce a method based on quantum theory to reduce the number of layers to a minimum while maximizing the distinguishability between the multilayer network and the corresponding aggregated graph. We validate our approach on synthetic benchmarks and we show that the number of informative layers in some real multilayer networks of protein-genetic interactions, social, economical and transportation systems can be reduced by up to 75%.

  5. 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.

  6. Syntheses, crystal structures, and characterization of three 1D, 2D and 3D complexes based on mixed multidentate N- and O-donor ligands

    SciTech Connect

    Yang, Huai-Xia; Liang, Zhen; Hao, Bao-Lian; Meng, Xiang-Ru

    2014-10-15

    Three new 1D to 3D complexes, namely, ([Ni(btec)(Himb){sub 2}(H{sub 2}O){sub 2}]·6H{sub 2}O){sub n} (1), ([Cd(btec){sub 0.5}(imb)(H{sub 2}O)]·1.5H{sub 2}O){sub n} (2), and ([Zn(btec){sub 0.5}(imb)]·H{sub 2}O){sub n} (3) (H{sub 4}btec=1,2,4,5-benzenetetracarboxylic acid, imb=2-(1H-imidazol-1-methyl)-1H-benzimidazole) have been synthesized by adjusting the central metal ions. Single-crystal X-ray diffraction analyses reveal that complex 1 possesses a 1D chain structure which is further extended into the 3D supramolecular architecture via hydrogen bonds. Complex 2 features a 2D network with Schla¨fli symbol (5{sup 3}·6{sup 2}·7)(5{sup 2}·6{sup 4}). Complex 3 presents a 3D framework with a point symbol of (4·6{sup 4}·8)(4{sup 2}·6{sup 2}·8{sup 2}). Moreover, their IR spectra, PXRD patterns, thermogravimetric curves, and luminescent emissions were studied at room temperature. - Graphical abstract: Three new 1D to 3D complexes with different structural and topological motifs have been obtained by modifying the central metal ions. Additionally, their IR, TG analyses and fluorescent properties are also investigated. - Highlights: • Three complexes based on mixed multidentate N- and O-donor ligands. • The complexes are characterized by IR, luminescence and TGA techniques. • Benzenetetracarboxylates display different coordination modes in complexes 1–3. • Changing the metal ions can result in complexes with completely different structures.

  7. Designing molecular structure to achieve ductile fracture behavior in a stiff and strong 2D polymer, ``graphylene''

    NASA Astrophysics Data System (ADS)

    Sandoz-Rosado, E.; Beaudet, T. D.; Balu, R.; Wetzel, E. D.

    2016-05-01

    As the simplest two-dimensional (2D) polymer, graphene has immensely high intrinsic strength and elastic stiffness but has limited toughness due to brittle fracture. We use atomistic simulations to explore a new class of graphene/polyethylene hybrid 2D polymer, ``graphylene'', that exhibits ductile fracture mechanisms and has a higher fracture toughness and flaw tolerance than graphene. A specific configuration of this 2D polymer hybrid, denoted ``GrE-2'' for the two-carbon-long ethylene chains connecting benzene rings in the inherent framework, is prioritized for study. MD simulations of crack propagation show that the energy release rate to propagate a crack in GrE-2 is twice that of graphene. We also demonstrate that GrE-2 exhibits delocalized failure and other energy-dissipating fracture mechanisms such as crack branching and bridging. These results demonstrate that 2D polymers can be uniquely tailored to achieve a balance of fracture toughness with mechanical stiffness and strength.As the simplest two-dimensional (2D) polymer, graphene has immensely high intrinsic strength and elastic stiffness but has limited toughness due to brittle fracture. We use atomistic simulations to explore a new class of graphene/polyethylene hybrid 2D polymer, ``graphylene'', that exhibits ductile fracture mechanisms and has a higher fracture toughness and flaw tolerance than graphene. A specific configuration of this 2D polymer hybrid, denoted ``GrE-2'' for the two-carbon-long ethylene chains connecting benzene rings in the inherent framework, is prioritized for study. MD simulations of crack propagation show that the energy release rate to propagate a crack in GrE-2 is twice that of graphene. We also demonstrate that GrE-2 exhibits delocalized failure and other energy-dissipating fracture mechanisms such as crack branching and bridging. These results demonstrate that 2D polymers can be uniquely tailored to achieve a balance of fracture toughness with mechanical stiffness and

  8. Gold-induced nanowires on the Ge(100) surface yield a 2D and not a 1D electronic structure

    NASA Astrophysics Data System (ADS)

    de Jong, N.; Heimbuch, R.; Eliëns, S.; Smit, S.; Frantzeskakis, E.; Caux, J.-S.; Zandvliet, H. J. W.; Golden, M. S.

    2016-06-01

    Atomic nanowires on semiconductor surfaces induced by the adsorption of metallic atoms have attracted a lot of attention as possible hosts of the elusive, one-dimensional Tomonaga-Luttinger liquid. The Au/Ge(100) system in particular is the subject of controversy as to whether the Au-induced nanowires do indeed host exotic, 1D (one-dimensional) metallic states. In light of this debate, we report here a thorough study of the electronic properties of high quality nanowires formed at the Au/Ge(100) surface. The high-resolution ARPES data show the low-lying Au-induced electronic states to possess a dispersion relation that depends on two orthogonal directions in k space. Comparison of the E (kx,ky) surface measured using high-resolution ARPES to tight-binding calculations yields hopping parameters in the two different directions that differ by approximately factor of two. Additionally, by pinpointing the Au-induced surface states in the first, second, and third surface Brillouin zones and analyzing their periodicity in k||, the nanowire propagation direction seen clearly in STM can be imported into the ARPES data. We find that the larger of the two hopping parameters corresponds, in fact, to the direction perpendicular to the nanowires (tperp). This proves that the Au-induced electron pockets possess a two-dimensional, closed Fermi surface, and this firmly places the Au/Ge(100) nanowire system outside potential hosts of a Tomonaga-Luttinger liquid. We combine these ARPES data with scanning tunneling spectroscopic measurements of the spatially resolved electronic structure and find that the spatially straight—wirelike—conduction channels observed up to energies of order one electron volt below the Fermi level do not originate from the Au-induced states seen in the ARPES data. The former are rather more likely to be associated with bulk Ge states that are localized to the subsurface region. Despite our proof of the 2D (two-dimentional) nature of the Au

  9. From network structure to network reorganization: implications for adult neurogenesis

    NASA Astrophysics Data System (ADS)

    Schneider-Mizell, Casey M.; Parent, Jack M.; Ben-Jacob, Eshel; Zochowski, Michal R.; Sander, Leonard M.

    2010-12-01

    Networks can be dynamical systems that undergo functional and structural reorganization. One example of such a process is adult hippocampal neurogenesis, in which new cells are continuously born and incorporate into the existing network of the dentate gyrus region of the hippocampus. Many of these introduced cells mature and become indistinguishable from established neurons, joining the existing network. Activity in the network environment is known to promote birth, survival and incorporation of new cells. However, after epileptogenic injury, changes to the connectivity structure around the neurogenic niche are known to correlate with aberrant neurogenesis. The possible role of network-level changes in the development of epilepsy is not well understood. In this paper, we use a computational model to investigate how the structural and functional outcomes of network reorganization, driven by addition of new cells during neurogenesis, depend on the original network structure. We find that there is a stable network topology that allows the network to incorporate new neurons in a manner that enhances activity of the persistently active region, but maintains global network properties. In networks having other connectivity structures, new cells can greatly alter the distribution of firing activity and destroy the initial activity patterns. We thus find that new cells are able to provide focused enhancement of network only for small-world networks with sufficient inhibition. Network-level deviations from this topology, such as those caused by epileptogenic injury, can set the network down a path that develops toward pathological dynamics and aberrant structural integration of new cells.

  10. Effects of network structure and routing strategy on network capacity

    NASA Astrophysics Data System (ADS)

    Chen, Zhen Yi; Wang, Xiao Fan

    2006-03-01

    The capacity of maximum end-to-end traffic flow the network is able to handle without overloading is an important index for network performance in real communication systems. In this paper, we estimate the variations of network capacity under different routing strategies for three different topologies. Simulation results reveal that the capacity depends on the underlying network structure and the capacity increases as the network becomes more homogeneous. It is also observed that the network capacity is greatly enhanced when the new traffic awareness routing strategy is adopted in each network structure.

  11. Residue-Specific Structural Kinetics of Proteins through the Union of Isotope Labeling, Mid-IR Pulse Shaping, and Coherent 2D IR Spectroscopy

    PubMed Central

    Middleton, Chris T.; Woys, Ann Marie; Mukherjee, Sudipta S.; Zanni, Martin T.

    2010-01-01

    We describe a methodology for studying protein kinetics using a rapid-scan technology for collecting 2D IR spectra. In conjunction with isotope labeling, 2D IR spectroscopy is able to probe the secondary structure and environment of individual residues in polypeptides and proteins. It is particularly useful for membrane and aggregate proteins. Our rapid-scan technology relies on a mid-IR pulse shaper that computer generates the pulse shapes, much like in an NMR spectrometer. With this device, data collection is faster, easier, and more accurate. We describe our 2D IR spectrometer, as well as protocols for 13C=18O isotope labeling, and then illustrate the technique with an application to the aggregation of the human islet amyloid polypeptide form type 2 diabetes. PMID:20472067

  12. 2D modeling of DC potential structures induced by RF sheaths with transverse currents in front of ICRF antenna

    SciTech Connect

    Faudot, E.; Heuraux, S.; Colas, L.

    2005-09-26

    Understanding DC potential generation in front of ICRF antennas is crucial for long pulse high RF power systems. DC potentials are produced by sheath rectification of these RF potentials. To reach this goal, near RF parallel electric fields have to be computed in 3D and integrated along open magnetic field lines to yield a 2D RF potential map in a transverse plane. DC potentials are produced by sheath rectification of these RF potentials. As RF potentials are spatially inhomogeneous, transverse polarization currents are created, modifying RF and DC maps. Such modifications are quantified on a 'test map' having initially a Gaussian shape and assuming that the map remains Gaussian near its summit,the time behavior of the peak can be estimated analytically in presence of polarization current as a function of its width r0 and amplitude {phi}0 (normalized to a characteristic length for transverse transport and to the local temperature). A 'peaking factor' is built from the DC peak potential normalized to {phi}0, and validated with a 2D fluid code and a 2D PIC code (XOOPIC). In an unexpected way transverse currents can increase this factor. Realistic situations of a Tore Supra antenna are also studied, with self-consistent near fields provided by ICANT code. Basic processes will be detailed and an evaluation of the 'peaking factor' for ITER will be presented for a given configuration.

  13. 2D MI-DRAGON: a new predictor for protein-ligands interactions and theoretic-experimental studies of US FDA drug-target network, oxoisoaporphine inhibitors for MAO-A and human parasite proteins.

    PubMed

    Prado-Prado, Francisco; García-Mera, Xerardo; Escobar, Manuel; Sobarzo-Sánchez, Eduardo; Yañez, Matilde; Riera-Fernandez, Pablo; González-Díaz, Humberto

    2011-12-01

    There are many pairs of possible Drug-Proteins Interactions that may take place or not (DPIs/nDPIs) between drugs with high affinity/non-affinity for different proteins. This fact makes expensive in terms of time and resources, for instance, the determination of all possible ligands-protein interactions for a single drug. In this sense, we can use Quantitative Structure-Activity Relationships (QSAR) models to carry out rational DPIs prediction. Unfortunately, almost all QSAR models predict activity against only one target. To solve this problem we can develop multi-target QSAR (mt-QSAR) models. In this work, we introduce the technique 2D MI-DRAGON a new predictor for DPIs based on two different well-known software. We use the software MARCH-INSIDE (MI) to calculate 3D structural parameters for targets and the software DRAGON was used to calculated 2D molecular descriptors all drugs showing known DPIs present in the Drug Bank (US FDA benchmark dataset). Both classes of parameters were used as input of different Artificial Neural Network (ANN) algorithms to seek an accurate non-linear mt-QSAR predictor. The best ANN model found is a Multi-Layer Perceptron (MLP) with profile MLP 21:21-31-1:1. This MLP classifies correctly 303 out of 339 DPIs (Sensitivity = 89.38%) and 480 out of 510 nDPIs (Specificity = 94.12%), corresponding to training Accuracy = 92.23%. The validation of the model was carried out by means of external predicting series with Sensitivity = 92.18% (625/678 DPIs; Specificity = 90.12% (730/780 nDPIs) and Accuracy = 91.06%. 2D MI-DRAGON offers a good opportunity for fast-track calculation of all possible DPIs of one drug enabling us to re-construct large drug-target or DPIs Complex Networks (CNs). For instance, we reconstructed the CN of the US FDA benchmark dataset with 855 nodes 519 drugs+336 targets). We predicted CN with similar topology (observed and predicted values of average distance are equal to 6.7 vs. 6.6). These CNs can be used to explore

  14. The structure of salt bridges between Arg(+) and Glu(-) in peptides investigated with 2D-IR spectroscopy: Evidence for two distinct hydrogen-bond geometries.

    PubMed

    Huerta-Viga, Adriana; Amirjalayer, Saeed; Domingos, Sérgio R; Meuzelaar, Heleen; Rupenyan, Alisa; Woutersen, Sander

    2015-06-01

    Salt bridges play an important role in protein folding and in supramolecular chemistry, but they are difficult to detect and characterize in solution. Here, we investigate salt bridges between glutamate (Glu(-)) and arginine (Arg(+)) using two-dimensional infrared (2D-IR) spectroscopy. The 2D-IR spectrum of a salt-bridged dimer shows cross peaks between the vibrational modes of Glu(-) and Arg(+), which provide a sensitive structural probe of Glu(-)⋯Arg(+) salt bridges. We use this probe to investigate a β-turn locked by a salt bridge, an α-helical peptide whose structure is stabilized by salt bridges, and a coiled coil that is stabilized by intra- and intermolecular salt bridges. We detect a bidentate salt bridge in the β-turn, a monodentate one in the α-helical peptide, and both salt-bridge geometries in the coiled coil. To our knowledge, this is the first time 2D-IR has been used to probe tertiary side chain interactions in peptides, and our results show that 2D-IR spectroscopy is a powerful method for investigating salt bridges in solution.

  15. The structure of salt bridges between Arg+ and Glu- in peptides investigated with 2D-IR spectroscopy: Evidence for two distinct hydrogen-bond geometries

    NASA Astrophysics Data System (ADS)

    Huerta-Viga, Adriana; Amirjalayer, Saeed; Domingos, Sérgio R.; Meuzelaar, Heleen; Rupenyan, Alisa; Woutersen, Sander

    2015-06-01

    Salt bridges play an important role in protein folding and in supramolecular chemistry, but they are difficult to detect and characterize in solution. Here, we investigate salt bridges between glutamate (Glu-) and arginine (Arg+) using two-dimensional infrared (2D-IR) spectroscopy. The 2D-IR spectrum of a salt-bridged dimer shows cross peaks between the vibrational modes of Glu- and Arg+, which provide a sensitive structural probe of Glu-⋯Arg+ salt bridges. We use this probe to investigate a β-turn locked by a salt bridge, an α-helical peptide whose structure is stabilized by salt bridges, and a coiled coil that is stabilized by intra- and intermolecular salt bridges. We detect a bidentate salt bridge in the β-turn, a monodentate one in the α-helical peptide, and both salt-bridge geometries in the coiled coil. To our knowledge, this is the first time 2D-IR has been used to probe tertiary side chain interactions in peptides, and our results show that 2D-IR spectroscopy is a powerful method for investigating salt bridges in solution.

  16. The impact of pore structure and surface roughness on capillary trapping for 2-D and 3-D porous media: Comparison with percolation theory

    NASA Astrophysics Data System (ADS)

    Geistlinger, Helmut; Ataei-Dadavi, Iman; Mohammadian, Sadjad; Vogel, Hans-Jörg

    2015-11-01

    We study the impact of pore structure and surface roughness on capillary trapping of nonwetting gas phase during imbibition with water for capillary numbers between 10-7 and 5 × 10-5, within glass beads, natural sands, glass beads monolayers, and 2-D micromodels. The materials exhibit different roughness of the pore-solid interface. We found that glass beads and natural sands, which exhibit nearly the same grain size distribution, pore size distribution, and connectivity, showed a significant difference of the trapped gas phase of about 15%. This difference can be explained by the microstructure of the pore-solid interface. Based on the visualization of the trapping dynamics within glass beads monolayers and 2-D micromodels, we could show that bypass trapping controls the trapping process in glass beads monolayers, while snap-off trapping controls the trapping process in 2-D micromodels. We conclude that these different trapping processes are the reason for the different trapping efficiency, when comparing glass beads packs with natural sand packs. Moreover, for small capillary numbers of 10-6, we found that the cluster size distribution of trapped gas clusters of all 2-D and 3-D porous media can be described by a universal power law behavior predicted from percolation theory. This cannot be expected a priori for 2-D porous media, because bicontinuity of the two bulk phases is violated. Obviously, bicontinuity holds for the thin-film water phase and the bulk gas phase. The snap-off trapping process leads to ordinary bond percolation in front of the advancing bulk water phase and is the reason for the observed universal power law behavior in 2-D micromodels with rough surfaces.

  17. revealing H{sub 2}D{sup +} depletion and compact structure in starless and protostellar cores with ALMA

    SciTech Connect

    Friesen, R. K.; Di Francesco, J.; Bourke, T. L.; Caselli, P.; Jørgensen, J. K.; Pineda, J. E.; Wong, M.

    2014-12-10

    We present Atacama Large Millimeter/submillimeter Array (ALMA) observations of the submillimeter dust continuum and H{sub 2}D{sup +} 1{sub 10}-1{sub 11} emission toward two evolved, potentially protostellar cores within the Ophiuchus molecular cloud, Oph A SM1 and SM1N. The data reveal small-scale condensations within both cores, with mass upper limits of M ≲ 0.02 M {sub ☉} (∼20 M {sub Jup}). The SM1 condensation is consistent with a nearly symmetric Gaussian source with a width of only 37 AU. The SM1N condensation is elongated and extends 500 AU along its major axis. No evidence for substructure is seen in either source. A Jeans analysis indicates that these sources are unlikely to fragment, suggesting that both will form single stars. H{sub 2}D{sup +} is only detected toward SM1N, offset from the continuum peak by ∼150-200 AU. This offset may be due to either heating from an undetected, young, low-luminosity protostellar source or first hydrostatic core, or HD (and consequently H{sub 2}D{sup +}) depletion in the cold center of the condensation. We propose that SM1 is protostellar and that the condensation detected by ALMA is a warm (T ∼ 30-50 K) accretion disk. The less concentrated emission of the SM1N condensation suggests that it is still starless, but we cannot rule out the presence of a low-luminosity source, perhaps surrounded by a pseudodisk. These data observationally reveal the earliest stages of the formation of circumstellar accretion regions and agree with theoretical predictions that disk formation can occur very early in the star formation process, coeval with or just after the formation of a first hydrostatic core or protostar.

  18. Hamiltonian structure of Dubrovin{close_quote}s equation of associativity in 2-d topological field theory

    SciTech Connect

    Galvao, C.A.; Nutku, Y.

    1996-12-01

    mA third order Monge-Amp{grave e}re type equation of associativity that Dubrovin has obtained in 2-d topological field theory is formulated in terms of a variational principle subject to second class constraints. Using Dirac{close_quote}s theory of constraints this degenerate Lagrangian system is cast into Hamiltonian form and the Hamiltonian operator is obtained from the Dirac bracket. There is a new type of Kac-Moody algebra that corresponds to this Hamiltonian operator. In particular, it is not a W-algebra. {copyright} {ital 1996 American Institute of Physics.}

  19. Synthesis and structure of a 2D → 3D framework with coexistence of hydrogen bonds and polythreading character

    SciTech Connect

    Zhang, Ming-Dao Zhuang, Qi-Fan; Xu, Jing; Cao, Hui

    2015-12-15

    The title complex, ([Co(BPPA)(5-OH-bdc)] · (H{sub 2}O)){sub n} was prepared under hydrothermal conditions based on two ligands, namely, bis(4-(pyridin-4-yl)phenyl)amine (BPPA) and 5-hydroxyisophthalic acid (5-OH-H{sub 2}bdc). 5-OH-bdc{sup 2–} anions coordinated to Co atoms to give layers in crystal. BPPA ligands coordinate to Co atoms and thread into the adjacent layers. There are hydrogen bonds between adjacent layers, giving rise to a 2D → 3D framework.

  20. Ultrafast 2D IR microscopy

    PubMed Central

    Baiz, Carlos R.; Schach, Denise; Tokmakoff, Andrei

    2014-01-01

    We describe a microscope for measuring two-dimensional infrared (2D IR) spectra of heterogeneous samples with μm-scale spatial resolution, sub-picosecond time resolution, and the molecular structure information of 2D IR, enabling the measurement of vibrational dynamics through correlations in frequency, time, and space. The setup is based on a fully collinear “one beam” geometry in which all pulses propagate along the same optics. Polarization, chopping, and phase cycling are used to isolate the 2D IR signals of interest. In addition, we demonstrate the use of vibrational lifetime as a contrast agent for imaging microscopic variations in molecular environments. PMID:25089490

  1. QCD prediction of jet structure in 2D trigger-associated momentum correlations and implications for multiple parton interactions

    NASA Astrophysics Data System (ADS)

    Trainor, Thomas A.

    2015-03-01

    The expression "multiple parton interactions" (MPI) denotes a conjectured QCD mechanism representing contributions from secondary (semi)hard parton scattering to the transverse azimuth region (TR) of jet-triggered p-p collisions. MPI is an object of underlying-event (UE) studies that consider variation of TR nch or pt yields relative to a trigger condition (leading hadron or jet pt). An alternative approach is 2D trigger-associated (TA) correlations on hadron transverse momentum pt or rapidity yt in which all hadrons from all p-p events are included. Based on a two-component (soft+hard) model (TCM) of TA correlations a jet-related TA hard component is isolated. Contributions to the hard component from the triggered dijet and from secondary dijets (MPI) can be distinguished, including their azimuth dependence relative to the trigger direction. Measured e+-e- and p-p¯ fragmentation functions and a minimum-bias jet spectrum from 200 GeV p-p¯ collisions are convoluted to predict the 2D hard component of TA correlations as a function of p-p collision multiplicity. The agreement between QCD predictions and TA correlation data is quantitative, confirming a dijet interpretation for the TCM hard component. The TA azimuth dependence is inconsistent with conventional UE assumptions.

  2. Social structure of Facebook networks

    NASA Astrophysics Data System (ADS)

    Traud, Amanda L.; Mucha, Peter J.; Porter, Mason A.

    2012-08-01

    We study the social structure of Facebook “friendship” networks at one hundred American colleges and universities at a single point in time, and we examine the roles of user attributes-gender, class year, major, high school, and residence-at these institutions. We investigate the influence of common attributes at the dyad level in terms of assortativity coefficients and regression models. We then examine larger-scale groupings by detecting communities algorithmically and comparing them to network partitions based on user characteristics. We thereby examine the relative importance of different characteristics at different institutions, finding for example that common high school is more important to the social organization of large institutions and that the importance of common major varies significantly between institutions. Our calculations illustrate how microscopic and macroscopic perspectives give complementary insights on the social organization at universities and suggest future studies to investigate such phenomena further.

  3. Synthesizing 2D and 3D Selenidostannates in Ionic Liquids: The Synergistic Structure-Directing Effects of Ionic Liquids and Metal-Amine Complexes.

    PubMed

    Du, Cheng-Feng; Shen, Nan-Nan; Li, Jian-Rong; Hao, Min-Ting; Wang, Zi; Huang, Xiao-Ying

    2016-05-20

    Presented are the ionothermal syntheses, characterizations, and properties of a series of two- and three-dimensional selenidostannate compounds synergistically directed by metal-amine complex (MAC) cations and ionic liquids (ILs) of [Bmmim]Cl (Bmmim=1-butyl-2,3-dimethylimidazolium). Four selenidostannates, namely, 2D-(Bmmim)3 [Ni(en)3 ]2 [Sn9 Se21 ]Cl (1, en=ethylenediamine), 2D-(Bmmim)8 [Ni2 (teta)2 (μ-teta)]Sn18 Se42 (2, teta=triethylenetetramine), 2D-(Bmmim)4 [Ni(tepa)Cl]2 [Ni(tepa)Sn12 Se28 ] (3, tepa=tetraethylenepentamine), and 3D-(Bmmim)2 [Ni(1,2-pda)3 ]Sn8 Se18 (4, 1,2-pda=1,2-diaminopropane), were obtained. Single-crystal X-ray diffraction analyses revealed that compounds 1 and 2 possess a lamellar anionic [Sn3 Se7 ]n (2n-) structure comprising distinct eight-membered ring units, whereas 3 features a MAC-decorated anionic [Ni(tepa)Sn12 Se28 ]n (6n-) layered structure. In contrast to 1-3, compound 4 exhibits a 3D open framework of anionic [Sn4 Se9 ]n (2n-) . The structural variation from 1 to 4 clearly indicates that on the basis of the synergistic structure-directing ability of the MACs and ILs, variation of the organic polyamine ligand has a significant impact on the formation of selenidostannates. PMID:27037731

  4. Efficient decoding of 2D structured illumination with linear phase stepping in X-ray phase contrast and dark-field imaging.

    PubMed

    Harmon, Katherine J; Bennett, Eric E; Gomella, Andrew A; Wen, Han

    2014-01-01

    The ability to map the phase distribution and lateral coherence of an x-ray wavefront offers the potential for imaging the human body through phase contrast, without the need to deposit significant radiation energy. The classic means to achieve this goal is structured illumination, in which a periodic intensity modulation is introduced into the image, and changes in the phase distribution of the wavefront are detected as distortions of the modulation pattern. Two-dimensional periodic patterns are needed to fully characterize a transverse wavefront. Traditionally, the information in a 2D pattern is retrieved at high resolution by acquiring multiple images while shifting the pattern over a 2D matrix of positions. Here we describe a method to decode 2D periodic patterns with single-axis phase stepping, without either a loss of information or increasing the number of sampling steps. The method is created to reduce the instrumentation complexity of high-resolution 2D wavefront sensing in general. It is demonstrated with motionless electromagnetic phase stepping and a flexible processing algorithm in x-ray dark-field and phase contrast imaging.

  5. Two-dimensional (2D) infrared correlation study of the structural characterization of a surface immobilized polypeptide film stimulated by pH

    NASA Astrophysics Data System (ADS)

    Chae, Boknam; Son, Seok Ho; Kwak, Young Jun; Jung, Young Mee; Lee, Seung Woo

    2016-11-01

    The pH-induced structural changes to surface immobilized poly (L-glutamic acid) (PLGA) films were examined by Fourier transform infrared (FTIR) spectroscopy and two-dimensional (2D) correlation analysis. Significant spectral changes were observed in the FTIR spectra of the surface immobilized PLGA film between pH 6 and 7. The 2D correlation spectra constructed from the pH-dependent FTIR spectra of the surface immobilized PLGA films revealed the spectral changes induced by the alternations of the protonation state of the carboxylic acid group in the PLGA side chain. When the pH was increased from 6 to 8, weak spectral changes in the secondary structure of the PLGA main chain were induced by deprotonation of the carboxylic acid side group.

  6. Social network structures and bank runs

    NASA Astrophysics Data System (ADS)

    Li, Shouwei; Li, Jiaheng

    2016-05-01

    This paper investigates the impact of social network structures of depositors on bank runs. The analyzed network structures include random networks, small-world networks and scale-free networks. Simulation results show that the probability of bank run occurrence in random networks is larger than that in small-world networks, but the probability of bank run occurrence in scale-free networks drops from the highest to the lowest among the three types of network structures with the increase of the proportion of impatient depositors. The average degree of depositor networks has a significant impact on bank runs, but this impact is related to the proportion of impatient depositors and the confidence levels of depositors in banks.

  7. Network structure exploration in networks with node attributes

    NASA Astrophysics Data System (ADS)

    Chen, Yi; Wang, Xiaolong; Bu, Junzhao; Tang, Buzhou; Xiang, Xin

    2016-05-01

    Complex networks provide a powerful way to represent complex systems and have been widely studied during the past several years. One of the most important tasks of network analysis is to detect structures (also called structural regularities) embedded in networks by determining group number and group partition. Most of network structure exploration models only consider network links. However, in real world networks, nodes may have attributes that are useful for network structure exploration. In this paper, we propose a novel Bayesian nonparametric (BNP) model to explore structural regularities in networks with node attributes, called Bayesian nonparametric attribute (BNPA) model. This model does not only take full advantage of both links between nodes and node attributes for group partition via shared hidden variables, but also determine group number automatically via the Bayesian nonparametric theory. Experiments conducted on a number of real and synthetic networks show that our BNPA model is able to automatically explore structural regularities in networks with node attributes and is competitive with other state-of-the-art models.

  8. Global Electricity Trade Network: Structures and Implications

    PubMed Central

    Ji, Ling; Jia, Xiaoping; Chiu, Anthony S. F.; Xu, Ming

    2016-01-01

    Nations increasingly trade electricity, and understanding the structure of the global power grid can help identify nations that are critical for its reliability. This study examines the global grid as a network with nations as nodes and international electricity trade as links. We analyze the structure of the global electricity trade network and find that the network consists of four sub-networks, and provide a detailed analysis of the largest network, Eurasia. Russia, China, Ukraine, and Azerbaijan have high betweenness measures in the Eurasian sub-network, indicating the degrees of centrality of the positions they hold. The analysis reveals that the Eurasian sub-network consists of seven communities based on the network structure. We find that the communities do not fully align with geographical proximity, and that the present international electricity trade in the Eurasian sub-network causes an approximately 11 million additional tons of CO2 emissions. PMID:27504825

  9. Global Electricity Trade Network: Structures and Implications.

    PubMed

    Ji, Ling; Jia, Xiaoping; Chiu, Anthony S F; Xu, Ming

    2016-01-01

    Nations increasingly trade electricity, and understanding the structure of the global power grid can help identify nations that are critical for its reliability. This study examines the global grid as a network with nations as nodes and international electricity trade as links. We analyze the structure of the global electricity trade network and find that the network consists of four sub-networks, and provide a detailed analysis of the largest network, Eurasia. Russia, China, Ukraine, and Azerbaijan have high betweenness measures in the Eurasian sub-network, indicating the degrees of centrality of the positions they hold. The analysis reveals that the Eurasian sub-network consists of seven communities based on the network structure. We find that the communities do not fully align with geographical proximity, and that the present international electricity trade in the Eurasian sub-network causes an approximately 11 million additional tons of CO2 emissions. PMID:27504825

  10. Analyzing network reliability using structural motifs

    NASA Astrophysics Data System (ADS)

    Khorramzadeh, Yasamin; Youssef, Mina; Eubank, Stephen; Mowlaei, Shahir

    2015-04-01

    This paper uses the reliability polynomial, introduced by Moore and Shannon in 1956, to analyze the effect of network structure on diffusive dynamics such as the spread of infectious disease. We exhibit a representation for the reliability polynomial in terms of what we call structural motifs that is well suited for reasoning about the effect of a network's structural properties on diffusion across the network. We illustrate by deriving several general results relating graph structure to dynamical phenomena.

  11. Centrality measures for networks with community structure

    NASA Astrophysics Data System (ADS)

    Gupta, Naveen; Singh, Anurag; Cherifi, Hocine

    2016-06-01

    Understanding the network structure, and finding out the influential nodes is a challenging issue in large networks. Identifying the most influential nodes in a network can be useful in many applications like immunization of nodes in case of epidemic spreading, during intentional attacks on complex networks. A lot of research is being done to devise centrality measures which could efficiently identify the most influential nodes in a network. There are two major approaches to this problem: On one hand, deterministic strategies that exploit knowledge about the overall network topology, while on the other end, random strategies are completely agnostic about the network structure. Centrality measures that can deal with a limited knowledge of the network structure are of prime importance. Indeed, in practice, information about the global structure of the overall network is rarely available or hard to acquire. Even if available, the structure of the network might be too large that it is too much computationally expensive to calculate global centrality measures. To that end, a centrality measure is proposed here that requires information only at the community level. Indeed, most of the real-world networks exhibit a community structure that can be exploited efficiently to discover the influential nodes. We performed a comparative evaluation of prominent global deterministic strategies together with stochastic strategies, an available and the proposed deterministic community-based strategy. Effectiveness of the proposed method is evaluated by performing experiments on synthetic and real-world networks with community structure in the case of immunization of nodes for epidemic control.

  12. A Structure-Activity Relationship Study of Imidazole-5-Carboxylic Acid Derivatives as Angiotensin II Receptor Antagonists Combining 2D and 3D QSAR Methods.

    PubMed

    Sharma, Mukesh C

    2016-03-01

    Two-dimensional (2D) and three-dimensional (3D) quantitative structure-activity relationship (QSAR) studies were performed for correlating the chemical composition of imidazole-5-carboxylic acid analogs and their angiotensin II [Formula: see text] receptor antagonist activity using partial least squares and k-nearest neighbor, respectively. For comparing the three different feature selection methods of 2D-QSAR, k-nearest neighbor models were used in conjunction with simulated annealing (SA), genetic algorithm and stepwise coupled with partial least square (PLS) showed variation in biological activity. The statistically significant best 2D-QSAR model having good predictive ability with statistical values of [Formula: see text] and [Formula: see text] was developed by SA-partial least square with the descriptors like [Formula: see text]count, 5Chain count, SdsCHE-index, and H-acceptor count, showing that increase in the values of these descriptors is beneficial to the activity. The 3D-QSAR studies were performed using the SA-PLS. A leave-one-out cross-validated correlation coefficient [Formula: see text] and predicate activity [Formula: see text] = 0.7226 were obtained. The information rendered by QSAR models may lead to a better understanding of structural requirements of substituted imidazole-5-carboxylic acid derivatives and also aid in designing novel potent antihypertensive molecules.

  13. High resolution spectroscopy of the Cs2 D 1Sigma u + -X 1Sigma g + transition and hyperfine structure

    NASA Astrophysics Data System (ADS)

    Kobayashi, Tooru; Usui, Takashi; Kumauchi, Takahiro; Baba, Masaaki; Ishikawa, Kiyoshi; Katô, Hajime

    1993-02-01

    The Doppler-free high resolution laser spectroscopy of Cs2 D 1Σu+-X 1Σg+ transition is extended up to v'=65. By comparing the spectral linewidth and the time-resolved fluorescence intensity, the line broadening observed for transitions to the D 1Σu+(v'=63,J'≤70) levels is identified as the lifetime broadening originating from the predissociation. Line splittings are observed for the D 1Σu+(v'=46,J'≥95)-X 1Σg+(v`= 1,J`) transitions and are identified as the hyperfine splitting due to a magnetic dipole interaction between nuclear spin and electron. The hyperfine splitting is attributed to mixing of the (2) 3Πu state, whose wave function changes from Hund's case (a) to case (b) at large J. The dependence of the electric dipole transition moment on the internuclear distance for the D 1Σu+-X 1Σg+ transition is determined by comparing the observed and calculated line intensities of the dispersed fluorescence.

  14. Structural modifications of Tilia cordata wood during heat treatment investigated by FT-IR and 2D IR correlation spectroscopy

    NASA Astrophysics Data System (ADS)

    Popescu, Maria-Cristina; Froidevaux, Julien; Navi, Parviz; Popescu, Carmen-Mihaela

    2013-02-01

    It is known that heat treatment of wood combined with a low percent of relative humidity causes transformations in the chemical composition of it. The modifications and/or degradation of wood components occur by hydrolysis, oxidation, and decarboxylation reactions. The aim of this study was to give better insights on wood chemical modifications during wood heat treatment under low temperature at about 140 °C and 10% percentage of relative humidity, by infrared, principal component analysis and two dimensional infrared correlation spectroscopy. For this purpose, hardwood samples of lime (Tilia cordata) were investigated and analysed. The infrared spectra of treated samples were compared with the reference ones, the most important differences being observed in the "fingerprint" region. Due to the complexity of this region, which have contributions from all the wood constituents the chemical changes during hydro-thermal treatment were examined in detail using principal component analysis and 2D IR correlation spectroscopy. By hydro-thermal treatment of wood results the formation of acetic acid, which catalyse the hydrolysis reactions of hemicelluloses and amorphous cellulose. The cleavage of the β-O-4 linkages and splitting of the aliphatic methoxyl chains from the aromatic lignin ring was also observed. For the first treatment interval, a higher extent of carbohydrates degradation was observed, then an increase of the extent of the lignin degradation also took place.

  15. Synthesis, magnetic properties, and magnetic structure of a natrochalcite structural variant, KM(II)2D3O2(MoO4)2 (M = Mn, Fe, or Co).

    PubMed

    Maalej, Wassim; Vilminot, Serge; André, Gilles; Damay, Françoise; Elaoud, Zakaria; Mhiri, Tahar; Kurmoo, Mohamedally

    2011-04-18

    We report the syntheses, crystal structures, and magnetic properties of KMn(2)(H(3)O(2))(MoO(4))(2) (MnH), KMn(2)(D(3)O(2))(MoO(4))(2) (MnD), KFe(2)(H(3)O(2))(MoO(4))(2) (FeH), KFe(2)(D(3)O(2))(MoO(4))(2) (FeD), KCo(2)(H(3)O(2))(MoO(4))(2) (CoH), and KCo(2)(D(3)O(2))(MoO(4))(2) (CoD), and the magnetic structures of MnD and FeD. They belong to the structural variant (space group I2/m) of the mineral natrochalcite NaCu(2)(H(3)O(2))(SO(4))(2) (space group C2/m) where the diagonal within the ac-plane of the latter become one axis of the former. The structure of MnD, obtained from Rietveld refinement of a high-resolution neutron pattern taken at 300 K, consists of chains of edge-sharing octahedra bridged by MoO(4) and D(3)O(2) to form layers, which are connected to K through the oxygen atoms to form the three-dimensional (3D)-network. The X-ray powder diffraction patterns of the other two compounds were found to belong to the same space group with similar parameters. The magnetic susceptibilities of MnH and FeH exhibit long-range ordering of the moments at a Néel temperature of 8 and 11 K, respectively, which are accompanied by additional strong Bragg reflections in the neutron diffraction in the ordered state, consistent with antiferromagnetism. Analyses of the neutron data for MnD and FeD reveal the presence of both long- and short-range orderings and commensurate magnetic structures with a propagation vector of (½, 0, ½). The moments are antiferromagnetically ordered within the chains with alternation between chains to generate four nonequivalent nuclear unit cells. For MnD the moments are perpendicular to the chain axis (b-axis) while for FeD they are parallel to the b-axis. The overall total is a fully compensated magnetic structure with zero moment in each case. Surprisingly, for KCo(2)(D(3)O(2))(MoO(4))(2) neither additional peaks nor increase of the nuclear peaks' intensities were observed in the neutron diffraction patterns below the magnetic anomaly at 12

  16. Synthesis and structure elucidation of a series of pyranochromene chalcones and flavanones using 1D and 2D NMR spectroscopy and X-ray crystallography.

    PubMed

    Pawar, Sunayna S; Koorbanally, Neil A

    2014-06-01

    A series of novel pyranochromene chalcones and corresponding flavanones were synthesized. This is the first report on the confirmation of the absolute configuration of chromene-based flavanones using X-ray crystallography. These compounds were characterized by 2D NMR spectroscopy, and their assignments are reported herein. The 3D structure of the chalcone 3b and flavanone 4g was determined by X-ray crystallography, and the structure of the flavanone was confirmed to be in the S configuration at C-2.

  17. Taxonomies of networks from community structure

    NASA Astrophysics Data System (ADS)

    Onnela, Jukka-Pekka; Fenn, Daniel J.; Reid, Stephen; Porter, Mason A.; Mucha, Peter J.; Fricker, Mark D.; Jones, Nick S.

    2012-09-01

    The study of networks has become a substantial interdisciplinary endeavor that encompasses myriad disciplines in the natural, social, and information sciences. Here we introduce a framework for constructing taxonomies of networks based on their structural similarities. These networks can arise from any of numerous sources: They can be empirical or synthetic, they can arise from multiple realizations of a single process (either empirical or synthetic), they can represent entirely different systems in different disciplines, etc. Because mesoscopic properties of networks are hypothesized to be important for network function, we base our comparisons on summaries of network community structures. Although we use a specific method for uncovering network communities, much of the introduced framework is independent of that choice. After introducing the framework, we apply it to construct a taxonomy for 746 networks and demonstrate that our approach usefully identifies similar networks. We also construct taxonomies within individual categories of networks, and we thereby expose nontrivial structure. For example, we create taxonomies for similarity networks constructed from both political voting data and financial data. We also construct network taxonomies to compare the social structures of 100 Facebook networks and the growth structures produced by different types of fungi.

  18. Taxonomies of networks from community structure

    PubMed Central

    Reid, Stephen; Porter, Mason A.; Mucha, Peter J.; Fricker, Mark D.; Jones, Nick S.

    2014-01-01

    The study of networks has become a substantial interdisciplinary endeavor that encompasses myriad disciplines in the natural, social, and information sciences. Here we introduce a framework for constructing taxonomies of networks based on their structural similarities. These networks can arise from any of numerous sources: they can be empirical or synthetic, they can arise from multiple realizations of a single process (either empirical or synthetic), they can represent entirely different systems in different disciplines, etc. Because mesoscopic properties of networks are hypothesized to be important for network function, we base our comparisons on summaries of network community structures. Although we use a specific method for uncovering network communities, much of the introduced framework is independent of that choice. After introducing the framework, we apply it to construct a taxonomy for 746 networks and demonstrate that our approach usefully identifies similar networks. We also construct taxonomies within individual categories of networks, and we thereby expose nontrivial structure. For example, we create taxonomies for similarity networks constructed from both political voting data and financial data. We also construct network taxonomies to compare the social structures of 100 Facebook networks and the growth structures produced by different types of fungi. PMID:23030977

  19. 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

  20. Structure and inference in annotated networks

    PubMed Central

    Newman, M. E. J.; Clauset, Aaron

    2016-01-01

    For many networks of scientific interest we know both the connections of the network and information about the network nodes, such as the age or gender of individuals in a social network. Here we demonstrate how this ‘metadata' can be used to improve our understanding of network structure. We focus in particular on the problem of community detection in networks and develop a mathematically principled approach that combines a network and its metadata to detect communities more accurately than can be done with either alone. Crucially, the method does not assume that the metadata are correlated with the communities we are trying to find. Instead, the method learns whether a correlation exists and correctly uses or ignores the metadata depending on whether they contain useful information. We demonstrate our method on synthetic networks with known structure and on real-world networks, large and small, drawn from social, biological and technological domains. PMID:27306566

  1. Structure and inference in annotated networks

    NASA Astrophysics Data System (ADS)

    Newman, M. E. J.; Clauset, Aaron

    2016-06-01

    For many networks of scientific interest we know both the connections of the network and information about the network nodes, such as the age or gender of individuals in a social network. Here we demonstrate how this `metadata' can be used to improve our understanding of network structure. We focus in particular on the problem of community detection in networks and develop a mathematically principled approach that combines a network and its metadata to detect communities more accurately than can be done with either alone. Crucially, the method does not assume that the metadata are correlated with the communities we are trying to find. Instead, the method learns whether a correlation exists and correctly uses or ignores the metadata depending on whether they contain useful information. We demonstrate our method on synthetic networks with known structure and on real-world networks, large and small, drawn from social, biological and technological domains.

  2. Entropy-controlled 2D supramolecular structures of N,N'-bis(n-alkyl)naphthalenediimides on a HOPG surface.

    PubMed

    Miyake, Yusuke; Nagata, Toshi; Tanaka, Hirofumi; Yamazaki, Masashi; Ohta, Masahiro; Kokawa, Ryohei; Ogawa, Takuji

    2012-05-22

    The two-dimensional supramolecular structures of a series of N,N'-bis(n-alkyl)naphthalenediimides (NDIs), whose chain lengths span from C3 to C18, at a liquid-HOPG surface interface, studied by STM and FM-AFM, are assigned with the help of molecular dynamics/molecular mechanics calculations to demonstrate that the C3- and C4-NDIs show lamellar structures, the C4- to C12-NDIs show honeycomb (KAGOME) structures, and the C14- to C18-NDIs show lamellar structures again. The change in supramolecular structure depending on chain length can be explained semiquantitatively by the balance of entropy and enthalpy terms to show the importance of "self-avoiding walk" of the alkyl chain in entropy terms.

  3. Simultaneous imaging of the topography and electrochemical activity of a 2D carbon nanotube network using a dual functional L-shaped nanoprobe.

    PubMed

    Lee, Eunjoo; Sung, Jungwoo; An, Taechang; Shin, Heungjoo; Nam, Hong Gil; Lim, Geunbae

    2015-05-01

    The application of nanomaterials for biosensors and fuel cells is becoming more common, but it requires an understanding of the relationship between the structure and electrochemical characteristics of the materials at the nanoscale. Herein, we report the development of scanning electrochemical microscopy-atomic force microscopy (SECM-AFM) nanoprobes for collecting spatially resolved data regarding the electrochemical activity of nanomaterials such as carbon nanotube (CNT) networks. The fabrication of the nanoprobe begins with the integration of a CNT-bundle wire into a conventional AFM probe followed by the deposition of an insulating layer and cutting of the probe end. In addition, a protrusive insulating tip is integrated at the end of the insulated CNT-bundle wire to maintain a constant distance between the nanoelectrode and the substrate; this yields an L-shaped nanoprobe. The resulting nanoprobes produced well-fitted maps of faradaic current data with less than 300 nm spatial resolution and topographical images of CNT networks owing to the small effective distance (of the order of tens of nanometers) between the electrode and the substrate. Electrochemical imaging using the L-shaped nanoprobe revealed that the electrochemical activity of the CNT network is not homogeneous and provided further understanding of the relationship between the topography and electrochemical characteristics of CNT networks.

  4. Structure-Activity Relationships and Pharmacophore Model of a Non-Competitive Pyrazoline Containing Class of GluN2C/GluN2D Selective Antagonists

    PubMed Central

    Acker, Timothy M.; Khatri, Alpa; Vance, Katie M.; Slabber, Cathryn; Bacsa, John; Snyder, James P.; Traynelis, Stephen F.; Liotta, Dennis C.

    2013-01-01

    Here we describe the synthesis and structure-activity relationship for a class of pyrazoline-containing dihydroquinolone negative allosteric modulators of the NMDA receptor that show strong subunit-selectivity for GluN2C- and GluN2D-containing receptors over GluN2A-and GluN2B-containing receptors. Several members of this class inhibit NMDA receptor responses in the nanomolar range, and are more than 50-fold selective over GluN1/GluN2A and GluN1/GluN2B NMDA receptors, as well as AMPA, kainate, GABA, glycine, nicotinic, serotonin, and purinergic receptors. Analysis of the purified enantiomers of one of the more potent and selective compounds shows that the S-enantiomer is both more potent and more selective than the R-enantiomer. The S-enantiomer had an IC50 value of 0.17–0.22 µM at GluN2D- and GluN2C-containing receptors, respectively, and showed over 70-fold selectivity over other NMDA receptor subunits. The subunit-selectivity of this class of compounds should be useful in defining the role of GluN2C- and GluN2D-containing receptors in specific brain circuits in both physiological and patho-physiological conditions. PMID:23909910

  5. Structure and Dynamics of Asymmetric Poly(styrene-b-1,4-isoprene) Diblock Copolymer under 1D and 2D Nanoconfinement.

    PubMed

    Kipnusu, Wycliffe K; Elmahdy, Mahdy M; Mapesa, Emmanuel U; Zhang, Jianqi; Böhlmann, Winfried; Smilgies, Detlef-M; Papadakis, Christine M; Kremer, Friedrich

    2015-06-17

    The impact of 1- and 2-dimensional (2D) confinement on the structure and dynamics of poly(styrene-b-1,4-isoprene) P(S-b-I) diblock copolymer is investigated by a combination of Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), Grazing-Incidence Small-Angle X-ray Scattering (GISAXS), and Broadband Dielectric Spectroscopy (BDS). 1D confinement is achieved by spin coating the P(S-b-I) to form nanometric thin films on silicon substrates, while in the 2D confinement, the copolymer is infiltrated into cylindrical anodized aluminum oxide (AAO) nanopores. After dissolving the AAO matrix having mean pore diameter of 150 nm, the SEM images of the exposed P(S-b-I) show straight nanorods. For the thin films, GISAXS and AFM reveal hexagonally packed cylinders of PS in a PI matrix. Three dielectrically active relaxation modes assigned to the two segmental modes of the styrene and isoprene blocks and the normal mode of the latter are studied selectively by BDS. The dynamic glass transition, related to the segmental modes of the styrene and isoprene blocks, is independent of the dimensionality and the finite sizes (down to 18 nm) of confinement, but the normal mode is influenced by both factors with 2D geometrical constraints exerting greater impact. This reflects the considerable difference in the length scales on which the two kinds of fluctuations take place. PMID:25660102

  6. Efficiently inferring community structure in bipartite networks

    NASA Astrophysics Data System (ADS)

    Larremore, Daniel B.; Clauset, Aaron; Jacobs, Abigail Z.

    2014-07-01

    Bipartite networks are a common type of network data in which there are two types of vertices, and only vertices of different types can be connected. While bipartite networks exhibit community structure like their unipartite counterparts, existing approaches to bipartite community detection have drawbacks, including implicit parameter choices, loss of information through one-mode projections, and lack of interpretability. Here we solve the community detection problem for bipartite networks by formulating a bipartite stochastic block model, which explicitly includes vertex type information and may be trivially extended to k-partite networks. This bipartite stochastic block model yields a projection-free and statistically principled method for community detection that makes clear assumptions and parameter choices and yields interpretable results. We demonstrate this model's ability to efficiently and accurately find community structure in synthetic bipartite networks with known structure and in real-world bipartite networks with unknown structure, and we characterize its performance in practical contexts.

  7. Self-assembly of 2D sandwich-structured MnFe{sub 2}O{sub 4}/graphene composites for high-performance lithium storage

    SciTech Connect

    Li, Songmei Wang, Bo; Li, Bin; Liu, Jianhua; Yu, Mei; Wu, Xiaoyu

    2015-01-15

    Highlights: • MFO/GN composites were synthesized by a facile in situ solvothermal approach. • The MFO microspheres are sandwiched between the graphene layers. • Each MFO microsphere is an interstitial cluster of nanoparticles. • The MFO/GN electrode exhibits an enhanced cyclability for Li-ion batteries anodes. - Abstract: In this study, two-dimensional (2D) sandwich-structured MnFe{sub 2}O{sub 4}/graphene (MFO/GN) composites are synthesized by a facile in situ solvothermal approach, using cetyltrimethylammonium bromide (CTAB) as cationic surfactant. As a consequence, the nanocomposites of MFO/GN self-assembled into a 2D sandwich structure, in which the interstitial cluster structure of microsphere-type MnFe{sub 2}O{sub 4} is sandwiched between the graphene layers. This special structure of the MFO/GN composites used as anodes for lithium-ion batteries will be favorable for the maximum accessible surface of electroactive materials, fast diffusion of lithium ions and migration of electron, and elastomeric space to accommodate volume changes during the discharge–charge processes. The as-synthesized MFO/GN composites deliver a high specific reversible capacity of 987.95 mA h g{sup −1} at a current density of 200 mA g{sup −1}, a good capacity retention of 69.27% after 80 cycles and excellent rate performance for lithium storage.

  8. Band structure of a 2D photonic crystal based on ferrofluids of Co(1-x)Znx Fe2O4 nanoparticles under perpendicular applied magnetic field

    NASA Astrophysics Data System (ADS)

    Lopez, Javier; Gonzalez, Luz Esther; Quinonez, Mario; Porras, Nelson; Zambrano, Gustavo; Gomez, Maria Elena

    2014-03-01

    Using a ferrfluid of cobalt-zinc ferrite nanoparticles Co(1 - x)ZnxFe2O4 coated with oleic acid and suspended in ethanol, we have fabricated a 2D photonic crystal (PC) by the application of an external magnetic field perpendicular to the plane of the ferrofluid. The 2D PC is made by rods of nanoparticles organized in a hexagonal structure. By means of the plane-wave expansion method, we study its photonic band structure (PBS) which depends on the effective permittivity and on the area ratio of the liquid phase. Additionaly, taking into account the Maxwell-Garnett theory we calculated the effective permittivity of the rods. We have found that the effective refractive index of the ferrofluid increases with its magnetization. Using these results we calculate the band structure of the photonic crystal at different applied magnetic fields, finding that the increase of the applied magnetic field shifts the band structure to lower frequencies with the appearance of more band gaps. Departamento de Física, Universidad del Valle, A.A. 25360, Cali, Colombia

  9. Genetic Network Inference Using Hierarchical Structure

    PubMed Central

    Kimura, Shuhei; Tokuhisa, Masato; Okada-Hatakeyama, Mariko

    2016-01-01

    Many methods for inferring genetic networks have been proposed, but the regulations they infer often include false-positives. Several researchers have attempted to reduce these erroneous regulations by proposing the use of a priori knowledge about the properties of genetic networks such as their sparseness, scale-free structure, and so on. This study focuses on another piece of a priori knowledge, namely, that biochemical networks exhibit hierarchical structures. Based on this idea, we propose an inference approach that uses the hierarchical structure in a target genetic network. To obtain a reasonable hierarchical structure, the first step of the proposed approach is to infer multiple genetic networks from the observed gene expression data. We take this step using an existing method that combines a genetic network inference method with a bootstrap method. The next step is to extract a hierarchical structure from the inferred networks that is consistent with most of the networks. Third, we use the hierarchical structure obtained to assign confidence values to all candidate regulations. Numerical experiments are also performed to demonstrate the effectiveness of using the hierarchical structure in the genetic network inference. The improvement accomplished by the use of the hierarchical structure is small. However, the hierarchical structure could be used to improve the performances of many existing inference methods. PMID:26941653

  10. Molecular phylogenetics in 2D: ITS2 rRNA evolution and sequence-structure barcode from Veneridae to Bivalvia.

    PubMed

    Salvi, Daniele; Mariottini, Paolo

    2012-11-01

    In this study, we analyzed the nuclear ITS2 rRNA primary sequence and secondary structure in Veneridae and comparatively with 20 Bivalvia taxa to test the phylogenetic resolution of this marker and its suitability for molecular diagnosis at different taxonomic levels. Maximum likelihood and Bayesian trees based on primary sequences were congruent with (profile-) neighbor-joining trees based on a combined model of sequence-structure evolution. ITS2 showed higher resolution below the subfamily level, providing a phylogenetic signal comparable to (mitochondrial/nuclear) gene fragments 2-5 times longer. Structural elements of the ITS2 folding, such as specific mismatch pairing and compensatory base changes, provided further support for the monophyly of some groups and for their phylogenetic relationships. Veneridae ITS2 folding is structured in six domains (DI-VI) and shows five striking sequence-structure features. Two of them, the Basal and Apical STEMs, are common to Bivalvia, while the presence of both the Branched STEM and the Y/R stretches occurs in five superfamilies of the two Heterodonta orders Myoida and Veneroida, thus questioning their reciprocal monophyly. Our results validated the ITS2 as a suitable marker for venerids phylogenetics and taxonomy, and underlined the significance of including secondary structure information for both applications at several systematic levels within bivalves.

  11. A 3D complex containing novel 2D Cu{sup II}-azido layers: Structure, magnetic properties and effects of 'Non-innocent' reagent

    SciTech Connect

    Gao, Xue-Miao; Guo, Qian; Zhao, Jiong-Peng; Liu, Fu-Chen

    2012-12-15

    A novel copper-azido coordination polymer, [Cu{sub 2}(N{sub 3}){sub 3}(L)]{sub n} (1, HL=pyrazine-2-carboxylic acid), has been synthesized by hydrothermal reaction with 'Non-innocent' reagent in the aqueous solution. In the reaction system, Cu{sup II} ions are avoided to reduce to Cu{sup I} ions due to the existence of Nd{sup III}. It is found that the complex is a 3D structure based on two double EO azido bridged trimmers and octahedron Cu{sup II} ions, in which the azide ligands take on EO and {mu}{sub 1,1,3} mode to form Cu{sup II}-azido 2D layers, furthermore L ligands pillar 2D layers into an infinite 3D framework with the Schlaefli symbol of {l_brace}4;6{sup 2}{r_brace}4{l_brace}4{sup 2};6{sup 12};8{sup 10};10{sup 4}{r_brace}{l_brace}4{sup 2};6{sup 4}{r_brace}. Magnetic studies revealed that the interactions between the Cu{sup II} ions in the trimmer are ferromagnetic for the Cu-N-Cu angle nearly 98 Degree-Sign , while the interactions between the trimmer and octahedron Cu{sup II} ion are antiferromgantic and result in an antiferromagnetic state. - Graphical abstract: A 3D complex containing novel 2D Cu{sup II}-azido layers, [Cu{sub 2}(N{sub 3}){sub 3}(L)]{sub n} (HL=pyrazine-2-carboxylic acid), was synthesized by hydrothermal reaction and exhibit interesting structure and magnetic properties. Highlights: Black-Right-Pointing-Pointer 'Non-innocent' reagents plays a key role in the process of formation of this complex. Black-Right-Pointing-Pointer 2D layer is formed only by Cu{sup II} ions and azido ligands. Black-Right-Pointing-Pointer Pyrazine-2-carboxylate ligands reinforce 2D layers and pillar them into an infinite 3D framework. Black-Right-Pointing-Pointer Magnetic study indicates that alternating FM-AF coupling exists in the complex.

  12. Exploring the hierarchical structure in road network

    NASA Astrophysics Data System (ADS)

    He, Jing; Zhang, Hong; Lan, Tian; Cao, Weiwei; Wu, Xun

    2015-12-01

    Hierarchical structure of road network has received intensive attention either in urban planning or multi-scale representation. On the one hand, high-efficiency traffic flow counts on a reasonable hierarchical structure. On the other hand, it is a guide-line for cartographic generalization of road network. The paper attempts to investigate the hierarchical structure of a road network from two perspectives, a) the ht-index in terms of the degree connectivity, which was proposed to quantify the scaling and hierarchical structure of the network, b) the renormalization process, originated from complex network analysis, which is able to uncover the self-similarity of a network and reveal its hierarchical structure. We argue that the first point exhibits a big picture of the whole network, revealing the depth of the hierarchy, while the second point further illustrates how the nodes are organized to form a hierarchical structure at different scales. The hierarchical structures of 6 road networks in reality are examined accordingly. Results show that both indices are able to reveal the complexity of the hierarchy of a network. These conclusions can be beneficial to the road network generalization.

  13. Synthesis, structure and temperature-depended 2D IR correlation spectroscopy of an organo-bismuth benzoate with 1,10-phenanthroline

    NASA Astrophysics Data System (ADS)

    Sun, Yan-Qiong; Zhong, Jie-Cen; Liu, Le-Hui; Qiu, Xing-Tai; Chen, Yi-Ping

    2016-11-01

    An organo-bismuth benzoate with phen as auxiliary ligand, [Bi(phen)(C6H5COO)(C6H4COO)] (1) (phen = 1,10-phenanthroline) has been hydrothermally synthesized from bismuth nitrate, 2-mercaptonbenzoic acid with phen as auxiliary ligand and characterized by single-crystal X-ray diffraction, elemental analyses, PXRD, IR spectra, TG analyses, temperature-depended 2D-IR COS (two-dimensional infrared correlation spectroscopy). Interestingly, benzoate anions in 1 came from the desulfuration reaction of 2-mercaptonbenzoic acid under hydrothermal condition. Compound 1 is a discrete organo-bismuth compound with benzoate and phen ligands. The offset face-to-face π-π stacking interactions and C-H⋯O hydrogen bonds link the isolate complex into a 3D supramolecular network. The temperature-depended 2D-IR COS indicates that the stretching vibrations of Cdbnd C/Cdbnd N of aromatic rings and Cdbnd O bonds are sensitive to the temperature change.

  14. Synthesis, structure and properties of one novel 2D Mn-heterocyclic carboxylic acid complex [Mn(TPA)Cl(H 2O)] n

    NASA Astrophysics Data System (ADS)

    Zhu, Peng; Li, Hui-Min

    2011-04-01

    A novel 2D layer complex [Mn(TPA)Cl(H 2O)] n ( 1) has been synthesized by two methods through the reaction of MnCl 2 and TPC or TPA under hydrothermal conditions and characterized by single crystal X-ray diffraction, elemental analysis, infrared spectrometry (IR), powder X-ray diffraction (XRD) and thermogravimetric analysis (TGA), where heterocyclic carboxylic acid ligand TPA = 2-(5-(pyridin-2-yl)-2H-tetrazol-2-yl)acetic acid, TPC = 2-(5-(pyridin-2-yl)-2H-tetrazol-2-yl)acetonitrile. The distorted octahedral Mn(II) centers are bridged by carboxylic O atoms resulting in the formation of a 1D chain. Then the 1D chains are connected with each other through TPA ligands into a 2D (3,3)-connected topology framework. The H-bonding interactions extend the complex into a three-dimensional network, and such weak interactions further stabilized the complex. Furthermore, solid-state fluorescence spectrum of complex 1 exhibits intense broad emissions at 396 nm at room temperature, which is red-shifted by 21 nm relative to that of free ligand TPA.

  15. 2D dual permeability modeling of flow and transport in a two-scale structured lignitic mine soil

    NASA Astrophysics Data System (ADS)

    Dusek, J.; Gerke, H. H.; Vogel, T.; Maurer, T.; Buczko, U.

    2009-04-01

    Two-dimensional single- and dual-permeability simulations are used to analyze water and solute fluxes in heterogeneous lignitic mine soil at a forest-reclaimed mine spoil heap. The soil heterogeneity on this experimental site "Bärenbrücker Höhe" resulted from inclined dumping structures and sediment mixtures that consist of sand with lignitic dust and embedded lignitic fragments. Observations on undisturbed field suction-cell lysimeters including tracer experiments revealed funneling-type preferential flow with lateral water and bromide movement along inclined sediment structures. The spatial distribution of soil structures and fragment distributions was acquired by a digital camera and identified by a supervised classification of the digital profile image. First, a classical single-domain modeling approach was used, with spatially variable scaling factors inferred from image analyses. In the next step, a two-continuum scenario was constructed to examine additional effects of nonequilibrium on the flow regime. The scaling factors used for the preferential flow domain are here obtained from the gradient of the grayscale images. So far, the single domain scenarios failed to predict the bromide leaching patterns although water effluent could be described. Dual-permeability model allows the incorporation of structural effects and can be used as a tool to further testing other approaches that account for structure effects. The numerical study suggests that additional experiments are required to obtain better understanding of the highly complex transport processes on this experimental site.

  16. Structure of triadic relations in multiplex networks

    NASA Astrophysics Data System (ADS)

    Cozzo, Emanuele; Kivelä, Mikko; De Domenico, Manlio; Solé-Ribalta, Albert; Arenas, Alex; Gómez, Sergio; Porter, Mason A.; Moreno, Yamir

    2015-07-01

    Recent advances in the study of networked systems have highlighted that our interconnected world is composed of networks that are coupled to each other through different ‘layers’ that each represent one of many possible subsystems or types of interactions. Nevertheless, it is traditional to aggregate multilayer networks into a single weighted network in order to take advantage of existing tools. This is admittedly convenient, but it is also extremely problematic, as important information can be lost as a result. It is therefore important to develop multilayer generalizations of network concepts. In this paper, we analyze triadic relations and generalize the idea of transitivity to multiplex networks. By focusing on triadic relations, which yield the simplest type of transitivity, we generalize the concept and computation of clustering coefficients to multiplex networks. We show how the layered structure of such networks introduces a new degree of freedom that has a fundamental effect on transitivity. We compute multiplex clustering coefficients for several real multiplex networks and illustrate why one must take great care when generalizing standard network concepts to multiplex networks. We also derive analytical expressions for our clustering coefficients for ensemble averages of networks in a family of random multiplex networks. Our analysis illustrates that social networks have a strong tendency to promote redundancy by closing triads at every layer and that they thereby have a different type of multiplex transitivity from transportation networks, which do not exhibit such a tendency. These insights are invisible if one only studies aggregated networks.

  17. Consensus between Pipelines in Structural Brain Networks

    PubMed Central

    Parker, Christopher S.; Deligianni, Fani; Cardoso, M. Jorge; Daga, Pankaj; Modat, Marc; Dayan, Michael; Clark, Chris A.

    2014-01-01

    Structural brain networks may be reconstructed from diffusion MRI tractography data and have great potential to further our understanding of the topological organisation of brain structure in health and disease. Network reconstruction is complex and involves a series of processesing methods including anatomical parcellation, registration, fiber orientation estimation and whole-brain fiber tractography. Methodological choices at each stage can affect the anatomical accuracy and graph theoretical properties of the reconstructed networks, meaning applying different combinations in a network reconstruction pipeline may produce substantially different networks. Furthermore, the choice of which connections are considered important is unclear. In this study, we assessed the similarity between structural networks obtained using two independent state-of-the-art reconstruction pipelines. We aimed to quantify network similarity and identify the core connections emerging most robustly in both pipelines. Similarity of network connections was compared between pipelines employing different atlases by merging parcels to a common and equivalent node scale. We found a high agreement between the networks across a range of fiber density thresholds. In addition, we identified a robust core of highly connected regions coinciding with a peak in similarity across network density thresholds, and replicated these results with atlases at different node scales. The binary network properties of these core connections were similar between pipelines but showed some differences in atlases across node scales. This study demonstrates the utility of applying multiple structural network reconstrution pipelines to diffusion data in order to identify the most important connections for further study. PMID:25356977

  18. 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.

  19. Finite Element Method for Analysis of Band Structures of 2D Phononic Crystals with Archimedean-like tilings

    NASA Astrophysics Data System (ADS)

    Li, Jianbao; Wang, Yue-Sheng; Zhang, Chuanzeng

    2010-05-01

    In this paper, a finite element method based on the ABAQUS code and user subroutine is presented to evaluate the propagation of acoustic waves in the two-dimensional phononic crystals with Archimedean-like tilings. Two systems composed of cylinder scatters embedded in a host in Ladybug and Bathroom lattices are considered. Complete and accurate band structures and transmission spectra are obtained to identify the band gaps and eigenmodes. We found that Archimedean-like structures can have some advantages over the traditional square lattice regarding the completeness of the gap and its position and width. Also, due to the same square primitive unit cell and the first Brillouin zone, the two square-like lattices have similar acoustic response in lower bands. The results indicate that the finite element method is precise for the band structure computation of the complex phononic crystals with Archimedean tilings.

  20. Large-area 2D periodic crystalline silicon nanodome arrays on nanoimprinted glass exhibiting photonic band structure effects.

    PubMed

    Becker, C; Lockau, D; Sontheimer, T; Schubert-Bischoff, P; Rudigier-Voigt, E; Bockmeyer, M; Schmidt, F; Rech, B

    2012-04-01

    Two-dimensional silicon nanodome arrays are prepared on large areas up to 50 cm² exhibiting photonic band structure effects in the near-infrared and visible wavelength region by downscaling a recently developed fabrication method based on nanoimprint-patterned glass, high-rate electron-beam evaporation of silicon, self-organized solid phase crystallization and wet-chemical etching. The silicon nanodomes, arranged in square lattice geometry with 300 nm lattice constant, are optically characterized by angular resolved reflection measurements, allowing the partial determination of the photonic band structure. This experimentally determined band structure agrees well with the outcome of three-dimensional optical finite-element simulations. A 16% photonic bandgap is predicted for an optimized geometry of the silicon nanodome arrays. By variation of the duration of the selective etching step, the geometry as well as the optical properties of the periodic silicon nanodome arrays can be controlled systematically.

  1. Structure and Magnetic Ordering of a 2-D MnII(TCNE)I(OH2) (TCNE = tetracyanoethylene) Organic-based Magnet (Tc = 171 K)

    SciTech Connect

    S Lapidus; A McConnell; P Stephens; J Miller

    2011-12-31

    Mn{sup II}(TCNE)I(OH{sub 2}) was isolated from the reaction of tetracyanoethylene (TCNE) and MnI{sub 2}(THF){sub 3}, and has a 2-D structure possessing an unusual, asymmetric bonded {mu}{sub 4}-[TCNE]{sup {sm_bullet}-}. Direct antiferromagnetic coupling between the S = 5/2 Mn{sup II} and S = 1/2 [TCNE]{sup {sm_bullet}-} leads to magnetic ordering as a canted antiferromagnet at a T{sub c} of 171 K.

  2. Assembly of 1D, 2D and 3D lanthanum(iii) coordination polymers with perchlorinated benzenedicarboxylates: positional isomeric effect, structural transformation and ring-opening polymerisation of glycolide.

    PubMed

    Chen, Sheng-Chun; Dai, An-Qi; Huang, Kun-Lin; Zhang, Zhi-Hui; Cui, Ai-Jun; He, Ming-Yang; Chen, Qun

    2016-02-28

    Utilizing a series of positional isomers of tetrachlorinated benzenedicarboxylic acid ligands, seven La(iii)-based coordination polymers were solvothermally synthesized and structurally characterized. Their structural dimensionalities varying from 1D double chains, to the 2D 3,4,5-connected network, to 3D 6-connected pcu topological nets are only governed by the positions of carboxyl groups on the tetrachlorinated benzene ring. A comprehensive analysis and comparison reveals that the size of the carbonyl solvent molecules (DMF, DEF, DMA, and NMP) can affect the coordination geometries around the La(iii) ions, the coordination modes of carboxylate groups, the packing arrangements, and the void volumes of the overall crystal lattices. One as-synthesized framework further shows an unprecedented structural transformation from a 3D 6-connected network to a 3D 4,5-connected net through the dissolution and reformation pathway in water, suggesting that these easily hydrolyzed lanthanide complexes may serve as precursors to produce new high-dimensional frameworks. The bulk solvent-free melt polymerisation of glycolide utilizing these La(iii) complexes as initiators has been reported herein for the first time. All complexes were found to promote the polymerization of glycolide over a temperature range of 200 to 220 °C, producing poly(glycolic acid) (PGA) with a molecular weight up to 93,280. Under the same experimental conditions, the different catalytic activities for these complexes may result from their structural discrepancy.

  3. Assembly of 1D, 2D and 3D lanthanum(iii) coordination polymers with perchlorinated benzenedicarboxylates: positional isomeric effect, structural transformation and ring-opening polymerisation of glycolide.

    PubMed

    Chen, Sheng-Chun; Dai, An-Qi; Huang, Kun-Lin; Zhang, Zhi-Hui; Cui, Ai-Jun; He, Ming-Yang; Chen, Qun

    2016-02-28

    Utilizing a series of positional isomers of tetrachlorinated benzenedicarboxylic acid ligands, seven La(iii)-based coordination polymers were solvothermally synthesized and structurally characterized. Their structural dimensionalities varying from 1D double chains, to the 2D 3,4,5-connected network, to 3D 6-connected pcu topological nets are only governed by the positions of carboxyl groups on the tetrachlorinated benzene ring. A comprehensive analysis and comparison reveals that the size of the carbonyl solvent molecules (DMF, DEF, DMA, and NMP) can affect the coordination geometries around the La(iii) ions, the coordination modes of carboxylate groups, the packing arrangements, and the void volumes of the overall crystal lattices. One as-synthesized framework further shows an unprecedented structural transformation from a 3D 6-connected network to a 3D 4,5-connected net through the dissolution and reformation pathway in water, suggesting that these easily hydrolyzed lanthanide complexes may serve as precursors to produce new high-dimensional frameworks. The bulk solvent-free melt polymerisation of glycolide utilizing these La(iii) complexes as initiators has been reported herein for the first time. All complexes were found to promote the polymerization of glycolide over a temperature range of 200 to 220 °C, producing poly(glycolic acid) (PGA) with a molecular weight up to 93,280. Under the same experimental conditions, the different catalytic activities for these complexes may result from their structural discrepancy. PMID:26811117

  4. Synthesis of 2D/2D Structured Mesoporous Co3O4 Nanosheet/N-Doped Reduced Graphene Oxide Composites as a Highly Stable Negative Electrode for Lithium Battery Applications.

    PubMed

    Sennu, Palanichamy; Kim, Hyo Sang; An, Jae Youn; Aravindan, Vanchiappan; Lee, Yun-Sung

    2015-08-01

    Mesoporous Co3O4 nanosheets (Co3 O4 -NS) and nitrogen-doped reduced graphene oxide (N-rGO) are synthesized by a facile hydrothermal approach, and the N-rGO/Co3O4 -NS composite is formulated through an infiltration procedure. Eventually, the obtained composites are subjected to various characterization techniques, such as XRD, Raman spectroscopy, surface area analysis, X-ray photoelectron spectroscopy (XPS), and TEM. The lithium-storage properties of N-rGO/Co3O4 -NS composites are evaluated in a half-cell assembly to ascertain their suitability as a negative electrode for lithium-ion battery applications. The 2D/2D nanostructured mesoporous N-rGO/Co3O4 -NS composite delivered a reversible capacity of about 1305 and 1501 mAh g(-1) at a current density of 80 mA g(-1) for the 1st and 50th cycles, respectively. Furthermore, excellent cyclability, rate capability, and capacity retention characteristics are noted for the N-rGO/Co3O4 -NS composite. This improved performance is mainly related to the existence of mesoporosity and a sheet-like 2D hierarchical morphology, which translates into extra space for lithium storage and a reduced electron pathway. Also, the presence of N-rGO and carbon shells in Co3O4 -NS should not be excluded from such exceptional performance, which serves as a reliable conductive channel for electrons and act as synergistically to accommodate volume expansion upon redox reactions. Ex-situ TEM, impedance spectroscopy, and XPS, are also conducted to corroborate the significance of the 2D morphology towards sustained lithium storage.

  5. Structure and function of complex brain networks.

    PubMed

    Sporns, Olaf

    2013-09-01

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

  6. Solution structure of GCCAAT recognition motif by 2D NMR, spectral simulation, molecular modeling, and distance geometry calculations.

    PubMed

    Nibedita, R; Kumar, R A; Majumdar, A; Hosur, R V; Govil, G; Majumder, K; Chauhan, V S

    1993-09-01

    Solution conformation of a self-complementary 14-mer DNA duplex (d-GGATTGGCCAATCC) containing the GCCAAT recognition motif of several transcription factors has been investigated by NMR spectroscopy. Complete resonance assignment of all the protons (except H5',H5'' protons) has been obtained following standard procedures based on two-dimensional NMR techniques. Three-bond coupling constants have been determined by spectral simulation procedures. New strategies have been described and employed for quantifying NOE intensities from the structural point of view. Approximate ranges of gamma torsion angles have been obtained from a selective NOESY experiment, by estimating the J(4'-5'), J(4'-5''), or their sum in the H1'-H4' cross peaks of the spectrum. Likewise, ranges of epsilon torsion angles have been obtained by monitoring the H3' multiplicities in the H8/H6-H3' cross peaks in selective NOESY spectra. With the help of such a total of 73 coupling constraints, 79 NOE intensity constraints, and 108 H-bond constraints, model building has been carried out to obtain a structure which satisfies the constraints. Starting from such a structure, an expanded distance constraint set has been created which has been used for the distance geometry calculations using the program TANDY. In the best structure thus derived, interesting irregularities similar to a BI-BII transition have been observed in the center. The molecule exhibits a bend. The overall base stacking is different from that in either B- or A-DNA models. The base pairs are tilted with respect to the local helix axes. The observed structural features are likely to have important implications for the recognition mechanism of the GCCAAT motif.

  7. Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.

    PubMed

    Fritzsching, K J; Yang, Y; Schmidt-Rohr, K; Hong, Mei

    2013-06-01

    We introduce a Python-based program that utilizes the large database of (13)C and (15)N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D (13)C-(13)C, (15)N-(13)C, or 3D (15)N-(13)C-(13)C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D (13)C-(13)C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the Cα and Cβ chemical shifts, the highest-ranked PLUQ assignments were 40-60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO-Cα-Cβ or N-Cα-Cβ), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

  8. Elucidating structural characteristics of biomass using solution-state 2 D NMR with a mixture of deuterated dimethylsulfoxide and hexamethylphosphoramide

    DOE PAGES

    Pu, Yunqiao; Ragauskas, Arthur J.; Yoo, Chang Geun; Li, Mi

    2016-04-26

    In recent developments of NMR methods for characterization of lignocellulosic biomass allow improved understanding of plant cell-wall structures with minimal deconstruction and modification of biomass. This study introduces a new NMR solvent system composed of dimethylsulfoxide (DMSO-d6) and hexamethylphosphoramide (HMPA-d18). HMPA as a co-solvent enhanced swelling and mobility of the biomass samples; thereby it allowed enhancing signals of NMR spectra. Moreover, the structural information of biomass was successfully analyzed by the proposed NMR solvent system (DMSO-d6/HMPA-d18; 4:1, v/v) with different biomass. The proposed bi-solvent system does not require derivatization or isolation of biomass, facilitating a facile sample preparation and involvingmore » with no signals overlapping with biomass peaks. Furthermore, it also allows analyzing biomass with a room-temperature NMR probe instead of cryo-probes, which are traditionally used for enhancing signal intensities.« less

  9. Ag (I)-based 2D metal frameworks with helical structures decorated by the homochiral camphor-10-sulfonic acid

    NASA Astrophysics Data System (ADS)

    Guo, Peng; Wang, Jing; Wang, Jun; Pan, Daocheng; Xu, Guohai

    2010-12-01

    Two two-dimension homochiral Ag (I) metal frameworks constructed from enantiopure camphor-10-sulfonic acid and hexamethylenetetramine have been synthesized at the room temperature. These two complexes with (6, 3) topology decorated by the homochiral camphor-10-sulfonic acid possess the unique helical structures. The result of Circular Dichroism (CD) spectroscopy confirms that the bulk materials are homochiral and also indicates the handedness of the single crystals can be controlled by the chirality of the camphor-10-sulfonic acid.

  10. Separation of experimental 2D IR frequency-frequency correlation functions into structural and reorientation-induced contributions

    NASA Astrophysics Data System (ADS)

    Kramer, Patrick L.; Nishida, Jun; Fayer, Michael D.

    2015-09-01

    A vibrational transition frequency can couple to its environment through a directional vector interaction. In such cases, reorientation of the vibrational transition dipole (molecular orientational relaxation) and its frequency fluctuations can be strongly coupled. It was recently shown [Kramer et al., J. Chem. Phys. 142, 184505 (2015)] that differing frequency-frequency correlation function (FFCF) decays, due to reorientation-induced spectral diffusion (RISD), are observed with different two-dimensional infrared polarization configurations when such strong coupling is present. The FFC functional forms were derived for the situation in which all spectral diffusion is due to reorientational motion. We extend the previous theory to include vibrational frequency evolution (spectral diffusion) caused by structural fluctuations of the medium. Model systems with diffusive reorientation and several regimes of structural spectral diffusion rates are analyzed for first order Stark effect interactions. Additionally, the transition dipole reorientational motion in complex environments is frequently not completely diffusive. Several periods of restricted angular motion (wobbling-in-a-cone) may precede the final diffusive orientational randomization. The polarization-weighted FFCF decays are presented in this case of restricted transition dipole wobbling. With these extensions to the polarization-dependent FFCF expressions, the structural spectral diffusion dynamics of methanol in the room temperature ionic liquid 1-hexyl-3-methylimidazolium hexafluorophosphate can be separated quantitatively from RISD using the experimental center line slope data. In addition, prior results on the spectral diffusion of water, methanol, and ethanol in 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide are re-examined to elucidate the influence of reorientation on the data, which were interpreted in terms of structural fluctuations.

  11. Quantitative Subsurface Atomic Structure Fingerprint for 2D Materials and Heterostructures by First-Principles-Calibrated Contact-Resonance Atomic Force Microscopy.

    PubMed

    Tu, Qing; Lange, Björn; Parlak, Zehra; Lopes, Joao Marcelo J; Blum, Volker; Zauscher, Stefan

    2016-07-26

    Interfaces and subsurface layers are critical for the performance of devices made of 2D materials and heterostructures. Facile, nondestructive, and quantitative ways to characterize the structure of atomically thin, layered materials are thus essential to ensure control of the resultant properties. Here, we show that contact-resonance atomic force microscopy-which is exquisitely sensitive to stiffness changes that arise from even a single atomic layer of a van der Waals-adhered material-is a powerful experimental tool to address this challenge. A combined density functional theory and continuum modeling approach is introduced that yields sub-surface-sensitive, nanomechanical fingerprints associated with specific, well-defined structure models of individual surface domains. Where such models are known, this information can be correlated with experimentally obtained contact-resonance frequency maps to reveal the (sub)surface structure of different domains on the sample. PMID:27263541

  12. A time series generalized functional model based method for vibration-based damage precise localization in structures consisting of 1D, 2D, and 3D elements

    NASA Astrophysics Data System (ADS)

    Sakaris, C. S.; Sakellariou, J. S.; Fassois, S. D.

    2016-06-01

    This study focuses on the problem of vibration-based damage precise localization via data-based, time series type, methods for structures consisting of 1D, 2D, or 3D elements. A Generalized Functional Model Based method is postulated based on an expanded Vector-dependent Functionally Pooled ARX (VFP-ARX) model form, capable of accounting for an arbitrary structural topology. The FP model's operating parameter vector elements are properly constrained to reflect any given topology. Damage localization is based on operating parameter vector estimation within the specified topology, so that the location estimate and its uncertainty bounds are statistically optimal. The method's effectiveness is experimentally demonstrated through damage precise localization on a laboratory spatial truss structure using various damage scenarios and a single pair of random excitation - vibration response signals in a low and limited frequency bandwidth.

  13. Quantitative Subsurface Atomic Structure Fingerprint for 2D Materials and Heterostructures by First-Principles-Calibrated Contact-Resonance Atomic Force Microscopy.

    PubMed

    Tu, Qing; Lange, Björn; Parlak, Zehra; Lopes, Joao Marcelo J; Blum, Volker; Zauscher, Stefan

    2016-07-26

    Interfaces and subsurface layers are critical for the performance of devices made of 2D materials and heterostructures. Facile, nondestructive, and quantitative ways to characterize the structure of atomically thin, layered materials are thus essential to ensure control of the resultant properties. Here, we show that contact-resonance atomic force microscopy-which is exquisitely sensitive to stiffness changes that arise from even a single atomic layer of a van der Waals-adhered material-is a powerful experimental tool to address this challenge. A combined density functional theory and continuum modeling approach is introduced that yields sub-surface-sensitive, nanomechanical fingerprints associated with specific, well-defined structure models of individual surface domains. Where such models are known, this information can be correlated with experimentally obtained contact-resonance frequency maps to reveal the (sub)surface structure of different domains on the sample.

  14. Synthesis and structure of a 2D Zn complex with mixed ligands stacked in offset ABAB manner

    NASA Astrophysics Data System (ADS)

    Qin, Ling; Wang, Yan-Qing; Ni, Gang

    2016-07-01

    The title complex, {[Zn(ODIB)1/2( bpdc)]·2DMF} n was prepared under hydrothermal conditions (dimethylformamide and water) based on two ligands, namely, 1,1'-oxy-bis[3,5-diimidazolyl-benzene] (ODIB) and biphenyldicarboxylic acid (H2 bpdc). ODIB ligands link Zn cations to give layers in crystal. bpdc 2- anions coordinate to Zn atoms, however, their introduction does not increase the dimension of the structure. Each layer is partially passes through the adjacent layers in the offset ABAB manner.

  15. Can fractional quantum Hall effect be due to the formation of coherent wave structures in a 2D electron gas?

    NASA Astrophysics Data System (ADS)

    Mirza, Babur M.

    2016-05-01

    A microscopic theory of integer and fractional quantum Hall effects is presented here. In quantum density wave representation of charged particles, it is shown that, in a two-dimensional electron gas coherent structures form under the low temperature and high density conditions. With a sufficiently high applied magnetic field, the combined N particle quantum density wave exhibits collective periodic oscillations. As a result the corresponding quantum Hall voltage function shows a step-wise change in multiples of the ratio h/e2. At lower temperatures further subdivisions emerge in the Hall resistance, exhibiting the fractional quantum Hall effect.

  16. Network structure of inter-industry flows

    NASA Astrophysics Data System (ADS)

    McNerney, James; Fath, Brian D.; Silverberg, Gerald

    2013-12-01

    We study the structure of inter-industry relationships using networks of money flows between industries in 45 national economies. We find these networks vary around a typical structure characterized by a Weibull link weight distribution, exponential industry size distribution, and a common community structure. The community structure is hierarchical, with the top level of the hierarchy comprising five industry communities: food industries, chemical industries, manufacturing industries, service industries, and extraction industries.

  17. An Easily Accessible Self-Healing Transparent Film Based on a 2D Supramolecular Network of Hydrogen-Bonding Interactions between Polymeric Chains.

    PubMed

    Roy, Nabarun; Tomović, Željko; Buhler, Eric; Lehn, Jean-Marie

    2016-09-12

    Self-healing polymers hold great promise for the future, enhancing in particular the longevity of polymeric materials. We describe a self-healing covalent polymer, presenting an extensive array of hydrogen-bonding sites based on the combination of urea, urethane, and bis-acyl-hydrazine units. Solvent-cast thin-films prepared by polycondensation of a commercially available dihydrazide and a diisocyanate prepolymer exhibited excellent room temperature autonomous healing with almost full recovery of mechanical properties when two parts of a cut film were overlapped and gently pressed together. This autonomous healing upon damage may be attributed to the supramolecular dynamics of multiple lateral inter-chain hydrogen-bonding interactions between the polymer chains. The solid-state structure of a model compound incorporating the same structural backbone corroborates the existence of an extensive two-dimensional supramolecular hydrogen-bonding network. PMID:27226034

  18. SPE-LEEM Studies on the Surface and Electronic Structure of 2-D Transition Metal Dichalcogenides (Part II)

    NASA Astrophysics Data System (ADS)

    Jin, Wencan; Yeh, Po-Chun; Zaki, Nader; Zhang, Datong; Sadowski, Jerzy; Al-Mahboob, Abdullah; van de Zande, Arend; Chenet, Daniel; Dadap, Jerry; Herman, Irving; Sutter, Peter; Hone, James; Osgood, Richard

    2014-03-01

    In this work, we studied the surface and electronic structure of monolayer and few-layer exfoliated MoS2 and WSe2, as well as chemical-vapor-deposition (CVD) grown MoS2, using Spectroscopic Photoemission and Low Energy Electron Microscope (SPE-LEEM). LEEM measurements reveal that, unlike exfoliated MoS2, CVD-grown MoS2 exhibits grain-boundary alterations due to surface strain. However, LEEM and micro-probe low energy electron diffraction show that the quality of CVD-grown MoS2 is comparable to that of exfoliated MoS2. Micrometer-scale angle-resolved photoemission spectroscopy (ARPES) measurement on exfoliated MoS2 and WSe2 single-crystals provides direct evidence for the shifting of the valence band maximum from Γ to K, when the layer number is thinned down to one, as predicted by density functional theory. Our measurements of the k-space resolved electronic structure allow for further comparison with other theoretical predictions and with transport measurements. This work is supported by DOE grant DE-FG 02-04-ER-46157, research carried out in part at the CFN and NSLS, Brookhaven National Laboratory.

  19. High Pressure Study of Delocalized Polarons in 2-D Lamellar Structure of Regio-Regular Poly(3-alkylthiophene) Films

    NASA Astrophysics Data System (ADS)

    An, C. P.; Jiang, X. M.; Vardeny, Z. V.

    2001-03-01

    The long-lived photoexcitations in poly(3-alkylthiophene) [P3AT] having a high head-to-tail ratio, the so called regio-regular (RR) P3AT, have been extensively studied by the photoinduced absorption (PA) spectroscopy using a FTIR spectrometer. In particular, delocalized polarons with DP1 (low energy) and DP2 (high energy) PA bands were observed in the self-assembled two-dimensional lamellar structure of RR P3AT films.(R. Osterbacka et al, Science, 287), p839 (2000) DP1 with a peak at ~0.1 eV is expected to red-shift as the interlayer distance decreases. This was indirectly confirmed before in the experiments by observing a red-shift in DP1 band as the aklyl sidegroup of the P3AT polymer decreases from dodecyl to hexyl.^2 In the present work we have succeeded, for the first time, to measure infrared PA spectra down to 400 cm-1 under high hydrostatic pressure up to 50 kbar with a diamond anvil cell. This technique was applied to RR P3AT in order to test the effect of the change in the interlayer distance for the same alkyl sidegroup, which is induced by the high pressure. We found that the first moment of the DP1 band red-shifts as the pressure increases. This result is in agreement with the delocalized polaron model in the lamellar structure.

  20. Origin and Structure of Dynamic Cooperative Networks

    NASA Astrophysics Data System (ADS)

    Wardil, Lucas; Hauert, Christoph

    2014-07-01

    Societies are built on social interactions among individuals. Cooperation represents the simplest form of a social interaction: one individual provides a benefit to another one at a cost to itself. Social networks represent a dynamical abstraction of social interactions in a society. The behaviour of an individual towards others and of others towards the individual shape the individual's neighbourhood and hence the local structure of the social network. Here we propose a simple theoretical framework to model dynamic social networks by focussing on each individual's actions instead of interactions between individuals. This eliminates the traditional dichotomy between the strategy of individuals and the structure of the population and easily complements empirical studies. As a consequence, altruists, egoists and fair types are naturally determined by the local social structures, while globally egalitarian networks or stratified structures arise. Cooperative interactions drive the emergence and shape the structure of social networks.

  1. Origin and Structure of Dynamic Cooperative Networks

    PubMed Central

    Wardil, Lucas; Hauert, Christoph

    2014-01-01

    Societies are built on social interactions among individuals. Cooperation represents the simplest form of a social interaction: one individual provides a benefit to another one at a cost to itself. Social networks represent a dynamical abstraction of social interactions in a society. The behaviour of an individual towards others and of others towards the individual shape the individual's neighbourhood and hence the local structure of the social network. Here we propose a simple theoretical framework to model dynamic social networks by focussing on each individual's actions instead of interactions between individuals. This eliminates the traditional dichotomy between the strategy of individuals and the structure of the population and easily complements empirical studies. As a consequence, altruists, egoists and fair types are naturally determined by the local social structures, while globally egalitarian networks or stratified structures arise. Cooperative interactions drive the emergence and shape the structure of social networks. PMID:25030202

  2. Structure of the Human Dopamine D3 Receptor in Complex with a D2/D3 Selective Antagonist

    SciTech Connect

    Chien, Ellen Y.T.; Liu, Wei; Zhao, Qiang; Katritch, Vsevolod; Han, Gye Won; Hanson, Michael A.; Shi, Lei; Newman, Amy Hauck; Javitch, Jonathan A.; Cherezov, Vadim; Stevens, Raymond C.

    2010-11-30

    Dopamine modulates movement, cognition, and emotion through activation of dopamine G protein-coupled receptors in the brain. The crystal structure of the human dopamine D3 receptor (D3R) in complex with the small molecule D2R/D3R-specific antagonist eticlopride reveals important features of the ligand binding pocket and extracellular loops. On the intracellular side of the receptor, a locked conformation of the ionic lock and two distinctly different conformations of intracellular loop 2 are observed. Docking of R-22, a D3R-selective antagonist, reveals an extracellular extension of the eticlopride binding site that comprises a second binding pocket for the aryl amide of R-22, which differs between the highly homologous D2R and D3R. This difference provides direction to the design of D3R-selective agents for treating drug abuse and other neuropsychiatric indications.

  3. Probing the 2D temperature structure of protoplanetary disks with Herschel observations of high-J CO lines

    NASA Astrophysics Data System (ADS)

    Fedele, D.; van Dishoeck, E. F.; Kama, M.; Bruderer, S.; Hogerheijde, M. R.

    2016-06-01

    The gas temperature structure of protoplanetary disks is a key ingredient for interpreting various disk observations and for quantifying the subsequent evolution of these systems. The comparison of low- and mid-J CO rotational lines is a powerful tool for assessing the temperature gradient in the warm molecular layer of disks. Spectrally resolved high-J (Ju> 14) CO lines probe intermediate distances and heights from the star that are not sampled by (sub-)millimeter CO spectroscopy. This paper presents new Herschel/HIFI and archival PACS observations of 12CO, 13CO, and [C ii] emission in four Herbig AeBe disks (HD 100546, HD 97048, IRS 48, HD 163296) and three T Tauri disks (AS 205, S CrA, TW Hya). In the case of the T Tauri systems AS 205 and S CrA, the CO emission has a single-peaked profile, likely due to a slow wind. For all the other systems, the Herschel CO spectra are consistent with pure disk emission and the spectrally resolved lines (HIFI) and the CO rotational ladder (PACS) are analyzed simultaneously assuming power-law temperature and column density profiles, using the velocity profile to locate the emission in the disk. The temperature profile varies substantially from disk to disk. In particular, Tgas in the disk surface layers can differ by up to an order of magnitude among the four Herbig AeBe systems; HD 100546 is the hottest and HD 163296 the coldest disk in the sample. Clear evidence of a warm disk layer where Tgas>Tdust is found in all the Herbig Ae disks. The observed CO fluxes and line profiles are compared to predictions of physical-chemical models. The primary parameters affecting the disk temperature structure are the flaring angle, the gas-to-dust mass ratio, the scale height, and the dust settling.

  4. Cross-linked structure of network evolution

    SciTech Connect

    Bassett, Danielle S.; Wymbs, Nicholas F.; Grafton, Scott T.; Porter, Mason A.; Mucha, Peter J.

    2014-03-15

    We study the temporal co-variation of network co-evolution via the cross-link structure of networks, for which we take advantage of the formalism of hypergraphs to map cross-link structures back to network nodes. We investigate two sets of temporal network data in detail. In a network of coupled nonlinear oscillators, hyperedges that consist of network edges with temporally co-varying weights uncover the driving co-evolution patterns of edge weight dynamics both within and between oscillator communities. In the human brain, networks that represent temporal changes in brain activity during learning exhibit early co-evolution that then settles down with practice. Subsequent decreases in hyperedge size are consistent with emergence of an autonomous subgraph whose dynamics no longer depends on other parts of the network. Our results on real and synthetic networks give a poignant demonstration of the ability of cross-link structure to uncover unexpected co-evolution attributes in both real and synthetic dynamical systems. This, in turn, illustrates the utility of analyzing cross-links for investigating the structure of temporal networks.

  5. Temporal network structures controlling disease spreading.

    PubMed

    Holme, Petter

    2016-08-01

    We investigate disease spreading on eight empirical data sets of human contacts (mostly proximity networks recording who is close to whom, at what time). We compare three levels of representations of these data sets: temporal networks, static networks, and a fully connected topology. We notice that the difference between the static and fully connected networks-with respect to time to extinction and average outbreak size-is smaller than between the temporal and static topologies. This suggests that, for these data sets, temporal structures influence disease spreading more than static-network structures. To explain the details in the differences between the representations, we use 32 network measures. This study concurs that long-time temporal structures, like the turnover of nodes and links, are the most important for the spreading dynamics. PMID:27627315

  6. Network Structure and Travel Time Perception

    PubMed Central

    Parthasarathi, Pavithra; Levinson, David; Hochmair, Hartwig

    2013-01-01

    The purpose of this research is to test the systematic variation in the perception of travel time among travelers and relate the variation to the underlying street network structure. Travel survey data from the Twin Cities metropolitan area (which includes the cities of Minneapolis and St. Paul) is used for the analysis. Travelers are classified into two groups based on the ratio of perceived and estimated commute travel time. The measures of network structure are estimated using the street network along the identified commute route. T-test comparisons are conducted to identify statistically significant differences in estimated network measures between the two traveler groups. The combined effect of these estimated network measures on travel time is then analyzed using regression models. The results from the t-test and regression analyses confirm the influence of the underlying network structure on the perception of travel time. PMID:24204932

  7. Network structure and travel time perception.

    PubMed

    Parthasarathi, Pavithra; Levinson, David; Hochmair, Hartwig

    2013-01-01

    The purpose of this research is to test the systematic variation in the perception of travel time among travelers and relate the variation to the underlying street network structure. Travel survey data from the Twin Cities metropolitan area (which includes the cities of Minneapolis and St. Paul) is used for the analysis. Travelers are classified into two groups based on the ratio of perceived and estimated commute travel time. The measures of network structure are estimated using the street network along the identified commute route. T-test comparisons are conducted to identify statistically significant differences in estimated network measures between the two traveler groups. The combined effect of these estimated network measures on travel time is then analyzed using regression models. The results from the t-test and regression analyses confirm the influence of the underlying network structure on the perception of travel time.

  8. Temporal network structures controlling disease spreading.

    PubMed

    Holme, Petter

    2016-08-01

    We investigate disease spreading on eight empirical data sets of human contacts (mostly proximity networks recording who is close to whom, at what time). We compare three levels of representations of these data sets: temporal networks, static networks, and a fully connected topology. We notice that the difference between the static and fully connected networks-with respect to time to extinction and average outbreak size-is smaller than between the temporal and static topologies. This suggests that, for these data sets, temporal structures influence disease spreading more than static-network structures. To explain the details in the differences between the representations, we use 32 network measures. This study concurs that long-time temporal structures, like the turnover of nodes and links, are the most important for the spreading dynamics.

  9. Modularity and community structure in networks.

    PubMed

    Newman, M E J

    2006-06-01

    Many networks of interest in the sciences, including social networks, computer networks, and metabolic and regulatory networks, are found to divide naturally into communities or modules. The problem of detecting and characterizing this community structure is one of the outstanding issues in the study of networked systems. One highly effective approach is the optimization of the quality function known as "modularity" over the possible divisions of a network. Here I show that the modularity can be expressed in terms of the eigenvectors of a characteristic matrix for the network, which I call the modularity matrix, and that this expression leads to a spectral algorithm for community detection that returns results of demonstrably higher quality than competing methods in shorter running times. I illustrate the method with applications to several published network data sets.

  10. Modularity and community structure in networks

    PubMed Central

    Newman, M. E. J.

    2006-01-01

    Many networks of interest in the sciences, including social networks, computer networks, and metabolic and regulatory networks, are found to divide naturally into communities or modules. The problem of detecting and characterizing this community structure is one of the outstanding issues in the study of networked systems. One highly effective approach is the optimization of the quality function known as “modularity” over the possible divisions of a network. Here I show that the modularity can be expressed in terms of the eigenvectors of a characteristic matrix for the network, which I call the modularity matrix, and that this expression leads to a spectral algorithm for community detection that returns results of demonstrably higher quality than competing methods in shorter running times. I illustrate the method with applications to several published network data sets. PMID:16723398

  11. Two Keggin-type heteropolytungstates with transition metal as a central atom: Crystal structure and magnetic study with 2D-IR correlation spectroscopy

    SciTech Connect

    Chai, Feng; Chen, YiPing; You, ZhuChai; Xia, ZeMin; Ge, SuZhi; Sun, YanQiong; Huang, BiHua

    2013-06-01

    Two Keggin-type heteropolytungstates, [Co(phen)₃]₃[CoW₁₂O₄₀]·9H₂O 1 (phen=1,10-phenanthroline) and [Fe(phen)₃]₂[FeW₁₂O₄₀]·H₃O·H₂O 2, have been synthesized via the hydrothermal technique and characterized by single crystal X-ray diffraction analyses, IR, XPS, TG analysis, UV–DRS, XRD, thermal-dependent and magnetic-dependent 2D-COS IR (two-dimensional infrared correlation spectroscopy). Crystal structure analysis reveals that the polyanions in compound 1 are linked into 3D supramolecule through hydrogen bonding interactions between lattice water molecules and terminal oxygen atoms of polyanion units, and [Co(phen)₃]²⁺ cations distributed in the polyanion framework with many hydrogen bonding interactions. The XPS spectra indicate that all the Co atoms in 1 are +2 oxidation state, the Fe atoms in 2 existing with +2 and +3 mixed oxidation states. - Graphical abstract: The magnetic-dependent synchronous 2D correlation IR spectra of 1 (a), 2 (b) over 0–50 mT in the range of 600–1000 cm⁻¹, the obvious response indicate two Keggin polyanions skeleton susceptible to applied magnetic field. Highlights: • Two Keggin-type heteropolytungstates with transition metal as a central atom has been obtained. • Compound 1 forms into 3D supramolecular architecture through hydrogen bonding between water molecules and polyanions. • Magnetic-dependent 2D-IR correlation spectroscopy was introduced to discuss the magnetism of polyoxometalate.

  12. Strain-Gated Field Effect Transistor of a MoS2-ZnO 2D-1D Hybrid Structure.

    PubMed

    Chen, Libo; Xue, Fei; Li, Xiaohui; Huang, Xin; Wang, Longfei; Kou, Jinzong; Wang, Zhong Lin

    2016-01-26

    Two-dimensional (2D) molybdenum disulfide (MoS2) is an exciting material due to its unique electrical, optical, and piezoelectric properties. Owing to an intrinsic band gap of 1.2-1.9 eV, monolayer or a-few-layer MoS2 is used for fabricating field effect transistors (FETs) with high electron mobility and on/off ratio. However, the traditional FETs are controlled by an externally supplied gate voltage, which may not be sensitive enough to directly interface with a mechanical stimulus for applications in electronic skin. Here we report a type of top-pressure/force-gated field effect transistors (PGFETs) based on a hybrid structure of a 2D MoS2 flake and 1D ZnO nanowire (NW) array. Once an external pressure is applied, the piezoelectric polarization charges created at the tips of ZnO NWs grown on MoS2 act as a gate voltage to tune/control the source-drain transport property in MoS2. At a 6.25 MPa applied stimulus on a packaged device, the source-drain current can be tuned for ∼25%, equivalent to the results of applying an extra -5 V back gate voltage. Another type of PGFET with a dielectric layer (Al2O3) sandwiched between MoS2 and ZnO also shows consistent results. A theoretical model is proposed to interpret the received data. This study sets the foundation for applying the 2D material-based FETs in the field of artificial intelligence.

  13. Strain-Gated Field Effect Transistor of a MoS2-ZnO 2D-1D Hybrid Structure.

    PubMed

    Chen, Libo; Xue, Fei; Li, Xiaohui; Huang, Xin; Wang, Longfei; Kou, Jinzong; Wang, Zhong Lin

    2016-01-26

    Two-dimensional (2D) molybdenum disulfide (MoS2) is an exciting material due to its unique electrical, optical, and piezoelectric properties. Owing to an intrinsic band gap of 1.2-1.9 eV, monolayer or a-few-layer MoS2 is used for fabricating field effect transistors (FETs) with high electron mobility and on/off ratio. However, the traditional FETs are controlled by an externally supplied gate voltage, which may not be sensitive enough to directly interface with a mechanical stimulus for applications in electronic skin. Here we report a type of top-pressure/force-gated field effect transistors (PGFETs) based on a hybrid structure of a 2D MoS2 flake and 1D ZnO nanowire (NW) array. Once an external pressure is applied, the piezoelectric polarization charges created at the tips of ZnO NWs grown on MoS2 act as a gate voltage to tune/control the source-drain transport property in MoS2. At a 6.25 MPa applied stimulus on a packaged device, the source-drain current can be tuned for ∼25%, equivalent to the results of applying an extra -5 V back gate voltage. Another type of PGFET with a dielectric layer (Al2O3) sandwiched between MoS2 and ZnO also shows consistent results. A theoretical model is proposed to interpret the received data. This study sets the foundation for applying the 2D material-based FETs in the field of artificial intelligence. PMID:26695840

  14. Structural Modeling of Network Systems in Citation Analysis.

    ERIC Educational Resources Information Center

    Yaru, Dang

    1997-01-01

    Describes construction of citation network systems and some subsystems (time sequence network, cocitation network, couple network). Establishes structural modeling of these systems by means of system engineering. Explains and analyzes citation network systems. Includes graphs and charts. (JAK)

  15. An analysis of electrochemical energy storage using electrodes fabricated from atomically thin 2D structures of MoS2, graphene and MoS2/graphene composites

    NASA Astrophysics Data System (ADS)

    Huffstutler, Jacob D.

    The behavior of 2D materials has become of great interest in the wake of development of electrochemical double-layer capacitors (EDLCs) and the discovery of monolayer graphene by Geim and Novoselov. This study aims to analyze the response variance of 2D electrode materials for EDLCs prepared through the liquid-phase exfoliation method when subjected to differing conditions. Once exfoliated, samples are tested with a series of structural characterization methods, including tunneling electron microscopy, atomic force microscopy, Raman spectroscopy, and x-ray photoelectron spectroscopy. A new ionic liquid for EDLC use, 1-butyl-1-methylpyrrolidinium tris(pentafluoroethyl)trifluorophosphate is compared in performance to 6M potassium hydroxide aqueous electrolyte. Devices composed of liquid-phase exfoliated graphene / MoS2 composites are analyzed by concentration for ideal performance. Device performance under cold extreme temperatures for the ionic fluid is presented as well. A brief overview of by-layer analysis of graphene electrode materials is presented as-is. All samples were tested with cyclic voltammetry, galvanostatic charge-discharge, and electrochemical impedance spectroscopy, with good capacitive results. The evolution of electrochemical behavior through the altered parameters is tracked as well.

  16. Crystal structure and antiferromagnetic ordering of quasi-2D [Cu(HF{sub 2})(pyz){sub 2}]TaF{sub 6} (pyz = pyrazine).

    SciTech Connect

    Manson, J. L.; Schlueter, J. A.; McDonald, R. D.; Singleton, J.; Materials Science Division; Eastern Washington Univ.; LANL

    2010-04-01

    The crystal structure of the title compound was determined by X-ray diffraction at 90 and 295 K. Copper(II) ions are coordinated to four bridging pyz ligands to form square layers in the ab-plane. Bridging HF{sub 2}{sup -} ligands join the layers together along the c-axis to afford a tetragonal, three-dimensional (3D) framework that contains Taf{sub 6}{sup -} anions in every cavity. At 295 K, the pyz rings lie exactly perpendicular to the layers and cooling to 90 K induces a canting of those rings. Magnetically, the compound exhibits 2D antiferromagnetic correlations within the 2D layers with an exchange interaction of -13.1(1) K. Weak interlayer interactions, as mediated by Cu-F-H-F-Cu, leads to long-range magnetic order below 4.2 K. Pulsed-field magnetization data at 0.5 K show a concave curvature with increasing B and reveal a saturation magnetization at 35.4 T.

  17. Hyperfine structure and lifetime measurements in the 4s2nd 2D3/2 Rydberg sequence of Ga I by time-resolved laser spectroscopy

    NASA Astrophysics Data System (ADS)

    Liu, Chunqing; Tian, Yanshan; Yu, Qi; Bai, Wanshuang; Wang, Xinghao; Wang, Chong; Dai, Zhenwen

    2016-05-01

    The hyperfine structure (HFS) constants of the 4s2nd 2D3/2 (n=6-18) Rydberg sequence and the 4s26p 2P3/2 level for two isotopes of 69Ga and 71Ga atoms were measured by means of the time-resolved laser-induced fluorescence (TR-LIF) technique and the quantum beat method. The observed hyperfine quantum beat spectra were analyzed and the magnetic-dipole HFS constants A as well as the electric-quadrupole HFS constants B of these levels were obtained by Fourier transform and a program for multiple regression analysis. Also using TR-LIF method radiative lifetimes of the above sequence states were determined at room temperature. The measured lifetime values range from 69 to 2279 ns with uncertainties no more than 10%. To our knowledge, the HFS constants of this Rydberg sequence and the lifetimes of the 4s2nd 2D3/2 (n=10-18) levels are reported for the first time. Good agreement between our results and the previous is achieved.

  18. Global optimization of data quality checks on 2-D and 3-D networks of GPR cross-well tomographic data for automatic correction of unknown well deviations

    SciTech Connect

    Sassen, D. S.; Peterson, J. E.

    2010-03-15

    .g. Bautu et al., 2006). In the technique of algebraic reconstruction tomography (ART), which is used herein for the travel time inversion (Peterson et al., 1985), a small relaxation parameter will smooth imaging artifacts caused by data errors at the expense of resolution and contrast (Figure 2). However, large data errors such as unaccounted well deviations cannot be adequately suppressed through inversion weighting schemes. Previously, problems with tomograms were treated manually. However, in large data sets and/or networks of data sets, trial and error changes to well geometries become increasingly difficult and ineffective. Mislocation of the transmitter and receiver stations of GPR cross-well tomography data sets can lead to serious imaging artifacts if not accounted for prior to inversion. Previously, problems with tomograms have been treated manually prior to inversion. In large data sets and/or networks of tomographic data sets, trial and error changes to well geometries become increasingly difficult and ineffective. Our approach is to use cross-well data quality checks and a simplified model of borehole deviation with particle swarm optimization (PSO) to automatically correct for source and receiver locations prior to tomographic inversion. We present a simple model of well deviation, which is designed to minimize potential corruption of actual data trends. We also provide quantitative quality control measures based on minimizing correlations between take-off angle and apparent velocity, and a quality check on the continuity of velocity between adjacent wells. This methodology is shown to be accurate and robust for simple 2-D synthetic test cases. Plus, we demonstrate the method on actual field data where it is compared to deviation logs. This study shows the promise for automatic correction of well deviations in GPR tomographic data. Analysis of synthetic data shows that very precise estimates of well deviation can be made for small deviations, even in the

  19. Information transfer in community structured multiplex networks

    NASA Astrophysics Data System (ADS)

    Solé Ribalta, Albert; Granell, Clara; Gómez, Sergio; Arenas, Alex

    2015-08-01

    The study of complex networks that account for different types of interactions has become a subject of interest in the last few years, specially because its representational power in the description of users interactions in diverse online social platforms (Facebook, Twitter, Instagram, etc.). The mathematical description of these interacting networks has been coined under the name of multilayer networks, where each layer accounts for a type of interaction. It has been shown that diffusive processes on top of these networks present a phenomenology that cannot be explained by the naive superposition of single layer diffusive phenomena but require the whole structure of interconnected layers. Nevertheless, the description of diffusive phenomena on multilayer networks has obviated the fact that social networks have strong mesoscopic structure represented by different communities of individuals driven by common interests, or any other social aspect. In this work, we study the transfer of information in multilayer networks with community structure. The final goal is to understand and quantify, if the existence of well-defined community structure at the level of individual layers, together with the multilayer structure of the whole network, enhances or deteriorates the diffusion of packets of information.

  20. Network Ecology and Adolescent Social Structure

    PubMed Central

    McFarland, Daniel A.; Moody, James; Diehl, David; Smith, Jeffrey A.; Thomas, Reuben J.

    2014-01-01

    Adolescent societies—whether arising from weak, short-term classroom friendships or from close, long-term friendships—exhibit various levels of network clustering, segregation, and hierarchy. Some are rank-ordered caste systems and others are flat, cliquish worlds. Explaining the source of such structural variation remains a challenge, however, because global network features are generally treated as the agglomeration of micro-level tie-formation mechanisms, namely balance, homophily, and dominance. How do the same micro-mechanisms generate significant variation in global network structures? To answer this question we propose and test a network ecological theory that specifies the ways features of organizational environments moderate the expression of tie-formation processes, thereby generating variability in global network structures across settings. We develop this argument using longitudinal friendship data on schools (Add Health study) and classrooms (Classroom Engagement study), and by extending exponential random graph models to the study of multiple societies over time. PMID:25535409

  1. Temporal network structures controlling disease spreading

    NASA Astrophysics Data System (ADS)

    Holme, Petter

    2016-08-01

    We investigate disease spreading on eight empirical data sets of human contacts (mostly proximity networks recording who is close to whom, at what time). We compare three levels of representations of these data sets: temporal networks, static networks, and a fully connected topology. We notice that the difference between the static and fully connected networks—with respect to time to extinction and average outbreak size—is smaller than between the temporal and static topologies. This suggests that, for these data sets, temporal structures influence disease spreading more than static-network structures. To explain the details in the differences between the representations, we use 32 network measures. This study concurs that long-time temporal structures, like the turnover of nodes and links, are the most important for the spreading dynamics.

  2. Exploiting Recurring Structure in a Semantic Network

    NASA Technical Reports Server (NTRS)

    Wolfe, Shawn R.; Keller, Richard M.

    2004-01-01

    With the growing popularity of the Semantic Web, an increasing amount of information is becoming available in machine interpretable, semantically structured networks. Within these semantic networks are recurring structures that could be mined by existing or novel knowledge discovery methods. The mining of these semantic structures represents an interesting area that focuses on mining both for and from the Semantic Web, with surprising applicability to problems confronting the developers of Semantic Web applications. In this paper, we present representative examples of recurring structures and show how these structures could be used to increase the utility of a semantic repository deployed at NASA.

  3. Aniso2D

    2005-07-01

    Aniso2d is a two-dimensional seismic forward modeling code. The earth is parameterized by an X-Z plane in which the seismic properties Can have monoclinic with x-z plane symmetry. The program uses a user define time-domain wavelet to produce synthetic seismograms anrwhere within the two-dimensional media.

  4. Towards 2D nanocomposites

    NASA Astrophysics Data System (ADS)

    Jang, Hyun-Sook; Yu, Changqian; Hayes, Robert; Granick, Steve

    2015-03-01

    Polymer vesicles (``polymersomes'') are an intriguing class of soft materials, commonly used to encapsulate small molecules or particles. Here we reveal they can also effectively incorporate nanoparticles inside their polymer membrane, leading to novel ``2D nanocomposites.'' The embedded nanoparticles alter the capacity of the polymersomes to bend and to stretch upon external stimuli.

  5. Cellulose Structural Polymorphism in Plant Primary Cell Walls Investigated by High-Field 2D Solid-State NMR Spectroscopy and Density Functional Theory Calculations.

    PubMed

    Wang, Tuo; Yang, Hui; Kubicki, James D; Hong, Mei

    2016-06-13

    The native cellulose of bacterial, algal, and animal origins has been well studied structurally using X-ray and neutron diffraction and solid-state NMR spectroscopy, and is known to consist of varying proportions of two allomorphs, Iα and Iβ, which differ in hydrogen bonding, chain packing, and local conformation. In comparison, cellulose structure in plant primary cell walls is much less understood because plant cellulose has lower crystallinity and extensive interactions with matrix polysaccharides. Here we have combined two-dimensional magic-angle-spinning (MAS) solid-state nuclear magnetic resonance (solid-state NMR) spectroscopy at high magnetic fields with density functional theory (DFT) calculations to obtain detailed information about the structural polymorphism and spatial distributions of plant primary-wall cellulose. 2D (13)C-(13)C correlation spectra of uniformly (13)C-labeled cell walls of several model plants resolved seven sets of cellulose chemical shifts. Among these, five sets (denoted a-e) belong to cellulose in the interior of the microfibril while two sets (f and g) can be assigned to surface cellulose. Importantly, most of the interior cellulose (13)C chemical shifts differ significantly from the (13)C chemical shifts of the Iα and Iβ allomorphs, indicating that plant primary-wall cellulose has different conformations, packing, and hydrogen bonding from celluloses of other organisms. 2D (13)C-(13)C correlation experiments with long mixing times and with water polarization transfer revealed the spatial distributions and matrix-polysaccharide interactions of these cellulose structures. Celluloses f and g are well mixed chains on the microfibril surface, celluloses a and b are interior chains that are in molecular contact with the surface chains, while cellulose c resides in the core of the microfibril, outside spin diffusion contact with the surface. Interestingly, cellulose d, whose chemical shifts differ most significantly from those of

  6. Cellulose Structural Polymorphism in Plant Primary Cell Walls Investigated by High-Field 2D Solid-State NMR Spectroscopy and Density Functional Theory Calculations.

    PubMed

    Wang, Tuo; Yang, Hui; Kubicki, James D; Hong, Mei

    2016-06-13

    The native cellulose of bacterial, algal, and animal origins has been well studied structurally using X-ray and neutron diffraction and solid-state NMR spectroscopy, and is known to consist of varying proportions of two allomorphs, Iα and Iβ, which differ in hydrogen bonding, chain packing, and local conformation. In comparison, cellulose structure in plant primary cell walls is much less understood because plant cellulose has lower crystallinity and extensive interactions with matrix polysaccharides. Here we have combined two-dimensional magic-angle-spinning (MAS) solid-state nuclear magnetic resonance (solid-state NMR) spectroscopy at high magnetic fields with density functional theory (DFT) calculations to obtain detailed information about the structural polymorphism and spatial distributions of plant primary-wall cellulose. 2D (13)C-(13)C correlation spectra of uniformly (13)C-labeled cell walls of several model plants resolved seven sets of cellulose chemical shifts. Among these, five sets (denoted a-e) belong to cellulose in the interior of the microfibril while two sets (f and g) can be assigned to surface cellulose. Importantly, most of the interior cellulose (13)C chemical shifts differ significantly from the (13)C chemical shifts of the Iα and Iβ allomorphs, indicating that plant primary-wall cellulose has different conformations, packing, and hydrogen bonding from celluloses of other organisms. 2D (13)C-(13)C correlation experiments with long mixing times and with water polarization transfer revealed the spatial distributions and matrix-polysaccharide interactions of these cellulose structures. Celluloses f and g are well mixed chains on the microfibril surface, celluloses a and b are interior chains that are in molecular contact with the surface chains, while cellulose c resides in the core of the microfibril, outside spin diffusion contact with the surface. Interestingly, cellulose d, whose chemical shifts differ most significantly from those of

  7. Structural requirements of 3-carboxyl-4(1H)-quinolones as potential antimalarials from 2D and 3D QSAR analysis.

    PubMed

    Li, Jiazhong; Li, Shuyan; Bai, Chongliang; Liu, Huanxiang; Gramatica, Paola

    2013-07-01

    Malaria is a fatal tropical and subtropical disease caused by the protozoal species Plasmodium. Many commonly available antimalarial drugs and therapies are becoming ineffective because of the emergence of multidrug resistant Plasmodium falciparum, which drives the need for the development of new antimalarial drugs. Recently, a series of 3-carboxyl-4(1H)-quinolone analogs, derived from the famous compound endochin, were reported as promising candidates for orally efficacious antimalarials. In this study, to analyze the structure-activity relationships (SAR) of these quinolones and investigate the structural requirements for antimalarial activity, the 2D multiple linear regressions (MLR) method and 3D comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods are employed to evolve different QSAR models. All these models give satisfactory results with highly accurate fitting and strong external predictive abilities for chemicals not used in model development. Furthermore, the contour maps from 3D models can provide an intuitive understanding of the key structure features responsible for the antimalarial activities. In conclusion, we summarize the detailed position-specific structural requirements of these derivatives accordingly. All these results are helpful for the rational design of new compounds with higher antimalarial bioactivities.

  8. Investigation of 2D photonic crystal structure based channel drop filter using quad shaped photonic crystal ring resonator for CWDM system

    NASA Astrophysics Data System (ADS)

    Chhipa, Mayur Kumar; Dusad, Lalit Kumar

    2016-05-01

    In this paper, the design & performance of two dimensional (2-D) photonic crystal structure based channel drop filter is investigated using quad shaped photonic crystal ring resonator. In this paper, Photonic Crystal (PhC) based on square lattice periodic arrays of Gallium Indium Phosphide (GaInP) rods in air structure have been investigated using Finite Difference Time Domain (FDTD) method and photonic band gap is being calculated using Plane Wave Expansion (PWE) method. The PhC designs have been optimized for telecommunication wavelength λ= 1571 nm by varying the rods lattice constant. The number of rods in Z and X directions is 21 and 20, with lattice constant 0.540 nm it illustrates that the arrangement of Gallium Indium Phosphide (GaInP) rods in the structure which gives the overall size of the device around 11.4 µm × 10.8 µm. The designed filter gives good dropping efficiency using 3.298, refractive index. The designed structure is useful for CWDM systems. This device may serve as a key component in photonic integrated circuits. The device is ultra compact with the overall size around 123 µm2.

  9. Network models of soil porous structure

    NASA Astrophysics Data System (ADS)

    Samec, M.; Santiago, A.; Cardenas, J. P.; Benito, R. M.; Tarquis, A. M.; Mooney, S. J.; Korošak, D.

    2010-05-01

    Soils sustain life on Earth. In times of increasing anthropogenic demands on soils [1] there is growing need to seek for novel approaches to understand the relationships between the soil porous structure and specific soil functions. Recently [2-4], soil pore structure was described as a complex network of pores using spatially embedded varying fitness network model [2] or heterogeneous preferential attachment scheme [3-4], both approaches revealing the apparent scale-free topology of soils. Here, we show, using a large set of soil images of structures obtained by X-ray computed tomography that both methods predict topological similar networks of soil pore structures. Furthermore, by analyzing the node-node link correlation properties of the obtained networks we suggest an approach to quantify the complexity of soil pore structure. [1] R. Lal, Soil science and the carbon civilization, Soil Sci. Soc. Am. J., 71: 1425-1437, 2007. [2] S. J. Mooney, D. Korošak, Using Complex Networks to Model Two- and Three-Dimensional Soil Porous Architecture, Soil Sci. Soc. Am. J., 73: 1094-1100, 2009. [3] A. Santiago, J. P. Cardenas, J. C. Losada, R. M. Benito, A. M. Tarquis, F. Borondo, Multiscaling of porous soils as heterogeneous complex networks, Nonlin. Proc. Geophys., 15: 893-902, 2008. [4] A. Santiago, R. M. Benito, An extended formalism for preferential attachment in heterogeneous complex networks, Eur. Phys. Lett., 82: 58004, 2008.

  10. Two-dimensional topological insulator molecular networks: dependence on structure, symmetry, and composition

    NASA Astrophysics Data System (ADS)

    Tan, Liang Z.; Louie, Steven G.

    2014-03-01

    2D molecular networks can be fabricated from a wide variety of molecular building blocks, arranged in many different configurations. Interactions between neighboring molecular building blocks result in the formation of new 2D materials. Examples of 2D organic topological insulators, that contain molecular building blocks and heavy elements arranged in a hexagonal lattice, have been recently proposed by Feng Liu and coworkers (Nano Lett., 13, 2842 (2013)). In this work, we present a systematic study of the design space of 2D molecular network topological insulators, elucidating the role of structure, symmetry, and composition of the networks. We show that the magnitude and presence of spin-orbit gaps in the electronic band structure is strongly dependent on the symmetry properties and arrangement of the individual components of the molecular lattice. We present general rules to maximize the magnitude of spin-orbit gaps and perform ab-initio calculations on promising structures derived from these guidelines. This work was supported by National Science Foundation Grant No. DMR10-1006184, the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Computational resources have been provided by the NSF through XSEDE resources at NICS.

  11. Nonparametric inference of network structure and dynamics

    NASA Astrophysics Data System (ADS)

    Peixoto, Tiago P.

    The network structure of complex systems determine their function and serve as evidence for the evolutionary mechanisms that lie behind them. Despite considerable effort in recent years, it remains an open challenge to formulate general descriptions of the large-scale structure of network systems, and how to reliably extract such information from data. Although many approaches have been proposed, few methods attempt to gauge the statistical significance of the uncovered structures, and hence the majority cannot reliably separate actual structure from stochastic fluctuations. Due to the sheer size and high-dimensionality of many networks, this represents a major limitation that prevents meaningful interpretations of the results obtained with such nonstatistical methods. In this talk, I will show how these issues can be tackled in a principled and efficient fashion by formulating appropriate generative models of network structure that can have their parameters inferred from data. By employing a Bayesian description of such models, the inference can be performed in a nonparametric fashion, that does not require any a priori knowledge or ad hoc assumptions about the data. I will show how this approach can be used to perform model comparison, and how hierarchical models yield the most appropriate trade-off between model complexity and quality of fit based on the statistical evidence present in the data. I will also show how this general approach can be elegantly extended to networks with edge attributes, that are embedded in latent spaces, and that change in time. The latter is obtained via a fully dynamic generative network model, based on arbitrary-order Markov chains, that can also be inferred in a nonparametric fashion. Throughout the talk I will illustrate the application of the methods with many empirical networks such as the internet at the autonomous systems level, the global airport network, the network of actors and films, social networks, citations among

  12. Edge direction and the structure of networks.

    PubMed

    Foster, Jacob G; Foster, David V; Grassberger, Peter; Paczuski, Maya

    2010-06-15

    Directed networks are ubiquitous and are necessary to represent complex systems with asymmetric interactions--from food webs to the World Wide Web. Despite the importance of edge direction for detecting local and community structure, it has been disregarded in studying a basic type of global diversity in networks: the tendency of nodes with similar numbers of edges to connect. This tendency, called assortativity, affects crucial structural and dynamic properties of real-world networks, such as error tolerance or epidemic spreading. Here we demonstrate that edge direction has profound effects on assortativity. We define a set of four directed assortativity measures and assign statistical significance by comparison to randomized networks. We apply these measures to three network classes--online/social networks, food webs, and word-adjacency networks. Our measures (i) reveal patterns common to each class, (ii) separate networks that have been previously classified together, and (iii) expose limitations of several existing theoretical models. We reject the standard classification of directed networks as purely assortative or disassortative. Many display a class-specific mixture, likely reflecting functional or historical constraints, contingencies, and forces guiding the system's evolution. PMID:20505119

  13. Edge direction and the structure of networks.

    PubMed

    Foster, Jacob G; Foster, David V; Grassberger, Peter; Paczuski, Maya

    2010-06-15

    Directed networks are ubiquitous and are necessary to represent complex systems with asymmetric interactions--from food webs to the World Wide Web. Despite the importance of edge direction for detecting local and community structure, it has been disregarded in studying a basic type of global diversity in networks: the tendency of nodes with similar numbers of edges to connect. This tendency, called assortativity, affects crucial structural and dynamic properties of real-world networks, such as error tolerance or epidemic spreading. Here we demonstrate that edge direction has profound effects on assortativity. We define a set of four directed assortativity measures and assign statistical significance by comparison to randomized networks. We apply these measures to three network classes--online/social networks, food webs, and word-adjacency networks. Our measures (i) reveal patterns common to each class, (ii) separate networks that have been previously classified together, and (iii) expose limitations of several existing theoretical models. We reject the standard classification of directed networks as purely assortative or disassortative. Many display a class-specific mixture, likely reflecting functional or historical constraints, contingencies, and forces guiding the system's evolution.

  14. Five inorganic–organic hybrids based on Keggin polyanion [SiMo{sub 12}O{sub 40}]{sup 4−}: From 0D to 2D network

    SciTech Connect

    Yu, Xiao-Yang; Cui, Xiao-Bing; Lu, Jing; Luo, Yu-Hui; Zhang, Hong; Gao, Wei-Ping

    2014-01-15

    Five new inorganic–organic hybrids based on 4,4′-bipyridine and Keggin-type polyoxometalate [SiMo{sub 12}O{sub 40}]{sup 4−}, (SiMo{sub 12}O{sub 40})(H{sub 2}bipy){sub 2}·2H{sub 2}O (1), [Cu(Hbipy){sub 4}(HSiMo{sub 12}O{sub 40})(SiMo{sub 12}O{sub 40})](H{sub 2}bipy){sub 0.5}·7H{sub 2}O (2), [Cu{sub 2}(Hbipy){sub 6}(bipy)(SiMo{sub 12}O{sub 40}){sub 3}](Hbipy){sub 2}·6H{sub 2}O (3), [Cu(bipy){sub 2}(SiMo{sub 12}O{sub 40})](H{sub 2}bipy)·2H{sub 2}O (4) and [Cu{sub 2}(bipy){sub 4}(H{sub 2}O){sub 4}](SiMo{sub 12}O{sub 40})·13H{sub 2}O (5) (bipy=4,4′-bipyridine), have been hydrothermally synthesized. 1 consists of H{sub 2}bipy{sup 2+} and [SiMo{sub 12}O{sub 40}]{sup 4−} units. In 2, two [SiMo{sub 12}O{sub 40}]{sup 4−} are bridged by [Cu(Hbipy){sub 4}]{sup 6+} to form a [Cu(Hbipy){sub 4}(SiMo{sub 12}O{sub 40}){sub 2}]{sup 2−} dimmer. In 3, [SiMo{sub 12}O{sub 40}]{sup 4−} polyanions acting as bidentated bridging ligands and monodentated auxiliary ligands connect [Cu{sub 2}(Hbipy){sub 6}(bipy)]{sup 8+} units into a 1D zigzag chain. In 4, [SiMo{sub 12}O{sub 40}]{sup 4−} polyanions bridge neighboring 1D [Cu(bipy){sub 2}]{sup 2+} double chains into a 2D extended layer. In 5, [SiMo{sub 12}O{sub 40}]{sup 4−} polyanions acting as templates site alternately upon the grids from both sides of the square grid [Cu{sub 2}(bipy){sub 4}(H{sub 2}O){sub 4}]{sup 4+} layer. In addition, the electrochemical behaviors of 1, 3 and 4 and the photocatalysis property of 1 have been investigated. - Graphical abstract: Five new compounds based on [SiMo{sub 12}O{sub 40}]{sup 4−} have been successfully generated. [SiMo{sub 12}O{sub 40}]{sup 4−} anions play different roles in the structures of the five compounds. Display Omitted - Highlights: • Five new compounds based on [SiMo{sub 12}O{sub 40}]{sup 4−} have been generated. • [SiMo{sub 12}O{sub 40}]{sup 4−} anions play different roles in the five structures. • The electrochemical behaviors of 1, 3 and 4 have been

  15. The structure and dynamics of multilayer networks

    NASA Astrophysics Data System (ADS)

    Boccaletti, S.; Bianconi, G.; Criado, R.; del Genio, C. I.; Gómez-Gardeñes, J.; Romance, M.; Sendiña-Nadal, I.; Wang, Z.; Zanin, M.

    2014-11-01

    In the past years, network theory has successfully characterized the interaction among the constituents of a variety of complex systems, ranging from biological to technological, and social systems. However, up until recently, attention was almost exclusively given to networks in which all components were treated on equivalent footing, while neglecting all the extra information about the temporal- or context-related properties of the interactions under study. Only in the last years, taking advantage of the enhanced resolution in real data sets, network scientists have directed their interest to the multiplex character of real-world systems, and explicitly considered the time-varying and multilayer nature of networks. We offer here a comprehensive review on both structural and dynamical organization of graphs made of diverse relationships (layers) between its constituents, and cover several relevant issues, from a full redefinition of the basic structural measures, to understanding how the multilayer nature of the network affects processes and dynamics.

  16. Detection of multi-scale secondary flow structures using anisotropic 2D Ricker wavelets in a bent tube model for curved arteries

    NASA Astrophysics Data System (ADS)

    Plesniak, Daniel H.; Bulusu, Kartik V.; Plesniak, Michael W.

    2012-11-01

    Interpretation of complex flow patterns observed in this study of a model curved artery required characterization of multiple, low-circulation secondary flow structures that were observed during the late systolic deceleration and diastolic phases under physiological inflow conditions. Phase-locked, planar vorticity PIV data were acquired at various cross-sectional locations of the 180-degree bent tube model. High circulation, deformed Dean- and Lyne-type vortices were observed during early stages of deceleration, while several smaller scale, highly deformed, low-circulation vortical patterns appeared in the core and near-wall regions during late systolic deceleration and diastolic phases. Due to the multiplicity of vortical scales and shapes, anisotropic 2D Ricker wavelets were used for coherent structure detection in a continuous wavelet transform algorithm (PIVlet 1.2). Our bio-inspired study is geared towards understanding whether optimizing the shape of the wavelet kernel will enable better resolution of several low-circulation, multi-scale secondary flow morphologies and whether new insights into the dynamics of arterial secondary flow structures can accordingly be gained. Supported by the National Science Foundation, Grant No. CBET-0828903 and GW Center for Biomimetics and Bioinspired Engineering (COBRE).

  17. Evaluating the structural identifiability of the parameters of the EBPR sub-model in ASM2d by the differential algebra method.

    PubMed

    Zhang, Tian; Zhang, Daijun; Li, Zhenliang; Cai, Qing

    2010-05-01

    The calibration of ASMs is a prerequisite for their application to simulation of a wastewater treatment plant. This work should be made based on the evaluation of structural identifiability of model parameters. An EBPR sub-model including denitrification phosphorus removal has been incorporated in ASM2d. Yet no report is presented on the structural identifiability of the parameters in the EBPR sub-model. In this paper, the differential algebra approach was used to address this issue. The results showed that the structural identifiability of parameters in the EBPR sub-model could be improved by increasing the measured variables. The reduction factor eta(NO)(3) was identifiable when combined data of aerobic process and anoxic process were assumed. For K(PP), X(PAO) and q(PHA) of the anaerobic process to be uniquely identifiable, one of them is needed to be determined by other ways. Likewise, if prior information on one of the parameters, K(PHA), X(PAO) and q(PP) of the aerobic process, is known, all the parameters are identifiable. The above results could be of interest to the parameter estimation of the EBPR sub-model. The algorithm proposed in the paper is also suitable for other sub-models of ASMs.

  18. 2D magnetotelluric imaging of the Anqing-Guichi ore district, Yangtze metallogenic belt, eastern China: An insight into the crustal structure and tectonic units

    NASA Astrophysics Data System (ADS)

    Chen, Xiangbin; Yan, Jiayong

    2016-08-01

    Two parallel NW-trending magnetotelluric (MT) profiles were placed perpendicularly to the main structures of the Anqing-Guichi ore district, one of the seven ore districts in the middle-lower Yangtze River metallogenic belt of eastern China. In October-December 2013, the MT data acquisition was carried out at 117 sites with 0.5-1 km site spacing. The MT data has a good quality in the frequency range between 320 and 0.01 Hz. The dimensionality analysis and 2D resistivity inversion results indicate that: (1) the deep of the ore district with three-dimensional structural characteristics, but two-dimensional structural characteristics for shallow; (2) there is a clear correlation between resistivity and the main geological units of the ore district, as well as correlation with mapped surface faults; (3) the Gandan deep fault (GDF) and Jiangnan deep fault (JNF) extend from the surface to 10 km deep, with dip of NW45°, and dip angles larger than 60°. A series of NE-trending acidic intrusive rocks were controlled by the GDF.

  19. Structure of entangled polymer network from primitive chain network simulations

    NASA Astrophysics Data System (ADS)

    Masubuchi, Yuichi; Uneyama, Takashi; Watanabe, Hiroshi; Ianniruberto, Giovanni; Greco, Francesco; Marrucci, Giuseppe

    2010-04-01

    The primitive chain network (PCN) model successfully employed to simulate the rheology of entangled polymers is here tested versus less coarse-grained (lattice or atomistic) models for what concerns the structure of the network at equilibrium (i.e., in the absence of flow). By network structure, we mean the distributions of some relevant quantities such as subchain length in space or in monomer number. Indeed, lattice and atomistic simulations are obviously more accurate, but are also more difficult to use in nonequilibrium flow situations, especially for long entangled polymers. Conversely, the coarse-grained PCN model that deals more easily with rheology lacks, strictly speaking, a rigorous foundation. It is therefore important to verify whether or not the equilibrium structure of the network predicted by the PCN model is consistent with the results recently obtained by using lattice and atomistic simulations. In this work, we focus on single chain properties of the entangled network. Considering the significant differences in modeling the polymer molecules, the results here obtained appear encouraging, thus providing a more solid foundation to Brownian simulations based on the PCN model. Comparison with the existing theories also proves favorable.

  20. Structural measures for multiplex networks

    NASA Astrophysics Data System (ADS)

    Battiston, Federico; Nicosia, Vincenzo; Latora, Vito

    2014-03-01

    Many real-world complex systems consist of a set of elementary units connected by relationships of different kinds. All such systems are better described in terms of multiplex networks, where the links at each layer represent a different type of interaction between the same set of nodes rather than in terms of (single-layer) networks. In this paper we present a general framework to describe and study multiplex networks, whose links are either unweighted or weighted. In particular, we propose a series of measures to characterize the multiplexicity of the systems in terms of (i) basic node and link properties such as the node degree, and the edge overlap and reinforcement, (ii) local properties such as the clustering coefficient and the transitivity, and (iii) global properties related to the navigability of the multiplex across the different layers. The measures we introduce are validated on a genuinely multiplex data set of Indonesian terrorists, where information among 78 individuals are recorded with respect to mutual trust, common operations, exchanged communications, and business relationships.

  1. Structural measures for multiplex networks.

    PubMed

    Battiston, Federico; Nicosia, Vincenzo; Latora, Vito

    2014-03-01

    Many real-world complex systems consist of a set of elementary units connected by relationships of different kinds. All such systems are better described in terms of multiplex networks, where the links at each layer represent a different type of interaction between the same set of nodes rather than in terms of (single-layer) networks. In this paper we present a general framework to describe and study multiplex networks, whose links are either unweighted or weighted. In particular, we propose a series of measures to characterize the multiplexicity of the systems in terms of (i) basic node and link properties such as the node degree, and the edge overlap and reinforcement, (ii) local properties such as the clustering coefficient and the transitivity, and (iii) global properties related to the navigability of the multiplex across the different layers. The measures we introduce are validated on a genuinely multiplex data set of Indonesian terrorists, where information among 78 individuals are recorded with respect to mutual trust, common operations, exchanged communications, and business relationships.

  2. Bifurcation structure of the special class of nonstationary regimes emerging in the 2D inertially coupled, unit-cell model: Analytical study

    NASA Astrophysics Data System (ADS)

    Vorotnikov, K.; Starosvetsky, Y.

    2016-09-01

    Present work is devoted to the analytical investigation of the bifurcation structure of special class of nonstationary low-energy regimes emerging in the locally resonant unit-cell model. System under consideration comprises an outer mass with internal rotator and subject to the 2D, nonlinear local potential. These regimes are characterized by the slow, purely rotational motion of the rotator synchronized with the periodic energy beats between the axial and the lateral vibrations of the outer element. Thus the angular speed of the rotator and the beating frequency of the outer element satisfy the 1:2 resonance condition. In the present study these regimes are referred to as regimes of synchronous nonlinear beats (RSNB). Using the regular muti-scale analysis in the limit of low energy excitation we derive the slow-flow model. To showcase the evolution of RSNBs we used the special Poincaré map technique applied on the slow-flow model. Results of the Poincaré sections unveiled some interesting local bifurcations undergone by these regimes. Further analysis of the slow-flow model enabled us to describe the RSNBs analytically as well as exposed their entire bifurcation structure. The bifurcation analysis has shown the coexistence of several branches of RSNBs corresponding to the regimes of weak and strong, two-dimensional, recurrent energy channeling. We substantiate the results of the analytical study with numerical simulations of the full model and find them to be in the very good agreement.

  3. Efficacy of very fast simulated annealing global optimization method for interpretation of self-potential anomaly by different forward formulation over 2D inclined sheet type structure

    NASA Astrophysics Data System (ADS)

    Biswas, A.; Sharma, S. P.

    2012-12-01

    best result without any ambiguity and smaller uncertainty. Keywords: SP anomaly, inclined sheet, 2D structure, forward problems, VFSA Optimization,

  4. Basement and Basin Structures of the Northwest Paraná Basin, Brazil: Illuminated by Matched-Filter Analysis and 2D Modeling of Gravity and Magnetic Data

    NASA Astrophysics Data System (ADS)

    Curto, J. B.; Blakely, R. J.; Vidotti, R. M.; Fuck, R. A.

    2015-12-01

    The South American Platform includes two major geological components with common structural roots: the Transbrasiliano Lineament (LTB) and the Paraná Basin. Important relationships between the two components occur within the northwest Paraná Basin and concealed beneath sedimentary cover. We integrated all available airborne magnetic and gravity surveys and ground-based gravity data to produce consistent, digital magnetic and Bouguer anomaly maps. Data-processing and modeling techniques then were used in order to reveal principal crustal compartments and basin-basement structures at various depths. Three large magnetic discontinuities delineate crustal compartments in the area with N30°E, N60°E, and N70°E strike, from east to west, respectively. These magnetic lineaments bound regions with distinct gravity anomaly character. Robust matched-filter analysis applied to magnetic and gravity data yielded important depth estimates: (i) 2.5 km to the top of the Paraná Basin Neoproterozoic basement; (ii) 4-6 km to the top of a second group of basement units; (iii) 20 km, possibly associated with the upper-lower crust interface; and (iv) 33-39 and 43 km related to crustal thicknesses west and southeast of a major N30°E trending lineament, respectively. The 2D joint modeling of gravity and magnetic data sheds light on the asymmetric geometry of the basement beneath the Paraná basin, with at least three half-grabens formed by LTB reactivated structures. The central region of the study area is characterized by thinner crust and higher crustal weakness, where important structures have developed in the Mesozoic, including NW trending reactivations, linked to crustal uplift and evolution of small NE-aligned Cretaceous basins. Important depocenters occur to the north and east of the study area, with N70ºE and N30°E - NS strike, respectively.

  5. 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

  6. A Topological Perspective of Neural Network Structure

    NASA Astrophysics Data System (ADS)

    Sizemore, Ann; Giusti, Chad; Cieslak, Matthew; Grafton, Scott; Bassett, Danielle

    The wiring patterns of white matter tracts between brain regions inform functional capabilities of the neural network. Indeed, densely connected and cyclically arranged cognitive systems may communicate and thus perform distinctly. However, previously employed graph theoretical statistics are local in nature and thus insensitive to such global structure. Here we present an investigation of the structural neural network in eight healthy individuals using persistent homology. An extension of homology to weighted networks, persistent homology records both circuits and cliques (all-to-all connected subgraphs) through a repetitive thresholding process, thus perceiving structural motifs. We report structural features found across patients and discuss brain regions responsible for these patterns, finally considering the implications of such motifs in relation to cognitive function.

  7. Fast motif-network scheme for extensive exploration of complex crystal structures in silicate cathodes

    NASA Astrophysics Data System (ADS)

    Ho, Kai-Ming; Zhao, Xin; Wu, Shunqing; Lv, Xiaobao; Nguyen, Manh Cuong; Wang, Cai-Zhuang; Lin, Zijing; Zhu, Zi-Zhong

    2015-03-01

    A motif-network search scheme is proposed to study the crystal structures of the dilithium/disodium transition metal orthosilicates A2MSiO4. Using this fast and efficient method, the structures of all six combinations with A = Li or Na and M = Mn, Fe or Co were extensively explored in this work. In addition to finding all previously reported experimental structures, we discover many other different crystal structures which are highly degenerate in energy. These tetrahedral-network-based structures can be classified into 1D, 2D and 3D types. A clear trend of the structural preference in different systems is revealed and possible indicators that affect the structure stabilities are introduced. For the case of Na systems which have been much less investigated in the literature relative to the Li systems, we predicted their ground state structures and found evidence for the existence of new structural motifs.

  8. Exploration of tetrahedral structures in silicate cathodes using a motif-network scheme

    NASA Astrophysics Data System (ADS)

    Zhao, Xin; Wu, Shunqing; Lv, Xiaobao; Nguyen, Manh Cuong; Wang, Cai-Zhuang; Lin, Zijing; Zhu, Zi-Zhong; Ho, Kai-Ming

    2015-10-01

    Using a motif-network search scheme, we studied the tetrahedral structures of the dilithium/disodium transition metal orthosilicates A2MSiO4 with A = Li or Na and M = Mn, Fe or Co. In addition to finding all previously reported structures, we discovered many other different tetrahedral-network-based crystal structures which are highly degenerate in energy. These structures can be classified into structures with 1D, 2D and 3D M-Si-O frameworks. A clear trend of the structural preference in different systems was revealed and possible indicators that affect the structure stabilities were introduced. For the case of Na systems which have been much less investigated in the literature relative to the Li systems, we predicted their ground state structures and found evidence for the existence of new structural motifs.

  9. Exploration of tetrahedral structures in silicate cathodes using a motif-network scheme

    SciTech Connect

    Zhao, Xin; Wu, Shunqing; Lv, Xiaobao; Nguyen, Manh Cuong; Wang, Cai -Zhuang; Lin, Zijing; Zhu, Zi -Zhong; Ho, Kai -Ming

    2015-10-26

    Using a motif-network search scheme, we studied the tetrahedral structures of the dilithium/disodium transition metal orthosilicates A2MSiO4 with A = Li or Na and M = Mn, Fe or Co. In addition to finding all previously reported structures, we discovered many other different tetrahedral-network-based crystal structures which are highly degenerate in energy. In addition, these structures can be classified into structures with 1D, 2D and 3D M-Si-O frameworks. A clear trend of the structural preference in different systems was revealed and possible indicators that affect the structure stabilities were introduced. For the case of Na systems which have been much less investigated in the literature relative to the Li systems, we predicted their ground state structures and found evidence for the existence of new structural motifs.

  10. Exploration of tetrahedral structures in silicate cathodes using a motif-network scheme

    PubMed Central

    Zhao, Xin; Wu, Shunqing; Lv, Xiaobao; Nguyen, Manh Cuong; Wang, Cai-Zhuang; Lin, Zijing; Zhu, Zi-Zhong; Ho, Kai-Ming

    2015-01-01

    Using a motif-network search scheme, we studied the tetrahedral structures of the dilithium/disodium transition metal orthosilicates A2MSiO4 with A = Li or Na and M = Mn, Fe or Co. In addition to finding all previously reported structures, we discovered many other different tetrahedral-network-based crystal structures which are highly degenerate in energy. These structures can be classified into structures with 1D, 2D and 3D M-Si-O frameworks. A clear trend of the structural preference in different systems was revealed and possible indicators that affect the structure stabilities were introduced. For the case of Na systems which have been much less investigated in the literature relative to the Li systems, we predicted their ground state structures and found evidence for the existence of new structural motifs. PMID:26497381

  11. Exploration of tetrahedral structures in silicate cathodes using a motif-network scheme

    DOE PAGES

    Zhao, Xin; Wu, Shunqing; Lv, Xiaobao; Nguyen, Manh Cuong; Wang, Cai -Zhuang; Lin, Zijing; Zhu, Zi -Zhong; Ho, Kai -Ming

    2015-10-26

    Using a motif-network search scheme, we studied the tetrahedral structures of the dilithium/disodium transition metal orthosilicates A2MSiO4 with A = Li or Na and M = Mn, Fe or Co. In addition to finding all previously reported structures, we discovered many other different tetrahedral-network-based crystal structures which are highly degenerate in energy. In addition, these structures can be classified into structures with 1D, 2D and 3D M-Si-O frameworks. A clear trend of the structural preference in different systems was revealed and possible indicators that affect the structure stabilities were introduced. For the case of Na systems which have been muchmore » less investigated in the literature relative to the Li systems, we predicted their ground state structures and found evidence for the existence of new structural motifs.« less

  12. Effect of strong phonon-phonon coupling on the temperature dependent structural stability and frequency shift of 2D hexagonal boron nitride.

    PubMed

    Anees, P; Valsakumar, M C; Panigrahi, B K

    2016-01-28

    The temperature dependent structural stability, frequency shift and linewidth of 2D hexagonal boron nitride (h-BN) are studied using a combination of lattice dynamics (LD) and molecular dynamics (MD) simulations. The in-plane lattice parameter shows a negative thermal expansion in the whole computed temperature range (0-2000 K). When the in-plane lattice parameter falls below the equilibrium value, the quasi-harmonic bending (ZA) mode frequency becomes imaginary along the Γ-M direction in the Brillouin zone, leading to a structural instability of the 2D sheet. The ZA mode is seen to be stabilized in the dispersion obtained from MD simulations, due to the automatic incorporation of higher order phonon scattering processes in MD, which are absent in a quasi-harmonic dispersion. The mode resolved phonon spectra computed with a quasi-harmonic method predict a blueshift of the longitudinal and transverse (LO/TO) optic mode frequencies with an increase in temperature. On the other hand, both canonical (NVT) and isobaric-isothermal (NPT) ensembles predict a redshift with an increase in temperature, which is more prominent in the NVT ensemble. The strong phonon-phonon coupling dominates over the thermal contraction effect and leads to a redshift in LO/TO mode frequency in the NPT ensemble simulations. The out-of-plane (ZO) optic mode quasi-harmonic frequencies are redshifted due to a membrane effect. The phonon-phonon coupling effects in the NVT and NPT ensemble simulations lead to a further reduction in the ZO mode frequencies. The linewidth of the LO/TO and ZO mode frequencies increases in a monotonic fashion. The temperature dependence of acoustic modes is also analyzed. The quasi-harmonic calculations predict a redshift of ZA mode, and at the same time the TA (transverse acoustic) and LA (longitudinal acoustic) mode frequencies are blueshifted. The strong phonon-phonon coupling in MD simulations causes a redshift of the LA and TA mode frequencies, while the ZA mode

  13. Structural networks in Alzheimer's disease.

    PubMed

    Reid, Andrew T; Evans, Alan C

    2013-01-01

    Alzheimer's disease (AD) appears to be a uniquely human condition, which is possibly attributable to our expanded longevity and peculiar capacity for episodic memory. Due to a lack of naturally-occurring animal model for investigating AD pathogenesis, our knowledge about the disease must be derived from correlational observation of humans, or from animal models produced by genetic manipulation of known risk factors in humans. Advances in neuroimaging, cellular and molecular science, and computational methods have proven useful for the improvement of such techniques, but the general limitation persists; as a result we remain without clear answers to some of the fundamental questions posed by AD. On the other hand, much progress has been made in characterizing the longitudinal progression of AD pathology, which includes the formation of "plaques and tangles", a distinct topological pattern of atrophy of grey and white matter, and the concurrent decline of specific cognitive functions, beginning with mild memory impairments and ending with general debilitating dementia. In this review, we first discuss the existing literature which characterizes AD etiology, pathology, and pathogenesis, with the intention of framing the disease as primarily a "disconnection syndrome". We next describe methodologies for investigating the topological properties of human brain networks, using graph theoretical techniques and connectivity information derived from anatomical and diffusion-weighted MR imaging. Finally, we discuss how these methodologies have been applied to systems-level analyses of AD, to help characterize the network changes underlying the disease process, and how these patterns relate to specific cognitive outcome measures. PMID:23294972

  14. 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.

  15. Interconnectivity structure of a general interdependent network.

    PubMed

    Van Mieghem, P

    2016-04-01

    A general two-layer network consists of two networks G_{1} and G_{2}, whose interconnection pattern is specified by the interconnectivity matrix B. We deduce desirable properties of B from a dynamic process point of view. Many dynamic processes are described by the Laplacian matrix Q. A regular topological structure of the interconnectivity matrix B (constant row and column sum) enables the computation of a nontrivial eigenmode (eigenvector and eigenvalue) of Q. The latter eigenmode is independent from G_{1} and G_{2}. Such a regularity in B, associated to equitable partitions, suggests design rules for the construction of interconnected networks and is deemed crucial for the interconnected network to show intriguing behavior, as discovered earlier for the special case where B=wI refers to an individual node to node interconnection with interconnection strength w. Extensions to a general m-layer network are also discussed.

  16. Network deconstruction reveals network structure in responsive microgels.

    PubMed

    Smith, Michael H; Herman, Emily S; Lyon, L Andrew

    2011-04-14

    Detailed characterization of hydrogel particle erosion revealed critical physicochemical differences between spheres, where network decomposition was informative of network structure. Real-time, in situ monitoring of the triggered erosion of colloidal hydrogels (microgels) was performed via multiangle light scattering. The solution-average molar mass and root-mean-square radii of eroding particles were measured as a function of time for microgels prepared from N-isopropylacrylamide (NIPAm) or N-isopropylmethacrylamide (NIPMAm), copolymerized with a chemically labile cross-linker (1,2-dihydroxylethylene)bisacrylamide (DHEA). Precipitation polymerization was employed to yield particles of comparable dimensions but with distinct topological features. Heterogeneous cross-linker incorporation resulted in a heterogeneous network structure for pNIPAm microgels. During the erosion reaction, mass loss proceeded from the exterior toward the interior of the polymer. In contrast, pNIPMAm microgels had a more homogeneous network structure, which resulted in a more uniform mass loss throughout the particle during erosion. Although both particle types degraded into low molar mass products, pNIPAm microgels were incapable of complete dissolution due to the presence of nondegradable cross-links arising from chain transfer and branching during particle synthesis. The observations described herein provide insight into key design parameters associated with the synthesis of degradable hydrogel particles, which may be of use in various biotechnological applications. PMID:21425815

  17. NAPS: Network Analysis of Protein Structures

    PubMed Central

    Chakrabarty, Broto; Parekh, Nita

    2016-01-01

    Traditionally, protein structures have been analysed by the secondary structure architecture and fold arrangement. An alternative approach that has shown promise is modelling proteins as a network of non-covalent interactions between amino acid residues. The network representation of proteins provide a systems approach to topological analysis of complex three-dimensional structures irrespective of secondary structure and fold type and provide insights into structure-function relationship. We have developed a web server for network based analysis of protein structures, NAPS, that facilitates quantitative and qualitative (visual) analysis of residue–residue interactions in: single chains, protein complex, modelled protein structures and trajectories (e.g. from molecular dynamics simulations). The user can specify atom type for network construction, distance range (in Å) and minimal amino acid separation along the sequence. NAPS provides users selection of node(s) and its neighbourhood based on centrality measures, physicochemical properties of amino acids or cluster of well-connected residues (k-cliques) for further analysis. Visual analysis of interacting domains and protein chains, and shortest path lengths between pair of residues are additional features that aid in functional analysis. NAPS support various analyses and visualization views for identifying functional residues, provide insight into mechanisms of protein folding, domain-domain and protein–protein interactions for understanding communication within and between proteins. URL:http://bioinf.iiit.ac.in/NAPS/. PMID:27151201

  18. NAPS: Network Analysis of Protein Structures.

    PubMed

    Chakrabarty, Broto; Parekh, Nita

    2016-07-01

    Traditionally, protein structures have been analysed by the secondary structure architecture and fold arrangement. An alternative approach that has shown promise is modelling proteins as a network of non-covalent interactions between amino acid residues. The network representation of proteins provide a systems approach to topological analysis of complex three-dimensional structures irrespective of secondary structure and fold type and provide insights into structure-function relationship. We have developed a web server for network based analysis of protein structures, NAPS, that facilitates quantitative and qualitative (visual) analysis of residue-residue interactions in: single chains, protein complex, modelled protein structures and trajectories (e.g. from molecular dynamics simulations). The user can specify atom type for network construction, distance range (in Å) and minimal amino acid separation along the sequence. NAPS provides users selection of node(s) and its neighbourhood based on centrality measures, physicochemical properties of amino acids or cluster of well-connected residues (k-cliques) for further analysis. Visual analysis of interacting domains and protein chains, and shortest path lengths between pair of residues are additional features that aid in functional analysis. NAPS support various analyses and visualization views for identifying functional residues, provide insight into mechanisms of protein folding, domain-domain and protein-protein interactions for understanding communication within and between proteins. URL:http://bioinf.iiit.ac.in/NAPS/. PMID:27151201

  19. The structure and evolution of story networks.

    PubMed

    Karsdorp, Folgert; van den Bosch, Antal

    2016-06-01

    With this study, we advance the understanding about the processes through which stories are retold. A collection of story retellings can be considered as a network of stories, in which links between stories represent pre-textual (or ancestral) relationships. This study provides a mechanistic understanding of the structure and evolution of such story networks: we construct a story network for a large diachronic collection of Dutch literary retellings of Red Riding Hood, and compare this network to one derived from a corpus of paper chain letters. In the analysis, we first provide empirical evidence that the formation of these story networks is subject to age-dependent selection processes with a strong lopsidedness towards shorter time-spans between stories and their pre-texts (i.e. 'young' story versions are preferred in producing new versions). Subsequently, we systematically compare these findings with and among predictions of various formal models of network growth to determine more precisely which kinds of attractiveness are also at play or might even be preferred as explicatory models. By carefully studying the structure and evolution of the two story networks, then, we show that existing stories are differentially preferred to function as a new version's pre-text given three types of attractiveness: (i) frequency-based and (ii) model-based attractiveness which (iii) decays in time.

  20. The structure and evolution of story networks.

    PubMed

    Karsdorp, Folgert; van den Bosch, Antal

    2016-06-01

    With this study, we advance the understanding about the processes through which stories are retold. A collection of story retellings can be considered as a network of stories, in which links between stories represent pre-textual (or ancestral) relationships. This study provides a mechanistic understanding of the structure and evolution of such story networks: we construct a story network for a large diachronic collection of Dutch literary retellings of Red Riding Hood, and compare this network to one derived from a corpus of paper chain letters. In the analysis, we first provide empirical evidence that the formation of these story networks is subject to age-dependent selection processes with a strong lopsidedness towards shorter time-spans between stories and their pre-texts (i.e. 'young' story versions are preferred in producing new versions). Subsequently, we systematically compare these findings with and among predictions of various formal models of network growth to determine more precisely which kinds of attractiveness are also at play or might even be preferred as explicatory models. By carefully studying the structure and evolution of the two story networks, then, we show that existing stories are differentially preferred to function as a new version's pre-text given three types of attractiveness: (i) frequency-based and (ii) model-based attractiveness which (iii) decays in time. PMID:27429767

  1. The structure and evolution of story networks

    PubMed Central

    Karsdorp, Folgert; van den Bosch, Antal

    2016-01-01

    With this study, we advance the understanding about the processes through which stories are retold. A collection of story retellings can be considered as a network of stories, in which links between stories represent pre-textual (or ancestral) relationships. This study provides a mechanistic understanding of the structure and evolution of such story networks: we construct a story network for a large diachronic collection of Dutch literary retellings of Red Riding Hood, and compare this network to one derived from a corpus of paper chain letters. In the analysis, we first provide empirical evidence that the formation of these story networks is subject to age-dependent selection processes with a strong lopsidedness towards shorter time-spans between stories and their pre-texts (i.e. ‘young’ story versions are preferred in producing new versions). Subsequently, we systematically compare these findings with and among predictions of various formal models of network growth to determine more precisely which kinds of attractiveness are also at play or might even be preferred as explicatory models. By carefully studying the structure and evolution of the two story networks, then, we show that existing stories are differentially preferred to function as a new version's pre-text given three types of attractiveness: (i) frequency-based and (ii) model-based attractiveness which (iii) decays in time. PMID:27429767

  2. The structure and stratigraphy of the sedimentary succession in the Swedish sector of the Baltic Basin: New insights from vintage 2D marine seismic data

    NASA Astrophysics Data System (ADS)

    Sopher, Daniel; Erlström, Mikael; Bell, Nicholas; Juhlin, Christopher

    2016-04-01

    We present five interpreted regional seismic profiles, describing the full sedimentary sequence across the Swedish sector of the Baltic Sea. The data for the study are part of an extensive and largely unpublished 2D seismic dataset acquired between 1970 and 1990 by the Swedish Oil Prospecting Company (OPAB). The Baltic Basin is an intracratonic basin located in northern Europe. Most of the Swedish sector of the basin constitutes the NW flank of a broad synclinal depression, the Baltic Basin. In the SW of the Swedish sector lies the Hanö Bay Basin, formed by subsidence associated with inversion of the Tornquist Zone during the Late Cretaceous. The geological history presented here is broadly consistent with previously published works. We observe an area between the Hanö Bay and the Baltic Basin where the Palaeozoic strata has been affected by transpression and subsequent inversion, associated with the Tornquist Zone during the late Carboniferous-Early Permian and Late Cretaceous, respectively. We propose that the Christiansø High was a structural low during the Late Jurassic, which was later inverted in the Late Cretaceous. We suggest that a fan shaped feature in the seismic data, adjacent to the Christiansø Fault within the Hanö Bay Basin, represents rapidly deposited, coarse-grained sediments eroded from the inverted Christiansø High during the Late Cretaceous. We identify a number of faults within the deeper part of the Baltic Basin, which we also interpret to be transpressional in nature, formed during the Caledonian Orogeny in the Late Silurian-Early Devonian. East of Gotland a number of sedimentary structures consisting of Silurian carbonate reefs and Ordovician carbonate mounds, as well as a large Quaternary glacial feature are observed. Finally, we use the seismic interpretation to infer the structural and stratigraphic history of the Baltic and Hanö Bay basins within the Swedish sector.

  3. Quantification of transition dipole strengths using 1D and 2D spectroscopy for the identification of molecular structures via exciton delocalization: Application to α-helices

    NASA Astrophysics Data System (ADS)

    Grechko, Maksim; Zanni, Martin T.

    2012-11-01

    Vibrational and electronic transition dipole strengths are often good probes of molecular structures, especially in excitonically coupled systems of chromophores. One cannot determine transition dipole strengths using linear spectroscopy unless the concentration is known, which in many cases it is not. In this paper, we report a simple method for measuring transition dipole moments from linear absorption and 2D IR spectra that does not require knowledge of concentrations. Our method is tested on several model compounds and applied to the amide I' band of a polypeptide in its random coil and α-helical conformation as modulated by the solution temperature. It is often difficult to confidently assign polypeptide and protein secondary structures to random coil or α-helix by linear spectroscopy alone, because they absorb in the same frequency range. We find that the transition dipole strength of the random coil state is 0.12 ± 0.013 D2, which is similar to a single peptide unit, indicating that the vibrational mode of random coil is localized on a single peptide unit. In an α-helix, the lower bound of transition dipole strength is 0.26 ± 0.03 D2. When taking into account the angle of the amide I' transition dipole vector with respect to the helix axis, our measurements indicate that the amide I' vibrational mode is delocalized across a minimum of 3.5 residues in an α-helix. Thus, one can confidently assign secondary structure based on exciton delocalization through its effect on the transition dipole strength. Our method will be especially useful for kinetically evolving systems, systems with overlapping molecular conformations, and other situations in which concentrations are difficult to determine.

  4. Graph Structure-Based Simultaneous Localization and Mapping Using a Hybrid Method of 2D Laser Scan and Monocular Camera Image in Environments with Laser Scan Ambiguity

    PubMed Central

    Oh, Taekjun; Lee, Donghwa; Kim, Hyungjin; Myung, Hyun

    2015-01-01

    Localization is an essential issue for robot navigation, allowing the robot to perform tasks autonomously. However, in environments with laser scan ambiguity, such as long corridors, the conventional SLAM (simultaneous localization and mapping) algorithms exploiting a laser scanner may not estimate the robot pose robustly. To resolve this problem, we propose a novel localization approach based on a hybrid method incorporating a 2D laser scanner and a monocular camera in the framework of a graph structure-based SLAM. 3D coordinates of image feature points are acquired through the hybrid method, with the assumption that the wall is normal to the ground and vertically flat. However, this assumption can be relieved, because the subsequent feature matching process rejects the outliers on an inclined or non-flat wall. Through graph optimization with constraints generated by the hybrid method, the final robot pose is estimated. To verify the effectiveness of the proposed method, real experiments were conducted in an indoor environment with a long corridor. The experimental results were compared with those of the conventional GMappingapproach. The results demonstrate that it is possible to localize the robot in environments with laser scan ambiguity in real time, and the performance of the proposed method is superior to that of the conventional approach. PMID:26151203

  5. Graph Structure-Based Simultaneous Localization and Mapping Using a Hybrid Method of 2D Laser Scan and Monocular Camera Image in Environments with Laser Scan Ambiguity.

    PubMed

    Oh, Taekjun; Lee, Donghwa; Kim, Hyungjin; Myung, Hyun

    2015-01-01

    Localization is an essential issue for robot navigation, allowing the robot to perform tasks autonomously. However, in environments with laser scan ambiguity, such as long corridors, the conventional SLAM (simultaneous localization and mapping) algorithms exploiting a laser scanner may not estimate the robot pose robustly. To resolve this problem, we propose a novel localization approach based on a hybrid method incorporating a 2D laser scanner and a monocular camera in the framework of a graph structure-based SLAM. 3D coordinates of image feature points are acquired through the hybrid method, with the assumption that the wall is normal to the ground and vertically flat. However, this assumption can be relieved, because the subsequent feature matching process rejects the outliers on an inclined or non-flat wall. Through graph optimization with constraints generated by the hybrid method, the final robot pose is estimated. To verify the effectiveness of the proposed method, real experiments were conducted in an indoor environment with a long corridor. The experimental results were compared with those of the conventional GMappingapproach. The results demonstrate that it is possible to localize the robot in environments with laser scan ambiguity in real time, and the performance of the proposed method is superior to that of the conventional approach. PMID:26151203

  6. Graph Structure-Based Simultaneous Localization and Mapping Using a Hybrid Method of 2D Laser Scan and Monocular Camera Image in Environments with Laser Scan Ambiguity.

    PubMed

    Oh, Taekjun; Lee, Donghwa; Kim, Hyungjin; Myung, Hyun

    2015-07-03

    Localization is an essential issue for robot navigation, allowing the robot to perform tasks autonomously. However, in environments with laser scan ambiguity, such as long corridors, the conventional SLAM (simultaneous localization and mapping) algorithms exploiting a laser scanner may not estimate the robot pose robustly. To resolve this problem, we propose a novel localization approach based on a hybrid method incorporating a 2D laser scanner and a monocular camera in the framework of a graph structure-based SLAM. 3D coordinates of image feature points are acquired through the hybrid method, with the assumption that the wall is normal to the ground and vertically flat. However, this assumption can be relieved, because the subsequent feature matching process rejects the outliers on an inclined or non-flat wall. Through graph optimization with constraints generated by the hybrid method, the final robot pose is estimated. To verify the effectiveness of the proposed method, real experiments were conducted in an indoor environment with a long corridor. The experimental results were compared with those of the conventional GMappingapproach. The results demonstrate that it is possible to localize the robot in environments with laser scan ambiguity in real time, and the performance of the proposed method is superior to that of the conventional approach.

  7. 2D Modelling of the Gorkha earthquake through the joint exploitation of Sentinel 1-A DInSAR measurements and geological, structural and seismological information

    NASA Astrophysics Data System (ADS)

    De Novellis, Vincenzo; Castaldo, Raffaele; Solaro, Giuseppe; De Luca, Claudio; Pepe, Susi; Bonano, Manuela; Casu, Francesco; Zinno, Ivana; Manunta, Michele; Lanari, Riccardo; Tizzani, Pietro

    2016-04-01

    A Mw 7.8 earthquake struck Nepal on 25 April 2015 at 06:11:26 UTC, killing more than 9,000 people, injuring more than 23,000 and producing extensive damages. The main seismic event, known as the Gorkha earthquake, had its epicenter localized at ~82 km NW of the Kathmandu city and the hypocenter at a depth of approximately 15 km. After the main shock event, about 100 aftershocks occurred during the following months, propagating toward the south-east direction; in particular, the most energetic shocks were the Mw 6.7 and Mw 7.3 occurred on 26 April and 12 May, respectively. In this study, we model the causative fault of the earthquake by jointly exploiting surface deformation retrieved by the DInSAR measurements collected through the Sentinel 1-A (S1A) space-borne sensor and the available geological, structural and seismological information. We first exploit the analytical solution performing a back-analysis of the ground deformation detected by the first co-seismic S1A interferogram, computed by exploiting the 17/04/2015 and 29/04/2015 SAR acquisitions and encompassing the main earthquake and some aftershocks, to search for the location and geometry of the fault plane. Starting from these findings and by benefiting from the available geological, structural and seismological data, we carry out a Finite Element (FE)-based 2D modelling of the causative fault, in order to evaluate the impact of the geological structures activated during the seismic event on the distribution of the ground deformation field. The obtained results show that the causative fault has a rather complex compressive structure, dipping northward, formed by segments with different dip angles: 6° the deep segment and 60° the shallower one. Therefore, although the hypocenters of the main shock and most of the more energetic aftershocks are located along the deeper plane, corresponding to a segment of the Main Himalayan Thrust (MHT), the FE solution also indicates the contribution of the shallower

  8. Structural covariance networks in the mouse brain.

    PubMed

    Pagani, Marco; Bifone, Angelo; Gozzi, Alessandro

    2016-04-01

    The presence of networks of correlation between regional gray matter volume as measured across subjects in a group of individuals has been consistently described in several human studies, an approach termed structural covariance MRI (scMRI). Complementary to prevalent brain mapping modalities like functional and diffusion-weighted imaging, the approach can provide precious insights into the mutual influence of trophic and plastic processes in health and pathological states. To investigate whether analogous scMRI networks are present in lower mammal species amenable to genetic and experimental manipulation such as the laboratory mouse, we employed high resolution morphoanatomical MRI in a large cohort of genetically-homogeneous wild-type mice (C57Bl6/J) and mapped scMRI networks using a seed-based approach. We show that the mouse brain exhibits robust homotopic scMRI networks in both primary and associative cortices, a finding corroborated by independent component analyses of cortical volumes. Subcortical structures also showed highly symmetric inter-hemispheric correlations, with evidence of distributed antero-posterior networks in diencephalic regions of the thalamus and hypothalamus. Hierarchical cluster analysis revealed six identifiable clusters of cortical and sub-cortical regions corresponding to previously described neuroanatomical systems. Our work documents the presence of homotopic cortical and subcortical scMRI networks in the mouse brain, thus supporting the use of this species to investigate the elusive biological and neuroanatomical underpinnings of scMRI network development and its derangement in neuropathological states. The identification of scMRI networks in genetically homogeneous inbred mice is consistent with the emerging view of a key role of environmental factors in shaping these correlational networks.

  9. Morphisms of reaction networks that couple structure to function

    PubMed Central

    2014-01-01

    Background The mechanisms underlying complex biological systems are routinely represented as networks. Network kinetics is widely studied, and so is the connection between network structure and behavior. However, similarity of mechanism is better revealed by relationships between network structures. Results We define morphisms (mappings) between reaction networks that establish structural connections between them. Some morphisms imply kinetic similarity, and yet their properties can be checked statically on the structure of the networks. In particular we can determine statically that a complex network will emulate a simpler network: it will reproduce its kinetics for all corresponding choices of reaction rates and initial conditions. We use this property to relate the kinetics of many common biological networks of different sizes, also relating them to a fundamental population algorithm. Conclusions Structural similarity between reaction networks can be revealed by network morphisms, elucidating mechanistic and functional aspects of complex networks in terms of simpler networks. PMID:25128194

  10. 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.

  11. Interaction Energy Based Protein Structure Networks

    PubMed Central

    Vijayabaskar, M.S.; Vishveshwara, Saraswathi

    2010-01-01

    The three-dimensional structure of a protein is formed and maintained by the noncovalent interactions among the amino-acid residues of the polypeptide chain. These interactions can be represented collectively in the form of a network. So far, such networks have been investigated by considering the connections based on distances between the amino-acid residues. Here we present a method of constructing the structure network based on interaction energies among the amino-acid residues in the protein. We have investigated the properties of such protein energy-based networks (PENs) and have shown correlations to protein structural features such as the clusters of residues involved in stability, formation of secondary and super-secondary structural units. Further we demonstrate that the analysis of PENs in terms of parameters such as hubs and shortest paths can provide a variety of biologically important information, such as the residues crucial for stabilizing the folded units and the paths of communication between distal residues in the protein. Finally, the energy regimes for different levels of stabilization in the protein structure have clearly emerged from the PEN analysis. PMID:21112295

  12. The structure of scientific collaboration networks

    PubMed Central

    Newman, M. E. J.

    2001-01-01

    The structure of scientific collaboration networks is investigated. Two scientists are considered connected if they have authored a paper together and explicit networks of such connections are constructed by using data drawn from a number of databases, including MEDLINE (biomedical research), the Los Alamos e-Print Archive (physics), and NCSTRL (computer science). I show that these collaboration networks form “small worlds,” in which randomly chosen pairs of scientists are typically separated by only a short path of intermediate acquaintances. I further give results for mean and distribution of numbers of collaborators of authors, demonstrate the presence of clustering in the networks, and highlight a number of apparent differences in the patterns of collaboration between the fields studied. PMID:11149952

  13. Uncovering the spatial structure of mobility networks

    NASA Astrophysics Data System (ADS)

    Louail, Thomas; Lenormand, Maxime; Picornell, Miguel; García Cantú, Oliva; Herranz, Ricardo; Frias-Martinez, Enrique; Ramasco, José J.; Barthelemy, Marc

    2015-01-01

    The extraction of a clear and simple footprint of the structure of large, weighted and directed networks is a general problem that has relevance for many applications. An important example is seen in origin-destination matrices, which contain the complete information on commuting flows, but are difficult to analyze and compare. We propose here a versatile method, which extracts a coarse-grained signature of mobility networks, under the form of a 2 × 2 matrix that separates the flows into four categories. We apply this method to origin-destination matrices extracted from mobile phone data recorded in 31 Spanish cities. We show that these cities essentially differ by their proportion of two types of flows: integrated (between residential and employment hotspots) and random flows, whose importance increases with city size. Finally, the method allows the determination of categories of networks, and in the mobility case, the classification of cities according to their commuting structure.

  14. Social Network Structures among Groundnut Farmers

    ERIC Educational Resources Information Center

    Thuo, Mary; Bell, Alexandra A.; Bravo-Ureta, Boris E.; Okello, David K.; Okoko, Evelyn Nasambu; Kidula, Nelson L.; Deom, C. Michael; Puppala, Naveen

    2013-01-01

    Purpose: Groundnut farmers in East Africa have experienced declines in production despite research and extension efforts to increase productivity. This study examined how social network structures related to acquisition of information about new seed varieties and productivity among groundnut farmers in Uganda and Kenya.…

  15. HOTCFGM-2D: A Coupled Higher-Order Theory for Cylindrical Structural Components with Bi-Directionally Components with Bi-Directionally Graded Microstructures

    NASA Technical Reports Server (NTRS)

    Pindera, Marek-Jerzy; Aboudi, Jacob

    2000-01-01

    The objective of this two-year project was to develop and deliver to the NASA-Glenn Research Center a two-dimensional higher-order theory, and related computer codes, for the analysis and design of cylindrical functionally graded materials/structural components for use in advanced aircraft engines (e.g., combustor linings, rotor disks, heat shields, brisk blades). To satisfy this objective, two-dimensional version of the higher-order theory, HOTCFGM-2D, and four computer codes based on this theory, for the analysis and design of structural components functionally graded in the radial and circumferential directions were developed in the cylindrical coordinate system r-Theta-z. This version of the higher-order theory is a significant generalization of the one-dimensional theory, HOTCFGM-1D, developed during the FY97 for the analysis and design of cylindrical structural components with radially graded microstructures. The generalized theory is applicable to thin multi-phased composite shells/cylinders subjected to steady-state thermomechanical, transient thermal and inertial loading applied uniformly along the axial direction such that the overall deformation is characterized by a constant average axial strain. The reinforcement phases are uniformly distributed in the axial direction, and arbitrarily distributed in the radial and circumferential direction, thereby allowing functional grading of the internal reinforcement in the r-Theta plane. The four computer codes fgmc3dq.cylindrical.f, fgmp3dq.cylindrical.f, fgmgvips3dq.cylindrical.f, and fgmc3dq.cylindrical.transient.f are research-oriented codes for investigating the effect of functionally graded architectures, as well as the properties of the multi-phase reinforcement, in thin shells subjected to thermomechanical and inertial loading, on the internal temperature, stress and (inelastic) strain fields. The reinforcement distribution in the radial and circumferential directions is specified by the user. The thermal

  16. Fine-scale thermohaline ocean structure retrieved with 2-D prestack full-waveform inversion of multichannel seismic data: Application to the Gulf of Cadiz (SW Iberia)

    NASA Astrophysics Data System (ADS)

    Dagnino, D.; Sallarès, V.; Biescas, B.; Ranero, C. R.

    2016-08-01

    This work demonstrates the feasibility of 2-D time-domain, adjoint-state acoustic full-waveform inversion (FWI) to retrieve high-resolution models of ocean physical parameters such as sound speed, temperature and salinity. The proposed method is first described and then applied to prestack multichannel seismic (MCS) data acquired in the Gulf of Cadiz (SW Iberia) in 2007 in the framework of the Geophysical Oceanography project. The inversion strategy flow includes specifically designed data preconditioning for acoustic noise reduction, followed by the inversion of sound speed in the shotgather domain. We show that the final sound speed model has a horizontal resolution of ˜ 70 m, which is two orders of magnitude better than that of the initial model constructed with coincident eXpendable Bathy Thermograph (XBT) data, and close to the theoretical resolution of O(λ). Temperature (T) and salinity (S) are retrieved with the same lateral resolution as sound speed by combining the inverted sound speed model with the thermodynamic equation of seawater and a local, depth-dependent T-S relation derived from regional conductivity-temperature-depth (CTD) measurements of the National Oceanic and Atmospheric Administration (NOAA) database. The comparison of the inverted T and S models with XBT and CTD casts deployed simultaneously to the MCS acquisition shows that the thermohaline contrasts are resolved with an accuracy of 0.18oC for temperature and 0.08 PSU for salinity. The combination of oceanographic and MCS data into a common, pseudo-automatic inversion scheme allows to quantitatively resolve submeso-scale features that ought to be incorporated into larger-scale ocean models of oceans structure and circulation.

  17. Synthesis and characterization of a new metal organic framework structure with a 2D porous system: (H 2NEt 2) 2[Zn 3(BDC) 4]ṡ3DEF

    NASA Astrophysics Data System (ADS)

    Biemmi, Enrica; Bein, Thomas; Stock, Norbert

    2006-03-01

    A new open-framework zinc terephthalate (H 2NEt 2) 2[Zn 3(BDC) 4]ṡ3DEF (BDC = 1,4-benzendicarboxylate, DEF=N,N-diethylformamide) was obtained under slightly acidic condition by reacting 1,4-benzendicarboxylic acid (H 2BDC) with ZnO in a DEF solution. The structure was obtained by single crystal X-ray diffraction and consists of trimetallic zinc building units, that are interconnected by eight BDC units each (crystal data: monoclinic, C2/c, a=3337.24(5), b=983.17(2), c=1819.67(2) pm, β=92.455(1, V=5965.0(2)×10 pm, Z=4, R=0.0395, wR=0.0843 for 4533 reflections I>2σ(I)). Six BDC ions together with the trimetallic zinc units form a two-dimensional (3,6)-net while the other two BDC unit pillar these layers. Thus a three-dimensional anionic framework with a 2D pore system is formed. The pore space is occupied by solvent molecules (DEF) and diethylammonium ions, produced by in situ hydrolysis of DEF. These are interconnected as well as connected to the framework by hydrogen-bonds. The TG investigation in combination with powder X-ray diffraction and vibrational-spectroscopy show a two-step loss of the pore filling molecules as well as one H 2BDC molecule leading to crystalline phases which are stable up to 250 and 400 °C, respectively. In addition, 13C MAS-NMR data of the title compound is presented.

  18. From 1D chain to 3D network: A theoretical study on TiO{sub 2} low dimensional structures

    SciTech Connect

    Guo, Ling-ju; He, Tao; Zeng, Zhi

    2015-06-14

    We have performed a systematic study on a series of low dimensional TiO{sub 2} nanostructures under density functional theory methods. The geometries, stabilities, growth mechanism, and electronic structures of 1D chain, 2D ring, 2D ring array, and 3D network of TiO{sub 2} nanostructures are analyzed. Based on the Ti{sub 2}O{sub 4} building unit, a series of 1D TiO{sub 2} nano chains and rings can be built. Furthermore, 2D ring array and 3D network nanostructures can be constructed from 1D chains and rings. Among non-periodic TiO{sub 2} chain and ring structures, one series of ring structures is found to be more stable. The geometry model of the 2D ring arrays and 3D network structures in this work has provided a theoretical understanding on the structure information in experiments. Based on these semiconductive low dimensional structures, moreover, it can help to understand and design new hierarchical TiO{sub 2} nanostructure in the future.

  19. Modeling Insurgent Network Structure and Dynamics

    NASA Astrophysics Data System (ADS)

    Gabbay, Michael; Thirkill-Mackelprang, Ashley

    2010-03-01

    We present a methodology for mapping insurgent network structure based on their public rhetoric. Indicators of cooperative links between insurgent groups at both the leadership and rank-and-file levels are used, such as joint policy statements or joint operations claims. In addition, a targeting policy measure is constructed on the basis of insurgent targeting claims. Network diagrams which integrate these measures of insurgent cooperation and ideology are generated for different periods of the Iraqi and Afghan insurgencies. The network diagrams exhibit meaningful changes which track the evolution of the strategic environment faced by insurgent groups. Correlations between targeting policy and network structure indicate that insurgent targeting claims are aimed at establishing a group identity among the spectrum of rank-and-file insurgency supporters. A dynamical systems model of insurgent alliance formation and factionalism is presented which evolves the relationship between insurgent group dyads as a function of their ideological differences and their current relationships. The ability of the model to qualitatively and quantitatively capture insurgent network dynamics observed in the data is discussed.

  20. Information diffusion in structured online social networks

    NASA Astrophysics Data System (ADS)

    Li, Pei; Zhang, Yini; Qiao, Fengcai; Wang, Hui

    2015-05-01

    Nowadays, due to the word-of-mouth effect, online social networks have been considered to be efficient approaches to conduct viral marketing, which makes it of great importance to understand the diffusion dynamics in online social networks. However, most research on diffusion dynamics in epidemiology and existing social networks cannot be applied directly to characterize online social networks. In this paper, we propose models to characterize the information diffusion in structured online social networks with push-based forwarding mechanism. We introduce the term user influence to characterize the average number of times that messages are browsed which is incurred by a given type user generating a message, and study the diffusion threshold, above which the user influence of generating a message will approach infinity. We conduct simulations and provide the simulation results, which are consistent with the theoretical analysis results perfectly. These results are of use in understanding the diffusion dynamics in online social networks and also critical for advertisers in viral marketing who want to estimate the user influence before posting an advertisement.

  1. Tensegrity II. How structural networks influence cellular information processing networks

    NASA Technical Reports Server (NTRS)

    Ingber, Donald E.

    2003-01-01

    The major challenge in biology today is biocomplexity: the need to explain how cell and tissue behaviors emerge from collective interactions within complex molecular networks. Part I of this two-part article, described a mechanical model of cell structure based on tensegrity architecture that explains how the mechanical behavior of the cell emerges from physical interactions among the different molecular filament systems that form the cytoskeleton. Recent work shows that the cytoskeleton also orients much of the cell's metabolic and signal transduction machinery and that mechanical distortion of cells and the cytoskeleton through cell surface integrin receptors can profoundly affect cell behavior. In particular, gradual variations in this single physical control parameter (cell shape distortion) can switch cells between distinct gene programs (e.g. growth, differentiation and apoptosis), and this process can be viewed as a biological phase transition. Part II of this article covers how combined use of tensegrity and solid-state mechanochemistry by cells may mediate mechanotransduction and facilitate integration of chemical and physical signals that are responsible for control of cell behavior. In addition, it examines how cell structural networks affect gene and protein signaling networks to produce characteristic phenotypes and cell fate transitions during tissue development.

  2. Fundamental structures of dynamic social networks.

    PubMed

    Sekara, Vedran; Stopczynski, Arkadiusz; Lehmann, Sune

    2016-09-01

    Social systems are in a constant state of flux, with dynamics spanning from minute-by-minute changes to patterns present on the timescale of years. Accurate models of social dynamics are important for understanding the spreading of influence or diseases, formation of friendships, and the productivity of teams. Although there has been much progress on understanding complex networks over the past decade, little is known about the regularities governing the microdynamics of social networks. Here, we explore the dynamic social network of a densely-connected population of ∼1,000 individuals and their interactions in the network of real-world person-to-person proximity measured via Bluetooth, as well as their telecommunication networks, online social media contacts, geolocation, and demographic data. These high-resolution data allow us to observe social groups directly, rendering community detection unnecessary. Starting from 5-min time slices, we uncover dynamic social structures expressed on multiple timescales. On the hourly timescale, we find that gatherings are fluid, with members coming and going, but organized via a stable core of individuals. Each core represents a social context. Cores exhibit a pattern of recurring meetings across weeks and months, each with varying degrees of regularity. Taken together, these findings provide a powerful simplification of the social network, where cores represent fundamental structures expressed with strong temporal and spatial regularity. Using this framework, we explore the complex interplay between social and geospatial behavior, documenting how the formation of cores is preceded by coordination behavior in the communication networks and demonstrating that social behavior can be predicted with high precision.

  3. Fundamental structures of dynamic social networks

    PubMed Central

    Sekara, Vedran; Stopczynski, Arkadiusz; Lehmann, Sune

    2016-01-01

    Social systems are in a constant state of flux, with dynamics spanning from minute-by-minute changes to patterns present on the timescale of years. Accurate models of social dynamics are important for understanding the spreading of influence or diseases, formation of friendships, and the productivity of teams. Although there has been much progress on understanding complex networks over the past decade, little is known about the regularities governing the microdynamics of social networks. Here, we explore the dynamic social network of a densely-connected population of ∼1,000 individuals and their interactions in the network of real-world person-to-person proximity measured via Bluetooth, as well as their telecommunication networks, online social media contacts, geolocation, and demographic data. These high-resolution data allow us to observe social groups directly, rendering community detection unnecessary. Starting from 5-min time slices, we uncover dynamic social structures expressed on multiple timescales. On the hourly timescale, we find that gatherings are fluid, with members coming and going, but organized via a stable core of individuals. Each core represents a social context. Cores exhibit a pattern of recurring meetings across weeks and months, each with varying degrees of regularity. Taken together, these findings provide a powerful simplification of the social network, where cores represent fundamental structures expressed with strong temporal and spatial regularity. Using this framework, we explore the complex interplay between social and geospatial behavior, documenting how the formation of cores is preceded by coordination behavior in the communication networks and demonstrating that social behavior can be predicted with high precision. PMID:27555584

  4. Fundamental structures of dynamic social networks.

    PubMed

    Sekara, Vedran; Stopczynski, Arkadiusz; Lehmann, Sune

    2016-09-01

    Social systems are in a constant state of flux, with dynamics spanning from minute-by-minute changes to patterns present on the timescale of years. Accurate models of social dynamics are important for understanding the spreading of influence or diseases, formation of friendships, and the productivity of teams. Although there has been much progress on understanding complex networks over the past decade, little is known about the regularities governing the microdynamics of social networks. Here, we explore the dynamic social network of a densely-connected population of ∼1,000 individuals and their interactions in the network of real-world person-to-person proximity measured via Bluetooth, as well as their telecommunication networks, online social media contacts, geolocation, and demographic data. These high-resolution data allow us to observe social groups directly, rendering community detection unnecessary. Starting from 5-min time slices, we uncover dynamic social structures expressed on multiple timescales. On the hourly timescale, we find that gatherings are fluid, with members coming and going, but organized via a stable core of individuals. Each core represents a social context. Cores exhibit a pattern of recurring meetings across weeks and months, each with varying degrees of regularity. Taken together, these findings provide a powerful simplification of the social network, where cores represent fundamental structures expressed with strong temporal and spatial regularity. Using this framework, we explore the complex interplay between social and geospatial behavior, documenting how the formation of cores is preceded by coordination behavior in the communication networks and demonstrating that social behavior can be predicted with high precision. PMID:27555584

  5. Synthesis, characterization and structure determination of two isotypes of a layered aluminophosphate with a new 2D network topology

    SciTech Connect

    Tuel, A. . E-mail: tuel@catalyse.cnrs.fr; Lorentz, Ch.; Gramlich, V.; Baerlocher, Ch.

    2005-07-15

    Two isotypes of a new layered aluminophosphate, further denoted MDAP-3 and MDAE-1, have been synthesized under hydrothermal conditions using N-methyl-1,3-propanediamine and N-methyl-ethylenediamine, respectively. MDAP-3, with the empirical formula [Al{sub 2}(HPO{sub 4})(PO{sub 4}){sub 2}](C{sub 4}N{sub 2}H{sub 14})(H{sub 2}O), crystallizes in the orthorhombic space group Pna2(1) (No. 33) with a=9.602(16)A, b=9.26(2)A, c=16.03(3)A, Z=4, R{sub 1}=0.0498 and wR{sub 2}=0.1217. The second solid, MDAE-1, with the empirical formula [Al{sub 2}(HPO{sub 4})(PO{sub 4}){sub 2}](C{sub 3}N{sub 2}H{sub 12})(H{sub 2}O), crystallizes in the same space group with a=9.4250(19)A, b=9.3170(19)A, c=15.907(3)A, Z=4, R{sub 1}=0.0407 and wR{sub 2}=0.0954. The two compounds possess the same layer topology. Inorganic layers contain PO{sub 3}=O, PO{sub 3}OH, AlO{sub 4} and AlO{sub 6} polyhedra, linked together to generate a new 4x8 net. MDAP-3 and MDAE-1 represent the first examples of two-dimensional layered aluminophosphates with the Al{sub 2}P{sub 3}O{sub 12} stoichiometry, and containing AlO{sub 6} octahedra.

  6. Network structure of multivariate time series.

    PubMed

    Lacasa, Lucas; Nicosia, Vincenzo; Latora, Vito

    2015-10-21

    Our understanding of a variety of phenomena in physics, biology and economics crucially depends on the analysis of multivariate time series. While a wide range tools and techniques for time series analysis already exist, the increasing availability of massive data structures calls for new approaches for multidimensional signal processing. We present here a non-parametric method to analyse multivariate time series, based on the mapping of a multidimensional time series into a multilayer network, which allows to extract information on a high dimensional dynamical system through the analysis of the structure of the associated multiplex network. The method is simple to implement, general, scalable, does not require ad hoc phase space partitioning, and is thus suitable for the analysis of large, heterogeneous and non-stationary time series. We show that simple structural descriptors of the associated multiplex networks allow to extract and quantify nontrivial properties of coupled chaotic maps, including the transition between different dynamical phases and the onset of various types of synchronization. As a concrete example we then study financial time series, showing that a multiplex network analysis can efficiently discriminate crises from periods of financial stability, where standard methods based on time-series symbolization often fail.

  7. Network structure of multivariate time series

    NASA Astrophysics Data System (ADS)

    Lacasa, Lucas; Nicosia, Vincenzo; Latora, Vito

    2015-10-01

    Our understanding of a variety of phenomena in physics, biology and economics crucially depends on the analysis of multivariate time series. While a wide range tools and techniques for time series analysis already exist, the increasing availability of massive data structures calls for new approaches for multidimensional signal processing. We present here a non-parametric method to analyse multivariate time series, based on the mapping of a multidimensional time series into a multilayer network, which allows to extract information on a high dimensional dynamical system through the analysis of the structure of the associated multiplex network. The method is simple to implement, general, scalable, does not require ad hoc phase space partitioning, and is thus suitable for the analysis of large, heterogeneous and non-stationary time series. We show that simple structural descriptors of the associated multiplex networks allow to extract and quantify nontrivial properties of coupled chaotic maps, including the transition between different dynamical phases and the onset of various types of synchronization. As a concrete example we then study financial time series, showing that a multiplex network analysis can efficiently discriminate crises from periods of financial stability, where standard methods based on time-series symbolization often fail.

  8. Network structure of multivariate time series

    PubMed Central

    Lacasa, Lucas; Nicosia, Vincenzo; Latora, Vito

    2015-01-01

    Our understanding of a variety of phenomena in physics, biology and economics crucially depends on the analysis of multivariate time series. While a wide range tools and techniques for time series analysis already exist, the increasing availability of massive data structures calls for new approaches for multidimensional signal processing. We present here a non-parametric method to analyse multivariate time series, based on the mapping of a multidimensional time series into a multilayer network, which allows to extract information on a high dimensional dynamical system through the analysis of the structure of the associated multiplex network. The method is simple to implement, general, scalable, does not require ad hoc phase space partitioning, and is thus suitable for the analysis of large, heterogeneous and non-stationary time series. We show that simple structural descriptors of the associated multiplex networks allow to extract and quantify nontrivial properties of coupled chaotic maps, including the transition between different dynamical phases and the onset of various types of synchronization. As a concrete example we then study financial time series, showing that a multiplex network analysis can efficiently discriminate crises from periods of financial stability, where standard methods based on time-series symbolization often fail. PMID:26487040

  9. Cu-PDC-bpa solid coordination frameworks (PDC=2,5-pyrindinedicarboxylate; bpa=1,2-DI(4-pyridil)ethane)): 2D and 3D structural flexibility producing a 3-c herringbone array next to ideal

    SciTech Connect

    Llano-Tomé, Francisco; Bazán, Begoña; Urtiaga, Miren-Karmele; Barandika, Gotzone; Antonia Señarís-Rodríguez, M.; and others

    2015-10-15

    Combination of polycarboxylate anions and dipyridyl ligands is an effective strategy to produce solid coordination frameworks (SCF) which are crystalline materials based on connections between metal ions through organic ligands. In this context, this work is focused on two novel Cu{sup II}-based SCFs exhibiting PDC (2,5-pyridinedicarboxylate) and bpa (1,2-di(4-pyridyl)ethane), being the first structures reported in literature containing both ligands. Chemical formula are [Cu{sub 2}[(PDC){sub 2}(bpa)(H{sub 2}O){sub 2}]·3H{sub 2}O·DMF (1), and [Cu{sub 2}(PDC){sub 2}(bpa)(H{sub 2}O){sub 2}]·7H{sub 2}O (2), where DMF is dimethylformamide. Compounds 1 and 2 have been characterized by means of X-ray diffraction (XRD), infrared spectroscopy (IR), thermogravimetric (TG) analysis, differential thermal analysis (DTA) and dielectric measurements. The crystallographic analysis revealed that compounds 1 and 2 can be described as herringbone-type layers formed by helicoidal Cu-PDC-Cu chains connected through bpa ligands. Solvent molecules are crystallized between the layers, providing the inter-layer connections through hydrogen bonds. Differences between both compounds are attributable to the flexibility of bpa (in 2D) as well as to the 3D packing of the layers which is solvent dependent. This fact results in the fact that compound 2 is the most regular 3-c herringbone array reported so far. The structural dynamism of these networks is responsible for the crystalline to-amorphous to-crystalline (CAC) transformation from compound 1 to compound 2. Crystallochemical features for both compounds have also been studied and compared to similar 3-connected herringbone-arrays. - Graphical abstract: Cu-PDC-bpa 3-c herringbone arrays. - Highlights: • The most ideal herringbone array reported so far is a Cu-PDC-bpa SCF. • Conformational freedom of bpa results in 2D and 3D flexibility of the SCFs. • The flexibility of the SCFs is related to a phase transformation. • Dielectric

  10. Color tunable and near white-light emission of two solvent-induced 2D lead(II) coordination networks based on a rigid ligand 1-tetrazole-4-imidazole-benzene.

    PubMed

    Chen, Jun; Zhang, Qing; Liu, Zhi-Fa; Wang, Shuai-Hua; Xiao, Yu; Li, Rong; Xu, Jian-Gang; Zhao, Ya-Ping; Zheng, Fa-Kun; Guo, Guo-Cong

    2015-06-01

    Two new lead(II) coordination polymers, [Pb(NO3)(tzib)]n (1) and [Pb(tzib)2]n (2), were successfully synthesized from the reaction of a rigid ligand 1-tetrazole-4-imidazole-benzene (Htzib) and lead(II) nitrate in different solvents. The obtained polymers have been characterized by single-crystal X-ray diffraction analyses, which show that both polymers feature 2D layer structures. The inorganic anion nitrate in 1 shows a μ2-κO3:κO3 bridging mode to connect adjacent lead ions into a zigzag chain, and then the organic ligands tzib(-) join the neighboring chains into a 2D layer by a μ3-κN1:κN2:κN6 connection mode. In 2, there are two different bridging modes of the tzib(-) ligand: μ3-κN1:κN2:κN6 and μ3-κN1:κN6 to coordinate the lead ions into a 2D layer structure. Interestingly, both polymers displayed broadband emissions covering the entire visible spectra, which could be tunable to near white-light emission by varying excitation wavelengths. PMID:25952460

  11. Design and characterization of low-loss 2D grating couplers for silicon photonics integrated circuits

    NASA Astrophysics Data System (ADS)

    Lacava, C.; Carrol, L.; Bozzola, A.; Marchetti, R.; Minzioni, P.; Cristiani, I.; Fournier, M.; Bernabe, S.; Gerace, D.; Andreani, L. C.

    2016-03-01

    We present the characterization of Silicon-on-insulator (SOI) photonic-crystal based 2D grating-couplers (2D-GCs) fabricated by CEA-Leti in the frame of the FP7 Fabulous project, which is dedicated to the realization of devices and systems for low-cost and high-performance passives-optical-networks. On the analyzed samples different test structures are present, including 2D-GC connected to another 2D-GC by different waveguides (in a Mach-Zehnder like configuration), and 2D-GC connected to two separate 2D-GCs, so as to allow a complete assessment of different parameters. Measurements were carried out using a tunable laser source operating in the extended telecom bandwidth and a fiber-based polarization controlling system at the input of device-under-test. The measured data yielded an overall fiber-to-fiber loss of 7.5 dB for the structure composed by an input 2D-GC connected to two identical 2D-GCs. This value was obtained at the peak wavelength of the grating, and the 3-dB bandwidth of the 2D-GC was assessed to be 43 nm. Assuming that the waveguide losses are negligible, so as to make a worst-case analysis, the coupling efficiency of the single 2D-GC results to be equal to -3.75 dB, constituting, to the best of our knowledge, the lowest value ever reported for a fully CMOS compatible 2D-GC. It is worth noting that both the obtained values are in good agreement with those expected by the numerical simulations performed using full 3D analysis by Lumerical FDTD-solutions.

  12. Self-Healing Networks: Redundancy and Structure

    PubMed Central

    Quattrociocchi, Walter; Caldarelli, Guido; Scala, Antonio

    2014-01-01

    We introduce the concept of self-healing in the field of complex networks modelling; in particular, self-healing capabilities are implemented through distributed communication protocols that exploit redundant links to recover the connectivity of the system. We then analyze the effect of the level of redundancy on the resilience to multiple failures; in particular, we measure the fraction of nodes still served for increasing levels of network damages. Finally, we study the effects of redundancy under different connectivity patterns—from planar grids, to small-world, up to scale-free networks—on healing performances. Small-world topologies show that introducing some long-range connections in planar grids greatly enhances the resilience to multiple failures with performances comparable to the case of the most resilient (and least realistic) scale-free structures. Obvious applications of self-healing are in the important field of infrastructural networks like gas, power, water, oil distribution systems. PMID:24533065

  13. Fast fixation with a generic network structure

    NASA Astrophysics Data System (ADS)

    Baxter, Gareth J.; Blythe, Richard A.; McKane, Alan J.

    2012-09-01

    We investigate the dynamics of a broad class of stochastic copying processes on a network that includes examples from population genetics (spatially structured Wright-Fisher models), ecology (Hubbell-type models), linguistics (the utterance selection model), and opinion dynamics (the voter model) as special cases. These models all have absorbing states of fixation where all the nodes are in the same state. Earlier studies of these models showed that the mean time when this occurs can be made to grow as different powers of the network size by varying the degree distribution of the network. Here we demonstrate that this effect can also arise if one varies the asymmetry of the copying dynamics while holding the degree distribution constant. In particular, we show that the mean time to fixation can be accelerated even on homogeneous networks when certain nodes are very much more likely to be copied from than copied to. We further show that there is a complex interplay between degree distribution and asymmetry when they may covary, and that the results are robust to correlations in the network or the initial condition.

  14. Structural determinants of criticality in biological networks

    PubMed Central

    Valverde, Sergi; Ohse, Sebastian; Turalska, Malgorzata; West, Bruce J.; Garcia-Ojalvo, Jordi

    2015-01-01

    Many adaptive evolutionary systems display spatial and temporal features, such as long-range correlations, typically associated with the critical point of a phase transition in statistical physics. Empirical and theoretical studies suggest that operating near criticality enhances the functionality of biological networks, such as brain and gene networks, in terms for instance of information processing, robustness, and evolvability. While previous studies have explained criticality with specific system features, we still lack a general theory of critical behavior in biological systems. Here we look at this problem from the complex systems perspective, since in principle all critical biological circuits have in common the fact that their internal organization can be described as a complex network. An important question is how self-similar structure influences self-similar dynamics. Modularity and heterogeneity, for instance, affect the location of critical points and can be used to tune the system toward criticality. We review and discuss recent studies on the criticality of neuronal and genetic networks, and discuss the implications of network theory when assessing the evolutionary features of criticality. PMID:26005422

  15. Community structure in the phonological network.

    PubMed

    Siew, Cynthia S Q

    2013-01-01

    Community structure, which refers to the presence of densely connected groups within a larger network, is a common feature of several real-world networks from a variety of domains such as the human brain, social networks of hunter-gatherers and business organizations, and the World Wide Web (Porter et al., 2009). Using a community detection technique known as the Louvain optimization method, 17 communities were extracted from the giant component of the phonological network described in Vitevitch (2008). Additional analyses comparing the lexical and phonological characteristics of words in these communities against words in randomly generated communities revealed several novel discoveries. Larger communities tend to consist of short, frequent words of high degree and low age of acquisition ratings, and smaller communities tend to consist of longer, less frequent words of low degree and high age of acquisition ratings. Real communities also contained fewer different phonological segments compared to random communities, although the number of occurrences of phonological segments found in real communities was much higher than that of the same phonological segments in random communities. Interestingly, the observation that relatively few biphones occur very frequently and a large number of biphones occur rarely within communities mirrors the pattern of the overall frequency of words in a language (Zipf, 1935). The present findings have important implications for understanding the dynamics of activation spread among words in the phonological network that are relevant to lexical processing, as well as understanding the mechanisms that underlie language acquisition and the evolution of language.

  16. Inner structure of capital control networks

    NASA Astrophysics Data System (ADS)

    Battiston, Stefano

    2004-07-01

    We study the topological structure of the network of shareholding relationships in the Italian stock market (MIB) and in two US stock markets (NYSE and NASDAQ). The portfolio diversification and the wealth invested on the market by economical agents have been shown in our previous work to have all a power law behavior. However, a further investigation shows that the inner structure of the capital control network are not at all the same across markets. The shareholding network is a weighted graph, therefore we introduce two quantities analogous to in-degree and out-degree for weighted graphs which measure, respectively: the number of effective shareholders of a stock and the number of companies effectively controlled by a single holder. Combining the information carried by the distributions of these two quantities we are able to extract the backbone of each market and we find that while the MIB splits into several separated groups of interest, the US markets is characterized by very large holders sharing control on overlapping subsets of stocks. This method seems promising for the analysis of the topology of capital control networks in general and not only in the stock market.

  17. Cu-PDC-bpa solid coordination frameworks (PDC=2,5-pyrindinedicarboxylate; bpa=1,2-DI(4-pyridil)ethane)): 2D and 3D structural flexibility producing a 3-c herringbone array next to ideal

    NASA Astrophysics Data System (ADS)

    Llano-Tomé, Francisco; Bazán, Begoña; Urtiaga, Miren-Karmele; Barandika, Gotzone; Antonia Señarís-Rodríguez, M.; Sánchez-Andújar, Manuel; Arriortua, María-Isabel

    2015-10-01

    Combination of polycarboxylate anions and dipyridyl ligands is an effective strategy to produce solid coordination frameworks (SCF) which are crystalline materials based on connections between metal ions through organic ligands. In this context, this work is focused on two novel CuII-based SCFs exhibiting PDC (2,5-pyridinedicarboxylate) and bpa (1,2-di(4-pyridyl)ethane), being the first structures reported in literature containing both ligands. Chemical formula are [Cu2[(PDC)2(bpa)(H2O)2]·3H2O·DMF (1), and [Cu2(PDC)2(bpa)(H2O)2]·7H2O (2), where DMF is dimethylformamide. Compounds 1 and 2 have been characterized by means of X-ray diffraction (XRD), infrared spectroscopy (IR), thermogravimetric (TG) analysis, differential thermal analysis (DTA) and dielectric measurements. The crystallographic analysis revealed that compounds 1 and 2 can be described as herringbone-type layers formed by helicoidal Cu-PDC-Cu chains connected through bpa ligands. Solvent molecules are crystallized between the layers, providing the inter-layer connections through hydrogen bonds. Differences between both compounds are attributable to the flexibility of bpa (in 2D) as well as to the 3D packing of the layers which is solvent dependent. This fact results in the fact that compound 2 is the most regular 3-c herringbone array reported so far. The structural dynamism of these networks is responsible for the crystalline to-amorphous to-crystalline (CAC) transformation from compound 1 to compound 2. Crystallochemical features for both compounds have also been studied and compared to similar 3-connected herringbone-arrays.

  18. Internal Photoemission Spectroscopy of 2-D Materials

    NASA Astrophysics Data System (ADS)

    Nguyen, Nhan; Li, Mingda; Vishwanath, Suresh; Yan, Rusen; Xiao, Shudong; Xing, Huili; Cheng, Guangjun; Hight Walker, Angela; Zhang, Qin

    Recent research has shown the great benefits of using 2-D materials in the tunnel field-effect transistor (TFET), which is considered a promising candidate for the beyond-CMOS technology. The on-state current of TFET can be enhanced by engineering the band alignment of different 2D-2D or 2D-3D heterostructures. Here we present the internal photoemission spectroscopy (IPE) approach to determine the band alignments of various 2-D materials, in particular SnSe2 and WSe2, which have been proposed for new TFET designs. The metal-oxide-2-D semiconductor test structures are fabricated and characterized by IPE, where the band offsets from the 2-D semiconductor to the oxide conduction band minimum are determined by the threshold of the cube root of IPE yields as a function of photon energy. In particular, we find that SnSe2 has a larger electron affinity than most semiconductors and can be combined with other semiconductors to form near broken-gap heterojunctions with low barrier heights which can produce a higher on-state current. The details of data analysis of IPE and the results from Raman spectroscopy and spectroscopic ellipsometry measurements will also be presented and discussed.

  19. Formation and properties of a terpyridine-based 2D MOF on the surface of water

    NASA Astrophysics Data System (ADS)

    Koitz, Ralph; Hutter, Jürg; Iannuzzi, Marcella

    2016-06-01

    Two-dimensional networks inspired by graphene are of prime importance in nanoscience. We present a computational study of an infinite molecular sheet confined on a water surface to assess its properties and formation mechanism. Terpyridine-based ligand molecules are interlinked by Zn ions to form an extended 2D metal-organic framework. We show that the network is stable on the water surface, and that the substrate affects the dynamic properties of the sheet, exhibiting a confining effect and flattening the sheet by 30%. We use metadynamics to characterize the process of network formation and breaking and determine an intra-network binding energy of 143 kJ mol‑1. Based on this mechanistic insight we propose that the 2D network strength can be tuned by varying the rigidity of the ligand through its chemical structure.

  20. Structural Connectivity Networks of Transgender People

    PubMed Central

    Hahn, Andreas; Kranz, Georg S.; Küblböck, Martin; Kaufmann, Ulrike; Ganger, Sebastian; Hummer, Allan; Seiger, Rene; Spies, Marie; Winkler, Dietmar; Kasper, Siegfried; Windischberger, Christian; Swaab, Dick F.; Lanzenberger, Rupert

    2015-01-01

    Although previous investigations of transsexual people have focused on regional brain alterations, evaluations on a network level, especially those structural in nature, are largely missing. Therefore, we investigated the structural connectome of 23 female-to-male (FtM) and 21 male-to-female (MtF) transgender patients before hormone therapy as compared with 25 female and 25 male healthy controls. Graph theoretical analysis of whole-brain probabilistic tractography networks (adjusted for differences in intracranial volume) showed decreased hemispheric connectivity ratios of subcortical/limbic areas for both transgender groups. Subsequent analysis revealed that this finding was driven by increased interhemispheric lobar connectivity weights (LCWs) in MtF transsexuals and decreased intrahemispheric LCWs in FtM patients. This was further reflected on a regional level, where the MtF group showed mostly increased local efficiencies and FtM patients decreased values. Importantly, these parameters separated each patient group from the remaining subjects for the majority of significant findings. This work complements previously established regional alterations with important findings of structural connectivity. Specifically, our data suggest that network parameters may reflect unique characteristics of transgender patients, whereas local physiological aspects have been shown to represent the transition from the biological sex to the actual gender identity. PMID:25217469

  1. Structural Connectivity Networks of Transgender People.

    PubMed

    Hahn, Andreas; Kranz, Georg S; Küblböck, Martin; Kaufmann, Ulrike; Ganger, Sebastian; Hummer, Allan; Seiger, Rene; Spies, Marie; Winkler, Dietmar; Kasper, Siegfried; Windischberger, Christian; Swaab, Dick F; Lanzenberger, Rupert

    2015-10-01

    Although previous investigations of transsexual people have focused on regional brain alterations, evaluations on a network level, especially those structural in nature, are largely missing. Therefore, we investigated the structural connectome of 23 female-to-male (FtM) and 21 male-to-female (MtF) transgender patients before hormone therapy as compared with 25 female and 25 male healthy controls. Graph theoretical analysis of whole-brain probabilistic tractography networks (adjusted for differences in intracranial volume) showed decreased hemispheric connectivity ratios of subcortical/limbic areas for both transgender groups. Subsequent analysis revealed that this finding was driven by increased interhemispheric lobar connectivity weights (LCWs) in MtF transsexuals and decreased intrahemispheric LCWs in FtM patients. This was further reflected on a regional level, where the MtF group showed mostly increased local efficiencies and FtM patients decreased values. Importantly, these parameters separated each patient group from the remaining subjects for the majority of significant findings. This work complements previously established regional alterations with important findings of structural connectivity. Specifically, our data suggest that network parameters may reflect unique characteristics of transgender patients, whereas local physiological aspects have been shown to represent the transition from the biological sex to the actual gender identity.

  2. Three new 2-D metal-organic frameworks containing 1-D metal chains bridged by N-benzesulfonyl-glutamic acid: Syntheses, crystal structures and properties

    SciTech Connect

    Ma Lufang; Huo Xiankuan; Wang Liya Wang Jiange; Fan Yaoting

    2007-05-15

    To explore the possibility of obtaining the metal-organic frameworks (MOFs) bearing the bsgluH{sub 2} ligand, two new Cd(II) and one Cu(II) coordination polymers, [Cd(bsglu)(bipy)] {sub n} (1), [Cd(bsglu).(H{sub 2}O)] {sub n} (2) and {l_brace}[Cu{sub 2}(bsglu){sub 2}(bipy){sub 2}].4H{sub 2}O{r_brace} {sub n} (3) (bsglu=N-benzesulfonyl-glutamic acid bianion, bipy=2,2'-bipyridine) were synthesized and characterized by IR, elemental analysis and X-ray diffraction analysis. Compounds 1 and 3 exhibit one-dimensional coordination chains, which are further connected to form two-dimensional supramolecular networks through {pi}-{pi} aromatic stacking interactions in a novel zipper-like way. Compound 2 presents a two-dimensional layer structure. To the best of our knowledge, 2 is the first two-dimensional complex formed from transition metal and bsgluH{sub 2} ligand. Interestingly, the bsglu anion exhibits remarkable versatile coordination modes in these complexes. Fluorescent analyses show that 1 exhibits photoluminescence in the solid state. Magnetic measurements for 3 revealed that the Cu(II) chain exhibit a weak antiferromagnetic behavior with a J value of -0.606 cm{sup -1}. - Graphical abstract: Three new complexes, [Cd(bsglu)(bipy)] {sub n} (1), [Cd(bsglu).(H{sub 2}O)] {sub n} (2) and {l_brace}[Cu{sub 2}(bsglu){sub 2}(bipy){sub 2}].4H{sub 2}O{r_brace} {sub n} (3), constructed from Cd(II) or Cu(II) salt with N-benzesulfonyl-glutamic acid were synthesized and characterized. Compounds 1 and 3 exhibit one-dimensional chains which are further connected to form two-dimensional supramolecular networks through {pi}-{pi} aromatic stacking interactions in a novel zipper-like way. Compound 2 presents a two-dimensional layer structure. Luminescence of 1 and magnetic properties of 3 are also investigated.

  3. Imidization induced structural changes of 6FDA-ODA poly(amic acid) by two-dimensional (2D) infrared correlation spectroscopy

    NASA Astrophysics Data System (ADS)

    Seo, Hyemi; Chae, Boknam; Im, Ji Hyuk; Jung, Young Mee; Lee, Seung Woo

    2014-07-01

    Two-dimensional (2D) gradient mapping method and 2D correlation analysis of in situ FTIR spectra were used to probe the thermal imidization-induced spectral changes in 6FDA-ODA poly(amic acid) (PAA) films prepared by a reaction of 4,4‧-(hexafluoroisopropylidene)diphthalic anhydride (6FDA) and 4,4‧-oxydianiline (ODA) in N,N‧-dimethylacetamide. Large spectral changes in the in situ FTIR spectra of 6FDA-ODA PAA film were observed in the range, 130-230 °C. The thermal imidization of 6FDA-ODA PAA films strongly affects the spectral changes in amic acid groups in the PAA unit. The spectral change in the amic acid groups occurred before those of the imide ring. The cyclic anhydrides, isoimdes and intermolecular links are present together with the imide ring in the thermally-cured 6FDA-ODA PAA films.

  4. 2-d Finite Element Code Postprocessor

    1996-07-15

    ORION is an interactive program that serves as a postprocessor for the analysis programs NIKE2D, DYNA2D, TOPAZ2D, and CHEMICAL TOPAZ2D. ORION reads binary plot files generated by the two-dimensional finite element codes currently used by the Methods Development Group at LLNL. Contour and color fringe plots of a large number of quantities may be displayed on meshes consisting of triangular and quadrilateral elements. ORION can compute strain measures, interface pressures along slide lines, reaction forcesmore » along constrained boundaries, and momentum. ORION has been applied to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.« less

  5. NUBOW-2D Inelastic

    2002-01-31

    This program solves the two-dimensional mechanical equilbrium configuration of a core restraint system, which is subjected to radial temperature and flux gradients, on a time increment basis. At each time increment, the code calculates the irradiation creep and swelling strains for each duct from user-specified creep and swelling correlations. Using the calculated thermal bowing, inelastic bowing and the duct dilation, the corresponding equilibrium forces, beam deflections, total beam displacements, and structural reactivity changes are calculated.

  6. Optimizing Dynamical Network Structure for Pinning Control.

    PubMed

    Orouskhani, Yasin; Jalili, Mahdi; Yu, Xinghuo

    2016-04-12

    Controlling dynamics of a network from any initial state to a final desired state has many applications in different disciplines from engineering to biology and social sciences. In this work, we optimize the network structure for pinning control. The problem is formulated as four optimization tasks: i) optimizing the locations of driver nodes, ii) optimizing the feedback gains, iii) optimizing simultaneously the locations of driver nodes and feedback gains, and iv) optimizing the connection weights. A newly developed population-based optimization technique (cat swarm optimization) is used as the optimization method. In order to verify the methods, we use both real-world networks, and model scale-free and small-world networks. Extensive simulation results show that the optimal placement of driver nodes significantly outperforms heuristic methods including placing drivers based on various centrality measures (degree, betweenness, closeness and clustering coefficient). The pinning controllability is further improved by optimizing the feedback gains. We also show that one can significantly improve the controllability by optimizing the connection weights.

  7. Optimizing Dynamical Network Structure for Pinning Control

    NASA Astrophysics Data System (ADS)

    Orouskhani, Yasin; Jalili, Mahdi; Yu, Xinghuo

    2016-04-01

    Controlling dynamics of a network from any initial state to a final desired state has many applications in different disciplines from engineering to biology and social sciences. In this work, we optimize the network structure for pinning control. The problem is formulated as four optimization tasks: i) optimizing the locations of driver nodes, ii) optimizing the feedback gains, iii) optimizing simultaneously the locations of driver nodes and feedback gains, and iv) optimizing the connection weights. A newly developed population-based optimization technique (cat swarm optimization) is used as the optimization method. In order to verify the methods, we use both real-world networks, and model scale-free and small-world networks. Extensive simulation results show that the optimal placement of driver nodes significantly outperforms heuristic methods including placing drivers based on various centrality measures (degree, betweenness, closeness and clustering coefficient). The pinning controllability is further improved by optimizing the feedback gains. We also show that one can significantly improve the controllability by optimizing the connection weights.

  8. High divergent 2D grating

    NASA Astrophysics Data System (ADS)

    Wang, Jin; Ma, Jianyong; Zhou, Changhe

    2014-11-01

    A 3×3 high divergent 2D-grating with period of 3.842μm at wavelength of 850nm under normal incidence is designed and fabricated in this paper. This high divergent 2D-grating is designed by the vector theory. The Rigorous Coupled Wave Analysis (RCWA) in association with the simulated annealing (SA) is adopted to calculate and optimize this 2D-grating.The properties of this grating are also investigated by the RCWA. The diffraction angles are more than 10 degrees in the whole wavelength band, which are bigger than the traditional 2D-grating. In addition, the small period of grating increases the difficulties of fabrication. So we fabricate the 2D-gratings by direct laser writing (DLW) instead of traditional manufacturing method. Then the method of ICP etching is used to obtain the high divergent 2D-grating.

  9. Structure and Interactions in Neurofilament Networks

    NASA Astrophysics Data System (ADS)

    Jones, Jayna; Ojeda-Lopez, Miguel; Safinya, Cyrus

    2004-03-01

    Neurofilaments (NFs) are a major constituent of myelinated axons of nerve cells, which assemble from three subunit proteins of low, medium, and high molecular weight to form a 10 nm diameter rod with sidearms radiating from the center. The sidearm interactions impart structural stability and result in an oriented network of NFs running parallel to the axon. Over or under expression of NF subunits is related to abnormal NF-networks, which are known hallmarks of motor neuron diseases (ALS). Here, we reassemble NFs from subunit proteins purified from bovine spinal cord. We demonstrate the formation of the NF network in vitro where synchrotron x-ray scattering (SSRL) reveals a well-defined interfilament spacing while the defect structure in polarized optical microcopy shows the liquid crystalline nature. The spacing varies depending on subunit molar ratios and salt conditions and we relate this change to the mechanical stability of the lattice. This change in lattice spacing yields insight into the stabilizing interactions between the NF sidearms. Supported by NSF DMR- 0203755, CTS-0103516, and NIH GM-59288.

  10. Measuring structural similarity in large online networks.

    PubMed

    Shi, Yongren; Macy, Michael

    2016-09-01

    Structural similarity based on bipartite graphs can be used to detect meaningful communities, but the networks have been tiny compared to massive online networks. Scalability is important in applications involving tens of millions of individuals with highly skewed degree distributions. Simulation analysis holding underlying similarity constant shows that two widely used measures - Jaccard index and cosine similarity - are biased by the distribution of out-degree in web-scale networks. However, an alternative measure, the Standardized Co-incident Ratio (SCR), is unbiased. We apply SCR to members of Congress, musical artists, and professional sports teams to show how massive co-following on Twitter can be used to map meaningful affiliations among cultural entities, even in the absence of direct connections to one another. Our results show how structural similarity can be used to map cultural alignments and demonstrate the potential usefulness of social media data in the study of culture, politics, and organizations across the social and behavioral sciences. PMID:27480374

  11. Optical modulators with 2D layered materials

    NASA Astrophysics Data System (ADS)

    Sun, Zhipei; Martinez, Amos; Wang, Feng

    2016-04-01

    Light modulation is an essential operation in photonics and optoelectronics. With existing and emerging technologies increasingly demanding compact, efficient, fast and broadband optical modulators, high-performance light modulation solutions are becoming indispensable. The recent realization that 2D layered materials could modulate light with superior performance has prompted intense research and significant advances, paving the way for realistic applications. In this Review, we cover the state of the art of optical modulators based on 2D materials, including graphene, transition metal dichalcogenides and black phosphorus. We discuss recent advances employing hybrid structures, such as 2D heterostructures, plasmonic structures, and silicon and fibre integrated structures. We also take a look at the future perspectives and discuss the potential of yet relatively unexplored mechanisms, such as magneto-optic and acousto-optic modulation.

  12. Structure Learning in Power Distribution Networks

    SciTech Connect

    Deka, Deepjyoti; Chertkov, Michael; Backhaus, Scott N.

    2015-01-13

    Traditionally power distribution networks are either not observable or only partially observable. This complicates development and implementation of new smart grid technologies, such as these related to demand response, outage detection and management, and improved load-monitoring. Here, inspired by proliferation of the metering technology, we discuss statistical estimation problems in structurally loopy but operationally radial distribution grids consisting in learning operational layout of the network from measurements, e.g. voltage data, which are either already available or can be made available with a relatively minor investment. Our newly suggested algorithms apply to a wide range of realistic scenarios. The algorithms are also computationally efficient – polynomial in time – which is proven theoretically and illustrated computationally on a number of test cases. The technique developed can be applied to detect line failures in real time as well as to understand the scope of possible adversarial attacks on the grid.

  13. THE STRUCTURE OF CRITICAL CARE TRANSFER NETWORKS

    PubMed Central

    Iwashyna, Theodore J.; Christie, Jason D.; Moody, James; Kahn, Jeremy M.; Asch, David A.

    2009-01-01

    Rationale Moving patients from low performing hospitals to high performing hospitals may improve patient outcomes. These transfers may be particularly important in critical care, where small relative improvements can yield substantial absolute changes in survival. Objective To characterize the existing critical care network in terms of the pattern of transfers. Methods In a retrospective cohort study, the nationwide 2005 Medicare fee-for-service claims were used to identify the interhospital transfer of critically ill patients, defined as instances where patients used critical care services in 2 temporally adjacent hospitalizations. Measurements We measured the characteristics of the interhospital transfer network and the extent to which ICU patients are referred towards each hospital in that network, a continuous quantitative measure at the hospital-level known as centrality. We evaluated associations between hospital centrality and organizational, medical, surgical and radiologic capabilities. Results There were 47,820 transfers of critically ill patients among 3,308 hospitals. 4.5% of all critical care stays of any length involved an inter-hospital critical care transfer. Hospitals transferred out to a mean of 4.4 other hospitals. More central hospital position was associated with multiple indicators of increased capability. Hospital characteristics explained 40.7% of the variance in hospitals’ centrality. Conclusions Critical care transfers are common, and traverse an informal but structured network. The centrality of a hospital is associated with increased capability in delivery of services, suggesting that existing transfers generally direct patients toward better resourced hospitals. Studies of this network promise further improvements in patient outcomes and efficiency of care. PMID:19536030

  14. Information diversity in structure and dynamics of simulated neuronal networks.

    PubMed

    Mäki-Marttunen, Tuomo; Aćimović, Jugoslava; Nykter, Matti; Kesseli, Juha; Ruohonen, Keijo; Yli-Harja, Olli; Linne, Marja-Leena

    2011-01-01

    Neuronal networks exhibit a wide diversity of structures, which contributes to the diversity of the dynamics therein. The presented work applies an information theoretic framework to simultaneously analyze structure and dynamics in neuronal networks. Information diversity within the structure and dynamics of a neuronal network is studied using the normalized compression distance. To describe the structure, a scheme for generating distance-dependent networks with identical in-degree distribution but variable strength of dependence on distance is presented. The resulting network structure classes possess differing path length and clustering coefficient distributions. In parallel, comparable realistic neuronal networks are generated with NETMORPH simulator and similar analysis is done on them. To describe the dynamics, network spike trains are simulated using different network structures and their bursting behaviors are analyzed. For the simulation of the network activity the Izhikevich model of spiking neurons is used together with the Tsodyks model of dynamical synapses. We show that the structure of the simulated neuronal networks affects the spontaneous bursting activity when measured with bursting frequency and a set of intraburst measures: the more locally connected networks produce more and longer bursts than the more random networks. The information diversity of the structure of a network is greatest in the most locally connected networks, smallest in random networks, and somewhere in between in the networks between order and disorder. As for the dynamics, the most locally connected networks and some of the in-between networks produce the most complex intraburst spike trains. The same result also holds for sparser of the two considered network densities in the case of full spike trains.

  15. Improving Network Structure can lead to Functional Failures.

    PubMed

    Pade, Jan Philipp; Pereira, Tiago

    2015-05-19

    In many real-world networks the ability to synchronize is a key property for their performance. Recent work on undirected networks with diffusive interaction revealed that improvements in the network connectivity such as making the network more connected and homogeneous enhances synchronization. However, real-world networks have directed and weighted connections. In such directed networks, understanding the impact of structural changes on the network performance remains a major challenge. Here, we show that improving the structure of a directed network can lead to a failure in the network function. For instance, introducing new links to reduce the minimum distance between nodes can lead to instabilities in the synchronized motion. This effect only occurs in directed networks. Our results allow to identify the dynamical importance of a link and thereby have a major impact on the design and control of directed networks.

  16. Generates 2D Input for DYNA NIKE & TOPAZ

    SciTech Connect

    Hallquist, J. O.; Sanford, Larry

    1996-07-15

    MAZE is an interactive program that serves as an input and two-dimensional mesh generator for DYNA2D, NIKE2D, TOPAZ2D, and CHEMICAL TOPAZ2D. MAZE also generates a basic template for ISLAND input. MAZE has been applied to the generation of input data to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  17. MAZE96. Generates 2D Input for DYNA NIKE & TOPAZ

    SciTech Connect

    Sanford, L.; Hallquist, J.O.

    1992-02-24

    MAZE is an interactive program that serves as an input and two-dimensional mesh generator for DYNA2D, NIKE2D, TOPAZ2D, and CHEMICAL TOPAZ2D. MAZE also generates a basic template for ISLAND input. MAZE has been applied to the generation of input data to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  18. Structure and Response in the World Trade Network

    NASA Astrophysics Data System (ADS)

    He, Jiankui; Deem, Michael W.

    2010-11-01

    We examine how the structure of the world trade network has been shaped by globalization and recessions over the last 40 years. We show that by treating the world trade network as an evolving system, theory predicts the trade network is more sensitive to recessionary shocks and recovers more slowly from them now than it did 40 years ago, due to structural changes in the world trade network induced by globalization. We also show that recession-induced change to the world trade network leads to an increased hierarchical structure of the global trade network for a few years after the recession.

  19. Soil Porous Structure as Heterogeneous Networks

    NASA Astrophysics Data System (ADS)

    Cárdenas, J. P.; Santiago, A.; Losada, J. C.; Borondo, F.; Benito, R. M.

    2010-05-01

    In this paper we present an application of the Complex Network theory to Geosciences. In particular, we show the implementation of the Heterogeneous Preferential Attachment (HPA) model [1] as a new way to quantify the structure of porous soils and closer relate them with soil texture. In the HPA model, already introduced in this context [2], pores are considered as nodes and their properties, such as position and size, are described by fixed states in a metric space. An affinity function is introduced in the HPA soil model in order to bias the attachment probabilities of links between pores according to their properties and soil texture. We perform an analytical study of the connectivity distributions of pores, P(k), and develop a numerical analysis for the HPA soil model considering a combination of parameters corresponding to eleven empirical soil samples with different physical properties and five different textures. [1] A. Santiago and R. M. Benito, An extended formalism for preferential attachment in heterogeneous complex networks, Europhysics Letters, 82 (2008) 58004. [2] A. Santiago, J.P. Cárdenas, J.C. Losada, R.M. Benito, A.M. Tarquis and F. Borondo, Multiscaling of porous soils as heterogeneous complex networks, Nonlinear Processes in Geophysics, 15 (2008) 893-902.

  20. Dynamics and control of diseases in networks with community structure.

    PubMed

    Salathé, Marcel; Jones, James H

    2010-04-08

    The dynamics of infectious diseases spread via direct person-to-person transmission (such as influenza, smallpox, HIV/AIDS, etc.) depends on the underlying host contact network. Human contact networks exhibit strong community structure. Understanding how such community structure affects epidemics may provide insights for preventing the spread of disease between communities by changing the structure of the contact network through pharmaceutical or non-pharmaceutical interventions. We use empirical and simulated networks to investigate the spread of disease in networks with community structure. We find that community structure has a major impact on disease dynamics, and we show that in networks with strong community structure, immunization interventions targeted at individuals bridging communities are more effective than those simply targeting highly connected individuals. Because the structure of relevant contact networks is generally not known, and vaccine supply is often limited, there is great need for efficient vaccination algorithms that do not require full knowledge of the network. We developed an algorithm that acts only on locally available network information and is able to quickly identify targets for successful immunization intervention. The algorithm generally outperforms existing algorithms when vaccine supply is limited, particularly in networks with strong community structure. Understanding the spread of infectious diseases and designing optimal control strategies is a major goal of public health. Social networks show marked patterns of community structure, and our results, based on empirical and simulated data, demonstrate that community structure strongly affects disease dynamics. These results have implications for the design of control strategies.

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

    PubMed Central

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

    2016-01-01

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

  2. 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.

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

    PubMed

    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.

  4. Computing with structured connections networks. Technical report

    SciTech Connect

    Feldman, J.A.; Fanty, M.A.; Goddard, N.; Lynne, K.

    1987-04-01

    Rapid advances both in the neurosciences and in computer science are beginning to lead to a new interest in computational models linking animal brains and behavior. In computer science, there is a large and growing body of knowledge about parallel computation and another, largely separate, science of artificial intelligence. The idea of looking directly at massively parallel realizations of intelligent activity promises to be fruitful for the study of both natural and artificial computations. Much attention has been directed towards the biological implications of this interdisciplinary effort, but there are equally important relations with computational theory, hardware and software. This article focuses on the design and use of massively parallel computational models, particularly in artificial intelligence. Much of the recent work on massively parallel computation has been carried out by physicists and examines the emergent behavior of large, unstructured collections of computing units. We are more concerned with how one can design, realize and analyze networks that embody the specific computational structures needed to solve hard problems. Adaptation and learning are treated as ways to improve structured networks, not as a replacement for analysis and design.

  5. Network models for 2D disordered superconductors

    NASA Astrophysics Data System (ADS)

    Kagalovsky, Victor; Horovitz, Baruch; Avishai, Yshai

    2004-04-01

    We study new random matrix symmetry classes which arise in models of non-interacting quasi-particles in disordered superconductors. Within the Altland-Zirnbauer classification scheme these are class C (with time-reversal symmetry broken and spin-rotaion invariance intact), and class D where both symmetries are broken. Preliminary studies of the two remaining symmetry classes CI and DIII are briefly mentioned. New results are presented pertaining to the 3d realization of class C, which, physically, corresponds to a layered superconductor.

  6. Effect of random structure on permeability and heat transfer characteristics for flow in 2D porous medium based on MRT lattice Boltzmann method

    NASA Astrophysics Data System (ADS)

    Yang, PeiPei; Wen, Zhi; Dou, RuiFeng; Liu, Xunliang

    2016-08-01

    Flow and heat transfer through a 2D random porous medium are studied by using the lattice Boltzmann method (LBM). For the random porous medium, the influence of disordered cylinder arrangement on permeability and Nusselt number are investigated. Results indicate that the permeability and Nusselt number for different cylinder locations are unequal even with the same number and size of cylinders. New correlations for the permeability and coefficient b‧Den of the Forchheimer equation are proposed for random porous medium composed of Gaussian distributed circular cylinders. Furthermore, a general set of heat transfer correlations is proposed and compared with existing experimental data and empirical correlations. Our results show that the Nu number increases with the increase of the porosity, hence heat transfer is found to be accurate considering the effect of porosity.

  7. Low-rank network decomposition reveals structural characteristics of small-world networks

    NASA Astrophysics Data System (ADS)

    Barranca, Victor J.; Zhou, Douglas; Cai, David

    2015-12-01

    Small-world networks occur naturally throughout biological, technological, and social systems. With their prevalence, it is particularly important to prudently identify small-world networks and further characterize their unique connection structure with respect to network function. In this work we develop a formalism for classifying networks and identifying small-world structure using a decomposition of network connectivity matrices into low-rank and sparse components, corresponding to connections within clusters of highly connected nodes and sparse interconnections between clusters, respectively. We show that the network decomposition is independent of node indexing and define associated bounded measures of connectivity structure, which provide insight into the clustering and regularity of network connections. While many existing network characterizations rely on constructing benchmark networks for comparison or fail to describe the structural properties of relatively densely connected networks, our classification relies only on the intrinsic network structure and is quite robust with respect to changes in connection density, producing stable results across network realizations. Using this framework, we analyze several real-world networks and reveal new structural properties, which are often indiscernible by previously established characterizations of network connectivity.

  8. Low-rank network decomposition reveals structural characteristics of small-world networks.

    PubMed

    Barranca, Victor J; Zhou, Douglas; Cai, David

    2015-12-01

    Small-world networks occur naturally throughout biological, technological, and social systems. With their prevalence, it is particularly important to prudently identify small-world networks and further characterize their unique connection structure with respect to network function. In this work we develop a formalism for classifying networks and identifying small-world structure using a decomposition of network connectivity matrices into low-rank and sparse components, corresponding to connections within clusters of highly connected nodes and sparse interconnections between clusters, respectively. We show that the network decomposition is independent of node indexing and define associated bounded measures of connectivity structure, which provide insight into the clustering and regularity of network connections. While many existing network characterizations rely on constructing benchmark networks for comparison or fail to describe the structural properties of relatively densely connected networks, our classification relies only on the intrinsic network structure and is quite robust with respect to changes in connection density, producing stable results across network realizations. Using this framework, we analyze several real-world networks and reveal new structural properties, which are often indiscernible by previously established characterizations of network connectivity.

  9. Correlation between structure and temperature in prokaryotic metabolic networks

    PubMed Central

    Takemoto, Kazuhiro; Nacher, Jose C; Akutsu, Tatsuya

    2007-01-01

    Background In recent years, an extensive characterization of network structures has been made in an effort to elucidate design principles of metabolic networks, providing valuable insights into the functional organization and the evolutionary history of organisms. However, previous analyses have not discussed the effects of environmental factors (i.e., exogenous forces) in shaping network structures. In this work, we investigate the effect of temperature, which is one of the environmental factors that may have contributed to shaping structures of metabolic networks. Results For this, we investigate the correlations between several structural properties characterized by graph metrics like the edge density, the degree exponent, the clustering coefficient, and the subgraph concentration in the metabolic networks of 113 prokaryotes and optimal growth temperature. As a result, we find that these structural properties are correlated with the optimal growth temperature. With increasing temperature, the edge density, the clustering coefficient and the subgraph concentration decrease and the degree exponent becomes large. Conclusion This result implies that the metabolic networks transit with temperature as follows. The density of chemical reactions becomes low, the connectivity of the networks becomes homogeneous such as random networks and both the network modularity, based on the graph-theoretic clustering coefficient, and the frequency of recurring subgraphs decay. In short, metabolic networks undergo a change from heterogeneous and high-modular structures to homogeneous and low-modular structures, such as random networks, with temperature. This finding may suggest that the temperature plays an important role in the design principles of metabolic networks. PMID:17711568

  10. Social inheritance can explain the structure of animal social networks

    PubMed Central

    Ilany, Amiyaal; Akçay, Erol

    2016-01-01

    The social network structure of animal populations has major implications for survival, reproductive success, sexual selection and pathogen transmission of individuals. But as of yet, no general theory of social network structure exists that can explain the diversity of social networks observed in nature, and serve as a null model for detecting species and population-specific factors. Here we propose a simple and generally applicable model of social network structure. We consider the emergence of network structure as a result of social inheritance, in which newborns are likely to bond with maternal contacts, and via forming bonds randomly. We compare model output with data from several species, showing that it can generate networks with properties such as those observed in real social systems. Our model demonstrates that important observed properties of social networks, including heritability of network position or assortative associations, can be understood as consequences of social inheritance. PMID:27352101

  11. Social inheritance can explain the structure of animal social networks.

    PubMed

    Ilany, Amiyaal; Akçay, Erol

    2016-01-01

    The social network structure of animal populations has major implications for survival, reproductive success, sexual selection and pathogen transmission of individuals. But as of yet, no general theory of social network structure exists that can explain the diversity of social networks observed in nature, and serve as a null model for detecting species and population-specific factors. Here we propose a simple and generally applicable model of social network structure. We consider the emergence of network structure as a result of social inheritance, in which newborns are likely to bond with maternal contacts, and via forming bonds randomly. We compare model output with data from several species, showing that it can generate networks with properties such as those observed in real social systems. Our model demonstrates that important observed properties of social networks, including heritability of network position or assortative associations, can be understood as consequences of social inheritance. PMID:27352101

  12. Electrical Transport and Network Percolation in Graphene and Boron Nitride Mixed-Platelet Structures.

    PubMed

    Debbarma, Rousan; Behura, Sanjay; Nguyen, Phong; Sreeprasad, T S; Berry, Vikas

    2016-04-01

    Percolating network of mixed 2D nanomaterials (2DNs) can leverage the unique electronic structures of different 2DNs, their interfacial doping, manipulable conduction pathways, and local traps. Here, we report on the percolation mechanism and electro-capacitive transport pathways of mixed-platelet network of hexagonal boron nitride (hBN) and reduced graphene oxide (rGO), two isostructural and isoelectronic 2DNs. The transport mechanism is explained in terms of electron hopping through isolated hBN defect traps between rGO (possibly via electron tunneling/hopping through "funneling" points). With optical bandgaps of 4.57 and 4.08 eV for the hBN-domains and 2.18 eV for the rGO domains, the network of hBN with rGO exhibits Poole-Frenkel emission-based transport with mean hopping gap of 1.12 nm (∼hBN trilayer) and an activation barrier of ∼15 ± 0.7 meV. Further, hBN (1.7 pF) has a 6-fold lower capacitance than 1:1 hBN:rGO, which has a resistance 2 orders of magnitude higher than that of rGO (1.46 MΩ). These carrier transport results can be applied to other multi-2DN networks for development of next-generation functional 2D-devices. PMID:27002378

  13. Functional approximation using artificial neural networks in structural mechanics

    NASA Technical Reports Server (NTRS)

    Alam, Javed; Berke, Laszlo

    1993-01-01

    The artificial neural networks (ANN) methodology is an outgrowth of research in artificial intelligence. In this study, the feed-forward network model that was proposed by Rumelhart, Hinton, and Williams was applied to the mapping of functions that are encountered in structural mechanics problems. Several different network configurations were chosen to train the available data for problems in materials characterization and structural analysis of plates and shells. By using the recall process, the accuracy of these trained networks was assessed.

  14. Non-experts' Recognition of Structure in Personal Network Data.

    PubMed

    Kennedy, David P; Green, Harold D; McCarty, Christopher; Tucker, Joan

    2011-08-01

    Network-based interventions are gaining prominence in the treatment of chronic illnesses; however, little is known about what aspects of network structure are easily identified by non-experts when shown network visualizations. This study examines which structural features are recognizable by non-experts. Nineteen non-experts were asked to pile-sort 68 network diagrams. Results were analyzed using multidimensional scaling, discriminant analysis, cluster analysis, and PROFIT analysis. Participants tended to sort networks along the dimensions of isolates and size of largest component, suggesting that interventions aimed at helping individuals understand and change their social environments could benefit from incorporating visualizations of social networks.

  15. Efficient Visible Quasi-2D Perovskite Light-Emitting Diodes.

    PubMed

    Byun, Jinwoo; Cho, Himchan; Wolf, Christoph; Jang, Mi; Sadhanala, Aditya; Friend, Richard H; Yang, Hoichang; Lee, Tae-Woo

    2016-09-01

    Efficient quasi-2D-structure perovskite light-emitting diodes (4.90 cd A(-1) ) are demonstrated by mixing a 3D-structured perovskite material (methyl ammonium lead bromide) and a 2D-structured perovskite material (phenylethyl ammonium lead bromide), which can be ascribed to better film uniformity, enhanced exciton confinement, and reduced trap density. PMID:27334788

  16. Efficient Visible Quasi-2D Perovskite Light-Emitting Diodes.

    PubMed

    Byun, Jinwoo; Cho, Himchan; Wolf, Christoph; Jang, Mi; Sadhanala, Aditya; Friend, Richard H; Yang, Hoichang; Lee, Tae-Woo

    2016-09-01

    Efficient quasi-2D-structure perovskite light-emitting diodes (4.90 cd A(-1) ) are demonstrated by mixing a 3D-structured perovskite material (methyl ammonium lead bromide) and a 2D-structured perovskite material (phenylethyl ammonium lead bromide), which can be ascribed to better film uniformity, enhanced exciton confinement, and reduced trap density.

  17. AnisWave 2D

    2004-08-01

    AnisWave2D is a 2D finite-difference code for a simulating seismic wave propagation in fully anisotropic materials. The code is implemented to run in parallel over multiple processors and is fully portable. A mesh refinement algorithm has been utilized to allow the grid-spacing to be tailored to the velocity model, avoiding the over-sampling of high-velocity materials that usually occurs in fixed-grid schemes.

  18. Distance metric learning for complex networks: Towards size-independent comparison of network structures

    NASA Astrophysics Data System (ADS)

    Aliakbary, Sadegh; Motallebi, Sadegh; Rashidian, Sina; Habibi, Jafar; Movaghar, Ali

    2015-02-01

    Real networks show nontrivial topological properties such as community structure and long-tail degree distribution. Moreover, many network analysis applications are based on topological comparison of complex networks. Classification and clustering of networks, model selection, and anomaly detection are just some applications of network comparison. In these applications, an effective similarity metric is needed which, given two complex networks of possibly different sizes, evaluates the amount of similarity between the structural features of the two networks. Traditional graph comparison approaches, such as isomorphism-based methods, are not only too time consuming but also inappropriate to compare networks with different sizes. In this paper, we propose an intelligent method based on the genetic algorithms for integrating, selecting, and weighting the network features in order to develop an effective similarity measure for complex networks. The proposed similarity metric outperforms state of the art methods with respect to different evaluation criteria.

  19. Numerical simulation of fibrous biomaterials with randomly distributed fiber network structure.

    PubMed

    Jin, Tao; Stanciulescu, Ilinca

    2016-08-01

    This paper presents a computational framework to simulate the mechanical behavior of fibrous biomaterials with randomly distributed fiber networks. A random walk algorithm is implemented to generate the synthetic fiber network in 2D used in simulations. The embedded fiber approach is then adopted to model the fibers as embedded truss elements in the ground matrix, which is essentially equivalent to the affine fiber kinematics. The fiber-matrix interaction is partially considered in the sense that the two material components deform together, but no relative movement is considered. A variational approach is carried out to derive the element residual and stiffness matrices for finite element method (FEM), in which material and geometric nonlinearities are both included. Using a data structure proposed to record the network geometric information, the fiber network is directly incorporated into the FEM simulation without significantly increasing the computational cost. A mesh sensitivity analysis is conducted to show the influence of mesh size on various simulation results. The proposed method can be easily combined with Monte Carlo (MC) simulations to include the influence of the stochastic nature of the network and capture the material behavior in an average sense. The computational framework proposed in this work goes midway between homogenizing the fiber network into the surrounding matrix and accounting for the fully coupled fiber-matrix interaction at the segment length scale, and can be used to study the connection between the microscopic structure and the macro-mechanical behavior of fibrous biomaterials with a reasonable computational cost. PMID:26342926

  20. Seismic Velocity Structure Across the Quebrada and Gofar Oceanic Transform Faults from 2D Refraction Tomography - A Comparison of Faults with High and Low Seismic Slip Deficits

    NASA Astrophysics Data System (ADS)

    Roland, E. C.; McGuire, J. J.; Collins, J. A.; Lizarralde, D.

    2009-12-01

    We perform two 2-D tomographic inversions using data collected as a part of the Quebrada-Discovery-Gofar (QDG) Transform Fault Active/Passive Experiment. The QDG transform faults are located in the southern Pacific Ocean and offset the East Pacific Rise (EPR) at approximately 4° south. In the spring of 2008, two ~100 km refraction profiles were collected, each using 8 short period Ocean Bottom Seismometers (OBS) from OBSIP and over 900 shots from the RV Marcus Langseth, across the easternmost segments of the Quebrada and Gofar transform faults. The two refraction profiles are modeled using a 2-D tomographic code that allows joint inversion of the Pg, PmP, and Pn arrivals (Korenaga et al., 2000). Variations in crustal velocity and thickness, as well as the width and depth extent of a significant low velocity zone within and below the transform valley provide some insight into the material properties of each of the fault-zones. Reduced seismic velocities that are 0.5 to over 1.0 km/s slower than velocities associated with the oceanic crust outside the fault zone may indicate the highly fractured fault zone lithology. The low velocity zone associated with the Quebrada fault also extends to the south of the active fault zone, beneath a fossil fault trace. Because Gofar is offset by an intratransform spreading center, we are able to compare ‘normal’ oceanic crust produced at the EPR to the south of the fault with crust associated with the ~15 km intratransform spreading center to the north. These two high slip rate (14 cm/yr) faults look similar morphologically and demonstrate comparable microseismicity characteristics, however their abilities to generate large earthquakes differ significantly. Gofar generates large earthquakes (Mw ~6) regularly every few years, but in the past 24 years only one large (Mw 5.6) event has been reliably located on Quebrada. The contrasting seismic behavior of these faults represents the range of behavior observed in the global

  1. Structure and Interactions in Neurofilament Networks

    NASA Astrophysics Data System (ADS)

    Jones, Jayna

    2005-03-01

    Neurofilaments (NFs) are a major constituent of nerve cell axons that assemble from three subunit proteins of low (NF-L), medium (NF-M), and high molecular weight (NF-H) to form a 10 nm diameter rod with radiating sidearms. The sidearm interactions result in an oriented network of NFs running parallel to the axon. Here, we reassemble NFs in vitro from varying weight ratios of two of the subunit proteins, NF-L and NF-M, purified from bovine spinal cord. We demonstrate the formation of the NF network where synchrotron x-ray scattering (SSRL) reveals a well-defined interfilament spacing, while the defect structure in polarized optical microcopy shows the liquid crystalline nature. The interfilament spacing varies depending on NF-M sidearm density and we relate this change to sidearm interactions. We show that at a low density of sidearms, repulsive forces dominate creating a lattice spacing that is regulated by the buffer volume. With an increasing sidearm density, the equilibrium interfilament spacing decreases as a result of competing repulsive and attractive forces. Supported by NIH GM-59288, NSF DMR- 0203755, & CTS-0404444.

  2. 2D quasi-planar or 3D structures? A comparison between CrBn(n = 2 - 10) wheel-like clusters and their corresponding 3D pyramidal clusters, and their hydrogen storage capability

    NASA Astrophysics Data System (ADS)

    Yildirim, E. K.

    2015-09-01

    In this study, we investigated stable structures for a transition metal atom-boron (CrB) wheel-like clusters and compared them with their corresponding 3D counterparts by means of density functional theory (DFT). In addition, hydrogen storage capability of the wheel-like system was investigated. All simulations were performed at the B3LYP/TZVP level of theory. We set out a complete route to the formation of CrB wheel-like clusters. Our results showed that, some of the clusters, investigated in this work (CrBn; n = 4, 6, 7, 8), either prefer to be in a 3D geometry rather than 2D quasi-planar or planar geometry. However, hydrogen doping has an interesting effect on both 2D quasi-planar and 3D geometries of this system. Simply it transforms the 3D structure, first, into a 2D quasi-planar, then a planar geometry. Furthermore, our results show that H-cluster interaction is too high for reversible hydrogen storage for these clusters.

  3. Utilizing Structures of CYP2D6 and BACE1 Complexes To Reduce Risk of Drug–Drug Interactions with a Novel Series of Centrally Efficacious BACE1 Inhibitors

    PubMed Central

    2016-01-01

    In recent years, the first generation of β-secretase (BACE1) inhibitors advanced into clinical development for the treatment of Alzheimer’s disease (AD). However, the alignment of drug-like properties and selectivity remains a major challenge. Herein, we describe the discovery of a novel class of potent, low clearance, CNS penetrant BACE1 inhibitors represented by thioamidine 5. Further profiling suggested that a high fraction of the metabolism (>95%) was due to CYP2D6, increasing the potential risk for victim-based drug–drug interactions (DDI) and variable exposure in the clinic due to the polymorphic nature of this enzyme. To guide future design, we solved crystal structures of CYP2D6 complexes with substrate 5 and its corresponding metabolic product pyrazole 6, which provided insight into the binding mode and movements between substrate/inhibitor complexes. Guided by the BACE1 and CYP2D6 crystal structures, we designed and synthesized analogues with reduced risk for DDI, central efficacy, and improved hERG therapeutic margins. PMID:25781223

  4. 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.

  5. Epidemic spreading on complex networks with community structures

    PubMed Central

    Stegehuis, Clara; van der Hofstad, Remco; van Leeuwaarden, Johan S. H.

    2016-01-01

    Many real-world networks display a community structure. We study two random graph models that create a network with similar community structure as a given network. One model preserves the exact community structure of the original network, while the other model only preserves the set of communities and the vertex degrees. These models show that community structure is an important determinant of the behavior of percolation processes on networks, such as information diffusion or virus spreading: the community structure can both enforce as well as inhibit diffusion processes. Our models further show that it is the mesoscopic set of communities that matters. The exact internal structures of communities barely influence the behavior of percolation processes across networks. This insensitivity is likely due to the relative denseness of the communities. PMID:27440176

  6. Epidemic spreading on complex networks with community structures.

    PubMed

    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

  7. 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.

  8. Evolving networks-Using past structure to predict the future

    NASA Astrophysics Data System (ADS)

    Shang, Ke-ke; Yan, Wei-sheng; Small, Michael

    2016-08-01

    Many previous studies on link prediction have focused on using common neighbors to predict the existence of links between pairs of nodes. More broadly, research into the structural properties of evolving temporal networks and temporal link prediction methods have recently attracted increasing attention. In this study, for the first time, we examine the use of links between a pair of nodes to predict their common neighbors and analyze the relationship between the weight and the structure in static networks, evolving networks, and in the corresponding randomized networks. We propose both new unweighted and weighted prediction methods and use six kinds of real networks to test our algorithms. In unweighted networks, we find that if a pair of nodes connect to each other in the current network, they will have a higher probability to connect common nodes both in the current and the future networks-and the probability will decrease with the increase of the number of neighbors. Furthermore, we find that the original networks have their particular structure and statistical characteristics which benefit link prediction. In weighted networks, the prediction algorithm performance of networks which are dominated by human factors decrease with the decrease of weight and are in general better in static networks. Furthermore, we find that geographical position and link weight both have significant influence on the transport network. Moreover, the evolving financial network has the lowest predictability. In addition, we find that the structure of non-social networks has more robustness than social networks. The structure of engineering networks has both best predictability and also robustness.

  9. Structure and formation of ant transportation networks

    PubMed Central

    Latty, Tanya; Ramsch, Kai; Ito, Kentaro; Nakagaki, Toshiyuki; Sumpter, David J. T.; Middendorf, Martin; Beekman, Madeleine

    2011-01-01

    Many biological systems use extensive networks for the transport of resources and information. Ants are no exception. How do biological systems achieve efficient transportation networks in the absence of centralized control and without global knowledge of the environment? Here, we address this question by studying the formation and properties of inter-nest transportation networks in the Argentine ant (Linepithema humile). We find that the formation of inter-nest networks depends on the number of ants involved in the construction process. When the number of ants is sufficient and networks do form, they tend to have short total length but a low level of robustness. These networks are topologically similar to either minimum spanning trees or Steiner networks. The process of network formation involves an initial construction of multiple links followed by a pruning process that reduces the number of trails. Our study thus illuminates the conditions under and the process by which minimal biological transport networks can be constructed. PMID:21288958

  10. Estimates of the statistical two-dimensional spatial structure in rain over a small network of disdrometers

    NASA Astrophysics Data System (ADS)

    Jameson, A. R.; Larsen, M. L.

    2016-06-01

    Microphysical understanding of the variability in rain requires a statistical characterization of different drop sizes both in time and in all dimensions of space. Temporally, there have been several statistical characterizations of raindrop counts. However, temporal and spatial structures are neither equivalent nor readily translatable. While there are recent reports of the one-dimensional spatial correlation functions in rain, they can only be assumed to represent the two-dimensional (2D) correlation function under the assumption of spatial isotropy. To date, however, there are no actual observations of the (2D) spatial correlation function in rain over areas. Two reasons for this deficiency are the fiscal and the physical impossibilities of assembling a dense network of instruments over even hundreds of meters much less over kilometers. Consequently, all measurements over areas will necessarily be sparsely sampled. A dense network of data must then be estimated using interpolations from the available observations. In this work, a network of 19 optical disdrometers over a 100 m by 71 m area yield observations of drop spectra every minute. These are then interpolated to a 1 m resolution grid. Fourier techniques then yield estimates of the 2D spatial correlation functions. Preliminary examples using this technique found that steadier, light rain decorrelates spatially faster than does the convective rain, but in both cases the 2D spatial correlation functions are anisotropic, reflecting an asymmetry in the physical processes influencing the rain reaching the ground not accounted for in numerical microphysical models.

  11. Temperature-induced structural phase transitions in a two-dimensional self-assembled network.

    PubMed

    Blunt, Matthew O; Adisoejoso, Jinne; Tahara, Kazukuni; Katayama, Keisuke; Van der Auweraer, Mark; Tobe, Yoshito; De Feyter, Steven

    2013-08-14

    Two-dimensional (2D) supramolecular self-assembly at liquid-solid interfaces is a thermodynamically complex process producing a variety of structures. The formation of multiple network morphologies from the same molecular building blocks is a common occurrence. We use scanning tunnelling microscopy (STM) to investigate a structural phase transition between a densely packed and a porous phase of an alkylated dehydrobenzo[12]annulene (DBA) derivative physisorbed at a solvent-graphite interface. The influence of temperature and concentration are studied and the results combined using a thermodynamic model to measure enthalpy and entropy changes associated with the transition. These experimental results are compared to corresponding values obtained from simulations and theoretical calculations. This comparison highlights the importance of considering the solvent when modeling porous self-assembled networks. The results also demonstrate the power of using structural phase transitions to study the thermodynamics of these systems and will have implications for the development of predictive models for 2D self-assembly.

  12. Health and the Structure of Adolescent Social Networks

    ERIC Educational Resources Information Center

    Haas, Steven A.; Schaefer, David R.; Kornienko, Olga

    2010-01-01

    Much research has explored the role of social networks in promoting health through the provision of social support. However, little work has examined how social networks themselves may be structured by health. This article investigates the link between individuals' health and the characteristics of their social network positions.We first develop…

  13. Detection of community structure in networks based on community coefficients

    NASA Astrophysics Data System (ADS)

    Lu, Hu; Wei, Hui

    2012-12-01

    Determining community structure in networks is fundamental to the analysis of the structural and functional properties of those networks, including social networks, computer networks, and biological networks. Modularity function Q, which was proposed by Newman and Girvan, was once the most widely used criterion for evaluating the partition of a network into communities. However, modularity Q is subject to a serious resolution limit. In this paper, we propose a new function for evaluating the partition of a network into communities. This is called community coefficient C. Using community coefficient C, we can automatically identify the ideal number of communities in the network, without any prior knowledge. We demonstrate that community coefficient C is superior to the modularity Q and does not have a resolution limit. We also compared the two widely used community structure partitioning methods, the hierarchical partitioning algorithm and the normalized cuts (Ncut) spectral partitioning algorithm. We tested these methods on computer-generated networks and real-world networks whose community structures were already known. The Ncut algorithm and community coefficient C were found to produce better results than hierarchical algorithms. Unlike several other community detection methods, the proposed method effectively partitioned the networks into different community structures and indicated the correct number of communities.

  14. Network structure, topology, and dynamics in generalized models of synchronization

    NASA Astrophysics Data System (ADS)

    Lerman, Kristina; Ghosh, Rumi

    2012-08-01

    Network structure is a product of both its topology and interactions between its nodes. We explore this claim using the paradigm of distributed synchronization in a network of coupled oscillators. As the network evolves to a global steady state, nodes synchronize in stages, revealing the network's underlying community structure. Traditional models of synchronization assume that interactions between nodes are mediated by a conservative process similar to diffusion. However, social and biological processes are often nonconservative. We propose a model of synchronization in a network of oscillators coupled via nonconservative processes. We study the dynamics of synchronization of a synthetic and real-world networks and show that the traditional and nonconservative models of synchronization reveal different structures within the same network.

  15. The National Biomedical Communications Network as a Developing Structure *

    PubMed Central

    Davis, Ruth M.

    1971-01-01

    The National Biomedical Communications Network has evolved both from a set of conceptual recommendations over the last twelve years and an accumulation of needs manifesting themselves in the requests of members of the medical community. With a short history of three years this network and its developing structure have exhibited most of the stresses of technology interfacing with customer groups, and of a structure attempting to build itself upon many existing fragmentary unconnected segments of a potentially viable resourcesharing capability. In addition to addressing these topics, the paper treats a design appropriate to any network devoted to information transfer in a special interest user community. It discusses fundamentals of network design, highlighting that network structure most appropriate to a national information network. Examples are given of cost analyses of information services and certain conjectures are offered concerning the roles of national networks. PMID:5542912

  16. 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.)

  17. Influence of Choice of Null Network on Small-World Parameters of Structural Correlation Networks

    PubMed Central

    Hosseini, S. M. Hadi; Kesler, Shelli R.

    2013-01-01

    In recent years, coordinated variations in brain morphology (e.g., volume, thickness) have been employed as a measure of structural association between brain regions to infer large-scale structural correlation networks. Recent evidence suggests that brain networks constructed in this manner are inherently more clustered than random networks of the same size and degree. Thus, null networks constructed by randomizing topology are not a good choice for benchmarking small-world parameters of these networks. In the present report, we investigated the influence of choice of null networks on small-world parameters of gray matter correlation networks in healthy individuals and survivors of acute lymphoblastic leukemia. Three types of null networks were studied: 1) networks constructed by topology randomization (TOP), 2) networks matched to the distributional properties of the observed covariance matrix (HQS), and 3) networks generated from correlation of randomized input data (COR). The results revealed that the choice of null network not only influences the estimated small-world parameters, it also influences the results of between-group differences in small-world parameters. In addition, at higher network densities, the choice of null network influences the direction of group differences in network measures. Our data suggest that the choice of null network is quite crucial for interpretation of group differences in small-world parameters of structural correlation networks. We argue that none of the available null models is perfect for estimation of small-world parameters for correlation networks and the relative strengths and weaknesses of the selected model should be carefully considered with respect to obtained network measures. PMID:23840672

  18. Influence of choice of null network on small-world parameters of structural correlation networks.

    PubMed

    Hosseini, S M Hadi; Kesler, Shelli R

    2013-01-01

    In recent years, coordinated variations in brain morphology (e.g., volume, thickness) have been employed as a measure of structural association between brain regions to infer large-scale structural correlation networks. Recent evidence suggests that brain networks constructed in this manner are inherently more clustered than random networks of the same size and degree. Thus, null networks constructed by randomizing topology are not a good choice for benchmarking small-world parameters of these networks. In the present report, we investigated the influence of choice of null networks on small-world parameters of gray matter correlation networks in healthy individuals and survivors of acute lymphoblastic leukemia. Three types of null networks were studied: 1) networks constructed by topology randomization (TOP), 2) networks matched to the distributional properties of the observed covariance matrix (HQS), and 3) networks generated from correlation of randomized input data (COR). The results revealed that the choice of null network not only influences the estimated small-world parameters, it also influences the results of between-group differences in small-world parameters. In addition, at higher network densities, the choice of null network influences the direction of group differences in network measures. Our data suggest that the choice of null network is quite crucial for interpretation of group differences in small-world parameters of structural correlation networks. We argue that none of the available null models is perfect for estimation of small-world parameters for correlation networks and the relative strengths and weaknesses of the selected model should be carefully considered with respect to obtained network measures.

  19. Basement blocks and basin inversion structures mapped using reprocessed Gulfrex 2D seismic data, Caribbean-South American oblique collisional zone

    NASA Astrophysics Data System (ADS)

    Escalona, A.; Sena, A.; Mann, P.

    2003-12-01

    We have reprocessed and reinterpreted more than 10,000 km of "Gulfrex" multi-channel 2D seismic reflection lines collected by Gulf Oil Corporation in 1972 along the northern margin of South America (offshore Venezuela and Trinidad). These digital data were donated to the University of Texas Institute for Geophysics and represent the largest single, digital reflection survey of the region. Reprocessing of these data included: format correction, filtering, post-stack multiple suppression, and fk migration. Reprocessed data were loaded and interpreted on a workstation. The data straddle a 2,000,000 km2 zone of Paleocene-Recent, time-transgressive, oblique collision between the Caribbean arc system and the passive continental margin of northern South America. Free-air, satellite gravity data shows the remarkable 1000-km-scale continuity of four basement ridges between the uncollided part of the Caribbean arc system (NS-trending Lesser Antilles arc) and the EW-trending collisional area north of Venezuela. The basement ridges involved in the Venezuelan collisional zone include: 1) Aruba-Bonaire-Curacao ridge that can be traced as a continuous feature to the Aves ridge remnant arc of the Lesser Antilles; 2) the partially inverted Blanquilla-Bonaire basin that can be traced into the Grenada back-arc basin; 3) Margarita-Los Testigos platform that can be traced to the Lesser Antilles volcanic arc; and 4) foreland basins and fold-thrust belts of eastern Venezuela (Serrania del Interior and Maturin basin) that can be traced to the Tobago forearc basin and Barbados accretionary prism. Gulfrex data document the progressive change of basinal fault systems from NS-striking normal faults formed in extensional, Lesser Antilles intra-arc settings to rotated and inverted, NE and EW-striking normal faults deformed in the collisional area north of Venezuela. Age of initial shortening of basinal areas and inversion of normal faults setting does not follow the simple, expected pattern of

  20. Multiple regimes of robust patterns between network structure and biodiversity.

    PubMed

    Jover, Luis F; Flores, Cesar O; Cortez, Michael H; Weitz, Joshua S

    2015-12-03

    Ecological networks such as plant-pollinator and host-parasite networks have structured interactions that define who interacts with whom. The structure of interactions also shapes ecological and evolutionary dynamics. Yet, there is significant ongoing debate as to whether certain structures, e.g., nestedness, contribute positively, negatively or not at all to biodiversity. We contend that examining variation in life history traits is key to disentangling the potential relationship between network structure and biodiversity. Here, we do so by analyzing a dynamic model of virus-bacteria interactions across a spectrum of network structures. Consistent with prior studies, we find plausible parameter domains exhibiting strong, positive relationships between nestedness and biodiversity. Yet, the same model can exhibit negative relationships between nestedness and biodiversity when examined in a distinct, plausible region of parameter space. We discuss steps towards identifying when network structure could, on its own, drive the resilience, sustainability, and even conservation of ecological communities.

  1. Multiple regimes of robust patterns between network structure and biodiversity

    NASA Astrophysics Data System (ADS)

    Jover, Luis F.; Flores, Cesar O.; Cortez, Michael H.; Weitz, Joshua S.

    2015-12-01

    Ecological networks such as plant-pollinator and host-parasite networks have structured interactions that define who interacts with whom. The structure of interactions also shapes ecological and evolutionary dynamics. Yet, there is significant ongoing debate as to whether certain structures, e.g., nestedness, contribute positively, negatively or not at all to biodiversity. We contend that examining variation in life history traits is key to disentangling the potential relationship between network structure and biodiversity. Here, we do so by analyzing a dynamic model of virus-bacteria interactions across a spectrum of network structures. Consistent with prior studies, we find plausible parameter domains exhibiting strong, positive relationships between nestedness and biodiversity. Yet, the same model can exhibit negative relationships between nestedness and biodiversity when examined in a distinct, plausible region of parameter space. We discuss steps towards identifying when network structure could, on its own, drive the resilience, sustainability, and even conservation of ecological communities.

  2. Multiple regimes of robust patterns between network structure and biodiversity

    PubMed Central

    Jover, Luis F.; Flores, Cesar O.; Cortez, Michael H.; Weitz, Joshua S.

    2015-01-01

    Ecological networks such as plant-pollinator and host-parasite networks have structured interactions that define who interacts with whom. The structure of interactions also shapes ecological and evolutionary dynamics. Yet, there is significant ongoing debate as to whether certain structures, e.g., nestedness, contribute positively, negatively or not at all to biodiversity. We contend that examining variation in life history traits is key to disentangling the potential relationship between network structure and biodiversity. Here, we do so by analyzing a dynamic model of virus-bacteria interactions across a spectrum of network structures. Consistent with prior studies, we find plausible parameter domains exhibiting strong, positive relationships between nestedness and biodiversity. Yet, the same model can exhibit negative relationships between nestedness and biodiversity when examined in a distinct, plausible region of parameter space. We discuss steps towards identifying when network structure could, on its own, drive the resilience, sustainability, and even conservation of ecological communities. PMID:26632996

  3. Multiple regimes of robust patterns between network structure and biodiversity.

    PubMed

    Jover, Luis F; Flores, Cesar O; Cortez, Michael H; Weitz, Joshua S

    2015-01-01

    Ecological networks such as plant-pollinator and host-parasite networks have structured interactions that define who interacts with whom. The structure of interactions also shapes ecological and evolutionary dynamics. Yet, there is significant ongoing debate as to whether certain structures, e.g., nestedness, contribute positively, negatively or not at all to biodiversity. We contend that examining variation in life history traits is key to disentangling the potential relationship between network structure and biodiversity. Here, we do so by analyzing a dynamic model of virus-bacteria interactions across a spectrum of network structures. Consistent with prior studies, we find plausible parameter domains exhibiting strong, positive relationships between nestedness and biodiversity. Yet, the same model can exhibit negative relationships between nestedness and biodiversity when examined in a distinct, plausible region of parameter space. We discuss steps towards identifying when network structure could, on its own, drive the resilience, sustainability, and even conservation of ecological communities. PMID:26632996

  4. Structural factoring approach for analyzing stochastic networks

    NASA Technical Reports Server (NTRS)

    Hayhurst, Kelly J.; Shier, Douglas R.

    1991-01-01

    The problem of finding the distribution of the shortest path length through a stochastic network is investigated. A general algorithm for determining the exact distribution of the shortest path length is developed based on the concept of conditional factoring, in which a directed, stochastic network is decomposed into an equivalent set of smaller, generally less complex subnetworks. Several network constructs are identified and exploited to reduce significantly the computational effort required to solve a network problem relative to complete enumeration. This algorithm can be applied to two important classes of stochastic path problems: determining the critical path distribution for acyclic networks and the exact two-terminal reliability for probabilistic networks. Computational experience with the algorithm was encouraging and allowed the exact solution of networks that have been previously analyzed only by approximation techniques.

  5. Exploring network structure, dynamics, and function using networkx

    SciTech Connect

    Hagberg, Aric; Swart, Pieter; S Chult, Daniel

    2008-01-01

    NetworkX is a Python language package for exploration and analysis of networks and network algorithms. The core package provides data structures for representing many types of networks, or graphs, including simple graphs, directed graphs, and graphs with parallel edges and self loops. The nodes in NetworkX graphs can be any (hashable) Python object and edges can contain arbitrary data; this flexibility mades NetworkX ideal for representing networks found in many different scientific fields. In addition to the basic data structures many graph algorithms are implemented for calculating network properties and structure measures: shortest paths, betweenness centrality, clustering, and degree distribution and many more. NetworkX can read and write various graph formats for eash exchange with existing data, and provides generators for many classic graphs and popular graph models, such as the Erdoes-Renyi, Small World, and Barabasi-Albert models, are included. The ease-of-use and flexibility of the Python programming language together with connection to the SciPy tools make NetworkX a powerful tool for scientific computations. We discuss some of our recent work studying synchronization of coupled oscillators to demonstrate how NetworkX enables research in the field of computational networks.

  6. Image-Based Structural Modeling of the Cardiac Purkinje Network

    PubMed Central

    Liu, Benjamin R.; Cherry, Elizabeth M.

    2015-01-01

    The Purkinje network is a specialized conduction system within the heart that ensures the proper activation of the ventricles to produce effective contraction. Its role during ventricular arrhythmias is less clear, but some experimental studies have suggested that the Purkinje network may significantly affect the genesis and maintenance of ventricular arrhythmias. Despite its importance, few structural models of the Purkinje network have been developed, primarily because current physical limitations prevent examination of the intact Purkinje network. In previous modeling efforts Purkinje-like structures have been developed through either automated or hand-drawn procedures, but these networks have been created according to general principles rather than based on real networks. To allow for greater realism in Purkinje structural models, we present a method for creating three-dimensional Purkinje networks based directly on imaging data. Our approach uses Purkinje network structures extracted from photographs of dissected ventricles and projects these flat networks onto realistic endocardial surfaces. Using this method, we create models for the combined ventricle-Purkinje system that can fully activate the ventricles through a stimulus delivered to the Purkinje network and can produce simulated activation sequences that match experimental observations. The combined models have the potential to help elucidate Purkinje network contributions during ventricular arrhythmias. PMID:26583120

  7. Measuring the robustness of network community structure using assortativity

    PubMed Central

    Shizuka, Daizaburo; Farine, Damien R.

    2016-01-01

    The existence of discrete social clusters, or ‘communities’, is a common feature of social networks in human and nonhuman animals. The level of such community structure in networks is typically measured using an index of modularity, Q. While modularity quantifies the degree to which individuals associate within versus between social communities and provides a useful measure of structure in the social network, it assumes that the network has been well sampled. However, animal social network data is typically subject to sampling errors. In particular, the associations among individuals are often not sampled equally, and animal social network studies are often based on a relatively small set of observations. Here, we extend an existing framework for bootstrapping network metrics to provide a method for assessing the robustness of community assignment in social networks using a metric we call community assortativity (rcom). We use simulations to demonstrate that modularity can reliably detect the transition from random to structured associations in networks that differ in size and number of communities, while community assortativity accurately measures the level of confidence based on the detectability of associations. We then demonstrate the use of these metrics using three publicly available data sets of avian social networks. We suggest that by explicitly addressing the known limitations in sampling animal social network, this approach will facilitate more rigorous analyses of population-level structural patterns across social systems. PMID:26949266

  8. Network analysis of cosmic structures: network centrality and topological environment

    NASA Astrophysics Data System (ADS)

    Hong, Sungryong; Dey, Arjun

    2015-06-01

    We apply simple analyses techniques developed for the study of complex networks to the study of the cosmic web, the large-scale galaxy distribution. In this paper, we measure three network centralities (ranks of topological importance): degree centrality (DC), closeness centrality (CL), and betweenness centrality (BC) from a network built from the Cosmological Evolution Survey (COSMOS) catalogue. We define eight galaxy populations according to the centrality measures: void, wall, and cluster by DC; main branch and dangling leaf by BC; and kernel, backbone, and fracture by CL. We also define three populations by Voronoi tessellation density to compare these with the DC selection. We apply the topological selections to galaxies in the (photometric) redshift range 0.91 < z < 0.94 from the COSMOS survey, and explore whether the red and blue galaxy populations show differences in colour, star formation rate, and stellar mass in the different topological regions. Despite the limitations and uncertainties associated with using photometric redshift and indirect measurements of galactic parameters, the preliminary results illustrate the potential of network analysis. Future surveys will provide better statistical samples to test and improve this `network cosmology'.

  9. Tensor Spectral Clustering for Partitioning Higher-order Network Structures

    PubMed Central

    Benson, Austin R.; Gleich, David F.; Leskovec, Jure

    2016-01-01

    Spectral graph theory-based methods represent an important class of tools for studying the structure of networks. Spectral methods are based on a first-order Markov chain derived from a random walk on the graph and thus they cannot take advantage of important higher-order network substructures such as triangles, cycles, and feed-forward loops. Here we propose a Tensor Spectral Clustering (TSC) algorithm that allows for modeling higher-order network structures in a graph partitioning framework. Our TSC algorithm allows the user to specify which higher-order network structures (cycles, feed-forward loops, etc.) should be preserved by the network clustering. Higher-order network structures of interest are represented using a tensor, which we then partition by developing a multilinear spectral method. Our framework can be applied to discovering layered flows in networks as well as graph anomaly detection, which we illustrate on synthetic networks. In directed networks, a higher-order structure of particular interest is the directed 3-cycle, which captures feedback loops in networks. We demonstrate that our TSC algorithm produces large partitions that cut fewer directed 3-cycles than standard spectral clustering algorithms.

  10. Climatic seasonality may affect ecological network structure: food webs and mutualistic networks.

    PubMed

    Takemoto, Kazuhiro; Kanamaru, Saori; Feng, Wenfeng

    2014-07-01

    Ecological networks exhibit non-random structural patterns, such as modularity and nestedness, which determine ecosystem stability with species diversity and connectance. Such structure-stability relationships are well known. However, another important perspective is less well understood: the relationship between the environment and structure. Inspired by theoretical studies that suggest that network structure can change due to environmental variability, we collected data on a number of empirical food webs and mutualistic networks and evaluated the effect of climatic seasonality on ecological network structure. As expected, we found that climatic seasonality affects ecological network structure. In particular, an increase in modularity due to climatic seasonality was observed in food webs; however, it is debatable whether this occurs in mutualistic networks. Interestingly, the type of climatic seasonality that affects network structure differs with ecosystem type. Rainfall and temperature seasonality influence freshwater food webs and mutualistic networks, respectively; food webs are smaller, and more modular, with increasing rainfall seasonality. Mutualistic networks exhibit a higher diversity (particularly of animals) with increasing temperature seasonality. These results confirm the theoretical prediction that the stability increases with greater perturbation. Although these results are still debatable because of several limitations in the data analysis, they may enhance our understanding of environment-structure relationships.

  11. Solution structure of the 45-residue MgATP-binding peptide of adenylate kinase as examined by 2-D NMR, FTIR, and CD spectroscopy.

    PubMed

    Fry, D C; Byler, D M; Susi, H; Brown, E M; Kuby, S A; Mildvan, A S

    1988-05-17

    The structure of a synthetic peptide corresponding to residues 1-45 of rabbit muscle adenylate kinase has been studied in aqueous solution by two-dimensional NMR, FTIR, and CD spectroscopy. This peptide, which binds MgATP and is believed to represent most of the MgATP-binding site of the enzyme [Fry, D.C., Kuby, S.A., & Mildvan, A.S. (1985) Biochemistry 24, 4680-4694], appears to maintain a conformation similar to that of residues 1-45 in the X-ray structure of intact porcine adenylate kinase [Sachsenheimer, W., & Schulz, G.E. (1977) J. Mol. Biol. 114, 23-26], with 42% of the residues of the peptide showing NOEs indicative of phi and psi angles corresponding to those found in the protein. The NMR studies suggest that the peptide is composed of two helical regions of residues 4-7 and 23-29, and three stretches of beta-strand at residues 8-15, 30-32, and 35-40, yielding an overall secondary structure consisting of 24% alpha-helix, 38% beta-structure, and 38% aperiodic. Although the resolution-enhanced amide I band of the peptide FTIR spectrum is broad and rather featureless, possibly due to disorder, it can be fit by using methods developed on well-characterized globular proteins. On this basis, the peptide consists of 35 +/- 10% beta-structure, 60 +/- 12% turns and aperiodic structure, and not more than 10% alpha-helix. The CD spectrum is best fit by assuming the presence of at most 13% alpha-helix in the peptide, 24 +/- 2% beta-structure, and 66 +/- 4% aperiodic. The inability of the high-frequency FTIR and CD methods to detect helices in the amount found by NMR may result from the short helical lengths as well as from static and dynamic disorder in the peptide. Upon binding of MgATP, numerous conformational changes in the backbone of the peptide are detected by NMR, with smaller alterations in the overall secondary structure as assessed by CD. Detailed assignments of resonances in the peptide spectrum and intermolecular NOEs between protons of bound MgATP and

  12. Finite difference time domain method for calculating the band structure of a 2D photonic crystal and simulating the lensing effect

    NASA Astrophysics Data System (ADS)

    Rafiee Dastjerdi, S.; Ghanaatshoar, M.

    2013-08-01

    A finite difference time domain method based on regular Yee's algorithm in an orthogonal coordinate system is utilized to calculate the band structure of a two-dimensional square-lattice photonic crystal comprising dielectric cylinders in air background and to simulate the image formation of mentioned structure incorporating the perfectly matched layer boundary condition. By analyzing the photonic band diagram of this system, we find that the frequency region of effective negative refraction exists in the second band in near-infrared domain. In this case, electromagnetic wave propagates with a negative phase velocity and the evanescent waves can be supported to perform higher image resolution.

  13. Hydrothermal syntheses and characterization of two novel luminescent Cadmium(II) frameworks: From 1D infinite triple Cd-(trz)-Cd bridges to a rare I2O0 network with 2D Cd-Br-Cd inorganic connectivity

    NASA Astrophysics Data System (ADS)

    Liu, Shi Xin; Li, Jian Hui; Wang, You You; Wu, Xiang Xia; Huo, Jian Zhong; Ding, Bin; Wang, Xiu Guang; Zhu, Zhao Zhou; Xia, Jun

    2015-05-01

    Using the 4-substituted-1,2,4-triazole derivate ligand 4-p-tolyl-1,2,4-triazole (L), two novel luminescent Cadmium(II) frameworks, namely {[Cd(μ2-L)3]·(NO3)2·L}n (1) and [Cd1.5(μ2-L)(μ2-Br)2(μ3-Br)]n (2) have been isolated under hydrothermal conditions. The structural analysis reveals that 1 presents a one-dimensional (1D) chain structural motif containing novel infinite triple Cd-(trz)-Cd bridges (triply trz-bridged M-M species). While 2 presents a rare I2O0 type framework, in which the infinite 2D Cd-Br-Cd inorganic connectivity with a 4-connected Kagome topology can be observed. The FT-IR, PXRD and thermal stabilities of 1-2 have investigated. The solid-state photo-luminescent spectra of organic ligand L and 1-2 also have been measured indicating strong emission bands.

  14. Modeling chemical interaction profiles: I. Spectral data-activity relationship and structure-activity relationship models for inhibitors and non-inhibitors of cytochrome P450 CYP3A4 and CYP2D6 isozymes.

    PubMed

    McPhail, Brooks; Tie, Yunfeng; Hong, Huixiao; Pearce, Bruce A; Schnackenberg, Laura K; Ge, Weigong; Valerio, Luis G; Fuscoe, James C; Tong, Weida; Buzatu, Dan A; Wilkes, Jon G; Fowler, Bruce A; Demchuk, Eugene; Beger, Richard D

    2012-03-15

    An interagency collaboration was established to model chemical interactions that may cause adverse health effects when an exposure to a mixture of chemicals occurs. Many of these chemicals--drugs, pesticides, and environmental pollutants--interact at the level of metabolic biotransformations mediated by cytochrome P450 (CYP) enzymes. In the present work, spectral data-activity relationship (SDAR) and structure-activity relationship (SAR) approaches were used to develop machine-learning classifiers of inhibitors and non-inhibitors of the CYP3A4 and CYP2D6 isozymes. The models were built upon 602 reference pharmaceutical compounds whose interactions have been deduced from clinical data, and 100 additional chemicals that were used to evaluate model performance in an external validation (EV) test. SDAR is an innovative modeling approach that relies on discriminant analysis applied to binned nuclear magnetic resonance (NMR) spectral descriptors. In the present work, both 1D ¹³C and 1D ¹⁵N-NMR spectra were used together in a novel implementation of the SDAR technique. It was found that increasing the binning size of 1D ¹³C-NMR and ¹⁵N-NMR spectra caused an increase in the tenfold cross-validation (CV) performance in terms of both the rate of correct classification and sensitivity. The results of SDAR modeling were verified using SAR. For SAR modeling, a decision forest approach involving from 6 to 17 Mold2 descriptors in a tree was used. Average rates of correct classification of SDAR and SAR models in a hundred CV tests were 60% and 61% for CYP3A4, and 62% and 70% for CYP2D6, respectively. The rates of correct classification of SDAR and SAR models in the EV test were 73% and 86% for CYP3A4, and 76% and 90% for CYP2D6, respectively. Thus, both SDAR and SAR methods demonstrated a comparable performance in modeling a large set of structurally diverse data. Based on unique NMR structural descriptors, the new SDAR modeling method complements the existing SAR

  15. Structural studies of an arabinan from the stems of Ephedra sinica by methylation analysis and 1D and 2D NMR spectroscopy.

    PubMed

    Xia, Yong-Gang; Liang, Jun; Yang, Bing-You; Wang, Qiu-Hong; Kuang, Hai-Xue

    2015-05-01

    Plant arabinan has important biological activity. In this study, a water-soluble arabinan (Mw∼6.15kDa) isolated from the stems of Ephedra sinica was found to consist of (1→5)-Araƒ, (1→3,5)-Araƒ, T-Araƒ, (1→3)-Araƒ and (1→2,5)-Araƒ residues at proportions of 10:2:3:2:1. A tentative structure was proposed by methylation analysis, nuclear magnetic resonance (NMR) spectroscopy ((1)H NMR, (13)C NMR, DEPT-135, (1)H-(1)H COSY, HSQC, HMBC and ROESY) and literature. The structure proposed includes a branched (1→5)-α-Araf backbone where branching occurs at the O-2 and O-3 positions of the residues with 7.7% and 15.4% of the 1,5-linked α-Araf substituted at the O-2 and O-3 positions. The presence of a branched structure was further observed by atomic force microscopy. This polymer was characterized as having a much longer linear (1→5)-α-Araf backbone as a repeating unit. In particular, the presence of α-Araf→3)-α-Araf-(1→3)-α-Araf-(1→ attached at the O-2 is a new finding. This study may facilitate a deeper understanding of structure-activity relationships of biological polysaccharides from the stems of E. sinica.

  16. CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6*15 and *35 Genotyping

    PubMed Central

    Riffel, Amanda K.; Dehghani, Mehdi; Hartshorne, Toinette; Floyd, Kristen C.; Leeder, J. Steven; Rosenblatt, Kevin P.; Gaedigk, Andrea

    2016-01-01

    TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs) some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false-positive CYP2D6*15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6*15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL)-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6*35) which is also located in exon 1. Although alternative CYP2D6*15 and *35 assays resolved the issue, we discovered a novel CYP2D6*15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6*15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696) SNP of CYP2D6*43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer and/or probe regions can impact

  17. CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6 (*) 15 and (*) 35 Genotyping.

    PubMed

    Riffel, Amanda K; Dehghani, Mehdi; Hartshorne, Toinette; Floyd, Kristen C; Leeder, J Steven; Rosenblatt, Kevin P; Gaedigk, Andrea

    2015-01-01

    TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs) some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false-positive CYP2D6 (*) 15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6 (*) 15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL)-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6 (*) 35) which is also located in exon 1. Although alternative CYP2D6 (*) 15 and (*) 35 assays resolved the issue, we discovered a novel CYP2D6 (*) 15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6 (*) 15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696) SNP of CYP2D6 (*) 43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer

  18. Topological effects of network structure on long-term social network dynamics in a wild mammal.

    PubMed

    Ilany, Amiyaal; Booms, Andrew S; Holekamp, Kay E

    2015-07-01

    Social structure influences ecological processes such as dispersal and invasion, and affects survival and reproductive success. Recent studies have used static snapshots of social networks, thus neglecting their temporal dynamics, and focused primarily on a limited number of variables that might be affecting social structure. Here, instead we modelled effects of multiple predictors of social network dynamics in the spotted hyena, using observational data collected during 20 years of continuous field research in Kenya. We tested the hypothesis that the current state of the social network affects its long-term dynamics. We employed stochastic agent-based models that allowed us to estimate the contribution of multiple factors to network changes. After controlling for environmental and individual effects, we found that network density and individual centrality affected network dynamics, but that social bond transitivity consistently had the strongest effects. Our results emphasise the significance of structural properties of networks in shaping social dynamics. PMID:25975663

  19. Topological effects of network structure on long-term social network dynamics in a wild mammal.

    PubMed

    Ilany, Amiyaal; Booms, Andrew S; Holekamp, Kay E

    2015-07-01

    Social structure influences ecological processes such as dispersal and invasion, and affects survival and reproductive success. Recent studies have used static snapshots of social networks, thus neglecting their temporal dynamics, and focused primarily on a limited number of variables that might be affecting social structure. Here, instead we modelled effects of multiple predictors of social network dynamics in the spotted hyena, using observational data collected during 20 years of continuous field research in Kenya. We tested the hypothesis that the current state of the social network affects its long-term dynamics. We employed stochastic agent-based models that allowed us to estimate the contribution of multiple factors to network changes. After controlling for environmental and individual effects, we found that network density and individual centrality affected network dynamics, but that social bond transitivity consistently had the strongest effects. Our results emphasise the significance of structural properties of networks in shaping social dynamics.

  20. Topological effects of network structure on long-term social network dynamics in a wild mammal

    PubMed Central

    Ilany, Amiyaal; Booms, Andrew S.; Holekamp, Kay E.

    2015-01-01

    Social structure influences ecological processes such as dispersal and invasion, and affects survival and reproductive success. Recent studies have used static snapshots of social networks, thus neglecting their temporal dynamics, and focused primarily on a limited number of variables that might be affecting social structure. Here, instead we modelled effects of multiple predictors of social network dynamics in the spotted hyena, using observational data collected during 20 years of continuous field research in Kenya. We tested the hypothesis that the current state of the social network affects its long-term dynamics. We employed stochastic agent-based models that allowed us to estimate the contribution of multiple factors to network changes. After controlling for environmental and individual effects, we found that network density and individual centrality affected network dynamics, but that social bond transitivity consistently had the strongest effects. Our results emphasise the significance of structural properties of networks in shaping social dynamics. PMID:25975663

  1. Network versus portfolio structure in financial systems

    NASA Astrophysics Data System (ADS)

    Kobayashi, Teruyoshi

    2013-10-01

    The question of how to stabilize financial systems has attracted considerable attention since the global financial crisis of 2007-2009. Recently, Beale et al. [Proc. Natl. Acad. Sci. USA 108, 12647 (2011)] demonstrated that higher portfolio diversity among banks would reduce systemic risk by decreasing the risk of simultaneous defaults at the expense of a higher likelihood of individual defaults. In practice, however, a bank default has an externality in that it undermines other banks’ balance sheets. This paper explores how each of these different sources of risk, simultaneity risk and externality, contributes to systemic risk. The results show that the allocation of external assets that minimizes systemic risk varies with the topology of the financial network as long as asset returns have negative correlations. In the model, a well-known centrality measure, PageRank, reflects an appropriately defined “infectiveness” of a bank. An important result is that the most infective bank needs not always to be the safest bank. Under certain circumstances, the most infective node should act as a firewall to prevent large-scale collective defaults. The introduction of a counteractive portfolio structure will significantly reduce systemic risk.

  2. 3D Chemical Similarity Networks for Structure-Based Target Prediction and Scaffold Hopping.

    PubMed

    Lo, Yu-Chen; Senese, Silvia; Damoiseaux, Robert; Torres, Jorge Z

    2016-08-19

    Target identification remains a major challenge for modern drug discovery programs aimed at understanding the molecular mechanisms of drugs. Computational target prediction approaches like 2D chemical similarity searches have been widely used but are limited to structures sharing high chemical similarity. Here, we present a new computational approach called chemical similarity network analysis pull-down 3D (CSNAP3D) that combines 3D chemical similarity metrics and network algorithms for structure-based drug target profiling, ligand deorphanization, and automated identification of scaffold hopping compounds. In conjunction with 2D chemical similarity fingerprints, CSNAP3D achieved a >95% success rate in correctly predicting the drug targets of 206 known drugs. Significant improvement in target prediction was observed for HIV reverse transcriptase (HIVRT) compounds, which consist of diverse scaffold hopping compounds targeting the nucleotidyltransferase binding site. CSNAP3D was further applied to a set of antimitotic compounds identified in a cell-based chemical screen and identified novel small molecules that share a pharmacophore with Taxol and display a Taxol-like mechanism of action, which were validated experimentally using in vitro microtubule polymerization assays and cell-based assays.

  3. DYNA2D96. Explicit 2-D Hydrodynamic FEM Program

    SciTech Connect

    Whirley, R.G.

    1992-04-01

    DYNA2D is a vectorized, explicit, two-dimensional, axisymmetric and plane strain finite element program for analyzing the large deformation dynamic and hydrodynamic response of inelastic solids. DYNA2D contains 13 material models and 9 equations of state (EOS) to cover a wide range of material behavior. The material models implemented in all machine versions are: elastic, orthotropic elastic, kinematic/isotropic elastic plasticity, thermoelastoplastic, soil and crushable foam, linear viscoelastic, rubber, high explosive burn, isotropic elastic-plastic, temperature-dependent elastic-plastic. The isotropic and temperature-dependent elastic-plastic models determine only the deviatoric stresses. Pressure is determined by one of 9 equations of state including linear polynomial, JWL high explosive, Sack Tuesday high explosive, Gruneisen, ratio of polynomials, linear polynomial with energy deposition, ignition and growth of reaction in HE, tabulated compaction, and tabulated.

  4. Structural bottlenecks for communication in networks

    NASA Astrophysics Data System (ADS)

    Sreenivasan, Sameet; Cohen, Reuven; López, Eduardo; Toroczkai, Zoltán; Stanley, H. Eugene

    2007-03-01

    We consider the effect of network topology on the optimality of packet routing which is quantified by γc , the rate of packet insertion beyond which congestion and queue growth occurs. We show that for any network, there exists an absolute upper bound, expressed in terms of vertex separators, for the scaling of γc with network size N , irrespective of the static routing protocol used. We then derive an estimate to this upper bound for scale-free networks and introduce a static routing protocol, the “hub avoidance protocol,” which, for large packet insertion rates, is superior to the shortest path routing protocol.

  5. 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.

  6. Structural determination of prunusins A and B, new C-alkylated flavonoids from Prunus domestica, by 1D and 2D NMR spectroscopy.

    PubMed

    Mahmood, Azhar; Fatima, Itrat; Kosar, Shaheen; Ahmed, Rehana; Malik, Abdul

    2010-02-01

    Prunusins A (1) and B (2), the new C-alkylated flavonoids, have been isolated from the seed kernels of Prunus domestica. Their structures were assigned from (1)H and (13)C nuclear magnetic resonating spectra, DEPT and by correlation spectroscopy, HMQC and HMBC experiments. 3, 5, 7, 4'-Tetrahydroxyflavone (3) and 3, 5, 7-trihydroxy-8, 4'-dimethoxyflavone (4) have also been reported from this species. Both compounds (1) and (2) showed significant antifungal activity against pathogenic fungus Trichophyton simmi.

  7. Integrated well log and 2-D seismic data interpretation to image the subsurface stratigraphy and structure in north-eastern Bornu (Chad) basin

    NASA Astrophysics Data System (ADS)

    Isyaku, Aminu A.; Rust, Derek; Teeuw, Richard; Whitworth, Malcolm

    2016-09-01

    Structural and stratigraphic mapping within the Bornu Basin in north east Nigeria was commonly carried out using traditional field geological methods. However, such traditional approaches remain inadequate in the semi-arid region characterised by topographically flat areas and lack of continuous bedrock outcrops that are mostly concealed beneath sand cover. Previous studies in the north-eastern part of the basin carried out using ditch cuttings from few wells and disconnected seismic data were largely inadequate and the resulting stratigraphic analyses were more often generalised. This paper presents an integrated structural and stratigraphic study of the basin using combined subsurface geophysical datasets. A Combined Log Pattern (CLP) method is a well log analysis, which utilises various well log data including gamma ray, resistivity, bulk density and sonic logs to identify lithology and stratigraphic boundaries of subsurface formations. This method is applied to constrain the subsurface stratigraphy of the north-eastern part of the Bornu Basin bordering the Lake Chad. In addition to qualitative combined well log analysis, the time-depth relationship of the sonic log and seismic data was quantitatively determined by tying a well with an intersecting seismic section to validate the stratigraphic facies horizons identified. Four well log facies and their environments of deposition were characterised from the combined well log analysis of the different log types. It is discovered that the Cretaceous basement structural features controlled the deposition of overlying formations in the basin. Without intact core data, the shallower wells were discovered to have bottomed over subsurface horst features while deeper wells penetrated into the basal facies contained mainly within the grabens. Main subsurface structural lineaments in the area include NW-SE, NE-SW and NNW-SSE trending faults, which mainly formed the horst and graben features. Some stratigraphic formations

  8. Magnetic structure and domain conversion of the quasi-2D frustrated antiferromagnet CuCrO{sub 2} probed by NMR

    SciTech Connect

    Sakhratov, Yu. A.; Svistov, L. E.; Kuhns, P. L.; Zhou, H. D.; Reyes, A. P.

    2014-11-15

    We have carried out {sup 63,65}Cu NMR spectra measurements in a magnetic field up to about 15.5 T on a single crystal of the multiferroic triangular-lattice antiferromagnet CuCrO{sub 2}. The measurements were performed for perpendicular and parallel orientations of the magnetic field with respect to the c axis of the crystal, and the detailed angle dependence of the spectra on the magnetic field direction in the ab plane was studied. The shape of the spectra can be well described in the model of spiral spin structure proposed by recent neutron diffraction experiments. When the field is rotated perpendicular to the crystal c axis, we observed, directly for the first time, a remarkable reorientation of the spin plane simultaneous with rotation of the incommensurate wavevector, by quantitatively deducing the conversion of the energetically less favorable domain to a more favorable one. At high enough fields parallel to the c axis, the data are consistent with either a field-induced commensurate spiral magnetic structure or an incommensurate spiral magnetic structure with a disorder in the c direction, suggesting that high fields may have influence on interplanar ordering.

  9. Two new Cu(ii) and La(iii) 2D coordination polymers, synthesis and in situ structural analysis by X-ray diffraction.

    PubMed

    Lundvall, F; Wragg, D S; Dietzel, P D C; Fjellvåg, H

    2016-08-01

    Two new coordination polymers were synthesized solvothermally using 4,4'-dimethoxy-3,3'-biphenyldicarboxylic acid (H2dmbpdc), and di- and trivalent metal salts (Cu(NO3)2·2.5H2O and La(NO3)3·6H2O). Their structures were determined by single-crystal X-ray diffraction analysis, and their thermal stability was evaluated by thermogravimetric analysis. The copper compound Cu(dmbpdc)(DMF; N,N-dimethylformamide), CPO-71-Cu, is based on the well known copper acetate paddlewheel secondary building unit. The asymmetric unit comprises one copper cation with one DMF molecule and one linker molecule coordinated. The lanthanum compound La2(dmbpdc)3(DMF)(H2O)3, CPO-72-La, is formed from a dimer of nine-coordinate, edge sharing lanthanum cations. To this dimer, three water molecules and one DMF molecule are coordinated in an ordered fashion. In addition, the asymmetric unit contains three crystallographically unique linker molecules. Both CPO-71-Cu and CPO-72-La form two-dimensional layered structures, and topological analyses reveal sql topologies with point symbol 4(4)·6(2) and vertex symbol 4·4·4·4·6(2)·6(2). The thermal behavior of CPO-71-Cu was investigated in an in situ structural analysis by variable temperature powder- and single-crystal X-ray diffraction. PMID:27469613

  10. Dynamic structure evolution of time-dependent network

    NASA Astrophysics Data System (ADS)

    Zhang, Beibei; Zhou, Yadong; Xu, Xiaoyan; Wang, Dai; Guan, Xiaohong

    2016-08-01

    In this paper, we research the long-voided problem of formulating the time-dependent network structure evolution scheme, it focus not only on finding new emerging vertices in evolving communities and new emerging communities over the specified time range but also formulating the complex network structure evolution schematic. Previous approaches basically applied to community detection on time static networks and thus failed to consider the potentially crucial and useful information latently embedded in the dynamic structure evolution process of time-dependent network. To address these problems and to tackle the network non-scalability dilemma, we propose the dynamic hierarchical method for detecting and revealing structure evolution schematic of the time-dependent network. In practice and specificity, we propose an explicit hierarchical network evolution uncovering algorithm framework originated from and widely expanded from time-dependent and dynamic spectral optimization theory. Our method yields preferable results compared with previous approaches on a vast variety of test network data, including both real on-line networks and computer generated complex networks.

  11. Network community structure detection for directional neural networks inferred from multichannel multisubject EEG data.

    PubMed

    Liu, Ying; Moser, Jason; Aviyente, Selin

    2014-07-01

    In many neuroscience applications, one is interested in identifying the functional brain modules from multichannel, multiple subject neuroimaging data. However, most of the existing network community structure detection algorithms are limited to single undirected networks and cannot reveal the common community structure for a collection of directed networks. In this paper, we propose a community detection algorithm for weighted asymmetric (directed) networks representing the effective connectivity in the brain. Moreover, the issue of finding a common community structure across subjects is addressed by maximizing the total modularity of the group. Finally, the proposed community detection algorithm is applied to multichannel multisubject electroencephalogram data.

  12. WFR-2D: an analytical model for PWAS-generated 2D ultrasonic guided wave propagation

    NASA Astrophysics Data System (ADS)

    Shen, Yanfeng; Giurgiutiu, Victor

    2014-03-01

    This paper presents WaveFormRevealer 2-D (WFR-2D), an analytical predictive tool for the simulation of 2-D ultrasonic guided wave propagation and interaction with damage. The design of structural health monitoring (SHM) systems and self-aware smart structures requires the exploration of a wide range of parameters to achieve best detection and quantification of certain types of damage. Such need for parameter exploration on sensor dimension, location, guided wave characteristics (mode type, frequency, wavelength, etc.) can be best satisfied with analytical models which are fast and efficient. The analytical model was constructed based on the exact 2-D Lamb wave solution using Bessel and Hankel functions. Damage effects were inserted in the model by considering the damage as a secondary wave source with complex-valued directivity scattering coefficients containing both amplitude and phase information from wave-damage interaction. The analytical procedure was coded with MATLAB, and a predictive simulation tool called WaveFormRevealer 2-D was developed. The wave-damage interaction coefficients (WDICs) were extracted from harmonic analysis of local finite element model (FEM) with artificial non-reflective boundaries (NRB). The WFR-2D analytical simulation results were compared and verified with full scale multiphysics finite element models and experiments with scanning laser vibrometer. First, Lamb wave propagation in a pristine aluminum plate was simulated with WFR-2D, compared with finite element results, and verified by experiments. Then, an inhomogeneity was machined into the plate to represent damage. Analytical modeling was carried out, and verified by finite element simulation and experiments. This paper finishes with conclusions and suggestions for future work.

  13. Structural and robustness properties of smart-city transportation networks

    NASA Astrophysics Data System (ADS)

    Zhang, Zhen-Gang; Ding, Zhuo; Fan, Jing-Fang; Meng, Jun; Ding, Yi-Min; Ye, Fang-Fu; Chen, Xiao-Song

    2015-09-01

    The concept of smart city gives an excellent resolution to construct and develop modern cities, and also demands infrastructure construction. How to build a safe, stable, and highly efficient public transportation system becomes an important topic in the process of city construction. In this work, we study the structural and robustness properties of transportation networks and their sub-networks. We introduce a complementary network model to study the relevance and complementarity between bus network and subway network. Our numerical results show that the mutual supplement of networks can improve the network robustness. This conclusion provides a theoretical basis for the construction of public traffic networks, and it also supports reasonable operation of managing smart cities. Project supported by the Major Projects of the China National Social Science Fund (Grant No. 11 & ZD154).

  14. Neighborhood Age Structure and Support Networks.

    ERIC Educational Resources Information Center

    Ward, Russell A.; And Others

    Studies conducted in specifically age-segregated housing for older persons suggest that such age-homogeneous settings encourage networks of friendships and mutual assistance. Since patterns of age segregation exist within communities, such segregation may result in similar social benefits. Interviews (N=1,185) assessing social networks were…

  15. 2-D or not 2-D, that is the question: A Northern California test

    SciTech Connect

    Mayeda, K; Malagnini, L; Phillips, W S; Walter, W R; Dreger, D

    2005-06-06

    Reliable estimates of the seismic source spectrum are necessary for accurate magnitude, yield, and energy estimation. In particular, how seismic radiated energy scales with increasing earthquake size has been the focus of recent debate within the community and has direct implications on earthquake source physics studies as well as hazard mitigation. The 1-D coda methodology of Mayeda et al. has provided the lowest variance estimate of the source spectrum when compared against traditional approaches that use direct S-waves, thus making it ideal for networks that have sparse station distribution. The 1-D coda methodology has been mostly confined to regions of approximately uniform complexity. For larger, more geophysically complicated regions, 2-D path corrections may be required. The complicated tectonics of the northern California region coupled with high quality broadband seismic data provides for an ideal ''apples-to-apples'' test of 1-D and 2-D path assumptions on direct waves and their coda. Using the same station and event distribution, we compared 1-D and 2-D path corrections and observed the following results: (1) 1-D coda results reduced the amplitude variance relative to direct S-waves by roughly a factor of 8 (800%); (2) Applying a 2-D correction to the coda resulted in up to 40% variance reduction from the 1-D coda results; (3) 2-D direct S-wave results, though better than 1-D direct waves, were significantly worse than the 1-D coda. We found that coda-based moment-rate source spectra derived from the 2-D approach were essentially identical to those from the 1-D approach for frequencies less than {approx}0.7-Hz, however for the high frequencies (0.7{le} f {le} 8.0-Hz), the 2-D approach resulted in inter-station scatter that was generally 10-30% smaller. For complex regions where data are plentiful, a 2-D approach can significantly improve upon the simple 1-D assumption. In regions where only 1-D coda correction is available it is still preferable over 2

  16. 1D and 2D assembly structures by imidazole···chloride hydrogen bonds of iron(II) complexes [Fe(II)(HL(n-Pr))3]Cl·Y (HL(n-Pr) = 2-methylimidazol-4-yl-methylideneamino-n-propyl; Y = AsF6, BF4) and their spin states.

    PubMed

    Fujinami, Takeshi; Nishi, Koshiro; Matsumoto, Naohide; Iijima, Seiichiro; Halcrow, Malcolm A; Sunatsuki, Yukinari; Kojima, Masaaki

    2011-12-01

    Two Fe(II) complexes fac-[Fe(II)(HL(n-Pr))(3)]Cl·Y (Y = AsF(6) (1) and BF(4) (2)) were synthesized, where HL(n-Pr) is 2-methylimidazole-4-yl-methylideneamino-n-propyl. Each complex-cation has the same octahedral N(6) geometry coordinated by three bidentate ligands and assumes facial-isomerism, fac-[Fe(II)(HL(n-Pr))(3)](2+) with Δ- and Λ-enantiomorphs. Three imidazole groups per Δ- or Λ-fac-[Fe(II)(HL(n-Pr))(3)](2+) are hydrogen-bonded to three Cl(-) ions or, from the viewpoint of the Cl(-) ion, one Cl(-) ion is hydrogen-bonded to three neighbouring fac-[Fe(II)(HL(n-Pr))(3)](2+) cations. The 3 : 3 NH···Cl(-) hydrogen bonds between Δ- or Λ-fac-[Fe(II)(HL(n-Pr))(3)](2+) and Cl(-) generate two kinds of assembly structures. The directions of the 3 : 3 NH···Cl(-) hydrogen bonds and hence the resulting assembly structures are determined by the size of the anion Y, though Y is not involved into the network structure and just accommodated in the cavity. Compound 1 has a 1D ladder structure giving a larger cavity, in which the Δ- and Λ-fac-[Fe(II)(HL(n-Pr))(3)](2+) enantiomorphs are bridged by two NH···Cl(-) hydrogen bonds. Compound 2 has a 2D network structure with a net unit of a cyclic trimer of {fac-[Fe(II)(HL(n-Pr))(3)](2+)···Cl(-)}(3) giving a smaller cavity, in which Δ- or Λ-fac-[Fe(II)(HL(n-Pr))(3)](2+) species with the same chirality are linked by NH···Cl(-) hydrogen bonds to give a homochiral 2D network structure. Magnetic susceptibility and Mössbauer spectral measurements demonstrated that compound 1 showed an abrupt one-step spin crossover with 4.0 K thermal hysteresis of T(c↓) = 125.5 K and T(c↑) = 129.5 K and compound 2 showed no spin transition and stayed in the high-spin state over the 5-300 K temperature range.

  17. KPLS-RWBFNN model for MFL 2D defect profile reconstruction

    NASA Astrophysics Data System (ADS)

    Xu, Chao; Wang, Changlong; Ji, Fengzhu

    2013-03-01

    Kernel partial least squares (KPLS) is normally very efficient for tackling nonlinear systems by mapping an original input space into a high-dimensional feature space and creating a linear PLS model in the feature space. Unlike other nonlinear PLS techniques, KPLS does not entail any nonlinear optimisation procedures. However, due to the linear inner model of PLS, KPLS is still inappropriate for describing the significant nonlinear characteristic data structure while dealing with complex physical systems in practical situations. Under this circumstance, radial wavelet basic function neural network (RWBFNN) can replace the linear inner model of PLS in the nonlinear kernel-based algorithm. Thus, KPLS-RWBFNN model is proposed in this paper and applied to multi-resolution approximation reconstruction of 2D defect profiles in magnetic flux leakage testing. The reconstructions of 2D defect profiles by this method are implemented, and the comparisons among reconstructions by KPLS, RWBFNN and the proposed approach are also undertaken. Meanwhile, the reconstructions of 2D defects by RWBFNN and the proposed approach at different SNR are also executed. The results indicate that KPLS-RWBFNN model could simplify the structure of the network while holding well-behaved generalisation and multi-resolution approximation and predict the 2D defect profiles accurately and rapidly with good robustness.

  18. Cornered Quadtrees/Octrees and Multiple Gateways Between Each Two Nodes; A Structure for Path Planning in 2D and 3D Environments

    NASA Astrophysics Data System (ADS)

    Namdari, Mohammad Hasan; Hejazi, Seyed Reza; Palhang, Maziar

    2016-06-01

    In this paper, modified versions of quadtree/octree, as structures used in path planning, are proposed which we call them cornered quadtree/octree. Also a new method of creating paths in quadtrees/octrees, once quadrants/octants to be passed are determined, is proposed both to improve traveled distance and path smoothness. In proposed modified versions of quadtree/octree, four corner cells of quadrants and eight corner voxels of octants are also considered as nodes of the graph to be searched for finding the shortest path. This causes better quadrant/octant selection during graph search relative to simple quadtrees and octrees. On the other hand, after that all quadrants/octants are determined, multiple gateways are nominated between each two selected nodes and path is constructed by passing through the gateway which its selection leads in shorter and smoother path. Proposed structures in this paper alongside the utilized path construction approach, creates better paths in terms of path length than those created if simple trees are used, somehow equal to the quality of the achieved paths by framed trees, meanwhile interestingly, consumed time and memory in our proposed method are closer to the used time and memory if simple trees are used.

  19. Synthesis, crystal structure of α-Keggin heteropolymolybdates with pyridine-2,6-dicarboxylate based frameworks, and associated RhB photocatalytic degradation and 2D-IR COS tests.

    PubMed

    Chen, Xiang-yi; Chen, Yi-ping; Xia, Ze-min; Hu, Heng-bin; Sun, Yan-qiong; Huang, Wei-yuan

    2012-09-01

    Three α-Keggin heteropolymolybdates with the formula [(C(5)H(4)NH)COOH](3)[PMo(12)O(40)] 1, {[Sm(H(2)O)(4)(pdc)](3)}{[Sm(H(2)O)(3)(pdc)]}[SiMo(12)O(40)]·3H(2)O 2 and {[La(H(2)O)(4)(pdc)](4)}[PMo(12)O(40)]F 3 (H(2)pdc = pyridine-2,6-dicarboxylate), have been synthesized under hydrothermal condition and characterized by single crystal X-ray diffraction analyses, elemental analyses, inductively coupled plasma atomic emission spectroscopy (ICP-AES), IR, thermal gravimetric analyses, thermal infrared spectrum analyses and powder X-ray diffraction (PXRD) analyses. Single crystal X-ray diffraction indicates all three compounds comprise ball-shaped Keggin type [XMo(12)O(40)](n-) polyoxometalates (POMs) (n = 3, X = P; n = 4, X = Si, respectively) with different types of carboxylic ligands derived from H(2)pdc, and these cluster anions are isostructural. In order to explore structural characteristics, Rhodamine B photocatalytic (RhB) degradation and two-dimensional infrared correlation spectroscopy (2D-IR COS) tests, are investigated for 1, 2 and 3. In RhB degradation, all compounds show good photocatalytic activity. For 1, the activity mainly comes from POMs. While in 2 and 3, POMs' photocatalytic activity is enhanced by the Ln(iii)-pdc metal-organic frameworks. Structural properties like POM's stability and magnetic sensitivity are discussed by 2D-IR COS under thermal/magnetic perturbations.

  20. Observation of the hyperfine structure of the {sup 2}S{sub 1/2}-{sup 2}D{sub 5/2} transition in {sup 87}Sr{sup +}

    SciTech Connect

    Barwood, G.P.; Gao, K.; Gill, P.; Huang, G.; Klein, H.A.

    2003-01-01

    The hyperfine structure of the {sup 2}S{sub 1/2}-{sup 2}D{sub 5/2} quadrupole transition at 674 nm in {sup 87}Sr{sup +} has been observed. The ion was confined in a Paul trap and cooled using laser radiation at 422 and 1092 nm. The quadrupole transition was observed by monitoring quantum jumps in the 422-nm fluorescence. The odd isotope of strontium has 'clock' transitions independent of the first-order Zeeman shift and the {sup 2}D{sub 5/2} state hyperfine structure constants have been determined as A{sub D{sub 5/2}}=2.1743(14) MHz and B{sub D{sub 5/2}}=49.11(6) MHz. Standard uncertainties have been added in parentheses. These values allow the second-order Zeeman shifts to be calculated. The {sup 88}Sr{sup +}-{sup 87}Sr{sup +} isotope shift for the 674-nm quadrupole transition has been measured to be 247.99(4) MHz.

  1. Diagnosis of helicopter gearboxes using structure-based networks

    NASA Technical Reports Server (NTRS)

    Jammu, Vinay B.; Danai, Kourosh; Lewicki, David G.

    1995-01-01

    A connectionist network is introduced for fault diagnosis of helicopter gearboxes that incorporates knowledge of the gearbox structure and characteristics of the vibration features as its fuzzy weights. Diagnosis is performed by propagating the abnormal features of vibration measurements through this Structure-Based Connectionist Network (SBCN), the outputs of which represent the fault possibility values for individual components of the gearbox. The performance of this network is evaluated by applying it to experimental vibration data from an OH-58A helicopter gearbox. The diagnostic results indicate that the network performance is comparable to those obtained from supervised pattern classification.

  2. Numerical models of diapiric structures: comparison of the 2D finite deformation field between Rayleigh-Taylor like and down-built like diapirs

    NASA Astrophysics Data System (ADS)

    Fuchs, Lukas; Schmeling, Harro; Koyi, Hemin

    2013-04-01

    Magmatic and salt diapirs are common structures in different tectonic regimes. Salt diapirs can act as possible hydrocarbon traps and, moreover, they could be used as repositories for nuclear waste disposal. Understanding the evolution and the dynamics of diapirs as well as their driving mechanisms has fundamental and applied significance. In general, salt diapirs seem to be driven by differential loading of sediments creating an uneven load that drives the salt from high to low pressure areas, e.g. a down-built diapir. Magmatic diapirs, instead, seem to be driven by buoyancy where lighter material rises vertically through a heavier overburden, i.e. a classical Rayleigh-Taylor instability [RTI]. These different driving mechanisms and dynamics strongly govern the internal deformation of the diapirs. In this study, we use a two-dimensional finite difference code (FDCON) in combination with a marker and cell method to calculate the finite deformation within diapiric structures. Thereby, we distinguish between the two different driving mechanisms, i.e. the differential loading and the buoyancy. We calculate the different finite deformation patterns during the evolution of RTI's and down-built diapirs for different viscosity ratios m = -?buoyant- ?overburden. The deformation pattern in the buoyant layer shows similarities for both diapiric structures, like high shear deformation at the bottom, a high finite deformation within the middle of the stem, and an increasing maximum finite deformation for a decreasing m. However, the strain partitioning between the overburden and the source layer is different within down-built diapirs compared to the RTI's, even for down-built diapirs with m = 1. Thus a higher amount of the total strain induced by down-building is concentrated within the buoyant layer. Moreover, in the case of viscosity ratios of m = 0.1 or 1 the sinking overburden units create an internal rotation within the diapiric bulb. This rotation depends indirectly on

  3. Synthesis, structural characterization and microbial activity of 2D Ag(I)-5-aminoisophthalate coordination polymer with a new coordination mode

    NASA Astrophysics Data System (ADS)

    Günay, Handan; Çolak, Alper Tolga; Yeşilel, Okan Zafer; Tunç, Tuncay; Çolak, Ferdağ

    2015-11-01

    In this study, a novel polynuclear Ag(I)-5-aminoisophthalate complex [Ag(μ4-Haip)]n (1) (H2aip = 5-aminoisophthalic acid) has been synthesized. The molecular structure of this complex has been determined by the single crystal X-ray diffraction. The two-dimens