Sample records for complex si-based structures

  1. A micro-structured Si-based electrodes for high capacity electrical double layer capacitors (United States)

    Krikscikas, Valdas; Oguchi, Hiroyuki; Yanazawa, Hiroshi; Hara, Motoaki; Kuwano, Hiroki


    We challenged to make basis for Si electrodes of electric double layer capacitors (EDLC) used as a power source of micro-sensor nodes. Mcroelectromechanical systems (MEMS) processes were successfully introduced to fabricate micro-structured Si-based electrodes to obtain high surface area which leads to high capacity of EDLCs. Study of fundamental properties revealed that the microstructured electrodes benefit from good wettability to electrolytes, but suffer from electric resistance. We found that this problem can be solved by metal-coating of the electrode surface. Finally we build an EDLC consisting of Au-coated micro-structured Si electrodes. This EDLC showed capacity of 14.3 mF/cm2, which is about 530 times larger than that of an EDLC consisting of flat Au electrodes.

  2. Design Optimization of Pixel Structure for α-Si based Uncooled Infrared Detector

    Directory of Open Access Journals (Sweden)

    Sudha Gupta


    Full Text Available In this paper authors present the design and simulation results achieved for pixel structure of amorphous Si (α-Si based bolometer array. Most uncooled IR detectors in the world are based on VOx material. But this is not a standard material in IC technology and has many inherent disadvantages. The α-Si, an alternative material with high TCR is becoming as popular. However, large TCR values, in this material are achieved only in films of high resistivity. To achieve TCR value more than 2.5%/K, α-Si film resistivity is ~ 80 ohms-cm. This gives rise to very large pixel resistance of the order of 100 Mega ohms depending upon the design of the leg structure. This high pixel resistance causes very large noise and hence lower sensitivity. If leg width or membrane thickness is increased in order to reduce the pixel resistance, then this results in higher thermal conductance which also decreases sensitivity. To overcome this problem, pixel structure is so designed that within a pixel, only part of the electrical conduction is through α-Si and rest is through metal. Simulation using Coventorware software has been done to optimize pixel resistance as well as thermal conductance through legs so that maximum sensitivity could be obtained. Optimization is also carried out in order to reduce sensitivity of pixel resistance to variation in material resistivity.

  3. Design optimization of Pixel Structure for α-Si based uncooled Infrared detector

    Directory of Open Access Journals (Sweden)

    Sudha Gupta


    Full Text Available In this paper authors present the design and simulation results achieved for pixel structure of amorphous Si (α-Si based bolometer array. Most uncooled IR detectors in the world are based on VOx material. But this is not a standard material in IC technology and has many inherent disadvantages. The α-Si, an alternative material with high TCR is becoming as popular. However, large TCR values, in this material are achieved only in films of high resistivity. To achieve TCR value more than 2.5%/K, α-Si film resistivity is ~ 80 ohms-cm. This gives rise to very large pixel resistance of the order of 100 Mega ohms depending upon the design of the leg structure. This high pixel resistance causes very large noise and hence lower sensitivity. If leg width or membrane thickness is increased in order to reduce the pixel resistance, then this results in higher thermal conductance which also decreases sensitivity. To overcome this problem, pixel structure is so designed that within a pixel, only part of the electrical conduction is through α-Si and rest is through metal. Simulation using Coventorware software has been done to optimize pixel resistance as well as thermal conductance through legs so that maximum sensitivity could be obtained. Optimization is also carried out in order to reduce sensitivity of pixel resistance to variation in material resistivity.Defence Science Journal, 2013, 63(6, pp.581-588, DOI:

  4. Controlled growth of Si-based heterostructure nanowires and their structural and electrical properties. (United States)

    Qian, Guanghan; Rahman, Saadah Abdul; Goh, Boon Tong


    Ni-catalyzed Si-based heterostructure nanowires grown on crystal Si substrates by hot-wire chemical vapor deposition (HWCVD) were studied. The nanowires which included NiSi nanowires, NiSi/Si core-shell nanowires, and NiSi/SiC core-shell nanowires were grown by varying the filament temperature T f from 1150 to 1850 °C. At a T f of 1450 °C, the heterostructure nanowires were formed by crystalline NiSi and crystalline Si that were attributed to the core and shell of the nanowires, respectively. The morphology of the nanowires showed significant changes with the increase in the filament temperature to 1850 °C. Moreover, the effect of hydrogen heat transfer from the filament temperature demonstrated significant phase changes from NiSi to Ni2Si with increase in the filament temperature. The increased filament temperature also enhanced reactions in the gas phase thus generating more SiC clusters and consequently formed the NiSi/SiC heterostructure core-shell nanowires at T f of 1850 °C. This paper discusses the role of filament temperatures on the growth and constituted phase change of the nanowires as well as their electrical characteristics.

  5. Controlled growth of Si-based heterostructure nanowires and their structural and electrical properties (United States)

    Qian, Guanghan; Rahman, Saadah Abdul; Goh, Boon Tong


    Ni-catalyzed Si-based heterostructure nanowires grown on crystal Si substrates by hot-wire chemical vapor deposition (HWCVD) were studied. The nanowires which included NiSi nanowires, NiSi/Si core-shell nanowires, and NiSi/SiC core-shell nanowires were grown by varying the filament temperature T f from 1150 to 1850 °C. At a T f of 1450 °C, the heterostructure nanowires were formed by crystalline NiSi and crystalline Si that were attributed to the core and shell of the nanowires, respectively. The morphology of the nanowires showed significant changes with the increase in the filament temperature to 1850 °C. Moreover, the effect of hydrogen heat transfer from the filament temperature demonstrated significant phase changes from NiSi to Ni2Si with increase in the filament temperature. The increased filament temperature also enhanced reactions in the gas phase thus generating more SiC clusters and consequently formed the NiSi/SiC heterostructure core-shell nanowires at T f of 1850 °C. This paper discusses the role of filament temperatures on the growth and constituted phase change of the nanowires as well as their electrical characteristics.

  6. Application of Ce3+ single-doped complexes as solar spectral downshifters for enhancing photoelectric conversion efficiencies of a-Si-based solar cells (United States)

    Song, Pei; Jiang, Chun


    The effect on photoelectric conversion efficiency of an a-Si-based solar cell by applying a solar spectral downshifter of rare earth ion Ce3+ single-doped complexes including yttrium aluminum garnet Y3Al5O12 single crystals, nanostructured ceramics, microstructured ceramics and B2O3-SiO2-Gd2O3-BaO glass is studied. The photoluminescence excitation spectra in the region 360-460 nm convert effectively into photoluminescence emission spectra in the region 450-550 nm where a-Si-based solar cells exhibit a higher spectral response. When these Ce3+ single-doped complexes are placed on the top of an a-Si-based solar cell as precursors for solar spectral downshifting, theoretical relative photoelectric conversion efficiencies of nc-Si:H and a-Si:H solar cells approach 1.09-1.13 and 1.04-1.07, respectively, by means of AMPS-1D numerical modeling, potentially benefiting an a-Si-based solar cell with a photoelectric efficiency improvement.

  7. Photoemission study of ferrocenes: insights into the electronic structure of Si-based hybrid materials

    Energy Technology Data Exchange (ETDEWEB)

    Boccia, A; Marrani, A G; Stranges, S; Zanoni, R [Dipartimento di Chimica, Universita degli Studi di Roma ' La Sapienza' , piazzale Aldo Moro 5, I-00185 Rome (Italy); Alagia, M [ISMN-CNR, Sezione Romal, Piazzale Aldo Moro 5, I-00185 Roma, Italy and Laboratorio Nazionale TASC-CNR SS-14, Km 163.5, Basovizza, I-34012 Trieste (Italy); Iozzi, M F; Cossi, M [Dipartimento di Scienze dell' Ambiente e della Vita, Universita del Piemonte Orientale, via V. Bellini 25/G, I-15100 Alessandria (Italy)], E-mail:


    We present here the results of synchrotron radiation-excited UV-photoemission investigation and DFT calculations on vinylferrocene (VFC), a redox molecule suitable for applications in molecular electronics. A detailed assignment is discussed of the valence photoelectron spectra (UPS), which provides new data on the electronic structure and offers a partial re-interpretation of previous assignments on VFC based on theoretical and experimental evidences. Furthermore, the present results can allow for a meaningful comparison of photoemission results from the corresponding hybrid obtained by covalently attaching VFC to Si oriented surfaces.

  8. Nanotubular structured Si-based multicomponent anodes for high-performance lithium-ion batteries with controllable pore size via coaxial electro-spinning. (United States)

    Ryu, Jaegeon; Choi, Sinho; Bok, Taesoo; Park, Soojin


    We demonstrate a simple but straightforward process for the synthesis of nanotube-type Si-based multicomponents by combining a coaxial electrospinning technique and subsequent metallothermic reduction reaction. Si-based multicomponent anodes consisting of Si, alumina and titanium silicide show several advantages for high-performance lithium-ion batteries. Alumina and titanium silicide, which have high mechanical properties, act as an effective buffer layer for the large volume change of Si, resulting in outstanding volume suppression behavior (volume expansion of only 14%). Moreover, electrically conductive titanium silicide layers located at the inner and outer layers of a Si nanotube exhibit a high initial coulombic efficiency of 88.5% and an extraordinary rate capability. Nanotubular structured Si-based multicomponents with mechanically and electrically improved components can be used as a promising alternative to conventional graphite anode materials. This synthetic route can be extended to other high capacity lithium-ion battery anode materials.

  9. On the Mass Fractal Character of Si-Based Structural Networks in Amorphous Polymer Derived Ceramics (United States)

    Sen, Sabyasachi; Widgeon, Scarlett


    The intermediate-range packing of SiNxC4−x (0 ≤ x ≤ 4) tetrahedra in polysilycarbodiimide and polysilazane-derived amorphous SiCN ceramics is investigated using 29Si spin-lattice relaxation nuclear magnetic resonance (SLR NMR) spectroscopy. The SiCN network in the polysilylcarbodiimide-derived ceramic consists predominantly of SiN4 tetrahedra that are characterized by a 3-dimensional spatial distribution signifying compact packing of such units to form amorphous Si3N4 clusters. On the other hand, the SiCN network of the polysilazane-derived ceramic is characterized by mixed bonded SiNxC4−x tetrahedra that are inefficiently packed with a mass fractal dimension of Df ~2.5 that is significantly lower than the embedding Euclidean dimension (D = 3). This result unequivocally confirms the hypothesis that the presence of dissimilar atoms, namely, 4-coordinated C and 3-coordinated N, in the nearest neighbor environment of Si along with some exclusion in connectivity between SiCxN4−x tetrahedra with widely different N:C ratios and the absence of bonding between C and N result in steric hindrance to an efficient packing of these structural units. It is noted that similar inefficiencies in packing are observed in polymer-derived amorphous SiOC ceramics as well as in proteins and binary hard sphere systems.

  10. On the Mass Fractal Character of Si-Based Structural Networks in Amorphous Polymer Derived Ceramics

    Directory of Open Access Journals (Sweden)

    Sabyasachi Sen


    Full Text Available The intermediate-range packing of SiNxC4−x (0 ≤ x ≤ 4 tetrahedra in polysilycarbodiimide and polysilazane-derived amorphous SiCN ceramics is investigated using 29Si spin-lattice relaxation nuclear magnetic resonance (SLR NMR spectroscopy. The SiCN network in the polysilylcarbodiimide-derived ceramic consists predominantly of SiN4 tetrahedra that are characterized by a 3-dimensional spatial distribution signifying compact packing of such units to form amorphous Si3N4 clusters. On the other hand, the SiCN network of the polysilazane-derived ceramic is characterized by mixed bonded SiNxC4−x tetrahedra that are inefficiently packed with a mass fractal dimension of Df ~2.5 that is significantly lower than the embedding Euclidean dimension (D = 3. This result unequivocally confirms the hypothesis that the presence of dissimilar atoms, namely, 4-coordinated C and 3-coordinated N, in the nearest neighbor environment of Si along with some exclusion in connectivity between SiCxN4−x tetrahedra with widely different N:C ratios and the absence of bonding between C and N result in steric hindrance to an efficient packing of these structural units. It is noted that similar inefficiencies in packing are observed in polymer-derived amorphous SiOC ceramics as well as in proteins and binary hard sphere systems.

  11. Stress influenced trapping processes in Si based multi-quantum well structures and heavy ions implanted Si

    Energy Technology Data Exchange (ETDEWEB)

    Ciurea, Magdalena Lidia, E-mail:; Lazanu, Sorina, E-mail: [National Institute for Materials Physics, 105bis Atomistilor Street, 077125 Magurele (Romania)


    Multi-quantum well structures and Si wafers implanted with heavy iodine and bismuth ions are studied in order to evaluate the influence of stress on the parameters of trapping centers. The experimental method of thermostimullatedcurrents without applied bias is used, and the trapping centers are filled by illumination. By modeling the discharge curves, we found in multilayered structures the parameters of both 'normal' traps and 'stress-induced' ones, the last having a Gaussian-shaped temperature dependence of the cross section. The stress field due to the presence of stopped heavy ions implanted into Si was modeled by a permanent electric field. The increase of the strain from the neighborhood of I ions to the neighborhood of Bi ions produces the broadening of some energy levels and also a temperature dependence of the cross sections for all levels.

  12. Stable generalized complex structures

    CERN Document Server

    Cavalcanti, Gil R


    A stable generalized complex structure is one that is generically symplectic but degenerates along a real codimension two submanifold, where it defines a generalized Calabi-Yau structure. We introduce a Lie algebroid which allows us to view such structures as symplectic forms. This allows us to construct new examples of stable structures, and also to define period maps for their deformations in which the background three-form flux is either fixed or not, proving the unobstructedness of both deformation problems. We then use the same tools to establish local normal forms for the degeneracy locus and for Lagrangian branes. Applying our normal forms to the four-dimensional case, we prove that any compact stable generalized complex 4-manifold has a symplectic completion, in the sense that it can be modified near its degeneracy locus to produce a compact symplectic 4-manifold.

  13. Structural complexity of quantum networks

    Energy Technology Data Exchange (ETDEWEB)

    Siomau, Michael [Physics Department, Jazan University, P.O.Box 114, 45142 Jazan (Saudi Arabia); Network Dynamics, Max Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen (Germany)


    Quantum network is a set of nodes connected with channels, through which the nodes communicate photons and classical information. Classical structural complexity of a quantum network may be defined through its physical structure, i.e. mutual position of nodes and channels connecting them. We show here that the classical structural complexity of a quantum network does not restrict the structural complexity of entanglement graphs, which may be created in the quantum network with local operations and classical communication. We show, in particular, that 1D quantum network can simulate both simple entanglement graphs such as lattices and random graphs and complex small-world graphs.

  14. Feasibility Studies on Si-Based Biosensors

    Directory of Open Access Journals (Sweden)

    Marcella Renis


    Full Text Available The aim of this paperis to summarize the efforts carried out so far in the fabrication of Si-based biosensors by a team of researchers in Catania, Italy. This work was born as a collaboration between the Catania section of the Microelectronic and Microsystem Institute (IMM of the CNR, the Surfaces and Interfaces laboratory (SUPERLAB of the Consorzio Catania Ricerche and two departments at the University of Catania: the Biomedical Science and the Biological Chemistry and Molecular Biology Departments. The first goal of our study was the definition and optimization of an immobilization protocol capable of bonding the biological sensing element on a Si-based surface via covalent chemical bonds. We chose SiO2 as the anchoring surface due to its biocompatibility and extensive presence in microelectronic devices. The immobilization protocol was tested and optimized, introducing a new step, oxide activation, using techniques compatible with microelectronic processing. The importance of the added step is described by the experimental results. We also tested different biological molecule concentrations in the immobilization solutions and the effects on the immobilized layer. Finally a MOS-like structure was designed and fabricated to test an electrical transduction mechanism. The results obtained so far and the possible evolution of the research field are described in this review paper.

  15. Progress of Si-based Optoelectronic Devices

    Institute of Scientific and Technical Information of China (English)

    PENG Ying-cai; FU Guang-sheng; WANG Ying-long; SHANG Yong


    Si-based optoelectronics is becoming a very active research area due to its potential applications to optical communications. One of the major goals of this study is to realize ali-Si optoelectronic integrated circuit. This is due to the fact that Si- based optoelectronic technology can be compatible with Si microelectronic technology. If Si-based optoelectronic devices and integrated circuits can be achieved,it will lead to a new informational technological revolution. In the article, the current developments of this exciting field are mainly reviewed in the recent years. The involved contents are the realization of various Si-based optoelectronic devices, such as light-emitting diodes,optical waveguides devices, Si photonic bandgap crystals,and Si laser,etc. Finally, the developed tendency of all-Si optoelectronic integrated technology are predicted in the near future.

  16. Structural insights into transcription complexes

    NARCIS (Netherlands)

    Berger, I.; Blanco, A.G.; Boelens, R.; Cavarelli, J.; Coll, M.; Folkers, G.E.; Nie, Y.; Pogenberg, V.; Schultz, P.; Wilmanns, M.; Moras, D.; Poterszman, A.


    Control of transcription allows the regulation of cell activity in response to external stimuli and research in the field has greatly benefited from efforts in structural biology. In this review, based on specific examples from the European SPINE2-COMPLEXES initiative, we illustrate the impact of

  17. The structure of rapidly quenched Fe–Co–B–Si based systems and the influence of addition of Cu and P

    Energy Technology Data Exchange (ETDEWEB)

    Janotová, I., E-mail:; Švec, P.; Mat’ko, I.; Janičkovič, D.; Švec, P.


    Highlights: • Amorphous materials in form of ribbons were prepared by planar flow casting. • Kinetics of crystallization was investigated by DSC and TGA. • Samples were annealed at 773 K, bcc-Fe(Si) and t-Fe{sub 2}B were determined by XRD. • In situ XRD using linear heating confirmed two-stage transformation. • Cu and P addition into base composition leads to changes of transformation parameters. - Abstract: Rapidly quenched systems based on Fe–Co–B–Si with addition of Cu and P are very interesting for their excellent soft magnetic and mechanical properties. These physical properties are given by the structure formed from amorphous state after controlled annealing. Selected amorphous systems of this type have been prepared by planar flow casting in form of thin ribbons. Materials after heat treatment exhibit fine-grains of bcc-Fe in amorphous matrix and subsequently borides. The influence of the substitution of Fe for Co, the substitution of B for Si and the additions of P and Cu on structure in nanocrystalline state was investigated. Transformations were detected using the methods of differential scanning calorimetry (DSC). X-ray diffraction (XRD), transmission electron microscopy (TEM) and electron diffraction (ED) analyses on samples heat-treated at selected temperatures were performed to obtain information about the structure, morphology, size and distribution of transformed grains in amorphous matrix of the investigated system.

  18. Structural insights into transcription complexes. (United States)

    Berger, Imre; Blanco, Alexandre G; Boelens, Rolf; Cavarelli, Jean; Coll, Miquel; Folkers, Gert E; Nie, Yan; Pogenberg, Vivian; Schultz, Patrick; Wilmanns, Matthias; Moras, Dino; Poterszman, Arnaud


    Control of transcription allows the regulation of cell activity in response to external stimuli and research in the field has greatly benefited from efforts in structural biology. In this review, based on specific examples from the European SPINE2-COMPLEXES initiative, we illustrate the impact of structural proteomics on our understanding of the molecular basis of gene expression. While most atomic structures were obtained by X-ray crystallography, the impact of solution NMR and cryo-electron microscopy is far from being negligible. Here, we summarize some highlights and illustrate the importance of specific technologies on the structural biology of protein-protein or protein/DNA transcription complexes: structure/function analysis of components the eukaryotic basal and activated transcription machinery with focus on the TFIID and TFIIH multi-subunit complexes as well as transcription regulators such as members of the nuclear hormone receptor families. We also discuss molecular aspects of promoter recognition and epigenetic control of gene expression. Copyright © 2011 Elsevier Inc. All rights reserved.

  19. Complex DNA structures and structures of DNA complexes

    Energy Technology Data Exchange (ETDEWEB)

    Chazin, W.J.; Carlstroem, G.; Shiow-Meei Chen; Miick, S.; Gomez-Paloma, L.; Smith, J.; Rydzewski, J. [Scripps Research Institute, La Jolla, CA (United States)


    Complex DNA structures (for example, triplexes, quadruplexes, junctions) and DNA-ligand complexes are more difficult to study by NMR than standard DNA duplexes are because they have high molecular weights, show nonstandard or distorted local conformations, and exhibit large resonance linewidths and severe {sup 1}H spectral overlap. These systems also tend to have limited solubility and may require specialized solution conditions to maintain favorable spectral characteristics, which adds to the spectroscopic difficulties. Furthermore, with more atoms in the system, both assignment and structure calculation become more challenging. In this article, we focus on demonstrating the current status of NMR studies of such systems and the limitations to further progress; we also indicate in what ways isotopic enrichment can be useful.

  20. Electro-physical properties of a Si-based MIS structure with a low-k SiOC(-H) film

    Energy Technology Data Exchange (ETDEWEB)

    Zakirov, Anvar Sagatovich; Navamathavan, Rangaswamy; Kim, Seung Hyun; Jang, Yong Jun; Jung, An Soo; Choi, Chi Kyu [Cheju National University, Jeju (Korea, Republic of)


    SiOC(-H) films with low dielectric constants have been prepared by using plasma enhanced chemical vapor deposition with a mixture of methyltriethoxysilane and oxygen precursors. The C-V characteristics of the structures, Al/SiOC(-H)/p-Si(100), were studied in the forward and the reverse directions by applying a polarizing potential. We found that the ratio of the maximum to the minimum capacitance (C{sub ma}x{sub /}C{sub min}) depended on the [MTES/(MTES+O{sub 2})] flow rate ratio. Annealed samples exhibited even greater reductions of the maximum capacitance and the dielectric constant of the SiOC(-H) samples. After annealing at 400 .deg. C, the measurement in the reverse direction revealed an interesting behavior in the form of strongly pronounced 'steps'. The bonds between Si-O and the -CH{sub 3} group reduced the surface charge density, and the distribution of the surface charge density depended on [MTES/(MTES+O{sub 2})] flow rate ratio and the annealing temperature because the fixed positive (Si-CH{sub 3}){sup +} and negative (Si-O){sup -} changed the configuration at the SiOC(-H)/p-Si(100) interface. The SiOC(-H) film had donor (O{sub 2}) and acceptor (Si-CH{sub 3} -groups) levels, and the electronic process at the SiOC(-H)/p-Si(100) interface was defined by the (Si-CH{sub 3}){sup +} and the (Si-O){sup -} bonds.

  1. Structural Analysis of Complex Networks

    CERN Document Server

    Dehmer, Matthias


    Filling a gap in literature, this self-contained book presents theoretical and application-oriented results that allow for a structural exploration of complex networks. The work focuses not only on classical graph-theoretic methods, but also demonstrates the usefulness of structural graph theory as a tool for solving interdisciplinary problems. Applications to biology, chemistry, linguistics, and data analysis are emphasized. The book is suitable for a broad, interdisciplinary readership of researchers, practitioners, and graduate students in discrete mathematics, statistics, computer science,

  2. Structural Complexity of DNA Sequence

    Directory of Open Access Journals (Sweden)

    Cheng-Yuan Liou


    Full Text Available In modern bioinformatics, finding an efficient way to allocate sequence fragments with biological functions is an important issue. This paper presents a structural approach based on context-free grammars extracted from original DNA or protein sequences. This approach is radically different from all those statistical methods. Furthermore, this approach is compared with a topological entropy-based method for consistency and difference of the complexity results.

  3. Efficient Analysis of Complex Structures (United States)

    Kapania, Rakesh K.


    Last various accomplishments achieved during this project are : (1) A Survey of Neural Network (NN) applications using MATLAB NN Toolbox on structural engineering especially on equivalent continuum models (Appendix A). (2) Application of NN and GAs to simulate and synthesize substructures: 1-D and 2-D beam problems (Appendix B). (3) Development of an equivalent plate-model analysis method (EPA) for static and vibration analysis of general trapezoidal built-up wing structures composed of skins, spars and ribs. Calculation of all sorts of test cases and comparison with measurements or FEA results. (Appendix C). (4) Basic work on using second order sensitivities on simulating wing modal response, discussion of sensitivity evaluation approaches, and some results (Appendix D). (5) Establishing a general methodology of simulating the modal responses by direct application of NN and by sensitivity techniques, in a design space composed of a number of design points. Comparison is made through examples using these two methods (Appendix E). (6) Establishing a general methodology of efficient analysis of complex wing structures by indirect application of NN: the NN-aided Equivalent Plate Analysis. Training of the Neural Networks for this purpose in several cases of design spaces, which can be applicable for actual design of complex wings (Appendix F).

  4. Progress of Si-based nanocrystalline luminescent materials

    Institute of Scientific and Technical Information of China (English)


    Si-based nanomaterials are some new photoelctronic and informational materials developed rapidly in recent years, and they have potential applications in the light emitting devices, e. g. Si light emitting diode, Si laser and integrated Si-based photoelectronics. Among them are nanoscale porous silicon (ps), Si nanocrystalline embedded SiO2 (SiOx, x < 2.0) matrices, Si nanoquantum dot and Si/SiO2 superlattice, etc. At present, there are various indications that if these materials can achieve efficient and stable luminescence, which are photoluminescence (PL) and electroluminescence (EL), it is possible for them to lead to a new informational revolution in the early days of the 21st century. In this article, we will mainly review the progress of study on Si-based nanomaterials in the past ten years. The involved contents are the fabricated methods, structural characterizations and light emitting properties. Finally, we predicate the developed tendency of this field in the following ten years.

  5. Structures of some surfactant–polyelectrolyte complexes

    Indian Academy of Sciences (India)

    Rema Krishnaswamy; V A Raghunathan; A K Sood


    Structures of complexes formed in aqueous solutions by some anionic polyelectrolytes (double and single stranded (ds and ss) DNA, poly(vinyl sulfonate) (PVS), and poly(styrene sulfonate) (PSS)) with a cationic surfactant system consisting of cetyltrimethylammonium bromide (CTAB) and sodium 3-hydroxy-2-naphthoate (SHN) have been determined using small angle X-ray diffraction. All complexes are found to have a two-dimensional (2-D) hexagonal structure at low SHN concentrations. Analysis of the diffraction data shows that the ds DNA–CTAB complex has an intercalated structure, with each DNA strand surrounded by three cylindrical micelles. On increasing SHN concentration, DNA–CTAB–SHN complexes exhibit a hexagonal-to-lamellar transition, whereas PVS complexes show a hexagonal → centered rectangular → lamellar transition. PSS complexes show yet another sequence of structures. These results indicate the significant influence of the chemical nature of the polyelectrolyte on the structure of the complexes.

  6. Computational Simulation of Complex Structure Fancy Yarns

    Institute of Scientific and Technical Information of China (English)


    A study is reported for mathematical model and simulation of complex structure fancy yarns. The investigated complex structure fancy yarns have a multithread structure composed of three components -core, effect, and binder yams. In current research the precondition was accepted that the cross-sections of the both two yarns of the effect intermediate product in the complex structure fancy yarn remain the circles shaped, and this shape does not change during manufacturing of the fancy yarn. Mathematical model of complex structure fancy yarn is established based on parameter equation of space helix line and computer simulation is further carried out using the computational mathematical tool Matlab 6.5. Theoretical structure of fancy yarn is compared with an experimental sample. The simulation system would help for further the set ofinformation in designing of new assortment of the complex structure fancy yarns and prediction of visual effects of fancy yarns in end-use fabrics.

  7. 3D complex: a structural classification of protein complexes.

    Directory of Open Access Journals (Sweden)

    Emmanuel D Levy


    Full Text Available Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.

  8. Predicting complex mineral structures using genetic algorithms. (United States)

    Mohn, Chris E; Kob, Walter


    We show that symmetry-adapted genetic algorithms are capable of finding the ground state of a range of complex crystalline phases including layered- and incommensurate super-structures. This opens the way for the atomistic prediction of complex crystal structures of functional materials and mineral phases.

  9. Active impedance matching of complex structural systems (United States)

    Macmartin, Douglas G.; Miller, David W.; Hall, Steven R.


    Viewgraphs on active impedance matching of complex structural systems are presented. Topics covered include: traveling wave model; dereverberated mobility model; computation of dereverberated mobility; control problem: optimal impedance matching; H2 optimal solution; statistical energy analysis (SEA) solution; experimental transfer functions; interferometer actuator and sensor locations; active strut configurations; power dual variables; dereverberation of complex structure; dereverberated transfer function; compensators; and relative power flow.

  10. TASI lectures on complex structures

    CERN Document Server

    Denef, Frederik


    These lecture notes give an introduction to a number of ideas and methods that have been useful in the study of complex systems ranging from spin glasses to D-branes on Calabi-Yau manifolds. Topics include the replica formalism, Parisi's solution of the Sherrington-Kirkpatrick model, overlap order parameters, supersymmetric quantum mechanics, D-brane landscapes and their black hole duals.

  11. TASI Lectures on Complex Structures (United States)

    Denef, Frederik


    These lecture notes give an introduction to a number of ideas and methods that have been useful in the study of complex systems ranging from spin glasses to D-branes on Calabi-Yau manifolds. Topics include the replica formalism, Parisi's solution of the Sherrington-Kirkpatrick model, overlap order parameters, supersymmetric quantum mechanics, D-brane landscapes and their black hole duals.

  12. Argument structure frames: a lexical complexity metric? (United States)

    Schmauder, A R


    The number of semantic argument structure frames associated with a verb has been reported to influence ease of processing during language comprehension. The present experiments tested the generality of the argument structure complexity effect with three dependent measures: eye-fixation times, naming latencies, and lexical decision latencies. Two eye-movement experiments and two experiments using cross-modal tasks failed to provide evidence supporting the argument structure complexity effect. The present experiments indicated that results reflecting verbs' argument structure complexity are not generalizable.

  13. Computational Complexity in Electronic Structure

    CERN Document Server

    Whitfield, James D; Aspuru-Guzik, Alan


    In quantum chemistry, the price paid by all known efficient model chemistries is either the truncation of the Hilbert space or uncontrolled approximations. Theoretical computer science suggests that these restrictions are not mere shortcomings of the algorithm designers and programmers but could stem from the inherent difficulty of simulating quantum systems. Extensions of computer science and information processing exploiting quantum mechanics has led to new ways of understanding the ultimate limitations of computational power. Interestingly, this perspective helps us understand widely used model chemistries in a new light. In this article, the fundamentals of computational complexity will be reviewed and motivated from the vantage point of chemistry. Then recent results from the computational complexity literature regarding common model chemistries including Hartree-Fock and density functional theory are discussed.

  14. Structures of photosynthetic membrane complexes


    Semchonok, Dmitry Alexandrovich


    Photosynthesis is essential to all life on Earth. It is the biological process that captures energy of sunlight and converts it into chemical compounds usable by any living organism. The processes occurring within photosynthesis can be divided into the light-dependent reactions and the light-independent reactions. In my PhD thesis several integral membrane protein complexes were investigated that catalyze the light dependent reactions. Primarily the photosystem I and II that are taking part i...

  15. Structure-based characterization of multiprotein complexes. (United States)

    Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J


    Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies.

  16. The structure of complex Lie groups

    CERN Document Server

    Lee, Dong Hoon


    Complex Lie groups have often been used as auxiliaries in the study of real Lie groups in areas such as differential geometry and representation theory. To date, however, no book has fully explored and developed their structural aspects.The Structure of Complex Lie Groups addresses this need. Self-contained, it begins with general concepts introduced via an almost complex structure on a real Lie group. It then moves to the theory of representative functions of Lie groups- used as a primary tool in subsequent chapters-and discusses the extension problem of representations that is essential for studying the structure of complex Lie groups. This is followed by a discourse on complex analytic groups that carry the structure of affine algebraic groups compatible with their analytic group structure. The author then uses the results of his earlier discussions to determine the observability of subgroups of complex Lie groups.The differences between complex algebraic groups and complex Lie groups are sometimes subtle ...

  17. Si-based Nanoparticles: a biocompatibility study (United States)

    Rivolta, I.; Lettiero, B.; Panariti, A.; D'Amato, R.; Maurice, V.; Falconieri, M.; Herlein, N.; Borsella, E.; Miserocchi, G.


    Exposure to silicon nanoparticles (Si-NPs) may occur in professional working conditions or for people undergoing a diagnostic screening test. Despite the fact that silicon is known as a non-toxic material, in the first case the risk is mostly related to the inhalation of nanoparticles, thus the most likely route of entry is across the lung alveolar epithelium. In the case of diagnostic imaging, nanoparticles are usually injected intravenously and Si-NPs could impact on the endothelial wall. In our study we investigated the interaction between selected Si-based NPs and an epithelial lung cell line. Our data showed that, despite the overall silicon biocompatibility, however accurate studies of the potential toxicity induced by the nanostructure and engineered surface characteristics need to be accurately investigated before Si nanoparticles can be safely used for in vivo applications as bio-imaging, cell staining and drug delivery.

  18. Structure of Complex Verb Forms in Meiteilon

    Directory of Open Access Journals (Sweden)

    Lourembam Surjit Singh


    Full Text Available This piece of work proposes to descriptively investigate the structures of complex verbs in Meiteilon. The categorization of such verbs is based on the nature of semantic and syntactic functions of a lexeme or verbal lexeme. A lexeme or verbal lexeme in Meiteilon may have multifunctional properties in the nature of occurrence. Such lexical items can be co-occurred together in a phrase as single functional word. Specifically, in the co-occurrences of two lexical items, the first component of lexical items has different semantic and syntactic functions in comparison to semantic and syntactic functions of the second component of lexical items. Such co-occurrences of two lexical items are the forms of complex verb that are covered with the term complex predicate in this work. The investigation in constructing complex predicate is thoroughly presenting in this work. Keywords: Structures, complex verb, conjunct verb, compound verb, complex predicate

  19. Alpha complexes in protein structure prediction

    DEFF Research Database (Denmark)

    Winter, Pawel; Fonseca, Rasmus


    Reducing the computational effort and increasing the accuracy of potential energy functions is of utmost importance in modeling biological systems, for instance in protein structure prediction, docking or design. Evaluating interactions between nonbonded atoms is the bottleneck of such computations......-complexes and kinetic a-complexes in protein related problems (e.g., protein structure prediction and protein-ligand docking) deserves furhter investigation.)...

  20. Modern structure of marketing communications complex

    Directory of Open Access Journals (Sweden)

    Hrebenyukova Elena


    Full Text Available The article presents the results of the desk research, in which the current structure of the marketing communications complex was analyzed. According to the results of the content analysis of scientific and educational literature in marketing it was proved that there is a certain structural asymmetry in today's complex of marketing communication: the rejection of impersonal tools and actualization of those which make possible personalized communication with the consumer.

  1. Structural Dissection for Controlling Complex Networks

    CERN Document Server

    Wang, Wen-Xu; Zhao, Chen; Liu, Yang-Yu; Lai, Ying-Cheng


    Controlling complex networked systems has been a central goal in different fields and understanding controllability of complex networks has been at the forefront of contemporary science. Despite the recent progress in the development of controllability theories for complex networks, we continue to lack efficient tools to fully understand the effect of network topology and interaction strengths among nodes on controllability. Here we establish a framework to discern the significance of links and nodes for controlling general complex networks in a simple way based on local information. A dissection process is offered by the framework to probe and classify nodes and links completely, giving rise to a criterion for strong structural controllability. Analytical results indicate phase transitions associated with link and node categories, and strong structural controllability. Applying the tools to real networks demonstrate that real technological networks are strong structurally controllable, whereas most of real s...

  2. Complex II from a structural perspective. (United States)

    Horsefield, Rob; Iwata, So; Byrne, Bernadette


    The super-macromolecular complex, succinate:quinone oxidoreductase (SQR, Complex II, succinate dehydrogenase) couples the oxidation of succinate in the matrix / cytoplasm to the reduction of quinone in the membrane. This function directly connects the Krebs cycle and the aerobic respiratory chain. Until the recent first report of the structure of SQR from Escherichia coli (E. coli) the structure-function relationships in SQR have been inferred from the structures of the homologous QFR, which catalyses the same reaction in the opposite direction. The structure of SQR from E. coli, analogous to the mitochondrial respiratory Complex II, has provided new insight into SQR's molecular design and mechanism, revealing the electron transport pathway through the enzyme. Comparison of the structures of SQR, QFR and other related flavoproteins shows how common amino acid residues at the interface of two domains facilitate the inter-conversion of succinate and fumarate. Additionally, the structure has provided a possible explanation as to why certain organisms utilise both SQR and QFR despite the fact that both can catalyse the inter-conversion of succinate and fumarate, in vitro and in vivo. Here we review how this structure has advanced our knowledge of this important enzyme and compare the structural information to other members of the Complex II superfamily and related flavoproteins.

  3. Stepwise redefinition of the SI base units

    CERN Document Server

    Issaev, L K; Khruschov, V V


    The four SI base units are proposed to be redefined in two stages: first, the kilogram, mole and ampere should be defined, and then the kelvin. To realize the redefinition of a base unit of the SI in terms of fundamental physical constant (FPC), a principle of coincidence of their physical dimensions is put forward. Direct applying this principle will lead to the changing of the sets of base and derived units in the new SI. If we want to preserve the continuity of the division between base and derived units in the new and the current SI, the principle is to be generalized with the time dimension factor be included. The status of the mole as the base unit of measurement is considered in the current and new SI. It is proposed to redefine the kilogram using a fixed value of the Avogadro constant and then to redefine the kelvin, after the measurement accuracy of the Boltzmann constant has been increased and agreed with the values of other constants of molecular physics.

  4. Si基Ge/SiGeⅠ型量子阱结构的理论设计和实验研究%Design and experiment of Si-based Ge/SiGe type-Ⅰ quantum well structure

    Institute of Scientific and Technical Information of China (English)

    陈城钊; 陈阳华; 黄诗浩; 李成; 赖虹凯; 陈松岩


    Si-based Ge/SiGe type-Ⅰ quantum well is theoretically designed based on the energy band engineering theory.High-quality Ge/ SiGe multiple quantum wells were grown on Si-based germanium virtual substrates by ultra-high vacuum chemical vapor deposition.When the thickness of the Ge quantum well is reduced from 15 nm to 12 nm and 11 nm,the quantum confinement effect in the Ge/SiGe quantum wells can be directly demonstrated by room temperature photoluminescence(PL),which is in good agreement with the theoretical prediction.But when the thickness of the Ge quantum well is gradually reduced to 9 nm and 7 nm,the experimental result doesn′t obey the theoretical prediction.Further experiments reveal the reason that when the thickness of the Ge quantum well is reduced to some extent,the photoluminescence from the direct band transition of the Ge well will be restrained and it mainly originates from the Ge virtual substrate.%基于能带工程理论,设计了Si基Ge/SiGeⅠ型量子阱结构。采用超高真空化学气相淀积系统,制备出高质量的Si基Ge/SiGe多量子阱系列材料。当样品中Ge量子阱宽从15nm减少到12nm和11nm时,室温下荧光(PL)光谱观测到量子限制效应引起的直接带跃迁发光峰位的蓝移,峰位的实验值与理论值符合得很好;当Ge量子阱宽逐渐减小到9nm和7nm时,测试得到样品的PL谱峰位却与理论预期出现了较大的差值。进一步的实验表明,这主要是由于量子阱厚度小到一定程度时,量子阱的直接带发光受到抑制,其发光主要源于Ge虚拟衬底。

  5. Probing complex RNA structures by mechanical force

    CERN Document Server

    Harlepp, S; Robert, J; Leger, J F; Xayaphoummine, A; Isambert, H; Chatenay, D


    RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by solely invoking successive openings of native helices. Indeed, typical force-extension responses of complex RNA molecules are largely shaped by stretching-induced, long-lived intermediates including non-native helices. This is first shown for a set of generic structural motifs found in larger RNA structures, and then for Escherichia coli's 1540-base long 16S ribosomal RNA, which exhibits a surprisingly well-structured and reproducible unfolding pathway under mechanical stretching. Using out-of-equilibrium stochastic simulations, we demonstrate that these experimental results reflect the slow relaxation of RNA structural rearrangements. Hence, micromanipulations of single RNA molecules probe both their native structures and long-lived intermediates, so-called "kinetic traps",...

  6. Structural and Topology Optimization of Complex Civil Engineering Structures

    DEFF Research Database (Denmark)

    Hald, Frederik; Kirkegaard, Poul Henning; Andersen, Lars Vabbersgaard


    will be optimized using the commercial code Abaqus CAE. The structures are: a bucket foundation for an off-shore submarine structure for a wind turbine, and a pedestrian footbridge over a freeway. The topology optimization method used is the SIMP method, based on minimizing the structures' compliance. Complex load...

  7. Structural Features of Caspase-Activating Complexes

    Directory of Open Access Journals (Sweden)

    Hyun Ho Park


    Full Text Available Apoptosis, also called programmed cell death, is an orderly cellular suicide program that is critical for the development, immune regulation and homeostasis of a multi-cellular organism. Failure to control this process can lead to serious human diseases, including many types of cancer, neurodegenerative diseases, and autoimmununity. The process of apoptosis is mediated by the sequential activation of caspases, which are cysteine proteases. Initiator caspases, such as caspase-2, -8, -9, and -10, are activated by formation of caspase-activating complexes, which function as a platform to recruit caspases, providing proximity for self-activation. Well-known initiator caspase-activating complexes include (1 DISC (Death Inducing Signaling Complex, which activates caspases-8 and 10; (2 Apoptosome, which activates caspase-9; and (3 PIDDosome, which activates caspase-2. Because of the fundamental biological importance of capases, many structural and biochemical studies to understand the molecular basis of assembly mechanism of caspase-activating complexes have been performed. In this review, we summarize previous studies that have examined the structural and biochemical features of caspase-activating complexes. By analyzing the structural basis for the assembly mechanism of the caspase-activating complex, we hope to provide a comprehensive understanding of caspase activation by these important oligomeric complexes.

  8. Detecting highly cyclic structure with complex eigenpairs

    CERN Document Server

    Klymko, Christine


    Many large, real-world complex networks have rich community structure that a network scientist seeks to understand. These communities may overlap or have intricate internal structure. Extracting communities with particular topological structure, even when they overlap with other communities, is a powerful capability that would provide novel avenues of focusing in on structure of interest. In this work we consider extracting highly-cyclic regions of directed graphs (digraphs). We demonstrate that embeddings derived from complex-valued eigenvectors associated with stochastic propagator eigenvalues near roots of unity are well-suited for this purpose. We prove several fundamental theoretic results demonstrating the connection between these eigenpairs and the presence of highly-cyclic structure and we demonstrate the use of these vectors on a few real-world examples.

  9. Modelling the structure of complex networks

    DEFF Research Database (Denmark)

    Herlau, Tue

    networks has been independently studied as mathematical objects in their own right. As such, there has been both an increased demand for statistical methods for complex networks as well as a quickly growing mathematical literature on the subject. In this dissertation we explore aspects of modelling complex....... The next chapters will treat some of the various symmetries, representer theorems and probabilistic structures often deployed in the modelling complex networks, the construction of sampling methods and various network models. The introductory chapters will serve to provide context for the included written...

  10. Structure of a copper-isoniazid complex. (United States)

    Hanson, J C; Camerman, N; Camerman, A


    It is well-known that complex formation with copper ions increases the in vitro mycobactericidal action of the antituberculosis agent isoniazid. We report here the preparation and structure of a copper(II)-isoniazid complex. Unit cell parameters are a = 9.575, b = 14.855, and c = 7.056 A and space group P2(1)2(1)2(1). Copper bonding geometry is square planar with the isoniazid carbonyl oxygen and hydrazide amino nitrogen atoms and two chlorines occupying coordination positions. Complexing with copper(II) does not significantly alter the isoniazid molecular conformation.

  11. The Electronic Structure of Heavy Element Complexes

    Energy Technology Data Exchange (ETDEWEB)

    Bursten, Bruce E.


    The area of study is the bonding in heavy element complexes, and the application of more sophisticated electronic structure theories. Progress is recounted in several areas: (a) technological advances and current methodologies - Relativistic effects are extremely important in gaining an understanding of the electronic structure of compounds of the actinides, transactinides, and other heavy elements. Therefore, a major part of the continual benchmarking was the proper inclusion of the appropriate relativistic effects for the properties under study. (b) specific applications - These include organoactinide sandwich complexes, CO activation by actinide atoms, and theoretical studies of molecules of the transactinide elements. Finally, specific directions in proposed research are described.

  12. Structural and Topology Optimization of Complex Civil Engineering Structures

    DEFF Research Database (Denmark)

    Hald, Frederik; Kirkegaard, Poul Henning; Andersen, Lars Vabbersgaard


    This paper shows the use of topology optimization for finding an optimized form for civil engineering structures. Today topology optimization and shape optimization have been integrated in several commercial finite element codes. Here, the topology of two complex civil engineering structures...

  13. Designing complex systems - a structured activity

    NARCIS (Netherlands)

    van der Veer, Gerrit C.; van Vliet, Johannes C.; Lenting, Bert; Olson, Gary M.; Schuon, Sue


    This paper concerns the development of complex systems from the point of view of design as a structure of activities, related both to the clients and the users. Several modeling approaches will be adopted for different aspects of design, and several views on design will be integrated. The proposed

  14. Designing complex systems - a structured activity

    NARCIS (Netherlands)

    van der Veer, Gerrit C.; van Vliet, Johannes C.; Lenting, Bert; Olson, Gary M.; Schuon, Sue


    This paper concerns the development of complex systems from the point of view of design as a structure of activities, related both to the clients and the users. Several modeling approaches will be adopted for different aspects of design, and several views on design will be integrated. The proposed a

  15. Structural studies of EF-Tu complexes

    DEFF Research Database (Denmark)

    Johansen, Jesper Sanderhoff


    elongation factor, EF-Ts, catalyse the dissociation of GDP from EF-Tu which in turn allows EF-Tu to bind another GTP molecule. The resulting EF-Tu:GTP complex is then cable of forming a ternary complex with a new aa-tRNA which can then associate with the ribosome. During my time as a Ph. D. student I have...... and in manuscript I. G. anatolicus is a hyperthermophilic bacteria isolated from a thermal vent. The structure of G. anatolicus EF-Ts has been determined in complex with E. coli EF-Tu by X-ray crystallography to a resolution of 2.8 Å. The structure of G. anatolicus EF-Ts is more similar to the previously determined...... structures of E. coli and bovine mitochondrial EF-Ts rather than EF-Ts from the thermophilic bacteria T. thermophilus. The structure of G. anatolicus EF-Ts in complex with E. coli EF-Tu is presented in chapter 3 and in manuscript II. Mammalian mitochondria contain an independent genome which encodes 13...

  16. Solution Structures of PPARγ2/RXRα Complexes

    Directory of Open Access Journals (Sweden)

    Judit Osz


    Full Text Available PPARγ is a key regulator of glucose homeostasis and insulin sensitization. PPARγ must heterodimerize with its dimeric partner, the retinoid X receptor (RXR, to bind DNA and associated coactivators such as p160 family members or PGC-1α to regulate gene networks. To understand how coactivators are recognized by the functional heterodimer PPARγ/RXRα and to determine the topological organization of the complexes, we performed a structural study using small angle X-ray scattering of PPARγ/RXRα in complex with DNA from regulated gene and the TIF2 receptor interacting domain (RID. The solution structures reveal an asymmetry of the overall structure due to the crucial role of the DNA in positioning the heterodimer and indicate asymmetrical binding of TIF2 to the heterodimer.

  17. Complex structures of dense lithium: Electronic origin (United States)

    Degtyareva, V. F.


    Lithium—the lightest alkali metal exhibits unexpected structures and electronic behavior at high pressures. Like the heavier alkali metals, Li is bcc at ambient pressure and transforms first to fcc (at 7.5 GPa). The post-fcc high-pressure form Li-cI 16 (at 40-60 GPa) is similar to Na-cI 16 and related to more complex structures of heavy alkalis Rb-oC52 and Cs- oC84. The other high pressure phases for Li (oC88, oC40, oC24) observed at pressures up to 130 GPa are found only in Li. The different route of Li high-pressure structures correlates with its special electronic configuration containing the only 3 electrons (at 1s and 2s levels). Crystal structures for Li are analyzed within the model of Fermi sphere-Brillouin zone interactions. Stability of post-fcc structures for Li are supported by the Hume-Rothery arguments when new diffraction plains appear close to the Fermi level producing pseudogaps near the Fermi level and decreasing the crystal energy. The filling of Brillouin-Jones zones by electron states for a given structure defines the physical properties as optical reflectivity, electrical resistivity and superconductivity. To understand the complexity of structural and physical properties of Li above 60 GPa it is necessary to assume the valence electron band overlap with the core electrons and increase the valence electron count under compression.

  18. Synthesis of crystalline Si-based nanosheets by extraction of Ca from CaSi2 in inositol hexakisphosphate solution (United States)

    Meng, Xiang; Sasaki, Kenta; Sano, Koki; Yuan, Peiling; Tatsuoka, Hirokazu


    Crystalline Si-based nanosheets were successfully synthesized from CaSi2 by a simple soft chemical synthetic method in solution. By immersing CaSi2 powder or CaSi2/Si substrates in an inositol hexakisphosphate (IP6) solution, Ca atoms were extracted from the CaSi2 particles, then Si-based nanosheets were formed. The morphological, structural and optical properties of the Si-based nanosheets were investigated. It is noted that the thin Si-based nanosheets stacked with a void space formed bundle structures, and the nanosheets were easily exfoliated from the bundles to expose the surfaces corresponding to the Si{111} planes. Meanwhile, the surface of the Si nanosheets might be terminated by O, H, or OH bonds. The Si-based nanosheet bundles were then formed and directly rooted to the Si(111) substrates, and had a remarkably highly symmetrical morphology. This study demonstrated a simple method for preparing Si-based nanosheets, and electro- and photo-chemical applications would possibly be expected, such as in lithium ion batteries.

  19. Structure of bacterial respiratory complex I. (United States)

    Berrisford, John M; Baradaran, Rozbeh; Sazanov, Leonid A


    Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. It is the largest protein assembly of respiratory chains and one of the most elaborate redox membrane proteins known. Bacterial enzyme is about half the size of mitochondrial and thus provides its important "minimal" model. Dysfunction of mitochondrial complex I is implicated in many human neurodegenerative diseases. The L-shaped complex consists of a hydrophilic arm, where electron transfer occurs, and a membrane arm, where proton translocation takes place. We have solved the crystal structures of the hydrophilic domain of complex I from Thermus thermophilus, the membrane domain from Escherichia coli and recently of the intact, entire complex I from T. thermophilus (536 kDa, 16 subunits, 9 iron-sulphur clusters, 64 transmembrane helices). The 95Å long electron transfer pathway through the enzyme proceeds from the primary electron acceptor flavin mononucleotide through seven conserved Fe-S clusters to the unusual elongated quinone-binding site at the interface with the membrane domain. Four putative proton translocation channels are found in the membrane domain, all linked by the central flexible axis containing charged residues. The redox energy of electron transfer is coupled to proton translocation by the as yet undefined mechanism proposed to involve long-range conformational changes. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.

  20. Structure of the haptoglobin-haemoglobin complex

    DEFF Research Database (Denmark)

    Andersen, Christian Brix Folsted; Torvund-Jensen, Morten; Nielsen, Marianne Jensby


    Red cell haemoglobin is the fundamental oxygen-transporting molecule in blood, but also a potentially tissue-damaging compound owing to its highly reactive haem groups. During intravascular haemolysis, such as in malaria and haemoglobinopathies, haemoglobin is released into the plasma, where...... it is captured by the protective acute-phase protein haptoglobin. This leads to formation of the haptoglobin-haemoglobin complex, which represents a virtually irreversible non-covalent protein-protein interaction. Here we present the crystal structure of the dimeric porcine haptoglobin-haemoglobin complex...... receptor CD163 (ref. 3) protrudes from the surface of the distal end of the complex, adjacent to the associated haemoglobin α-subunit. Small-angle X-ray scattering measurements of human haptoglobin-haemoglobin bound to the ligand-binding fragment of CD163 confirm receptor binding in this area, and show...

  1. Crystal structure of putrescine aspartic acid complex


    Ramaswamy, S.; Murthy, MRN


    Polyamines, putrescine, spermidine and spermine are ubiquitous biogenic cations believed to be important for a variety of cellular processes. In order to obtain structural information on the interaction of these amines with other biomolecules, the structure of a complex of putrescine with aspartic acid was determined using single crystal X-ray diffraction methods. The crystals belong monoclinic space group $C_2$ with $a = 21.504 \\AA$, $b = 4.779 \\AA$, $c = 8.350 \\AA$ and $\\beta = {97.63}^{\\ci...

  2. Electromagnetic Detection and Identification of Complex Structures (United States)


    1 ELECTROMAGNETIC DETECTION AND IDENTIFICATION OF COMPLEX STRUCTURES I. Kohlberg Kohlberg Associates Reston, Virginia, 20190-4440 S.A...TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Kohlberg Associates Reston, Virginia, 20190-4440 8...Electromagnetic Theory, 2 nd ed. IEEE Press, New York. von Laven, S.A., Albritton, N.G., Baginski, T.A., Hodel, A.S., McMillan, R.W., Kohlberg

  3. Structural alignment of RNA with complex pseudoknot structure. (United States)

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


    The secondary structure of an ncRNA molecule is known to play an important role in its biological functions. Aligning a known ncRNA to a target candidate to determine the sequence and structural similarity helps in identifying de novo ncRNA molecules that are in the same family of the known ncRNA. However, existing algorithms cannot handle complex pseudoknot structures which are found in nature. In this article, we propose algorithms to handle two types of complex pseudoknots: simple non-standard pseudoknots and recursive pseudoknots. Although our methods are not designed for general pseudoknots, it already covers all known ncRNAs in both Rfam and PseudoBase databases. An evaluation of our algorithms shows that it is useful to identify ncRNA molecules in other species which are in the same family of a known ncRNA.

  4. Morphologically complex protostellar envelopes : structure and kinematics (United States)

    Tobin, John J.

    I present an in-depth study of protostars and their surrounding envelopes of dense gas and dust, using a multitude of observational methods to reveal new details of the star formation process. I use mid-infrared imaging from the Spitzer Space Telescope, combined with photometry spanning the near-infrared to millimeter wavelengths, to construct a model of the L1527 protostellar system. I modeled both the spectral energy distribution and resolved scattered light images to determine physical properties of the protostellar system. The nature of the apparent central point source in the Spitzer images was uncertain until high-resolution L-band imaging from the Gemini observatory resolved the point source into a disk in scattered light, having a radius of 200 AU. Protostellar envelopes are also often found to cast shadows against the 8 micron Galactic background in Spitzer imaging, enabling direct probes of envelope structure. The shadow images show that the dense envelopes around twenty-two Class 0 protostars are generally morphologically complex from 0.1 pc scales down to ˜1000 AU; they are often filamentary, and frequently non-axisymmetric. The observed envelope structure indicates a likely origin in turbulent cloud structure rather than a quasi-static/equilibrium formation. The complex envelope structure also may indicate an increased likelihood of fragmentation during collapse, forming close binaries. To further characterize these envelopes, I have observed them in the dense molecular gas tracers nthp and nht, both of which closely follow the 8 micron extinction morphology. The magnitude of the velocity gradients and envelope complexity on ˜10000 AU scales indicates that the velocity structure may reflect large-scale infall in addition to the often assumed rotation. Comparisons with three-dimensional filamentary and symmetric rotating collapse models reinforce the interpretation of velocities reflecting large-scale infall, showing that the structure of the envelope

  5. Structured analysis and modeling of complex systems (United States)

    Strome, David R.; Dalrymple, Mathieu A.


    The Aircrew Evaluation Sustained Operations Performance (AESOP) facility at Brooks AFB, Texas, combines the realism of an operational environment with the control of a research laboratory. In recent studies we collected extensive data from the Airborne Warning and Control Systems (AWACS) Weapons Directors subjected to high and low workload Defensive Counter Air Scenarios. A critical and complex task in this environment involves committing a friendly fighter against a hostile fighter. Structured Analysis and Design techniques and computer modeling systems were applied to this task as tools for analyzing subject performance and workload. This technology is being transferred to the Man-Systems Division of NASA Johnson Space Center for application to complex mission related tasks, such as manipulating the Shuttle grappler arm.

  6. The complex channel networks of bone structure

    CERN Document Server

    Costa, Luciano da Fontoura; Beletti, Marcelo E


    Bone structure in mammals involves a complex network of channels (Havers and Volkmann channels) required to nourish the bone marrow cells. This work describes how three-dimensional reconstructions of such systems can be obtained and represented in terms of complex networks. Three important findings are reported: (i) the fact that the channel branching density resembles a power law implies the existence of distribution hubs; (ii) the conditional node degree density indicates a clear tendency of connection between nodes with degrees 2 and 4; and (iii) the application of the recently introduced concept of hierarchical clustering coefficient allows the identification of typical scales of channel redistribution. A series of important biological insights is drawn and discussed

  7. Topological structural classes of complex networks (United States)

    Estrada, Ernesto


    We use theoretical principles to study how complex networks are topologically organized at large scale. Using spectral graph theory we predict the existence of four different topological structural classes of networks. These classes correspond, respectively, to highly homogenous networks lacking structural bottlenecks, networks organized into highly interconnected modules with low inter-community connectivity, networks with a highly connected central core surrounded by a sparser periphery, and networks displaying a combination of highly connected groups (quasicliques) and groups of nodes partitioned into disjoint subsets (quasibipartites). Here we show by means of the spectral scaling method that these classes really exist in real-world ecological, biological, informational, technological, and social networks. We show that neither of three network growth mechanisms—random with uniform distribution, preferential attachment, and random with the same degree sequence as real network—is able to reproduce the four structural classes of complex networks. These models reproduce two of the network classes as a function of the average degree but completely fail in reproducing the other two classes of networks.

  8. Hierarchical community structure in complex (social) networks

    CERN Document Server

    Massaro, Emanuele


    The investigation of community structure in networks is a task of great importance in many disciplines, namely physics, sociology, biology and computer science where systems are often represented as graphs. One of the challenges is to find local communities from a local viewpoint in a graph without global information in order to reproduce the subjective hierarchical vision for each vertex. In this paper we present the improvement of an information dynamics algorithm in which the label propagation of nodes is based on the Markovian flow of information in the network under cognitive-inspired constraints \\cite{Massaro2012}. In this framework we have introduced two more complex heuristics that allow the algorithm to detect the multi-resolution hierarchical community structure of networks from a source vertex or communities adopting fixed values of model's parameters. Experimental results show that the proposed methods are efficient and well-behaved in both real-world and synthetic networks.

  9. Electronic structure and magnetism of complex materials

    CERN Document Server

    Papaconstantopoulos, D A


    Recent developments in electronic structure theory have led to a new understanding of magnetic materials at the microscopic level. This enables a truly first-principles approach to investigations of technologically important magnetic materials. Among these advances have been practical schemes for handling non-collinear magnetic systems, including relativity, understanding of the origins and role of orbital magnetism within band structure formalisms, density functional approaches for magnons and low-lying spin excitations, understanding of the interplay of orbital, spin and lattice orderings in complex oxides, transport theories for layered systems, and the theory of magnetic interactions in doped semiconductors. The book covers these recent developments with review articles by some of the main originators of these advances.

  10. Learning Latent Structure in Complex Networks

    DEFF Research Database (Denmark)

    Mørup, Morten; Hansen, Lars Kai

    as in the previous Bayesian approaches and in addition allows learning of node specific link properties similar to that in the modularity objective. We employ a new relaxation method for efficient inference in these generative models that allows us to learn the behavior of very large networks. We compare the link...... such as the Modularity, it has recently been shown that latent structure in complex networks is learnable by Bayesian generative link distribution models (Airoldi et al., 2008, Hofman and Wiggins, 2008). In this paper we propose a new generative model that allows representation of latent community structure...... prediction performance of the learning based approaches and other widely used link prediction approaches in 14 networks ranging from medium size to large networks with more than a million nodes. While link prediction is typically well above chance for all networks, we find that the learning based mixed...

  11. Complex band structure and superlattice electronic states (United States)

    Schulman, J. N.; McGill, T. C.


    The complex band structures of the bulk materials which constitute the alternating layer (001) semiconductor-semiconductor superlattice are investigated. The complex bands near the center of the Brillouin zone in the [001] direction are studied in detail. The decay lengths of superlattice states whose energies lie in the bulk band gaps of one of the semiconductors are determined from the dispersion curves of these bands for imaginary k-->. This method is applied using a tight-binding band-structure calculation to two superlattices: the AlAs-GaAs superlattice and the CdTe-HgTe superlattice. The decay lengths of AlAs-GaAs superlattice conduction-band minimum states are found to be substantially shorter than those for the CdTe-HgTe superlattice. These differences in the decay of the states in the two superlattices result in differences in the variation of the conduction-band effective masses with the thickness of the AlAs and CdTe layers. The conduction-band effective masses increase more rapidly with AlAs thickness in the AlAs-GaAs superlattice than with CdTe thickness in the CdTe-HgTe superlattice.

  12. Issues in Complex Structure Moduli Inflation

    CERN Document Server

    Hayashi, Hirotaka; Watari, Taizan


    Supersymmetric compactification with moderately large radius (${\\rm Re} \\sim {\\cal O}(10)$ or more) not only accommodates supersymmetric unification, but also provides candidates for an inflaton in the form of geometric moduli; the value of ${\\rm Re} > 1$ may be used as a parameter that brings corrections to the inflaton potential under control. Motivated by a bottom-up idea "right-handed sneutrino inflation" scenario, we study whether complex structure moduli can play some role during the slow-roll inflation and/or reheating process in this moderately large radius regime. Even when we allow a tuning introduced by Kallosh and Linde, the barrier of volume stabilization potential from gaugino condensation racetrack superpotential can hardly be as high as $(10^{16} \\; {\\rm GeV})^4$ for generic choice of parameters in this regime. It is also found that even very small deformation of complex structure during inflation/reheating distorts the volume stabilization potential, so that the volume stabilization imposes t...

  13. Ab initio lattice dynamics of complex structures

    DEFF Research Database (Denmark)

    Voss, Johannes


    systems in particular. A more detailed analysis of the phonon spectrum has been performed for the compound Mg(BH4)2, where several crystal symmetries have been proposed theoretically and experimentally. By means of an analysis of the instabilities of these structures, a new, stable phase has been......In this thesis, density functional theory is applied in a study of thermodynamic properties of so-called complex metal hydrides, which are promising materials for hydrogen storage applications. Since the unit cells of these crystals can be relatively large with many symmetrically inequivalent...... determined. Aiming at finding scaling relationships between alloy stabilities and computationally inexpensive properties, the stabilities of cation-alloyed metal aluminum hexahydrides have been studied. The analysis shows that charge density symmetries are correlated to the stability. In addition...

  14. Superelement Verification in Complex Structural Models

    Directory of Open Access Journals (Sweden)

    B. Dupont


    Full Text Available The objective of this article is to propose decision indicators to guide the analyst in the optimal definition of an ensemble of superelements in a complex structural assembly. These indicators are constructed based on comparisons between the unreduced physical model and the approximate solution provided by a nominally reduced superelement model. First, the low contribution substructure slave modes are filtered. Then, the minimum dynamical residual expansion is used to localize the superelements which are the most responsible for the response prediction errors. Moreover, it is shown that static residual vectors, which are a natural result of these calculations, can be included to represent the contribution of important truncated slave modes and consequently correct the deficient superelements. The proposed methodology is illustrated on a subassembly of an aeroengine model.

  15. Structure and spectroscopy of uranyl salicylaldiminate complexes

    Energy Technology Data Exchange (ETDEWEB)

    Tamasi, A.L.; Barnes, C.L.; Walensky, J.R. [Missouri Univ., Columbia, MO (United States). Dept. of Chemistry


    The synthesis of uranyl complexes coordinated to tridentate, monoanionic salicylaldiminate (Schiff base) ligands was achieved by the reaction of UO{sub 2}Cl{sub 2}(THF){sub 3}, 1, with one equivalent of the corresponding sodium salicylaldiminate salts affording [(C{sub 9}H{sub 6}N)N=C(H)C{sub 6}H{sub 2}'Bu{sub 2}O]UO{sub 2}Cl(THF), 2, [(NC{sub 5}H{sub 4})N=C(H)C{sub 6}H{sub 2}'Bu{sub 2}O]UO{sub 2}Cl(THF), 3, and [(C{sub 6}H{sub 4}SCH{sub 3})N=C(H)C{sub 6}H{sub 2}'Bu{sub 2}O]UO{sub 2}Cl(THF), 4. These are uncommon examples of uranyl complexes with a monoanionic ancillary ligand to stabilize the coordination sphere and one chloride ligand. Compounds 2-4 have been characterized by {sup 1}H and {sup 13}C NMR spectroscopy as well as IR and UVVis spectroscopy and their structures determined by X-ray crystallography. (orig.)

  16. Coherent structures in a supersonic complex nozzle (United States)

    Magstadt, Andrew; Berry, Matthew; Glauser, Mark


    The jet flow from a complex supersonic nozzle is studied through experimental measurements. The nozzle's geometry is motivated by future engine designs for high-performance civilian and military aircraft. This rectangular jet has a single plane of symmetry, an additional shear layer (referred to as a wall jet), and an aft deck representative of airframe integration. The core flow operates at a Mach number of Mj , c = 1 . 6 , and the wall jet is choked (Mj , w = 1 . 0). This high Reynolds number jet flow is comprised of intense turbulence levels, an intricate shock structure, shear and boundary layers, and powerful corner vortices. In the present study, stereo PIV measurements are simultaneously sampled with high-speed pressure measurements, which are embedded in the aft deck, and far-field acoustics in the anechoic chamber at Syracuse University. Time-resolved schlieren measurements have indicated the existence of strong flow events at high frequencies, at a Strouhal number of St = 3 . 4 . These appear to result from von Kàrmàn vortex shedding within the nozzle and pervade the entire flow and acoustic domain. Proper orthogonal decomposition is applied on the current data to identify coherent structures in the jet and study the influence of this vortex street. AFOSR Turbulence and Transition Program (Grant No. FA9550-15-1-0435) with program managers Dr. I. Leyva and Dr. R. Ponnappan.

  17. Organization structures for dealing with complexity

    NARCIS (Netherlands)

    Meijer, B.R.


    "Complexity is in the eye of the beholder" is a well known quote in the research field of complexity. In the world of managers the word complex is often a synonym for difficult, complicated, involving many factors and highly uncertain. A complex business decision requires careful preparation and clo

  18. Organization structures for dealing with complexity

    NARCIS (Netherlands)

    Meijer, B.R.


    "Complexity is in the eye of the beholder" is a well known quote in the research field of complexity. In the world of managers the word complex is often a synonym for difficult, complicated, involving many factors and highly uncertain. A complex business decision requires careful preparation and

  19. Si-based light emitter in an integrated photonic circuit for smart biosensor applications (United States)

    Germer, S.; Cherkouk, C.; Rebohle, L.; Helm, M.; Skorupa, W.


    The motivation for integrated Silicon-based optoelectronics is the creation of low-cost photonics for mass-market applications. Especially, the growing demand for sensitive biochemical sensors in the environmental control or medicine leads to the development of integrated high resolution sensors. Here we present initial results in the integration and butt-coupling of a Si-based light emitting device (LED) [1-3] to a waveguide into a photonic circuit. Our first approach deals with the design, fabrication and characterization of the dielectric high contrast waveguide as an important component, beside the LED, for the development of a Si-based biodetection system. In this work we demonstrate design examples of Si3N4/SiO2-waveguides, which were calculated using MATLAB, the effective index method (EIM) and the finite element method (FEM), with a 0.45μm thick and 0.7μm wide core which shows a high confinement factor of ~74% and coupling efficiency of ~66% at 1.55μm, respectively. The fabrication was done by plasma enhanced chemical vapour deposition (PECVD), optical lithography and reactive ion etching (RIE). Additionally, we characterized the deposited layers via ellipsometry and the etched structures by scanning electron microscopy (SEM). The obtained results establish principles for Si-based LED butt-coupling to a powerful optical waveguide-based interconnect with effective light absorption and an adequate coupling efficiency.

  20. Complex Convective Thermal Fluxes and Vorticity Structure (United States)

    Redondo, Jose M.; Tellez, Jackson; Sotillos, Laura; Lopez Gonzalez-Nieto, Pilar; Sanchez, Jesus M.; Furmanek, Petr; Diez, Margarita


    Local Diffusion and the topological structure of vorticity and velocity fields is measured in the transition from a homogeneous linearly stratified fluid to a cellular or layered structure by means of convective cooling and/or heating[1,2]. Patterns arise by setting up a convective flow generated by an array of Thermoelectric devices (Peltier/Seebeck cells) these are controlled by thermal PID generating a buoyant heat flux [2]. The experiments described here investigate high Prandtl number mixing using brine and fresh water in order to form density interfaces and low Prandtl number mixing with temperature gradients. The set of dimensionless parameters define conditions of numeric and small scale laboratory modeling of environmental flows. Fields of velocity, density and their gradients were computed and visualized [3,4]. When convective heating and cooling takes place the combination of internal waves and buoyant turbulence is much more complicated if the Rayleigh and Reynolds numbers are high in order to study entrainment and mixing. Using ESS and selfsimilarity structures in the velocity and vorticity fieds and intermittency [3,5] that forms in the non-homogeneous flow is related to mixing and stiring. The evolution of the mixing fronts are compared and the topological characteristics of the merging of plumes and jets in different configurations presenting detailed comparison of the evolution of RM and RT, Jets and Plumes in overall mixing. The relation between structure functions, fractal analysis and spectral analysis can be very useful to determine the evolution of scales. Experimental and numerical results on the advance of a mixing or nonmixing front occurring at a density interface due to body forces [6]and gravitational acceleration are analyzed considering the fractal and spectral structure of the fronts like in removable plate experiments for Rayleigh-Taylor flows. The evolution of the turbulent mixing layer and its complex configuration is studied

  1. The structure and singularities of arc complexes

    DEFF Research Database (Denmark)

    Penner, Robert

    boundary components. The main result of this paper is the determination of those arc complexes Arc(F) that are also spherical. This classification has consequences for Riemann's moduli space via its known identification with an analogous arc complex in the punctured case with no boundary. Namely...

  2. The structure and singularities of arc complexes

    DEFF Research Database (Denmark)

    Penner, Robert

    A classical combinatorial fact is that the simplicial complex consisting of disjointly embedded chords in a convex planar polygon is a sphere. For any surface F with non-empty boundary, there is an analogous complex Arc(F) consisting of suitable equivalence classes of arcs in F connecting its bou...

  3. Structure, dynamics, assembly, and evolution of protein complexes. (United States)

    Marsh, Joseph A; Teichmann, Sarah A


    The assembly of individual proteins into functional complexes is fundamental to nearly all biological processes. In recent decades, many thousands of homomeric and heteromeric protein complex structures have been determined, greatly improving our understanding of the fundamental principles that control symmetric and asymmetric quaternary structure organization. Furthermore, our conception of protein complexes has moved beyond static representations to include dynamic aspects of quaternary structure, including conformational changes upon binding, multistep ordered assembly pathways, and structural fluctuations occurring within fully assembled complexes. Finally, major advances have been made in our understanding of protein complex evolution, both in reconstructing evolutionary histories of specific complexes and in elucidating general mechanisms that explain how quaternary structure tends to evolve. The evolution of quaternary structure occurs via changes in self-assembly state or through the gain or loss of protein subunits, and these processes can be driven by both adaptive and nonadaptive influences.

  4. Three Dimensional Topological Field Theory induced from Generalized Complex Structure

    CERN Document Server

    Ikeda, N


    We construct a three-dimensional topological sigma model which is induced from a generalized complex structure on a target generalized complex manifold. This model is constructed from maps from a three-dimensional manifold $X$ to an arbitrary generalized complex manifold $M$. The theory is invariant under the diffeomorphism on the world volume and the $b$-transformation on the generalized complex structure. Moreover the model is manifestly invariant under the mirror symmetry. We derive from this model the Zucchini's two dimensional topological sigma model with a generalized complex structure as a boundary action on $\\partial X$. As a special case, we obtain three dimensional realization of a WZ-Poisson manifold.

  5. Synthesis, Structure and Reactivity of Lanthanocene Complexes

    Institute of Scientific and Technical Information of China (English)

    QIAN, Chang-Tao(钱长涛); ZHU, Cheng-Jian(朱成建)


    A variety of lanthanocene complexes,e.g.chlorides,hydrocarbyls,amides,hydrides and divalent derivatives,were synthesized by using a series of destgned cyclopentadienyl,indenyl and fluorenyl ligands with ring bridges or dornor-functionalized sidearms.X-Ray crystallographic analyses reveal the formation of intramolecular coordination bonds between central metals and heteroatoms(O,N)in sidearms or bridging chains.Some applications of these complexes are also discussed in this account.

  6. 纳米梁的金硅原电池腐蚀和无损释放技术研究%Study on the galvanic cell etching for Si-based nano beam with Au pad and release method without structure damage

    Institute of Scientific and Technical Information of China (English)

    戴斌; 杨恒; 陆松涛


    Hydrofluoric acid(HF) was widely used in wet etching operation to release Si-based micronano beams. However,corrosion of silicon may occur when silicon beam is electrically connected to Au Pad, which seriously damages the feature and performance of nano beams. According to the measurements of polarization curves of Au/ Si in HF, galvanic etching was suggested to play a major role in the etching of Si. Galvanic etching can be alleviated by changing the Au/Si area ratio and HF solution content based on the experiments. In the end, HF vapor phase etching devices was designed to totally eliminate the galvanic cell etching and 120 nm thickness two double-clamped nano beams was successfully fabricated by this method without structure damage.%采用金电极的硅纳米梁在通过HF湿法腐蚀SiO2牺牲层释放结构的时候会发生硅纳米梁被腐蚀现象,消除此效应对于纳米尺度梁制造非常重要:通过电化学工作站测量不同条件下金/硅在HF中的极化曲线和腐蚀电流,从定性和定量研究此腐蚀的原理和影响因素:金硅在HF中形成的原电池效应是此腐蚀的主要原因;改变金硅面积比和改变HF构成可以减缓此腐蚀.设计了一种简单可控的HF蒸气腐蚀装置彻底消除原电池腐蚀效应的影响,并实现了120 nm厚双端固支纳米梁的无损释放.

  7. Si-Based Anode Materials for Li-Ion Batteries:A Mini Review

    Institute of Scientific and Technical Information of China (English)

    Delong Ma; Zhanyi Cao; Anming Hu


    Si has been considered as one of the most attractive anode materials for Li-ion batteries (LIBs) because of its high gravimetric and volumetric capacity. Importantly, it is also abundant, cheap, and environmentally benign. In this review, we summarized the recent progress in developments of Si anode materials. First, the electrochemical reaction and failure are outlined, and then, we summarized various methods for improving the battery performance, including those of nanostructuring, alloying, forming hierarchic structures, and using suitable binders. We hope that this review can be of benefit to more intensive investigation of Si-based anode materials.

  8. Structural studies of EF-Tu complexes

    DEFF Research Database (Denmark)

    Johansen, Jesper Sanderhoff


    proteins and 22 tRNAs and 2 rRNAs. The mammalian mitochondria have their own specialised translational system for maintaining the synthesis of the 13 proteins. The mammalian mitochondrial protein synthesis resembles the prokaryotic system more than the cytosolic system from eukaryotes. Some of the t...... and tRNASerGCU was produced by in vitro transcription. The ternary complex composed of EF-Tu:GDPNP:tRNASerGCU was reconstituted for crystallisation experiments. Unfortunately, we have not succeeding in crystallising neither the free components nor the ternary complex so far. The results of this project...

  9. Complex photonic structures for energy efficiency

    Directory of Open Access Journals (Sweden)

    Wiersma D. S.


    Full Text Available Photonic structures are playing an increasingly important role in energy efficiency. In particular, they can help to control the flow of light and improve the optical properties of photovoltaic solar cells. We will explain the physics of light transport in such structures with a special focus on disordered materials.

  10. Structural Complexity in Linguistic Systems Research Topic 3: Mathematical Sciences (United States)


    SECURITY CLASSIFICATION OF: We adapted computational mechanics to determine the role of structural complexity in linguistic systems, including language...Jan-2015 Approved for Public Release; Distribution Unlimited Final Report: Structural Complexity in Linguistic Systems (Research Topic 3: Mathematical...hidden Markov model, epsilon-machine, entropy, quantitative linguistics , computational linguistics REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S

  11. Research progress of Si-based germanium materials and devices (United States)

    Buwen, Cheng; Cheng, Li; Zhi, Liu; Chunlai, Xue


    Si-based germanium is considered to be a promising platform for the integration of electronic and photonic devices due to its high carrier mobility, good optical properties, and compatibility with Si CMOS technology. However, some great challenges have to be confronted, such as: (1) the nature of indirect band gap of Ge; (2) the epitaxy of dislocation-free Ge layers on Si substrate; and (3) the immature technology for Ge devices. The aim of this paper is to give a review of the recent progress made in the field of epitaxy and optical properties of Ge heterostructures on Si substrate, as well as some key technologies on Ge devices. High crystal quality Ge epilayers, as well as Ge/SiGe multiple quantum wells with high Ge content, were successfully grown on Si substrate with a low-temperature Ge buffer layer. A local Ge condensation technique was proposed to prepare germanium-on-insulator (GOI) materials with high tensile strain for enhanced Ge direct band photoluminescence. The advances in formation of Ge n+p shallow junctions and the modulation of Schottky barrier height of metal/Ge contacts were a significant progress in Ge technology. Finally, the progress of Si-based Ge light emitters, photodetectors, and MOSFETs was briefly introduced. These results show that Si-based Ge heterostructure materials are promising for use in the next-generation of integrated circuits and optoelectronic circuits. Project supported in part by the National Natural Science Foundation (Nos. 61036003, 61435013) and the Major State Basic Research Development Program of China (No. 2013CB632103).

  12. Crystallization and Structure Determination of Superantigens and Immune Receptor Complexes. (United States)

    Rödström, Karin E J; Lindkvist-Petersson, Karin


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

  13. Synthesis and Crystal Structure of a New Salen Complex

    Institute of Scientific and Technical Information of China (English)

    LI Li-Jun; LI Ying; SUN Wen-Hua


    @@ Salen Schiff base complexes are some of the most important stereochemical models in transition metal coordina tion chemistry, with their ease of preparation and structural variation. [1] Salen complexes are extensively used as organic reaction catalysts, it was reported to be used in asymmetric cyclopropanation, epoxidation, aziridination, hydrolysis, alkylation, Diels-Alder reaction, reduction, oxidation etc. Here we report the synthesis and structure of a new salen nickel complex 4.

  14. Gelled Complex Fluids: Combining Unique Structures with Mechanical Stability. (United States)

    Stubenrauch, Cosima; Gießelmann, Frank


    Gelled complex fluids are soft materials in which the microstructure of the complex fluid is combined with the mechanical stability of a gel. To obtain a gelled complex fluid one either adds a gelator to a complex fluid or replaces the solvent in a gel by a complex fluid. The most prominent example of a "natural" gelled complex fluid is the cell. There are various strategies by which one can form a gelled complex fluid; one such strategy is orthogonal self-assembly, that is, the independent but simultaneous formation of two coexisting self-assembled structures within one system. The aim of this Review is to describe the structure and potential applications of various man-made gelled complex fluids and to clarify whether or not the respective system is formed by orthogonal self-assembly.

  15. Relationships between structural complexity, coral traits, and reef fish assemblages (United States)

    Darling, Emily S.; Graham, Nicholas A. J.; Januchowski-Hartley, Fraser A.; Nash, Kirsty L.; Pratchett, Morgan S.; Wilson, Shaun K.


    With the ongoing loss of coral cover and the associated flattening of reef architecture, understanding the links between coral habitat and reef fishes is of critical importance. Here, we investigate whether considering coral traits and functional diversity provides new insights into the relationship between structural complexity and reef fish communities, and whether coral traits and community composition can predict structural complexity. Across 157 sites in Seychelles, Maldives, the Chagos Archipelago, and Australia's Great Barrier Reef, we find that structural complexity and reef zone are the strongest and most consistent predictors of reef fish abundance, biomass, species richness, and trophic structure. However, coral traits, diversity, and life histories provided additional predictive power for models of reef fish assemblages, and were key drivers of structural complexity. Our findings highlight that reef complexity relies on living corals—with different traits and life histories—continuing to build carbonate skeletons, and that these nuanced relationships between coral assemblages and habitat complexity can affect the structure of reef fish assemblages. Seascape-level estimates of structural complexity are rapid and cost effective with important implications for the structure and function of fish assemblages, and should be incorporated into monitoring programs.

  16. Development of numerical procedures for analysis of complex structures (United States)

    Gupta, K. K.


    The paper is concerned with the development of novel numerical procedures for the solution of static, stability, free vibration and dynamic response analysis of large, complex practical structures. Thus, details of numerical algorithms evolved for dynamic analysis of usual non-rotating and also rotating structures as well as finite dynamic elements are presented in the paper. Furthermore, the article provides some description of a general-purpose computer program STARS specifically developed for efficient analysis of complex practical structures.

  17. Structurally simple complexes of CO2


    Murphy, Luke J.; Robertson, Katherine N.; Richard A. Kemp; TUONONEN, Heikki; Clyburne, Jason A. C.


    The ability to bind CO2 through the formation of low-energy, easily-broken, bonds could prove invaluable in a variety of chemical contexts. For example, weak bonds to CO2 would greatly decrease the cost of the energy-intensive sorbent-regeneration step common to most carbon capture technologies. Furthermore, exploration of this field could lead to the discovery of novel CO2 chemistry. Reduction of complexed carbon dioxide might generate chemical feedstocks for the preparation of value-added p...

  18. In situ structural analysis of the human nuclear pore complex. (United States)

    von Appen, Alexander; Kosinski, Jan; Sparks, Lenore; Ori, Alessandro; DiGuilio, Amanda L; Vollmer, Benjamin; Mackmull, Marie-Therese; Banterle, Niccolo; Parca, Luca; Kastritis, Panagiotis; Buczak, Katarzyna; Mosalaganti, Shyamal; Hagen, Wim; Andres-Pons, Amparo; Lemke, Edward A; Bork, Peer; Antonin, Wolfram; Glavy, Joseph S; Bui, Khanh Huy; Beck, Martin


    Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a formidable challenge and requires in situ structural biology approaches. Of approximately 30 nucleoporins (Nups), 15 are structured and form the Y and inner-ring complexes. These two major scaffolding modules assemble in multiple copies into an eight-fold rotationally symmetric structure that fuses the inner and outer nuclear membranes to form a central channel of ~60 nm in diameter. The scaffold is decorated with transport-channel Nups that often contain phenylalanine-repeat sequences and mediate the interaction with cargo complexes. Although the architectural arrangement of parts of the Y complex has been elucidated, it is unclear how exactly it oligomerizes in situ. Here we combine cryo-electron tomography with mass spectrometry, biochemical analysis, perturbation experiments and structural modelling to generate, to our knowledge, the most comprehensive architectural model of the human nuclear pore complex to date. Our data suggest previously unknown protein interfaces across Y complexes and to inner-ring complex members. We show that the transport-channel Nup358 (also known as Ranbp2) has a previously unanticipated role in Y-complex oligomerization. Our findings blur the established boundaries between scaffold and transport-channel Nups. We conclude that, similar to coated vesicles, several copies of the same structural building block--although compositionally identical--engage in different local sets of interactions and conformations.

  19. Structure and Dynamics of the VAULT COMPLEX

    NARCIS (Netherlands)

    A. van Zon (Arend)


    textabstractVaults are the largest ribonucleoprotein particles found in eukaryotic cells. The maincomponent of these 13 MDa structures is the Mr 100,000 major vault protein (MVP).In mammalian cells, about 96 copies of this protein are necessary to form one vaultparticle. Two additional proteins are

  20. Supramolecular Multiblock Copolymers Featuring Complex Secondary Structures. (United States)

    Elacqua, Elizabeth; Manning, Kylie B; Lye, Diane S; Pomarico, Scott K; Morgia, Federica; Weck, Marcus


    This contribution introduces main-chain supramolecular ABC and ABB'A block copolymers sustained by orthogonal metal coordination and hydrogen bonding between telechelic polymers that feature distinct secondary structure motifs. Controlled polymerization techniques in combination with supramolecular assembly are used to engineer heterotelechelic π-sheets that undergo high-fidelity association with both helical and coil-forming synthetic polymers. Our design features multiple advances to achieve our targeted structures, in particular, those emulating sheet-like structural aspects using poly(p-phenylenevinylene)s (PPVs). To engineer heterotelechelic PPVs in a sheet-like design, we engineer an iterative one-pot cross metathesis-ring-opening metathesis polymerization (CM-ROMP) strategy that affords functionalized Grubbs-II initiators that subsequently polymerize a paracyclophanediene. Supramolecular assembly of two heterotelechelic PPVs is used to realize a parallel π-sheet, wherein further orthogonal assembly with helical motifs is possible. We also construct an antiparallel π-sheet, wherein terminal PPV blocks are adjacent to a flexible coil-like poly(norbornene) (PNB). The PNB is designed, through supramolecular chain collapse, to expose benzene and perfluorobenzene motifs that promote a hairpin turn via charge-transfer-aided folding. We demonstrate that targeted helix-(π-sheet)-helix and helix-(π-sheet)-coil assemblies occur without compromising intrinsic helicity, while both parallel and antiparallel β-sheet-like structures are realized. Our main-chain orthogonal assembly approach allows the engineering of multiblock copolymer scaffolds featuring diverse secondary structures via the directional assembly of telechelic building blocks. The targeted assemblies, a mix of sequence-defined helix-sheet-coil and helix-sheet-helix architectures, are Nature-inspired synthetic mimics that expose α/β and α+β protein classes via de novo design and cooperative assembly

  1. Community structure of complex networks based on continuous neural network (United States)

    Dai, Ting-ting; Shan, Chang-ji; Dong, Yan-shou


    As a new subject, the research of complex networks has attracted the attention of researchers from different disciplines. Community structure is one of the key structures of complex networks, so it is a very important task to analyze the community structure of complex networks accurately. In this paper, we study the problem of extracting the community structure of complex networks, and propose a continuous neural network (CNN) algorithm. It is proved that for any given initial value, the continuous neural network algorithm converges to the eigenvector of the maximum eigenvalue of the network modularity matrix. Therefore, according to the stability of the evolution of the network symbol will be able to get two community structure.

  2. Reinforcing Visual Grouping Cues to Communicate Complex Informational Structure. (United States)

    Bae, Juhee; Watson, Benjamin


    In his book Multimedia Learning [7], Richard Mayer asserts that viewers learn best from imagery that provides them with cues to help them organize new information into the correct knowledge structures. Designers have long been exploiting the Gestalt laws of visual grouping to deliver viewers those cues using visual hierarchy, often communicating structures much more complex than the simple organizations studied in psychological research. Unfortunately, designers are largely practical in their work, and have not paused to build a complex theory of structural communication. If we are to build a tool to help novices create effective and well structured visuals, we need a better understanding of how to create them. Our work takes a first step toward addressing this lack, studying how five of the many grouping cues (proximity, color similarity, common region, connectivity, and alignment) can be effectively combined to communicate structured text and imagery from real world examples. To measure the effectiveness of this structural communication, we applied a digital version of card sorting, a method widely used in anthropology and cognitive science to extract cognitive structures. We then used tree edit distance to measure the difference between perceived and communicated structures. Our most significant findings are: 1) with careful design, complex structure can be communicated clearly; 2) communicating complex structure is best done with multiple reinforcing grouping cues; 3) common region (use of containers such as boxes) is particularly effective at communicating structure; and 4) alignment is a weak structural communicator.

  3. Complex banded structures in directional solidification processes. (United States)

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


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

  4. Complexity and dynamics of topological and community structure in complex networks (United States)

    Berec, Vesna


    Complexity is highly susceptible to variations in the network dynamics, reflected on its underlying architecture where topological organization of cohesive subsets into clusters, system's modular structure and resulting hierarchical patterns, are cross-linked with functional dynamics of the system. Here we study connection between hierarchical topological scales of the simplicial complexes and the organization of functional clusters - communities in complex networks. The analysis reveals the full dynamics of different combinatorial structures of q-th-dimensional simplicial complexes and their Laplacian spectra, presenting spectral properties of resulting symmetric and positive semidefinite matrices. The emergence of system's collective behavior from inhomogeneous statistical distribution is induced by hierarchically ordered topological structure, which is mapped to simplicial complex where local interactions between the nodes clustered into subcomplexes generate flow of information that characterizes complexity and dynamics of the full system.

  5. Landau theory of martensitic transformation in Fe-Mn-Si based alloys

    Institute of Scientific and Technical Information of China (English)


    Considering the features of martensitic transformation in Fe-Mn-Si based alloys, the Landau theory is established by introducing the density of stacking faults as a new order parameter ηand the corresponding free energy function. By using such an order parameter, the stacking fault mechanism of the nucleation and growth for the γ(fcc)→ε(hcp) martensitic transformation can be reasonably explained, and a further detailed mechanism is proposed. The stacking faults are generated and overlapped in an irregular form at the beginning and then becoming regular to create some transition structures till a stable phase forms at a certain temperature. The importance of the interface soliton is to complete the transformations into various structures of martensite but not the twinned one. The thermodynamics of fcc→hcp transformation and those between different transition structures are described by the free energy function established in the present note.

  6. Structural and dynamical properties of complex networks (United States)

    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


    Energy Technology Data Exchange (ETDEWEB)



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

  8. The structure and function of bacterial light-harvesting complexes. (United States)

    Law, Christopher J; Roszak, Aleksander W; Southall, June; Gardiner, Alastair T; Isaacs, Neil W; Cogdell, Richard J


    The harvesting of solar radiation by purple photosynthetic bacteria is achieved by circular, integral membrane pigment-protein complexes. There are two main types of light-harvesting complex, termed LH2 and LH1, that function to absorb light energy and to transfer that energy rapidly and efficiently to the photochemical reaction centres where it is trapped. This mini-review describes our present understanding of the structure and function of the purple bacterial light-harvesting complexes.

  9. [Problems of formal organizational structure of industrial health care complexes]. (United States)

    Włodarczyk, C


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

  10. Synthesis and Crystal Structure of a New Manganese Complex

    Institute of Scientific and Technical Information of China (English)

    WANG Jian; LIU Ping; CHEN Yun


    @@ In order to study the relationship between the manganese ion and the biological coordination agent, the role ofmanganese ion in the active sites and the structure of the active sites in the manganese enzymes, small molecule complexes are often applied to modeling the structure and the properties of reaction in the active centers. In this pa per, we will report the synthesis and crystal structure of a new manganese(Ⅱ) complex, catena[ aqua-(p-methoxybenzoato- O, O′ ) - (p-methoxybenzoato- O )- (2,2′-bipyridine)-manganese (Ⅱ) ] (p-methoxybenzoic acid). The crystal structure was confirmeded by X-ray crystallography analysis.

  11. Studies on the structure and function of pyruvate dehydrogenase complexes

    NARCIS (Netherlands)

    Abreu, de R.A.


    The aim of the present investigation was to obtain more information of the structure and function of the pyruvate dehydrogenase complexes from Azotobacter vinelandii and Escherichia coli.In chapter 2 a survey is given of the recent literature on pyruvate dehydrogenase complexes.In chapter 3 results

  12. Ge-Photodetectors for Si-Based Optoelectronic Integration

    Directory of Open Access Journals (Sweden)

    Sungjoo Lee


    Full Text Available High speed photodetectors are a key building block, which allow a large wavelength range of detection from 850 nm to telecommunication standards at optical fiber band passes of 1.3–1.55 µm. Such devices are key components in several applications such as local area networks, board to board, chip to chip and intrachip interconnects. Recent technological achievements in growth of high quality SiGe/Ge films on Si wafers have opened up the possibility of low cost Ge-based photodetectors for near infrared communication bands and high resolution spectral imaging with high quantum efficiencies. In this review article, the recent progress in the development and integration of Ge-photodetectors on Si-based photonics will be comprehensively reviewed, along with remaining technological issues to be overcome and future research trends.

  13. Structural assembly of molecular complexes based on residual dipolar couplings. (United States)

    Berlin, Konstantin; O'Leary, Dianne P; Fushman, David


    We present and evaluate a rigid-body molecular docking method, called PATIDOCK, that relies solely on the three-dimensional structure of the individual components and the experimentally derived residual dipolar couplings (RDCs) for the complex. We show that, given an accurate ab initio predictor of the alignment tensor from a protein structure, it is possible to accurately assemble a protein-protein complex by utilizing the RDCs' sensitivity to molecular shape to guide the docking. The proposed docking method is robust against experimental errors in the RDCs and computationally efficient. We analyze the accuracy and efficiency of this method using experimental or synthetic RDC data for several proteins, as well as synthetic data for a large variety of protein-protein complexes. We also test our method on two protein systems for which the structure of the complex and steric-alignment data are available (Lys48-linked diubiquitin and a complex of ubiquitin and a ubiquitin-associated domain) and analyze the effect of flexible unstructured tails on the outcome of docking. The results demonstrate that it is fundamentally possible to assemble a protein-protein complex solely on the basis of experimental RDC data and the prediction of the alignment tensor from 3D structures. Thus, despite the purely angular nature of RDCs, they can be converted into intermolecular distance/translational constraints. Additionally, we show a method for combining RDCs with other experimental data, such as ambiguous constraints from interface mapping, to further improve structure characterization of protein complexes.

  14. Mesoscopic hydrothermodynamics of complex-structured materials (United States)

    Vasconcellos, Áurea R.; Silva, A. A. P.; Luzzi, Roberto; Casas-Vázquez, J.; Jou, David


    Some experimental results in the study of disordered systems, polymeric fluids, solutions of micelles and surfactants, ionic-glass conductors, and others show a hydrodynamic behavior labeled “anomalous” with properties described by some kind of fractional power laws in place of the standard ones. This is a consequence of the fractal-like structure that is present in these systems of which we do not have a detailed description, thus impairing the application of the conventional ensemble formalism of statistical mechanics. In order to obtain a physical picture of the phenomenon for making predictions which may help with technological and industrial decisions, one may resort to different styles (so-called nonconventional) in statistical mechanics. In that way can be introduced a theory for handling such impaired situations, a nonconventional mesoscopic hydrothermodynamics (MHT). We illustrate the question presenting an application in a contracted description of such nonconventional MHT, consisting in the use of the Renyi approach to derive a set of coupled nonstandard evolution equations, one for the density, a nonconventional Maxwell-Cattaneo equation, which in a limiting case goes over a non-Fickian diffusion equation, and other for the velocity in fluids under forced flow. For illustration the theory is applied to the study of the hydrodynamic motion in several soft-matter systems under several conditions such as streaming flow appearing in electrophoretic techniques and flow generated by harmonic forces arising in optical traps. The equivalence with Lévy processes is discussed and comparison with experiment is done.

  15. The Structure Inventory of the Nuclear Pore Complex. (United States)

    Schwartz, Thomas U


    The nuclear pore complex (NPC) is the principal gateway for molecular exchange between nucleus and cytoplasm across the nuclear envelope. Due to its sheer size of estimated 50-112MDa and its complex buildup from about 500-1000 individual proteins, it is a difficult object to study for structural biologists. Here, I review the extensive ensemble of high-resolution structures of the building blocks of the NPC. Concurrent with the increase in size and complexity, these latest, large structures and assemblies can now be used as the basis for hybrid approaches, primarily in combination with cryo-electron microscopic analysis, generating the first structure-based assembly models of the NPC. Going forward, the structures will be critically important for a detailed analysis of the NPC, including function, evolution, and assembly.

  16. Methods for behavior descriptions of structure-complex Petri nets

    Institute of Scientific and Technical Information of China (English)

    Qingtian ZENG; Zhehui WU


    Petri net language is a powerful tool for describing dynamic behaviors of physical systems. However, it is not easy to obtain the language expression for a given Petri net especially a structure-complex net. In this paper, we first analyze the behaviors of S-nets, which are structure-simple. With the decomposition method based on a given index function on the place set, a given structure-complex Petri net can be decomposed into a set of structure-simple S-nets. With the language relationships between the original system and the decomposed subnets, an algorithm to obtain the language expression of a given structure-complex net system is presented, which benefits the analysis of physical systems based on the Petri net language.

  17. How to Measure Significance of Community Structure in Complex Networks

    CERN Document Server

    Hu, Yanqing; Fan, Ying; Di, Zengru


    Community structure analysis is a powerful tool for complex networks, which can simplify their functional analysis considerably. Recently, many approaches were proposed to community structure detection, but few works were focused on the significance of community structure. Since real networks obtained from complex systems always contain error links, and most of the community detection algorithms have random factors, evaluate the significance of community structure is important and urgent. In this paper, we use the eigenvectors' stability to characterize the significance of community structures. By employing the eigenvalues of Laplacian matrix of a given network, we can evaluate the significance of its community structure and obtain the optimal number of communities, which are always hard for community detection algorithms. We apply our method to many real networks. We find that significant community structures exist in many social networks and C.elegans neural network, and that less significant community stru...

  18. Photonic crystals, light manipulation, and imaging in complex nematic structures (United States)

    Ravnik, Miha; Å timulak, Mitja; Mur, Urban; Čančula, Miha; Čopar, Simon; Žumer, Slobodan


    Three selected approaches for manipulation of light by complex nematic colloidal and non-colloidal structures are presented using different own custom developed theoretical and modelling approaches. Photonic crystals bands of distorted cholesteric liquid crystal helix and of nematic colloidal opals are presented, also revealing distinct photonic modes and density of states. Light propagation along half-integer nematic disclinations is shown with changes in the light polarization of various winding numbers. As third, simulated light transmission polarization micrographs of nematic torons are shown, offering a new insight into the complex structure characterization. Finally, this work is a contribution towards using complex soft matter in optics and photonics for advanced light manipulation.

  19. On the complexity and the information content of cosmic structures (United States)

    Vazza, F.


    The emergence of cosmic structure is commonly considered one of the most complex phenomena in nature. However, this complexity has never been defined nor measured in a quantitative and objective way. In this work, we propose a method to measure the information content of cosmic structure and to quantify the complexity that emerges from it, based on Information Theory. The emergence of complex evolutionary patterns is studied with a statistical symbolic analysis of the datastream produced by state-of-the-art cosmological simulations of forming galaxy clusters. This powerful approach allows us to measure how many bits of information is necessary to predict the evolution of energy fields in a statistical way, and it offers a simple way to quantify when, where and how the cosmic gas behaves in complex ways. The most complex behaviours are found in the peripheral regions of galaxy clusters, where supersonic flows drive shocks and large energy fluctuations over a few tens of million years. Describing the evolution of magnetic energy requires at least twice as large amount of bits as required for the other energy fields. When radiative cooling and feedback from galaxy formation are considered, the cosmic gas is overall found to double its degree of complexity. In the future, Cosmic Information Theory can significantly increase our understanding of the emergence of cosmic structure as it represents an innovative framework to design and analyse complex simulations of the Universe in a simple, yet powerful way.

  20. Structural and evolutionary versatility in protein complexes with uneven stoichiometry. (United States)

    Marsh, Joseph A; Rees, Holly A; Ahnert, Sebastian E; Teichmann, Sarah A


    Proteins assemble into complexes with diverse quaternary structures. Although most heteromeric complexes of known structure have even stoichiometry, a significant minority have uneven stoichiometry--that is, differing numbers of each subunit type. To adopt this uneven stoichiometry, sequence-identical subunits must be asymmetric with respect to each other, forming different interactions within the complex. Here we first investigate the occurrence of uneven stoichiometry, demonstrating that it is common in vitro and is likely to be common in vivo. Next, we elucidate the structural determinants of uneven stoichiometry, identifying six different mechanisms by which it can be achieved. Finally, we study the frequency of uneven stoichiometry across evolution, observing a significant enrichment in bacteria compared with eukaryotes. We show that this arises due to a general increased tendency for bacterial proteins to self-assemble and form homomeric interactions, even within the context of a heteromeric complex.

  1. Structuring and assessing large and complex decision problems using MCDA

    DEFF Research Database (Denmark)

    Barfod, Michael Bruhn

    This paper presents an approach for the structuring and assessing of large and complex decision problems using multi-criteria decision analysis (MCDA). The MCDA problem is structured in a decision tree and assessed using the REMBRANDT technique featuring a procedure for limiting the number of pair...

  2. Homoclinic (Heteroclinic) Orbit of Complex Dynamical System and Spiral Structure

    Institute of Scientific and Technical Information of China (English)

    FU Zun-Tao; LIU Shi-Da; LIU Shi-Kuo; LIANG Fu-Ming; XIN Guo-Jun


    Starting from iterated systems, it is shown that the homoclinic (heteroclinic) orbit is a kind of spiral structure. The emphasis is laid to show that there are homoclinic or heteroclinic orbits in complex discrete and continuous systems, and these homoclinic or heteroclinic orbits are some kind of spiral structure.

  3. A new entropy based method for computing software structural complexity

    CERN Document Server

    Roca, J L


    In this paper a new methodology for the evaluation of software structural complexity is described. It is based on the entropy evaluation of the random uniform response function associated with the so called software characteristic function SCF. The behavior of the SCF with the different software structures and their relationship with the number of inherent errors is investigated. It is also investigated how the entropy concept can be used to evaluate the complexity of a software structure considering the SCF as a canonical representation of the graph associated with the control flow diagram. The functions, parameters and algorithms that allow to carry out this evaluation are also introduced. After this analytic phase follows the experimental phase, verifying the consistency of the proposed metric and their boundary conditions. The conclusion is that the degree of software structural complexity can be measured as the entropy of the random uniform response function of the SCF. That entropy is in direct relation...

  4. Universal structural estimator and dynamics approximator for complex networks

    CERN Document Server

    Chen, Yu-Zhong


    Revealing the structure and dynamics of complex networked systems from observed data is of fundamental importance to science, engineering, and society. Is it possible to develop a universal, completely data driven framework to decipher the network structure and different types of dynamical processes on complex networks, regardless of their details? We develop a Markov network based model, sparse dynamical Boltzmann machine (SDBM), as a universal network structural estimator and dynamics approximator. The SDBM attains its topology according to that of the original system and is capable of simulating the original dynamical process. We develop a fully automated method based on compressive sensing and machine learning to find the SDBM. We demonstrate, for a large variety of representative dynamical processes on model and real world complex networks, that the equivalent SDBM can recover the network structure of the original system and predicts its dynamical behavior with high precision.

  5. Statistical energy analysis of complex structures, phase 2 (United States)

    Trudell, R. W.; Yano, L. I.


    A method for estimating the structural vibration properties of complex systems in high frequency environments was investigated. The structure analyzed was the Materials Experiment Assembly, (MEA), which is a portion of the OST-2A payload for the space transportation system. Statistical energy analysis (SEA) techniques were used to model the structure and predict the structural element response to acoustic excitation. A comparison of the intial response predictions and measured acoustic test data is presented. The conclusions indicate that: the SEA predicted the response of primary structure to acoustic excitation over a wide range of frequencies; and the contribution of mechanically induced random vibration to the total MEA is not significant.

  6. Repression and activation by multiprotein complexes that alter chromatin structure. (United States)

    Kingston, R E; Bunker, C A; Imbalzano, A N


    Recent studies have provided strong evidence that macromolecular complexes are used in the cell to remodel chromatin structure during activation and to create an inaccessible structure during repression, Although there is not yet any rigorous demonstration that modification of chromatin structure plays a direct, causal role in either activation or repression, there is sufficient smoke to indicate the presence of a blazing inferno nearby. It is clear that complexes that remodel chromatin are tractable in vitro; hopefully this will allow the establishment of systems that provide a direct analysis of the role that remodeling might play in activation. These studies indicate that establishment of functional systems to corroborate the elegant genetic studies on repression might also be tractable. As the mechanistic effects of these complexes are sorted out, it will become important to understand how the complexes are regulated. In many of the instances discussed above, the genes whose products make up these complexes were identified in genetic screens for effects on developmental processes. This implies a regulation of the activity of these complexes in response to developmental cues and further implies that the work to fully understand these complexes will occupy a generation of scientists.

  7. The Ccr4-Not Complex: Architecture and Structural Insights. (United States)

    Collart, Martine A; Panasenko, Olesya O


    The Ccr4-Not complex is an essential multi-subunit protein complex that plays a fundamental role in eukaryotic mRNA metabolism and has a multitude of different roles that impact eukaryotic gene expression . It has a conserved core of three Not proteins, the Ccr4 protein, and two Ccr4 associated factors, Caf1 and Caf40. A fourth Not protein, Not4, is conserved, but is only a stable subunit of the complex in yeast. Certain subunits have been duplicated during evolution, with functional divergence, such as Not3 in yeast, and Ccr4 or Caf1 in human. However the complex includes only one homolog for each protein. In addition, species-specific subunits are part of the complex, such as Caf130 in yeast or Not10 and Not11 in human. Two conserved catalytic functions are associated with the complex, deadenylation and ubiquitination . The complex adopts an L-shaped structure, in which different modules are bound to a large Not1 scaffold protein. In this chapter we will summarize our current knowledge of the architecture of the complex and of the structure of its constituents.

  8. Geometric modeling of subcellular structures, organelles, and multiprotein complexes (United States)

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


    SUMMARY Recently, the structure, function, stability, and dynamics of subcellular structures, organelles, and multi-protein complexes have emerged as a leading interest in structural biology. Geometric modeling not only provides visualizations of shapes for large biomolecular complexes but also fills the gap between structural information and theoretical modeling, and enables the understanding of function, stability, and dynamics. This paper introduces a suite of computational tools for volumetric data processing, information extraction, surface mesh rendering, geometric measurement, and curvature estimation of biomolecular complexes. Particular emphasis is given to the modeling of cryo-electron microscopy data. Lagrangian-triangle meshes are employed for the surface presentation. On the basis of this representation, algorithms are developed for surface area and surface-enclosed volume calculation, and curvature estimation. Methods for volumetric meshing have also been presented. Because the technological development in computer science and mathematics has led to multiple choices at each stage of the geometric modeling, we discuss the rationales in the design and selection of various algorithms. Analytical models are designed to test the computational accuracy and convergence of proposed algorithms. Finally, we select a set of six cryo-electron microscopy data representing typical subcellular complexes to demonstrate the efficacy of the proposed algorithms in handling biomolecular surfaces and explore their capability of geometric characterization of binding targets. This paper offers a comprehensive protocol for the geometric modeling of subcellular structures, organelles, and multiprotein complexes. PMID:23212797

  9. MMDB and VAST+: tracking structural similarities between macromolecular complexes. (United States)

    Madej, Thomas; Lanczycki, Christopher J; Zhang, Dachuan; Thiessen, Paul A; Geer, Renata C; Marchler-Bauer, Aron; Bryant, Stephen H


    The computational detection of similarities between protein 3D structures has become an indispensable tool for the detection of homologous relationships, the classification of protein families and functional inference. Consequently, numerous algorithms have been developed that facilitate structure comparison, including rapid searches against a steadily growing collection of protein structures. To this end, NCBI's Molecular Modeling Database (MMDB), which is based on the Protein Data Bank (PDB), maintains a comprehensive and up-to-date archive of protein structure similarities computed with the Vector Alignment Search Tool (VAST). These similarities have been recorded on the level of single proteins and protein domains, comprising in excess of 1.5 billion pairwise alignments. Here we present VAST+, an extension to the existing VAST service, which summarizes and presents structural similarity on the level of biological assemblies or macromolecular complexes. VAST+ simplifies structure neighboring results and shows, for macromolecular complexes tracked in MMDB, lists of similar complexes ranked by the extent of similarity. VAST+ replaces the previous VAST service as the default presentation of structure neighboring data in NCBI's Entrez query and retrieval system. MMDB and VAST+ can be accessed via


    Institute of Scientific and Technical Information of China (English)

    J.H. Peng; G.L. Chen


    The mechanical behavior of Fe3Si based alloy with B2 structure was studied by tensionand fracture toughness test in various testing media. The fracture strength σb ofFe3Si alloy decreased in the following order: oxygen, air and hydrogen respectively.The fracture toughness in different testing environment showed that KiC in oxygenis 11.5±0.3MPa. m1/2, and is 8.6±0.4MPa. m1/2 in distilled water. The reductionof fracture toughness is contributed to the environmental reaction of Si with water.Addition of Al element in Fe3Si is not beneficial to improve the intrinsic ductility ofFe-14Si-3Al alloy. The scattering phenomenon of fracture strength was found, andexplained by fracture mechanics. It was found by means of SEM that the fracture modechanged from transgranular in oxygen to intergranular in hydrogen gas and distilledwater.

  11. Information structure and reference tracking in complex sentences

    CERN Document Server

    Gijn, Rik van; Matic, Dejan


    This paper discusses argument marking and reference tracking in Mekens complex clauses and their correlation to information structure. The distribution of pronominal arguments in Mekens simple clauses follows an absolutive pattern with main verbs. Complex clauses maintain the morphological absolutive argument marking, but show a nominative pattern with respect to argument reference tracking, since transitive and intransitive subjects function as syntactic pivots. The language extends the use of argument-marking verb morphology to control the reference of discourse participants across clauses.

  12. Structure of a human rhinovirus complexed with its receptor molecule.



    Cryoelectron microscopy has been used to determine the structure of a virus when complexed with its glycoprotein cellular receptor. Human rhinovirus 16 complexed with the two amino-terminal, immunoglobulin-like domains of the intercellular adhesion molecule 1 shows that the intercellular adhesion molecule 1 binds into the 12-A deep "canyon" on the viral surface. This result confirms the prediction that the viral-receptor attachment site lies in a cavity inaccessible to the host's antibodies. ...

  13. Complex Network Structure of Flocks in the Standard Vicsek Model (United States)

    Baglietto, Gabriel; Albano, Ezequiel V.; Candia, Julián


    In flocking models, the collective motion of self-driven individuals leads to the formation of complex spatiotemporal patterns. The Standard Vicsek Model (SVM) considers individuals that tend to adopt the direction of movement of their neighbors under the influence of noise. By performing an extensive complex network characterization of the structure of SVM flocks, we show that flocks are highly clustered, assortative, and non-hierarchical networks with short-tailed degree distributions. Moreover, we also find that the SVM dynamics leads to the formation of complex structures with an effective dimension higher than that of the space where the actual displacements take place. Furthermore, we show that these structures are capable of sustaining mean-field-like orientationally ordered states when the displacements are suppressed, thus suggesting a linkage between the onset of order and the enhanced dimensionality of SVM flocks.

  14. Solvent structure improves docking prediction in lectin-carbohydrate complexes. (United States)

    Gauto, Diego F; Petruk, Ariel A; Modenutti, Carlos P; Blanco, Juan I; Di Lella, Santiago; Martí, Marcelo A


    Recognition and complex formation between proteins and carbohydrates is a key issue in many important biological processes. Determination of the three-dimensional structure of such complexes is thus most relevant, but particularly challenging because of their usually low binding affinity. In silico docking methods have a long-standing tradition in predicting protein-ligand complexes, and allow a potentially fast exploration of a number of possible protein-carbohydrate complex structures. However, determining which of these predicted complexes represents the correct structure is not always straightforward. In this work, we present a modification of the scoring function provided by AutoDock4, a widely used docking software, on the basis of analysis of the solvent structure adjacent to the protein surface, as derived from molecular dynamics simulations, that allows the definition and characterization of regions with higher water occupancy than the bulk solvent, called water sites. They mimic the interaction held between the carbohydrate -OH groups and the protein. We used this information for an improved docking method in relation to its capacity to correctly predict the protein-carbohydrate complexes for a number of tested proteins, whose ligands range in size from mono- to tetrasaccharide. Our results show that the presented method significantly improves the docking predictions. The resulting solvent-structure-biased docking protocol, therefore, appears as a powerful tool for the design and optimization of development of glycomimetic drugs, while providing new insights into protein-carbohydrate interactions. Moreover, the achieved improvement also underscores the relevance of the solvent structure to the protein carbohydrate recognition process.

  15. Computational RNA secondary structure design: empirical complexity and improved methods

    Directory of Open Access Journals (Sweden)

    Condon Anne


    Full Text Available Abstract Background We investigate the empirical complexity of the RNA secondary structure design problem, that is, the scaling of the typical difficulty of the design task for various classes of RNA structures as the size of the target structure is increased. The purpose of this work is to understand better the factors that make RNA structures hard to design for existing, high-performance algorithms. Such understanding provides the basis for improving the performance of one of the best algorithms for this problem, RNA-SSD, and for characterising its limitations. Results To gain insights into the practical complexity of the problem, we present a scaling analysis on random and biologically motivated structures using an improved version of the RNA-SSD algorithm, and also the RNAinverse algorithm from the Vienna package. Since primary structure constraints are relevant for designing RNA structures, we also investigate the correlation between the number and the location of the primary structure constraints when designing structures and the performance of the RNA-SSD algorithm. The scaling analysis on random and biologically motivated structures supports the hypothesis that the running time of both algorithms scales polynomially with the size of the structure. We also found that the algorithms are in general faster when constraints are placed only on paired bases in the structure. Furthermore, we prove that, according to the standard thermodynamic model, for some structures that the RNA-SSD algorithm was unable to design, there exists no sequence whose minimum free energy structure is the target structure. Conclusion Our analysis helps to better understand the strengths and limitations of both the RNA-SSD and RNAinverse algorithms, and suggests ways in which the performance of these algorithms can be further improved.

  16. Complex quantum networks as structured environments: engineering and probing (United States)

    Nokkala, Johannes; Galve, Fernando; Zambrini, Roberta; Maniscalco, Sabrina; Piilo, Jyrki


    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.

  17. Net-Shape Tailored Fabrics For Complex Composite Structures (United States)

    Farley, Gary L.


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


    Institute of Scientific and Technical Information of China (English)

    Guanghui Ma; Fangling Gong; Guohua Hu; Dongxia Hao; Rong Liu; Renwei Wang


    Multi-scale structures involved in emulsion and microsphere complex systems are presented and discussed. The stability and spatio-temporal structures of emulsions, as well as nano-structures formed on the surface of microspheres after polymerization, are affected by the molecular emulsifier/stabilizer structures and the adsorbed emulsifier/stabilizer nano-structures on the oil/water interface. The broad size distribution and variation of surface features of droplets are responsible for variations of the adsorbed emulsifier/stabilizer structures and the stability of the emulsions.On the other hand, preparation of a uniformly sized emulsion and employment of a combined emulsifier/stabilizer system can preserve the stability of the emulsions and microspheres. The above phenomena should be modeled by a multiscale method, in order to maintain the stability of individual emulsion systems and realize the desired nano-structures of microspheres by choosing adequate emulsifier/stabilizer and experimental parameters.

  19. Protein-complex structure completion using IPCAS (Iterative Protein Crystal structure Automatic Solution). (United States)

    Zhang, Weizhe; Zhang, Hongmin; Zhang, Tao; Fan, Haifu; Hao, Quan


    Protein complexes are essential components in many cellular processes. In this study, a procedure to determine the protein-complex structure from a partial molecular-replacement (MR) solution is demonstrated using a direct-method-aided dual-space iterative phasing and model-building program suite, IPCAS (Iterative Protein Crystal structure Automatic Solution). The IPCAS iteration procedure involves (i) real-space model building and refinement, (ii) direct-method-aided reciprocal-space phase refinement and (iii) phase improvement through density modification. The procedure has been tested with four protein complexes, including two previously unknown structures. It was possible to use IPCAS to build the whole complex structure from one or less than one subunit once the molecular-replacement method was able to give a partial solution. In the most challenging case, IPCAS was able to extend to the full length starting from less than 30% of the complex structure, while conventional model-building procedures were unsuccessful.

  20. The complex band structure for armchair graphene nanoribbons

    Institute of Scientific and Technical Information of China (English)

    Zhang Liu-Jun; Xia Tong-Sheng


    Using a tight binding transfer matrix method, we calculate the complex band structure of armchair graphene nanoribbons. The real part of the complex band structure calculated by the transfer matrix method fits well with the bulk band structure calculated by a Hermitian matrix. The complex band structure gives extra information on carrier's decay behaviour. The imaginary loop connects the conduction and valence band, and can profoundly affect the characteristics of nanoscale electronic device made with graphene nanoribbons. In this work, the complex band structure calculation includes not only the first nearest neighbour interaction, but also the effects of edge bond relaxation and the third nearest neighbour interaction. The band gap is classified into three classes. Due to the edge bond relaxation and the third nearest neighbour interaction term, it opens a band gap for N= 3M-1. The band gap is almost unchanged for N = 3M + 1, but decreased for N = 3M. The maximum imaginary wave vector length provides additional information about the electrical characteristics of graphene nmaoribbons, and is also classified into three classes.

  1. Structural Dynamics of the MecA-ClpC Complex (United States)

    Liu, Jing; Mei, Ziqing; Li, Ningning; Qi, Yutao; Xu, Yanji; Shi, Yigong; Wang, Feng; Lei, Jianlin; Gao, Ning


    The MecA-ClpC complex is a bacterial type II AAA+ molecular machine responsible for regulated unfolding of substrates, such as transcription factors ComK and ComS, and targeting them to ClpP for degradation. The six subunits of the MecA-ClpC complex form a closed barrel-like structure, featured with three stacked rings and a hollow passage, where substrates are threaded and translocated through successive pores. Although the general concepts of how polypeptides are unfolded and translocated by internal pore loops of AAA+ proteins have long been conceived, the detailed mechanistic model remains elusive. With cryoelectron microscopy, we captured four different structures of the MecA-ClpC complexes. These complexes differ in the nucleotide binding states of the two AAA+ rings and therefore might presumably reflect distinctive, representative snapshots from a dynamic unfolding cycle of this hexameric complex. Structural analysis reveals that nucleotide binding and hydrolysis modulate the hexameric complex in a number of ways, including the opening of the N-terminal ring, the axial and radial positions of pore loops, the compactness of the C-terminal ring, as well as the relative rotation between the two nucleotide-binding domain rings. More importantly, our structural and biochemical data indicate there is an active allosteric communication between the two AAA+ rings and suggest that concerted actions of the two AAA+ rings are required for the efficiency of the substrate unfolding and translocation. These findings provide important mechanistic insights into the dynamic cycle of the MecA-ClpC unfoldase and especially lay a foundation toward the complete understanding of the structural dynamics of the general type II AAA+ hexamers. PMID:23595989

  2. Structure and Semiconducting Character of a Polymeric Iodoplumbate Coordination Complex

    Institute of Scientific and Technical Information of China (English)

    SONG De-Sheng; LIU Chang-Chun; CHEN Heng-Jun; SU Dong-Po; FU Zhi-Yong


    A new polymeric iodoplumbate complex [Zn(DMF)6][Pb2I6] 1 has been prepared and characterized by elemental analysis and single-crystal X-ray analysis. Its structure contains infinite iodoplumbate chains constructed by the [PbI5] subunit. EHT crystal orbital calculation and the experimental results show that this material is an unconventional semiconductor and the electrical character is associated with its structural feature.

  3. On the complexity and the information content of cosmic structures

    CERN Document Server

    Vazza, Franco


    The emergence of cosmic structure is commonly considered one of the most complex phenomena in Nature. However, this complexity has never been defined nor measured in a quantitative and objective way. In this work we propose a method to measure the information content of cosmic structure and to quantify the complexity that emerges from it, based on Information Theory. The emergence of complex evolutionary patterns is studied with a statistical symbolic analysis of the datastream produced by state-of-the-art cosmological simulations of forming galaxy clusters. This powerful approach allows us to measure how many bits of information are necessary to predict the evolution of energy fields in a statistical way, and it offers a simple way to quantify when, where and how the cosmic gas behaves in complex ways. The most complex behaviors are found in the peripheral regions of galaxy clusters, where supersonic flows drive shocks and large energy fluctuations over a few tens of million years. Describing the evolution o...

  4. Structural study of coacervation in protein-polyelectrolyte complexes (United States)

    Chodankar, S.; Aswal, V. K.; Kohlbrecher, J.; Vavrin, R.; Wagh, A. G.


    Coacervation is a dense liquid-liquid phase separation and herein we report coacervation of protein bovine serum albumin (BSA) in the presence of polyelectrolyte sodium polystyrene sulfonate (NaPSS) under varying solution conditions. Small-angle neutron scattering (SANS) measurements have been performed on above protein-polyelectrolyte complexes to study the structural evolution of the process that leads to coacervation and the phase separated coacervate as a function of solution pH , protein-polyelectrolyte ratio and ionic strength. SANS study prior to phase separation on the BSA-NaPSS complex shows a fractal structure representing a necklace model of protein macromolecules randomly distributed along the polystyrene sulfonate chain. The fractal dimension of the complex decreases as pH is shifted away from the isoelectric point (˜4.7) of BSA protein, which indicates the decrease in the compactness of the complex structure due to increase in the charge repulsion between the protein macromolecules bound to the polyelectrolyte. Concentration-dependence studies of the polyelectrolyte in the complex suggest coexistence of two populations of polyelectrolytes, first one fully saturated with proteins and another one free from proteins. Coacervation phase has been obtained through the turbidity measurement by varying pH of the aqueous solution containing protein and polyelectrolyte from neutral to acidic regime to get them to where the two components are oppositely charged. The spontaneous formation of coacervates is observed for pH values less than 4. SANS study on coacervates shows two length scales related to complex aggregations (mesh size and overall extent of the complex) hierarchically branched to form a larger network. The mesh size represents the distance between cross-linked points in the primary complex, which decreases with increase in ionic strength and remains the same on varying the protein-polyelectrolyte ratio. On the other hand, the overall extent of the

  5. Managing structure complexity in a multi-physic simulation software


    Huynh, Quoc Hung; Maréchal, Yves; Coulomb, Jean-Louis


    International audience; This paper presents an efficient method for managing the complexity of software structure by implementing the business rules over the data model using a combination of logical programming and object-oriented programming, concretely applied in a multiphysics application.

  6. Investigation of fine and complex vortex circulation structures

    Institute of Scientific and Technical Information of China (English)


    The formation and evolution of fine and complicated vortex circulation structures were investigated using a two-dimensional quasi-geostrophic barotropic model simulation.We find that the highly localized asymmetric and complex configuration of energy transfer flux between large-and small-scale components is caused by the nonlinear interaction between a large-scale vortex with an initial axi-symmetric flow and four beta meso-scale vortices.The complex structure is characterized by a fine pattern,which contains seven closed systems with spatial scales of less than 100 km,embedded in a positive flux wave train and a negative wave train,respectively.The average wind speed decreased with time in the positive flux region,but was nearly unchanged in the negative flux region.This pattern reveals the evolutionary asymmetry and localization of wind speed of the major vortex.The track of the major vortex center has a trend toward the center of the negative flux center,indicating that there is a certain relation between the complex structure of the energy transfer flux and the motion of the major vortex center.These results imply that the formation and evolution of the fine and complex structure should be attributed to the nonlinear interaction between the vortices at different spatial scales.

  7. Crystalline molecular complexes and compounds structures and principles

    CERN Document Server

    Herbstein, Frank H


    This book provides an account of the structure and properties of crystalline binary adducts. Such crystals are perhaps better known as molecular compounds and complexes and are estimated to make up one quarter of the world's crystals. More than 600 figures, 200 tables and 3500 references are included in the book.

  8. Functional reconstruction of structurally complex epitopes using CLIPS™ technology

    NARCIS (Netherlands)

    Timmerman, P.; Puijk, W.C.; Boshuizen, R.S.; van Dijken, P.; Slootstra, J.W.; Beurskens, F.J.; Parren, P.W.H.I.; Huber, A.; Bachmann, M.F.; Meloen, R.H.


    This review summarizes an illustrative set of data from our research on the reconstruction of structurally complex protein surfaces, i.e. those that fail to be mimicked properly by linear peptides. In the past 5 years, our newly developed CLIPS™ technology has proven an extremely valuable tool for 1

  9. Structure, Agency, Complexity Theory and Interdisciplinary Research in Education Studies (United States)

    Smith, John A.


    This article argues that Education Studies needs to develop its existing interdisciplinarity understanding of structures and agencies by giving greater attention to the modern process theories of self-organisation in the physical, biological, psychological and social sciences, sometimes given the umbrella term "complexity theory". The…

  10. School Structures: Transforming Urban Complex Schools into Better Learning Communities (United States)

    Haimendorf, Max; Kestner, Jacob


    This article, which forms part of the policy booklet "Lessons from the Front" written by participants and Ambassadors of the Teach First scheme, argues that educational outcomes are often adversely affected by the size and structure of many urban complex schools. Rather than multiplying the efforts of teachers, too often the organisational model…

  11. Purple Bacterial Light-harvesting Complexes: From Dreams to Structures. (United States)

    Cogdell, Richard J; Hashimoto, Hideki; Gardiner, Alastair T


    This paper describes the main stages involved in the research efforts designed to try and understand the structure and function of purple bacterial antenna complexes. Wherever possible the work has been illustrated by pictures of the major people who carried it out.

  12. Structure, Agency, Complexity Theory and Interdisciplinary Research in Education Studies (United States)

    Smith, John A.


    This article argues that Education Studies needs to develop its existing interdisciplinarity understanding of structures and agencies by giving greater attention to the modern process theories of self-organisation in the physical, biological, psychological and social sciences, sometimes given the umbrella term "complexity theory". The…

  13. Structural insight into the UNC-45–myosin complex

    DEFF Research Database (Denmark)

    Fratev, Filip; Jonsdottir, Svava Osk; Pajeva, Ilza


    in silico methods. Initially, the human UNC-45B binding epitope was identified and the protein was docked to the cardiac myosin (MYH7) motor domain. The final UNC45B–MYH7 structure was obtained by performing of total 630 ns molecular dynamics simulations. The results indicate a complex formation, which...

  14. Optimizing controllability of complex networks by minimum structural perturbations. (United States)

    Wang, Wen-Xu; Ni, Xuan; Lai, Ying-Cheng; Grebogi, Celso


    To drive a large, complex, networked dynamical system toward some desired state using as few external signals as possible is a fundamental issue in the emerging field of controlling complex networks. Optimal control is referred to the situation where such a network can be fully controlled using only one driving signal. We propose a general approach to optimizing the controllability of complex networks by judiciously perturbing the network structure. The principle of our perturbation method is validated theoretically and demonstrated numerically for homogeneous and heterogeneous random networks and for different types of real networks as well. The applicability of our method is discussed in terms of the relative costs of establishing links and imposing external controllers. Besides the practical usage of our approach, its implementation elucidates, interestingly, the intricate relationship between certain structural properties of the network and its controllability.

  15. Chlorine Nuclear Quadrupole Hyperfine Structure in the Vinyl - Chloride Complex (United States)

    Leung, Helen O.; Marshall, Mark D.; Messinger, Joseph P.


    The microwave spectrum of the vinyl chloride--hydrogen chloride complex, presented at last year's symposium, is greatly complicated by the presence of two chlorine nuclei as well as an observed, but not fully explained tunneling motion. Indeed, although it was possible at that time to demonstrate conclusively that the complex is nonplanar, the chlorine nuclear quadrupole hyperfine splitting in the rotational spectrum resisted analysis. With higher resolution, Balle-Flygare Fourier transform microwave spectra, the hyperfine structure has been more fully resolved, but appears to be perturbed for some rotational transitions. It appears that knowledge of the quadrupole coupling constants will provide essential information regarding the structure of the complex, specifically the location of the hydrogen atom in HCl. Our progress towards obtaining values for these constants will be presented.

  16. Structural Study of Mismatched Disila-Crown Ether Complexes

    Directory of Open Access Journals (Sweden)

    Kirsten Reuter


    Full Text Available Mismatched complexes of the alkali metals cations Li+ and Na+ were synthesized from 1,2-disila[18]crown-6 (1 and 2 and of K+ from 1,2,4,5-tetrasila[18]crown-6 (4. In these alkali metal complexes, not all crown ether O atoms participate in the coordination, which depicts the coordination ability of the C-, Si/C-, and Si-bonded O atoms. Furthermore, the inverse case—the coordination of the large Ba2+ ion by the relatively small ligand 1,2-disila[15]crown-5—was investigated, yielding the dinuclear complex 5. This structure represents a first outlook on sandwich complexes based on hybrid crown ethers.

  17. Significance tests for functional data with complex dependence structure

    KAUST Repository

    Staicu, Ana-Maria


    We propose an L (2)-norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a multilevel structure of the form groups-clusters or subjects-units, where the unit-level profiles are spatially correlated within the cluster, and the cluster-level data are independent. Orthogonal series expansions are used to approximate the group mean functions and the test statistic is estimated using the basis coefficients. The asymptotic null distribution of the test statistic is developed, under mild regularity conditions. To our knowledge this is the first work that studies hypothesis testing, when data have such complex multilevel functional and spatial structure. Two small-sample alternatives, including a novel block bootstrap for functional data, are proposed, and their performance is examined in simulation studies. The paper concludes with an illustration of a motivating experiment.

  18. Structure and stability of complex coacervate core micelles with lysozyme. (United States)

    Lindhoud, Saskia; Vries, Renko de; Norde, Willem; Stuart, Martien A Cohen


    Encapsulation of enzymes by polymers is a promising method to influence their activity and stability. Here, we explore the use of complex coacervate core micelles for encapsulation of enzymes. The core of the micelles consists of negatively charged blocks of the diblock copolymer PAA42PAAm417 and the positively charged homopolymer PDMAEMA150. For encapsulation, part of the positively charged homopolymer was replaced by the positively charged globular protein lysozyme. We have studied the formation, structure, and stability of the resulting micelles for three different mixing ratios of homopolymer and lysozyme: a system predominantly consisting of homopolymer, a system predominantly consisting of lysozyme, and a system where the molar ratio between the two positively charged molecules was almost one. We also studied complexes made of only lysozyme and PAA42PAAm417. Complex formation and the salt-induced disintegration of the complexes were studied using dynamic light-scattering titrations. Small-angle neutron scattering was used to investigate the structures of the cores. We found that micelles predominantly consisting of homopolymer are spherical but that complex coacervate core micelles predominantly consisting of lysozyme are nonspherical. The stability of the micelles containing a larger fraction of lysozyme is lower.

  19. Bim Automation: Advanced Modeling Generative Process for Complex Structures (United States)

    Banfi, F.; Fai, S.; Brumana, R.


    The new paradigm of the complexity of modern and historic structures, which are characterised by complex forms, morphological and typological variables, is one of the greatest challenges for building information modelling (BIM). Generation of complex parametric models needs new scientific knowledge concerning new digital technologies. These elements are helpful to store a vast quantity of information during the life cycle of buildings (LCB). The latest developments of parametric applications do not provide advanced tools, resulting in time-consuming work for the generation of models. This paper presents a method capable of processing and creating complex parametric Building Information Models (BIM) with Non-Uniform to NURBS) with multiple levels of details (Mixed and ReverseLoD) based on accurate 3D photogrammetric and laser scanning surveys. Complex 3D elements are converted into parametric BIM software and finite element applications (BIM to FEA) using specific exchange formats and new modelling tools. The proposed approach has been applied to different case studies: the BIM of modern structure for the courtyard of West Block on Parliament Hill in Ottawa (Ontario) and the BIM of Masegra Castel in Sondrio (Italy), encouraging the dissemination and interaction of scientific results without losing information during the generative process.

  20. A uranium (VI) complex: Synthesis, structural and thermal kinetic analysis (United States)

    Goel, Nidhi


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

  1. On String Topology Operations and Algebraic Structures on Hochschild Complexes (United States)

    Rivera, Manuel

    The field of string topology is concerned with the algebraic structure of spaces of paths and loops on a manifold. It was born with Chas and Sullivan's observation of the fact that the intersection product on the homology of a smooth manifold M can be combined with the concatenation product on the homology of the based loop space on M to obtain a new product on the homology of LM, the space of free loops on M. Since then, a vast family of operations on the homology of LM have been discovered. In this thesis we focus our attention on a non trivial coproduct of degree 1--dim(M) on the homology of LM modulo constant loops. This coproduct was described by Sullivan on chains on general position and by Goresky and Hingston in a Morse theory context. We give a Thom-Pontryagin type description for the coproduct. Using this description we show that the resulting coalgebra is an invariant on the oriented homotopy type of the underlying manifold. The coproduct together with the loop product induce an involutive Lie bialgebra structure on the S 1-equivariant homology of LM modulo constant loops. It follows from our argument that this structure is an oriented homotopy invariant as well. There is also an algebraic theory of string topology which is concerned with the structure of Hochschild complexes of DG Frobenius algebras and their homotopy versions. We make several observations about the algebraic theory around products, coproducts and their compatibilities. In particular, we describe a BV-coalgebra structure on the coHochschild complex of a DG cocommutative Frobenius coalgebra. Some conjectures and partial results regarding homotopy versions of this structure are discussed. Finally, we explain how Poincare duality may be incorporated into Chen's theory of iterated integrals to relate the geometrically constructed string topology operations to algebraic structures on Hochschild complexes.

  2. The Similar Structures and Control Problems of Complex Systems

    Institute of Scientific and Technical Information of China (English)


    In this paper, the naturally evolving complex systems, such as biotic and social ones, are considered. Focusing on their structures, a feature is noteworthy, i.e., the similarity in structures. The relations between the functions and behaviors of these systems and their similar structures will be studied. Owing to the management of social systems and the course of evolution of biotic systems may be regarded as control processes, the researches will be within the scope of control problems. Moreover, since it is difficult to model for biotic and social systems, it will start with the control problems of complex systems, possessing similar structures, in engineering.The obtained results show that for either linear or nonlinear systems and for a lot of control problemssimilar structures lead to a series of simplifications. In general, the original system may be decomposed into reduced amount of subsystems with lower dimensions and simpler structures. By virtue of such subsystems, the control problems of original system can be solved more simply.At last, it turns round to observe the biotic and social systems and some analyses are given.

  3. Structural rearrangement through lanthanide contraction in dinuclear complexes. (United States)

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


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

  4. Supramolecular structures constructed from three novel rare earth metal complexes

    Indian Academy of Sciences (India)

    Huaze Dong; Xiaojun Feng; Xia Liu; BiN Zheng; Jianhong Bi; Yan Xue; Shaohua Gou; Yanping Wang


    Three rare earth metal supramolecular complexes, {[Tb(2)4](ClO4)3·2H2O(1), [Eu(2)2(H2O)5] (ClO4)3(2) and [Gd(NO3)3(2)2]·2CH3CH2OH(3) ( 2 = 3-Dimethylamino-1-pyridin-2-yl-propenone), have been synthesized and characterized by elemental analysis, IR and single crystal X-ray diffraction. The crystal structure analysis reveals that the coordination numbers of three complexes (1–3) are 8, 9 and 10, respectively. Three complexes assembled into 3D frameworks based on C-H⋯O, O-H⋯O hydrogen bond linkages.

  5. Classification of smooth structures on a homotopy complex projective space

    Indian Academy of Sciences (India)

    Ramesh Kasilingam


    We classify, up to diffeomorphism, all closed smooth manifolds homeomorphic to the complex projective $n$-space ${\\mathbb C}{\\bf P}^n$, where $n = 3$ and 4. Let $M^{2n}$ be a closed smooth $2n$-manifold homotopy equivalent to ${\\mathbb C}{\\bf P}^n$. We show that, up to diffeomorphism, $M^6$ has a unique differentiable structure and $M^8$ has at most two distinct differentiable structures. We also show that, up to concordance, there exist at least two distinct differentiable structures on a finite sheeted cover $N^2n$ of ${\\mathbb C}{\\bf P}^n$ for = 4, 7 or 8 and six distinct differentiable structures on $N^{10}$.

  6. Variable structure control of complex systems analysis and design

    CERN Document Server

    Yan, Xing-Gang; Edwards, Christopher


    This book systematizes recent research work on variable-structure control. It is self-contained, presenting necessary mathematical preliminaries so that the theoretical developments can be easily understood by a broad readership. The text begins with an introduction to the fundamental ideas of variable-structure control pertinent to their application in complex nonlinear systems. In the core of the book, the authors lay out an approach, suitable for a large class of systems, that deals with system uncertainties with nonlinear bounds. Its treatment of complex systems in which limited measurement information is available makes the results developed convenient to implement. Various case-study applications are described, from aerospace, through power systems to river pollution control with supporting simulations to aid the transition from mathematical theory to engineering practicalities. The book addresses systems with nonlinearities, time delays and interconnections and considers issues such as stabilization, o...

  7. Emergence of hierarchical structural complexities in nanoparticles and their assembly (United States)

    Zeng, Chenjie; Chen, Yuxiang; Kirschbaum, Kristin; Lambright, Kelly J.; Jin, Rongchao


    We demonstrate that nanoparticle self-assembly can reach the same level of hierarchy, complexity, and accuracy as biomolecules. The precise assembly structures of gold nanoparticles (246 gold core atoms with 80 p-methylbenzenethiolate surface ligands) at the atomic, molecular, and nanoscale levels were determined from x-ray diffraction studies. We identified the driving forces and rules that guide the multiscale assembly behavior. The protecting ligands self-organize into rotational and parallel patterns on the nanoparticle surface via C-Hṡṡṡπ interaction, and the symmetry and density of surface patterns dictate directional packing of nanoparticles into crystals with orientational, rotational, and translational orders. Through hierarchical interactions and symmetry matching, the simple building blocks evolve into complex structures, representing an emergent phenomenon in the nanoparticle system.

  8. Structural insights into the YAP and TEAD complex. (United States)

    Li, Ze; Zhao, Bin; Wang, Ping; Chen, Fei; Dong, Zhenghong; Yang, Huirong; Guan, Kun-Liang; Xu, Yanhui


    The Yes-associated protein (YAP) transcriptional coactivator is a key regulator of organ size and a candidate human oncogene inhibited by the Hippo tumor suppressor pathway. The TEAD family of transcription factors binds directly to and mediates YAP-induced gene expression. Here we report the three-dimensional structure of the YAP (residues 50-171)-TEAD1 (residues 194-411) complex, in which YAP wraps around the globular structure of TEAD1 and forms extensive interactions via three highly conserved interfaces. Interface 3, including YAP residues 86-100, is most critical for complex formation. Our study reveals the biochemical nature of the YAP-TEAD interaction, and provides a basis for pharmacological intervention of YAP-TEAD hyperactivation in human diseases.

  9. Dynamical evolution of the community structure of complex earthquake network

    CERN Document Server

    Abe, Sumiyoshi


    Earthquake network is known to be complex in the sense that it is scale-free, small-world, hierarchically organized and assortatively mixed. Here, the time evolution of earthquake networks is analyzed around main shocks in the context of the community structure. It is found that the maximum of the modularity measure quantifying existence of communities exhibits a peculiar behavior: its maximum value stays at a large value before a main shock, suddenly drops to a small values at the main shock, and then increases to relax to a large value again relatively slowly. In this way, a main shock is characterized in the language of theory of complex networks. The result is also interpreted in terms of the clustering structure of the earthquake network.

  10. Algorithms and Complexity Results for Exact Bayesian Structure Learning

    CERN Document Server

    Ordyniak, Sebastian


    Bayesian structure learning is the NP-hard problem of discovering a Bayesian network that optimally represents a given set of training data. In this paper we study the computational worst-case complexity of exact Bayesian structure learning under graph theoretic restrictions on the super-structure. The super-structure (a concept introduced by Perrier, Imoto, and Miyano, JMLR 2008) is an undirected graph that contains as subgraphs the skeletons of solution networks. Our results apply to several variants of score-based Bayesian structure learning where the score of a network decomposes into local scores of its nodes. Results: We show that exact Bayesian structure learning can be carried out in non-uniform polynomial time if the super-structure has bounded treewidth and in linear time if in addition the super-structure has bounded maximum degree. We complement this with a number of hardness results. We show that both restrictions (treewidth and degree) are essential and cannot be dropped without loosing uniform ...

  11. The structure of complex networks theory and applications

    CERN Document Server

    Estrada, Ernesto


    This book deals with the analysis of the structure of complex networks by combining results from graph theory, physics, and pattern recognition. The book is divided into two parts. 11 chapters are dedicated to the development of theoretical tools for the structural analysis of networks, and 7 chapters are illustrating, in a critical way, applications of these tools to real-world scenarios. The first chapters provide detailed coverage of adjacency and metric and topologicalproperties of networks, followed by chapters devoted to the analysis of individual fragments and fragment-based global inva

  12. Structural properties of complex plasmas in a homogeneous dc discharge. (United States)

    Mitic, S; Klumov, B A; Konopka, U; Thoma, M H; Morfill, G E


    We report on the first three-dimensional (3D) complex plasma structure analysis for an experiment that was performed in an elongated discharge tube in the absence of striations. The low frequency discharge was established with 1 kHz alternating dc current through a cylindrical glass tube filled with neon at 30 Pa. The injected particle cloud consisted of monodisperse microparticles. A scanning laser sheet and a camera were used to determine the particle position in 3D. The observed cylindrical-shaped particle cloud showed an ordered structure with a distinct outer particle shell. The observations are in agreement with performed molecular dynamics simulations.

  13. Optimal structure of complex networks for minimizing traffic congestion. (United States)

    Zhao, Liang; Cupertino, Thiago Henrique; Park, Kwangho; Lai, Ying-Cheng; Jin, Xiaogang


    To design complex networks to minimize traffic congestion, it is necessary to understand how traffic flow depends on network structure. We study data packet flow on complex networks, where the packet delivery capacity of each node is not fixed. The optimal configuration of capacities to minimize traffic congestion is derived and the critical packet generating rate is determined, below which the network is at a free flow state but above which congestion occurs. Our analysis reveals a direct relation between network topology and traffic flow. Optimal network structure, free of traffic congestion, should have two features: uniform distribution of load over all nodes and small network diameter. This finding is confirmed by numerical simulations. Our analysis also makes it possible to theoretically compare the congestion conditions for different types of complex networks. In particular, we find that network with low critical generating rate is more susceptible to congestion. The comparison has been made on the following complex-network topologies: random, scale-free, and regular.

  14. An Algebraic Approach to Inference in Complex Networked Structures (United States)


    44], [45],[46] where the shift is the elementary non-trivial filter that generates, under an appropriate notion of shift invariance, all linear ... elementary filter, and its output is a graph signal with the value at vertex n of the graph given approximately by a weighted linear combination of...AFRL-AFOSR-VA-TR-2015-0265 An Algebraic Approach to Inference in Complex Networked Structures Jose Moura CARNEGIE MELLON UNIVERSITY Final Report 07

  15. Acoustic Wave Dispersion and Scattering in Complex Marine Sediment Structures (United States)


    Acoustic wave dispersion and scattering in complex marine sediment structures Charles W. Holland The Pennsylvania State University Applied...volume scattering and 2) the effects of shear waves in general layered media. These advances will provide the basis for measuring dispersion in in-situ...shear waves on dispersion in marine sediments. The first step will be development of the theory. WORK COMPLETED A brief summary of the work

  16. Improvement of seismic imaging of complex geologic structures

    Energy Technology Data Exchange (ETDEWEB)

    Duquet, B.


    Successful imaging of complex geologic structures by pre-stack depth migration requires a correct velocity model of the subsurface. In recent years, it has been proposed to use pre-stack depth migration of the cube of pre-stack depth migrated images and the subsequent use of the interpretation for velocity model update. However, in complex geologic structures, pre-stack depth migration does not yield results of sufficient quality for interpretation. We therefore propose a new wave-field imaging technique based on linearized inversion using the paraxial approximation of the wave equation. Using this technique we can remove the artifacts contaminating the individual depth images by integrating a priori information in the inverse problem. The application of the method to synthetic and real data shows that it allows us to largely improve the quality of the depth images at reasonable cost.We thus obtain an interpretable cube of depth images that makes migration velocity analysis feasible in complex structures. In 3D, due to the size of the problem there is still a large interest in using post stack techniques for velocity model determination. The quality of the results of such techniques relies on the quality of the stacking process. Classical data stacking techniques rely on simplifications that are not valid anymore in case of complex geologic structures. We propose a data stacking technique based on depth domain stacking after pre-stack depth migration, followed by explosive reflector modeling, to obtain the stacked seismic data. This method which is totally automatic yield 3 D stacked data that are suitable for 3D post stack velocity determination techniques.

  17. Generating a 2D Representation of a Complex Data Structure (United States)

    James, Mark


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

  18. Designing smart particles for the assembly of complex macroscopic structures. (United States)

    Garcia-Tunon, Esther; Barg, Suelen; Bell, Robert; Weaver, Jonathan V M; Walter, Claudia; Goyos, Lidia; Saiz, Eduardo


    Particle get-together: Surface functionalization with a branched copolymer surfactant is used to create responsive inorganic particles that can self-assemble in complex structures. The assembly process is triggered by a pH switch that reversibly activates multiple hydrogen bonds between ceramic particles (see picture; yellow) and soft templates (n-decane; green). Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Optical spectroscopy study of nc-Si-based p-i-n solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Sancho-Parramon, Jordi; Gracin, Davor; Gajovic, Andreja [Rudjer Boskovic Institute, Bijenicka cesta 54, 10000 Zagreb (Croatia); Modreanu, Mircea [Tyndall Institute, Lee Maltings, Prospect Row, Cork (Ireland)


    In the present study we analyzed nanocrystalline silicon (nc-Si)-based p-i-n thin film structures (SiC/nc-Si/n-doped amorphous Si) on glass produced by radio-frequency plasma-enhanced chemical vapor deposition. The crystallinity of the nc-Si layer was modified by varying the deposition conditions ([SiH{sub 4}]/[H{sub 2}] ratio in the plasma and radio-frequency power). Structural properties of the samples (crystalline fraction and crystal size distribution) were inferred by Raman spectroscopy. Different optical spectroscopy methods were combined for the determination of the optical constants in different spectral ranges: spectrophotometry, ellipsometry and photothermal deflection spectroscopy. Characterization results evidence that the optical properties of the nc-Si layers are strongly connected with the layer structural properties. Thus, the correlation between density of defects, Urbach energy, band-gap and line-shape of dielectric function critical points with the crystalline properties of the films is established. (author)

  20. Polymer supported nickel complex: Synthesis, structure and catalytic application

    Indian Academy of Sciences (India)

    Alekha Kumar Sutar; Tungabidya Maharana; Yasobanta Das; Prasanta Rath


    In the present investigation, a new synthetic route for a novel recyclable free [3-MOBdMBn-Ni] and polystyrene-anchored [P-3-MOBdMBn-Ni] nickel complexes is presented. The free and polymer-anchored metal complexes were synthesized by the reaction of nickel (II) with one molar equivalent of unsupported N N′-bis (2-Hydroxy-3-methoxybenzaldehyde) 4-Methylbenzene-1,2-diamine (3-MOBdMBn) or polymersupported (P-3-MOBdMBn) Schiff-base ligand in methanol under nitrogen atmosphere. The advantages of these polymer-supported catalysts are the low cost of catalyst and recyclability up to six times, due to easy availability of materials and simple synthetic route. The higher efficiency of complexation of nickel on the polymer-anchored 3-MOBdMBn Schiff base than the unsupported analogue is another advantage of this catalyst system. The structural study reveals that nickel(II) complex of 3-MOBdMBn is square planar in geometry. The catalytic activity of nickel complex towards the oxidation of phenol was investigated in the presence of hydrogen peroxide. Experimental results indicate that the reactivity of P-3-MOBdMBn-Ni was dramatically affected by the polymer support compared to free 3-MOBdMBn-Ni. The rates of oxidation (R) for unsupported and supported catalysts are 1.37 × 10-6 mole dm-3 s-1 and 2.33 × 10-6 mole dm-3 s-1 respectively.

  1. Complexation of Flavonoids with Iron: Structure and Optical Signatures (United States)

    Ren, Jun; Meng, Sheng; Lekka, Ch. E.; Kaxiras, Efthimios


    Flavonoids exhibit antioxidant behavior believed to be related to their metal ion chelation ability. We investigate the complexation mechanism of several flavonoids, quercetin, luteolin, galangin, kaempferol and chrysin with iron, the most abundant type of metal ions in the body, through first- principles electronic structure calculations based on Density Functional Theory (DFT). We find that the most likely chelation site for Fe is the 3-hydroxyl-4-carbonyl group, followed by 4- carbonyl-5-hydroxyl group and the 3'-4' hydroxyl (if present) for all the flavonoid molecules studied. Three quercetin molecules are required to saturate the bonds of a single Fe ion by forming six orthogonal Fe-O bonds, though the binding energy per molecule is highest for complexes consisting of two quercetin molecules and one Fe atom, in agreement with experiment. Optical absorption spectra calculated with time- dependent DFT serve as signatures to identify various complexes. For the iron-quercetin complexes, we find a redshift of the first absorbance peak upon complexation in good agreement with experiment; this behavior is explained by the narrowing of the optical gap of quercetin due to Fe(d)--O(p) orbital hybridization.

  2. Structure and function of the mitochondrial calcium uniporter complex. (United States)

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


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

  3. Complexity of Soils Porous Structure: A Simple Question (United States)

    Benito, R. M.; Cardenas, J. P.; Santiago, A.; Borondo, F.; Losada, J. C.; Tarquis, A. M.; Grupo de Sistemas Complejos


    In the last decades scientist have realized that soil processes are implicated the biggest global challenges facing humanity such as soil aeration, sequestration or emission of greenhouse gasses, volatilization of volatile organic chemicals among other phenomena. Progress in these challenges will depend on being able to understand the integrated behavior of soil as a system, and dealing with the complexity in describing soil in these terms. In this work we focus in one of the critical soil issues: soil structure and pore connectivity. A quantitative and explicit characterization of soil structure is difficult because of the complexity of the pore space. We proposed a model to attempt to capture the complexity of the system in which we interpret porous soils as heterogeneous networks, where pores are represented by nodes and the links representing flows between them. Pore properties such as position and size are described by fixed states in a metric space, while an affinity function is introduced to bias the attachment probabilities of links according to these properties taking in account soil texture. These types of models are named as Heterogeneous Preferential Attachment (HPA). We perform an analytical study of the degree distributions in the soil model and show that under reasonable conditions all the model variants yield a multiscaling behavior in the connectivity degrees, leaving an empirically testable signature of heterogeneity in the topology of pore networks. With the aim to study in more detail topological properties of these networks, for different real soils samples an analysis of the community structure have been applied and studied depending on the values of the parameters of the porous soil model used. The detection of communities of pores, as groups densely connected with only sparser connections between groups, could contribute to understand the mechanisms of the diffusion phenomena in soils. References Cardenas, J. P. Cardenas, A. M. Tarquis, J. C

  4. Structural Analysis in Shoufengsi Area of Tananao Complex, Eastern Taiwan

    Directory of Open Access Journals (Sweden)

    Gong-Ruei Ho and Wei Lo


    Full Text Available The subduction and collision boundaries of the Eurasia and Philippine Sea Plates in the Taiwan mountain belt expose a NE-trending coherent crustal section in the Tananao Complex. This study investigates the structures in three dimensions in the Shoufengsi area, which is located in the middle section of the Tananao Complex to understand the Taiwan orogeny mountain building processes. Detailed geological mapping and structural analyses shows the eastward shortening associated with metamorphism indicative of three deformation events. Three sets of axial plane foliation S1, S2, and S3 can be recognized by Type-1 and Type-3 fold interference patterns. Different structural characteristics can be further revealed in five domains based on domain analysis. Each domain shows the superposed process characteristics. Synthetic structural mapping and microstructure examination analyses on the Shoufengsi area show that NE-trending isoclinal folds and axial D1 and D2 plane foliation events represent shortening deformation and NW-trending crenulation cleavage. Normal D3 event faults display the gravity collapse deformation. These observations are consistent with shortening to extension stage predictions during Eurasia and Philippine Sea Plate collisions.

  5. Syntheses and structural characterization of new dithiophosphinato cadmium complexes

    Indian Academy of Sciences (India)

    Ertuğrul Gazi̇ Sağlam; Nurcan Acar; Yasemi̇n Süzen; Berline Mougang-Soumé; Tuncer Hökelek


    New cadmium complexes of 4-methoxyphenyl dithiophosphinic acids, H3CO-C6H4-(R)PS2H were prepared. The five dithiophosphinato ligands (L) involved were of the general structure H3CO-C6H4-(R)PS2−with R= 3-methylbutyl, (L1); n-butyl, (L2); 2-methylpropyl, (L3); 1-methylpropyl, (L4) and 2-propyl, (L5).To the best of our knowledge, this is the first report on the preparation and characterization of the n-butyl-derivative. The acid forms of the ligands were obtained by treatment of the Lawesson reagent, (LR) [2,4-bis(4-methoxyphenyl)-1,3,2,4-dithiadiphosphetane-2,4-disulfide] with the corresponding Grignard reagent in dry diethylether. The acids formed were transformed into easily crystallizable ammonium salts (NH4L) for purification. These salts were treated with CdCl2 in ethanol at room temperature to produce the bis-dithiophosphinato cadmium complexes ([Cd(L)2]2) exclusively. The structures of the complexes were elucidated by elemental analysis, MS, FTIR and Raman spectroscopy techniques as well as 1H-, 13C- and 31P- NMR. The crystal structures of [Cd(L1)2]2 and [Cd(L2)2]2 were also studied as examples. X-ray studies confirmed the nonplanar, four-coordination geometry of the complexes and indicate that electron delocalization prevails in the PS$_{−}^{2}$ moiety of the dithiophosphinato groups.

  6. Random field Ising model and community structure in complex networks (United States)

    Son, S.-W.; Jeong, H.; Noh, J. D.


    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.)

  7. Measuring robustness of community structure in complex networks

    CERN Document Server

    Li, Hui-Jia; Chen, Luonan


    The theory of community structure is a powerful tool for real networks, which can simplify their topological and functional analysis considerably. However, since community detection methods have random factors and real social networks obtained from complex systems always contain error edges, evaluating the robustness of community structure is an urgent and important task. In this letter, we employ the critical threshold of resolution parameter in Hamiltonian function, $\\gamma_C$, to measure the robustness of a network. According to spectral theory, a rigorous proof shows that the index we proposed is inversely proportional to robustness of community structure. Furthermore, by utilizing the co-evolution model, we provides a new efficient method for computing the value of $\\gamma_C$. The research can be applied to broad clustering problems in network analysis and data mining due to its solid mathematical basis and experimental effects.

  8. Complex Dynamic Flows in Solar Flare Sheet Structures (United States)

    McKenzie, David E.; Reeves, Katharine K.; Savage, Sabrina


    Observations of high-energy emission from solar flares often reveal the presence of large sheet-like structures, sometimes extending over a space comparable to the Sun's radius. Given that these structures are found between a departing coronal mass ejection and the post-eruption flare arcade, it is natural to associate the structure with a current sheet; though the relationship is unclear. Moreover, recent high-resolution observations have begun to reveal that the motions in this region are highly complex, including reconnection outflows, oscillations, and apparent wakes and eddies. We present a detailed first look at the complicated dynamics within this supra-arcade plasma, and consider implications for the interrelationship between the plasma and its embedded magnetic field.

  9. Integrated lithography to produce complex structures for spectral engineering

    CERN Document Server

    Csete, Maria; Szalai, Aniko; Szabo, Gabor


    An integrated interference and colloid sphere lithography (IICL) method is presented capable of producing complex plasmonic structures consisting of wavelength-scaled periodic arrays of nano-objects with arbitrary array symmetry and controllable nano-scaled sub-structures. The IICL method is based on illumination of colloid sphere monolayers by interference patterns synchronized with sphere arrays along arbitrary crystallographic directions. This nano-kaleidoscope method enables to tune four structure parameters independently: the symmetry and characteristic periodicity of the interference pattern might be varied by the wavelength, number and angle of incidence of the interfering beams; the colloid-spheres' diameter-scaled distance between the nano-objects is controllable by the relative orientation of the interference pattern with respect to the hexagonal lattice of colloid spheres; the size of the individual nano-objects is determined by the colloid-spheres diameter and by the illumination light wavelength ...

  10. The encoding complexity of two dimensional range minimum data structures

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Brodnik, Andrej; Davoodi, Pooya


    In the two-dimensional range minimum query problem an input matrix A of dimension m ×n, m ≤ n, has to be preprocessed into a data structure such that given a query rectangle within the matrix, the position of a minimum element within the query range can be reported. We consider the space complexity...... of the encoding variant of the problem where queries have access to the constructed data structure but can not access the input matrix A, i.e. all information must be encoded in the data structure. Previously it was known how to solve the problem with space O(mn min {m,logn}) bits (and with constant query time...

  11. Structural Complexity and Phonon Physics in 2D Arsenenes. (United States)

    Carrete, Jesús; Gallego, Luis J; Mingo, Natalio


    In the quest for stable 2D arsenic phases, four different structures have been recently claimed to be stable. We show that, due to phonon contributions, the relative stability of those structures differs from previous reports and depends crucially on temperature. We also show that one of those four phases is in fact mechanically unstable. Furthermore, our results challenge the common assumption of an inverse correlation between structural complexity and thermal conductivity. Instead, a richer picture emerges from our results, showing how harmonic interactions, anharmonicity, and symmetries all play a role in modulating thermal conduction in arsenenes. More generally, our conclusions highlight how vibrational properties are an essential element to be carefully taken into account in theoretical searches for new 2D materials.

  12. Seismic Imaging of Complex Structures in the Tarim Basin

    Institute of Scientific and Technical Information of China (English)

    Ning Guo; Chao Wu; Stuart Fagin


    Conventional time imaging techniques are not capable of producing accurate seismic imaging of the subsurface in the mountain front of the Tarim Basin, China. Their imaged structures have led to some major drilling failures before, bearing a disrepute that “their structural closures have wheels and their structural highs have springs”. This article first lists the imaging challenges, and explains in a schematic why the time imaging techniques fail in this area. Then through a series of real data examples, it demonstrates that when there exist lateral velocity variations, depth imaging is the only solution to tackle the imaging challenges in this area. Depth imaging accounts for the com-plexity of the wavefield, therefore produces superior and geological plausible images. The core task in properly performing depth imaging is building the velocity model. This article stresses some the main aspects in this regard.

  13. The Interplay between Microscopic and Mesoscopic Structures in Complex Networks (United States)

    Reichardt, Jörg; Alamino, Roberto; Saad, David


    Understanding a complex network's structure holds the key to understanding its function. The physics community has contributed a multitude of methods and analyses to this cross-disciplinary endeavor. Structural features exist on both the microscopic level, resulting from differences between single node properties, and the mesoscopic level resulting from properties shared by groups of nodes. Disentangling the determinants of network structure on these different scales has remained a major, and so far unsolved, challenge. Here we show how multiscale generative probabilistic exponential random graph models combined with efficient, distributive message-passing inference techniques can be used to achieve this separation of scales, leading to improved detection accuracy of latent classes as demonstrated on benchmark problems. It sheds new light on the statistical significance of motif-distributions in neural networks and improves the link-prediction accuracy as exemplified for gene-disease associations in the highly consequential Online Mendelian Inheritance in Man database. PMID:21829597

  14. The interplay between microscopic and mesoscopic structures in complex networks.

    Directory of Open Access Journals (Sweden)

    Jörg Reichardt

    Full Text Available Understanding a complex network's structure holds the key to understanding its function. The physics community has contributed a multitude of methods and analyses to this cross-disciplinary endeavor. Structural features exist on both the microscopic level, resulting from differences between single node properties, and the mesoscopic level resulting from properties shared by groups of nodes. Disentangling the determinants of network structure on these different scales has remained a major, and so far unsolved, challenge. Here we show how multiscale generative probabilistic exponential random graph models combined with efficient, distributive message-passing inference techniques can be used to achieve this separation of scales, leading to improved detection accuracy of latent classes as demonstrated on benchmark problems. It sheds new light on the statistical significance of motif-distributions in neural networks and improves the link-prediction accuracy as exemplified for gene-disease associations in the highly consequential Online Mendelian Inheritance in Man database.

  15. Manufacturing of a 3D complex hyperstable Cesic structure (United States)

    Kroedel, Matthias; Courteau, Pascal; Poupinet, Anne; Sarri, Giuseppe


    Global astrometry requires extremely stable materials for instrument structures, such as optical benches. Cesic®, developed by ECM and Thales Alenia Space for mirrors and high stability structures, offers an excellent compromise in terms of structural strength, stability and very high lightweight capability, with a coefficient of thermal expansion that is virtually zero at cryogenic T°. The High-Stability Optical Bench (HSOB) GAIA study, realized by Thales Alenia Space under ESA contract, aimed to design, develop and test a full-scale representative of the HSOB bench, made entirely of Cesic®. The bench has been equipped with SAGEIS-CSO laser metrology system MOUSE1, a Michelson interferometer composed of integrated optics with nm-resolution. The HSOB bench has been submitted to a homogeneous T° step under vacuum to characterize 3-D expansion behavior of its two arms. The quite negligible interarm differential, measured with a nm-range reproducibility, demonstrates that a complete 3-D structure made of Cesic® has the same CTE homogeneity as do characterization samples, fully in line with the stringent GAIA requirements (1ppm at 120K). This demonstrates that Cesic® properties at cryogenic temperatures are fully appropriate to the manufacturing of complex highly stable optical structures. This successful study confirms ECM's and Thales Alenia Space's ability to design and manufacture monolithic lightweight highly stable optical structures, based on inner-cell triangular design made possible by the unique Cesic® manufacturing process.

  16. Structural and spectroscopic insights into BolA-glutaredoxin complexes. (United States)

    Roret, Thomas; Tsan, Pascale; Couturier, Jérémy; Zhang, Bo; Johnson, Michael K; Rouhier, Nicolas; Didierjean, Claude


    BolA proteins are defined as stress-responsive transcriptional regulators, but they also participate in iron metabolism. Although they can form [2Fe-2S]-containing complexes with monothiol glutaredoxins (Grx), structural details are lacking. Three Arabidopsis thaliana BolA structures were solved. They differ primarily by the size of a loop referred to as the variable [H/C] loop, which contains an important cysteine (BolA_C group) or histidine (BolA_H group) residue. From three-dimensional modeling and spectroscopic analyses of A. thaliana GrxS14-BolA1 holo-heterodimer (BolA_H), we provide evidence for the coordination of a Rieske-type [2Fe-2S] cluster. For BolA_C members, the cysteine could replace the histidine as a ligand. NMR interaction experiments using apoproteins indicate that a completely different heterodimer was formed involving the nucleic acid binding site of BolA and the C-terminal tail of Grx. The possible biological importance of these complexes is discussed considering the physiological functions previously assigned to BolA and to Grx-BolA or Grx-Grx complexes. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Complex band structure of topological insulator Bi2Se3 (United States)

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


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

  18. Structural and Biochemical Insights into MLL1 Core Complex Assembly

    Energy Technology Data Exchange (ETDEWEB)

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


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

  19. Structural genomic variation in childhood epilepsies with complex phenotypes

    DEFF Research Database (Denmark)

    Helbig, Ingo; Swinkels, Marielle E M; Aten, Emmelien


    A genetic contribution to a broad range of epilepsies has been postulated, and particularly copy number variations (CNVs) have emerged as significant genetic risk factors. However, the role of CNVs in patients with epilepsies with complex phenotypes is not known. Therefore, we investigated the role...... of CNVs in patients with unclassified epilepsies and complex phenotypes. A total of 222 patients from three European countries, including patients with structural lesions on magnetic resonance imaging (MRI), dysmorphic features, and multiple congenital anomalies, were clinically evaluated and screened...... for CNVs. MRI findings including acquired or developmental lesions and patient characteristics were subdivided and analyzed in subgroups. MRI data were available for 88.3% of patients, of whom 41.6% had abnormal MRI findings. Eighty-eight rare CNVs were discovered in 71 out of 222 patients (31...

  20. Structure and function of florigen and the receptor complex. (United States)

    Taoka, Ken-ichiro; Ohki, Izuru; Tsuji, Hiroyuki; Kojima, Chojiro; Shimamoto, Ko


    In the 1930s, the flowering hormone, florigen, was proposed to be synthesized in leaves under inductive day length and transported to the shoot apex, where it induces flowering. More recently, generated genetic and biochemical data suggest that florigen is a protein encoded by the gene, FLOWERING LOCUS T (FT). A rice (Oryza sativa) FT homolog, Hd3a, interacts with the rice FD homolog, OsFD1, via a 14-3-3 protein. Formation of this tri-protein complex is essential for flowering promotion by Hd3a in rice. In addition, the multifunctionality of FT homologs, other than for flowering promotion, is an emerging concept. Here we review the structural and biochemical features of the florigen protein complex and discuss the molecular basis for the multifunctionality of FT proteins.

  1. The Beta Ansatz: A Tale of Two Complex Structures

    CERN Document Server

    Hanany, Amihay; Jejjala, Vishnu; Pasukonis, Jurgis; Ramgoolam, Sanjaye; Rodriguez-Gomez, Diego


    Brane tilings, sometimes called dimer models, are a class of bipartite graphs on a torus which encode the gauge theory data of four-dimensional SCFTs dual to D3-branes probing toric Calabi--Yau threefolds. An efficient way of encoding this information exploits the theory of dessin d'enfants, expressing the structure in terms of a permutation triple, which is in turn related to a Belyi pair, namely a holomorphic map from a torus to a P^1 with three marked points. The procedure of a-maximization, in the context of isoradial embeddings of the dimer, also associates a complex structure to the torus, determined by the R-charges in the SCFT, which can be compared with the Belyi complex structure. Algorithms for the explicit construction of the Belyi pairs are described in detail. In the case of orbifolds, these algorithms are related to the construction of covers of elliptic curves, which exploits the properties of Weierstrass elliptic functions. We present a counterexample to a previous conjecture identifying the ...

  2. Synthesis and structure of didysprosium complexes with a tetraketone (United States)

    Yang, Luqin; Yang, Rudong


    Two novel didysprosium (Dy 2) complexes of 1,5-bis(1'-phenyl-3'-methyl-5'-pyrazolone-4')-1,5-pentanedione (H 2L), Dy 2L 3·2H 2O and Dy 2L 3·5DMF (DMF = dimethylformamide), have been synthesized. The crystal structure of Dy 2L 3·5DMF was determined by X-ray diffraction. Crystals are triclinic, space group P1¯, with a = 16.99(1), b = 17.970(9), c = 18.28(1) Å, α = 110.36(4), β = 101.47(6), γ = 111.11(5)°, V = 4533(9) Å 3, Mr = 2017.91, Z = 2, D x = 1.48 g cm -3, μ = 17.22 cm -1, F(000) = 2056, R = 0.074 with 3804 reflections used in the refinement. In the complex, each L bonds two dysprosium atoms with its two β-diketone groups. Two DMF solvent molecules bond to each dysprosium ion. The coordination number of the two dysprosium ions is eight. The eight oxygen atoms around the dysprosium ion make up a distorted square antiprism coordination polyhedron. The resonance structures of coordinated β-diketonates are also discussed. Different lanthanide ions may stabilize the specific structure.

  3. Temporal structure and complexity affect audio-visual correspondence detection

    Directory of Open Access Journals (Sweden)

    Rachel N Denison


    Full Text Available Synchrony between events in different senses has long been considered the critical temporal cue for multisensory integration. Here, using rapid streams of auditory and visual events, we demonstrate how humans can use temporal structure (rather than mere temporal coincidence to detect multisensory relatedness. We find psychophysically that participants can detect matching auditory and visual streams via shared temporal structure for crossmodal lags of up to 200 ms. Performance on this task reproduced features of past findings based on explicit timing judgments but did not show any special advantage for perfectly synchronous streams. Importantly, the complexity of temporal patterns influences sensitivity to correspondence. Stochastic, irregular streams – with richer temporal pattern information – led to higher audio-visual matching sensitivity than predictable, rhythmic streams. Our results reveal that temporal structure and its complexity are key determinants for human detection of audio-visual correspondence. The distinctive emphasis of our new paradigms on temporal patterning could be useful for studying special populations with suspected abnormalities in audio-visual temporal perception and multisensory integration.

  4. Changes in protein structure at the interface accompanying complex formation

    Directory of Open Access Journals (Sweden)

    Devlina Chakravarty


    Full Text Available Protein interactions are essential in all biological processes. The changes brought about in the structure when a free component forms a complex with another molecule need to be characterized for a proper understanding of molecular recognition as well as for the successful implementation of docking algorithms. Here, unbound (U and bound (B forms of protein structures from the Protein–Protein Interaction Affinity Database are compared in order to enumerate the changes that occur at the interface atoms/residues in terms of the solvent-accessible surface area (ASA, secondary structure, temperature factors (B factors and disorder-to-order transitions. It is found that the interface atoms optimize contacts with the atoms in the partner protein, which leads to an increase in their ASA in the bound interface in the majority (69% of the proteins when compared with the unbound interface, and this is independent of the root-mean-square deviation between the U and B forms. Changes in secondary structure during the transition indicate a likely extension of helices and strands at the expense of turns and coils. A reduction in flexibility during complex formation is reflected in the decrease in B factors of the interface residues on going from the U form to the B form. There is, however, no distinction in flexibility between the interface and the surface in the monomeric structure, thereby highlighting the potential problem of using B factors for the prediction of binding sites in the unbound form for docking another protein. 16% of the proteins have missing (disordered residues in the U form which are observed (ordered in the B form, mostly with an irregular conformation; the data set also shows differences in the composition of interface and non-interface residues in the disordered polypeptide segments as well as differences in their surface burial.

  5. Crystal structure of eukaryotic ribosome and its complexes with inhibitors. (United States)

    Yusupova, Gulnara; Yusupov, Marat


    A high-resolution structure of the eukaryotic ribosome has been determined and has led to increased interest in studying protein biosynthesis and regulation of biosynthesis in cells. The functional complexes of the ribosome crystals obtained from bacteria and yeast have permitted researchers to identify the precise residue positions in different states of ribosome function. This knowledge, together with electron microscopy studies, enhances our understanding of how basic ribosome processes, including mRNA decoding, peptide bond formation, mRNA, and tRNA translocation and cotranslational transport of the nascent peptide, are regulated. In this review, we discuss the crystal structure of the entire 80S ribosome from yeast, which reveals its eukaryotic-specific features, and application of X-ray crystallography of the 80S ribosome for investigation of the binding mode for distinct compounds known to inhibit or modulate the protein-translation function of the ribosome. We also refer to a challenging aspect of the structural study of ribosomes, from higher eukaryotes, where the structures of major distinctive features of higher eukaryote ribosome-the high-eukaryote-specific long ribosomal RNA segments (about 1MDa)-remain unresolved. Presently, the structures of the major part of these high-eukaryotic expansion ribosomal RNA segments still remain unresolved.This article is part of the themed issue 'Perspectives on the ribosome'.

  6. Synthesis, structural, spectroscopic and biological studies of Schiff base complexes (United States)

    Diab, M. A.; El-Sonbati, A. Z.; Shoair, A. F.; Eldesoky, A. M.; El-Far, N. M.


    Schiff base ligand 4-((pyridin-2- yl)methyleneamino)-1,2-dihydro-2,3-dimethyl-1-phenylpyrazol-5-one (PDMP) and its complexes were prepared and characterized on the basis of elemental analysis, IR, mass spectra and thermogravimetric analysis. All results confirm that the complexes have 1:1 (M: PMDP) stoichiometric formula [M(PMDP)Cl2H2O ] (M = Cu(II), Co(II), Ni(II) and Mn(II)), [Cd(PMDP)Cl2] and the ligand behaves as a bi/tridentate forming five-membered chelating ring towards the metal ions, bonding through azomethine nitrogen/exocyclic carbonyl oxygen, azomethine pyridine nitrogen and exocyclic carbonyl oxygen. The shift in the band positions of the groups involved in coordination has been utilized to estimate the metal-nitrogen and/or oxygen bond lengths. The complexes of Co(II), Ni(II) and Cu(II) are paramagnetic and the magnetic as well as spectral data suggest octahedral geometry, whereas the Cd(II) complex is tetrahedral. The XRD studies show that both the ligand and its metal complexes (1 and 3) show polycrystalline with crystal structure. Molecular docking was used to predict the binding between PMDP ligand and the receptors. The corrosion inhibition of mild steel in 2 M HCl solution by PDMP was explored utilizing potentiodynamic polarization, electrochemical impedance spectroscopy (EIS) and (EFM) electrochemical frequency modulation method. Potentiodynamic polarization demonstrated that PDMP compound is mixed-type inhibitor. EIS spectra exhibit one capacitive loop and confirm the protective ability. The percentage of inhibition efficiency was found to increase with increasing the inhibitor concentration.

  7. Analysis of residue conformations in peptides in Cambridge structural database and protein-peptide structural complexes. (United States)

    Raghavender, Upadhyayula Surya


    A comprehensive statistical analysis of the geometric parameters of peptide chains in a reduced dataset of protein-peptide complexes in Protein Data Bank (PDB) is presented. The angular variables describing the backbone conformations of amino acid residues in peptide chains shed insights into the conformational preferences of peptide residues interacting with protein partners. Nonparametric statistical approaches are employed to evaluate the interrelationships and associations in structural variables. Grouping of residues based on their structure into chemical classes reveals characteristic trends in parameter relationships. A comparison of canonical amino acid residues in free peptide structures in Cambridge structural database (CSD) with identical residues in PDB complexes, suggests that the information can be integrated from both the structural repositories enabling efficient and accurate modeling of biologically active peptides. © 2016 John Wiley & Sons A/S.

  8. Synthesis and Structure of a New Dinuclear Uranyl Complex

    Institute of Scientific and Technical Information of China (English)


    With a heptadentate compartmental Schiff-base ligand H3L (1, 3-di[o-(salicylimino) ph-enoxyl]-2-propanol), a new binuclear diuranyl complex [(UO2)2L(OH)]?3DMF, C38H45N5O13U2, was synthesized and the crystal structure was determined by X-ray diffraction techniques. The coordination geometry are two pentagonal bipyramids. In each pentagon four kinds of U-O (phenoxido, hydroxo, alkoxo and ether oxo) bonds are discussed.

  9. Unveiling the Multi-fractal Structure of Complex Networks

    CERN Document Server

    Jalan, Sarika; Sarkar, Camellia; Boccaletti, Stefano


    The fractal nature of graphs has traditionally been investigated by using the nodes of networks as the basic units. Here, instead, we propose to concentrate on the graph edges, and introduce a practical and computationally not demanding method for revealing changes in the fractal behavior of networks, and particularly for allowing distinction between mono-fractal, quasi mono-fractal, and multi-fractal structures. We show that degree homogeneity plays a crucial role in determining the fractal nature of the underlying network, and report on six different protein-protein interaction networks along with their corresponding random networks. Our analysis allows to identify varying levels of complexity in the species.

  10. Structural and Electronic Investigations of Complex Intermetallic Compounds

    Energy Technology Data Exchange (ETDEWEB)

    Ko, Hyunjin [Iowa State Univ., Ames, IA (United States)


    In solid state chemistry, numerous investigations have been attempted to address the relationships between chemical structure and physical properties. Such questions include: (1) How can we understand the driving forces of the atomic arrangements in complex solids that exhibit interesting chemical and physical properties? (2) How do different elements distribute themselves in a solid-state structure? (3) Can we develop a chemical understanding to predict the effects of valence electron concentration on the structures and magnetic ordering of systems by both experimental and theoretical means? Although these issues are relevant to various compound classes, intermetallic compounds are especially interesting and well suited for a joint experimental and theoretical effort. For intermetallic compounds, the questions listed above are difficult to answer since many of the constituent atoms simply do not crystallize in the same manner as in their separate, elemental structures. Also, theoretical studies suggest that the energy differences between various structural alternatives are small. For example, Al and Ga both belong in the same group on the Periodic Table of Elements and share many similar chemical properties. Al crystallizes in the fcc lattice with 4 atoms per unit cell and Ga crystallizes in an orthorhombic unit cell lattice with 8 atoms per unit cell, which are both fairly simple structures (Figure 1). However, when combined with Mn, which itself has a very complex cubic crystal structure with 58 atoms per unit cell, the resulting intermetallic compounds crystallize in a completely different fashion. At the 1:1 stoichiometry, MnAl forms a very simple tetragonal lattice with two atoms per primitive unit cell, while MnGa crystallizes in a complicated rhombohedral unit cell with 26 atoms within the primitive unit cell. The mechanisms influencing the arrangements of atoms in numerous crystal structures have been studied theoretically by calculating electronic

  11. Structure of Block Copolymer Hydrogel Formed by Complex Coacervate Process (United States)

    Choi, Soohyung; Ortony, Julia; Krogstad, Daniel; Spruell, Jason; Lynd, Nathaniel; Han, Songi; Kramer, Edward


    Complex coacervation occurs when oppositely charged polyelectrolytes associate in solution, forming dense micron-sized droplets. Hydrogels with coacervate block domains were formed by mixing two ABA and A'BA' triblock copolymer solutions in water where the A and A' blocks are oppositely charged. Small-angle neutron scattering (SANS) was used to investigate the structure of hydrogels formed by ABA triblock copolymers (A block: poly(allyl glycidyl ether) functionalized with guanidinium (A) or sulfonate (A'), B block: poly(ethylene oxide)). By using an appropriate fitting model, structural information such as coacervate core block radius and water volume fraction w can be extracted from SANS data. The results reveal that w in the coacervate core block was significantly higher than in conventional triblock copolymer hydrogels where microphase separation is driven by the hydrophobicity of the core-forming blocks.

  12. Frequency and Complexity of De Novo Structural Mutation in Autism (United States)

    Brandler, William M.; Antaki, Danny; Gujral, Madhusudan; Noor, Amina; Rosanio, Gabriel; Chapman, Timothy R.; Barrera, Daniel J.; Lin, Guan Ning; Malhotra, Dheeraj; Watts, Amanda C.; Wong, Lawrence C.; Estabillo, Jasper A.; Gadomski, Therese E.; Hong, Oanh; Fajardo, Karin V. Fuentes; Bhandari, Abhishek; Owen, Renius; Baughn, Michael; Yuan, Jeffrey; Solomon, Terry; Moyzis, Alexandra G.; Maile, Michelle S.; Sanders, Stephan J.; Reiner, Gail E.; Vaux, Keith K.; Strom, Charles M.; Zhang, Kang; Muotri, Alysson R.; Akshoomoff, Natacha; Leal, Suzanne M.; Pierce, Karen; Courchesne, Eric; Iakoucheva, Lilia M.; Corsello, Christina; Sebat, Jonathan


    Genetic studies of autism spectrum disorder (ASD) have established that de novo duplications and deletions contribute to risk. However, ascertainment of structural variants (SVs) has been restricted by the coarse resolution of current approaches. By applying a custom pipeline for SV discovery, genotyping, and de novo assembly to genome sequencing of 235 subjects (71 affected individuals, 26 healthy siblings, and their parents), we compiled an atlas of 29,719 SV loci (5,213/genome), comprising 11 different classes. We found a high diversity of de novo mutations, the majority of which were undetectable by previous methods. In addition, we observed complex mutation clusters where combinations of de novo SVs, nucleotide substitutions, and indels occurred as a single event. We estimate a high rate of structural mutation in humans (20%) and propose that genetic risk for ASD is attributable to an elevated frequency of gene-disrupting de novo SVs, but not an elevated rate of genome rearrangement. PMID:27018473

  13. Structure-based control of complex networks with nonlinear dynamics

    CERN Document Server

    Zañudo, Jorge G T; Albert, Réka


    Given the network of interactions underlying a complex system, what can we learn about controlling such a system solely from its structure? Over a century of research in control theory has given us tools to answer this question, which were widely applied in science and engineering. Yet the current tools do not always consider the inherently nonlinear dynamics of real systems and the naturally occurring system states in their definition of "control", a term whose interpretation varies across disciplines. Here we use a new mathematical framework for structure-based control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic models of biological, technological, and social processes. This framework provides realizable node overrides that steer a system towards any of its natural long term dynamic behaviors and which are guaranteed to be effective regardless of the dynamic details and parameters of the underlying system. We use this framework on several real networks, compar...

  14. Structural complexities in the active layers of organic electronics. (United States)

    Lee, Stephanie S; Loo, Yueh-Lin


    The field of organic electronics has progressed rapidly in recent years. However, understanding the direct structure-function relationships between the morphology in electrically active layers and the performance of devices composed of these materials has proven difficult. The morphology of active layers in organic electronics is inherently complex, with heterogeneities existing across multiple length scales, from subnanometer to micron and millimeter range. A major challenge still facing the organic electronics community is understanding how the morphology across all of the length scales in active layers collectively determines the device performance of organic electronics. In this review we highlight experiments that have contributed to the elucidation of structure-function relationships in organic electronics and also point to areas in which knowledge of such relationships is still lacking. Such knowledge will lead to the ability to select active materials on the basis of their inherent properties for the fabrication of devices with prespecified characteristics.

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

    Energy Technology Data Exchange (ETDEWEB)

    Xia Junchao; Margulis, Claudio [University of Iowa, Department of Chemistry (United States)], E-mail:


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

  16. Microstructure and texture evolution of Ti-Nb-Si based alloys for biomedical applications

    Institute of Scientific and Technical Information of China (English)

    KIM Won-Yong; KIM Han-Sol


    Microstructure and texture of Ti-Nb-Si based alloys, prepared by water quenching from β-phase field, cold rolling and recrystallization heat treatment followed by water quenching, were investigated in terms of optical microstructure and analysis of X-ray pole figure result.In as-quenched sample, relatively random distribution of pole figure was detected without showing a specific texture component.In as-cold rolled sample, however, it is found well-developed several texture components consisting of rotated cube, α-fiber and γ-fiber texture components which are frequently observed in bcc-structured metals and alloys were found.Therefore, texture components developed in the present alloys are closely related to the deformation of β-phase even though small amount of α″ phase co-exist in the microstructure.In recrystallized sample, α-fiber texture component is weakly detected while the other texture components, rotated cube and γ-fiber components, appears to be relatively unchanged.No additional texture components were detected besides those texture components observed in the cold rolled samples.

  17. Correlations between community structure and link formation in complex networks.

    Directory of Open Access Journals (Sweden)

    Zhen Liu

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

  18. The structure and proteolytic processing of Cbln1 complexes. (United States)

    Bao, Dashi; Pang, Zhen; Morgan, James I


    The hexadecapeptide cerebellin is present in the brains of many vertebrate species and is derived from a larger protein, Cbln1 (cerebellin 1 precursor protein). Although cerebellin has features of a neuropeptide, Cbln1 belongs to the C1q/tumor necrosis factor superfamily of secreted proteins, suggesting that it is the biologically active molecule and the proteolytic events that generate cerebellin serve another function. Therefore, we assessed whether Cbln1 undergoes proteolytic processing and determined what consequences the cleavage events necessary to produce cerebellin have on the structure of Cbln1. Substantial degradation of Cbln1 was evident in the synaptic compartment of cerebellum and lysates of cultured cerebellar neurons and cells transfected with Cbln1 expression vectors. However, only uncleaved Cbln1 containing the cerebellin motif was released and assembled into hexameric complexes. Using yeast two hybrid and mammalian expression systems we show that the cleavages required to produce cerebellin influence the subunit stoichiometry of Cbln1 complexes. Cleavage at the N-terminus of the cerebellin sequence in Cbln1 yields trimeric complexes by separating the trimer-mediating C-terminal C1q domain from conserved N-terminal cysteine residues that mediate higher order oligomerization. Cleavage at the C-terminus of the cerebellin motif disrupts the C1q domain and abolishes subunit interactions. Functional implications of these data are discussed.

  19. A Method for Measuring the Structure Complexity of Web Application

    Institute of Scientific and Technical Information of China (English)


    The precise and effective measure results of Web applications not only facilitate good comprehension of them, but also benefit to the macro-management of software activities, such as testing, reverse engineering, reuse, etc. The paper exploits some researches on measuring the structure complexity of Web application. Through a deep analysis of the configuration and objects' interactions of Web system, two conclusions have been drawn:①A generic Web application consists of static web page, dynamic page, component and database object;②The main interactions have only three styles, that is static link, dynamic link and call/return relation. Based on analysis and modeling of the content of a Web page (static or dynamic), complexity measure methods of both control logic of script and nesting of HTML code are further discussed. In addition, two methods for measuring the complexity of inter-page navigation are also addressed by modeling the inter-page navigation behaviors of Web application via WNG graph.

  20. Crystal structure of KLHL3 in complex with Cullin3.

    Directory of Open Access Journals (Sweden)

    Alan X Ji

    Full Text Available KLHL3 is a BTB-BACK-Kelch family protein that serves as a substrate adapter in Cullin3 (Cul3 E3 ubiquitin ligase complexes. KLHL3 is highly expressed in distal nephron tubules where it is involved in the regulation of electrolyte homeostasis and blood pressure. Mutations in KLHL3 have been identified in patients with inherited hypertension disorders, and several of the disease-associated mutations are located in the presumed Cul3 binding region. Here, we report the crystal structure of a complex between the KLHL3 BTB-BACK domain dimer and two copies of an N terminal fragment of Cul3. We use isothermal titration calorimetry to directly demonstrate that several of the disease mutations in the KLHL3 BTB-BACK domains disrupt the association with Cul3. Both the BTB and BACK domains contribute to the Cul3 interaction surface, and an extended model of the dimeric CRL3 complex places the two E2 binding sites in a suprafacial arrangement with respect to the presumed substrate-binding sites.

  1. Structural and Operational Complexity of the Geobacter Sulfurreducens Genome

    Energy Technology Data Exchange (ETDEWEB)

    Qiu, Yu; Cho, Byung-Kwan; Park, Young S.; Lovley, Derek R.; Palsson, Bernhard O.; Zengler, Karsten


    Prokaryotic genomes can be annotated based on their structural, operational, and functional properties. These annotations provide the pivotal scaffold for understanding cellular functions on a genome-scale, such as metabolism and transcriptional regulation. Here, we describe a systems approach to simultaneously determine the structural and operational annotation of the Geobacter sulfurreducens genome. Integration of proteomics, transcriptomics, RNA polymerase, and sigma factor-binding information with deep-sequencing-based analysis of primary 59-end transcripts allowed for a most precise annotation. The structural annotation is comprised of numerous previously undetected genes, noncoding RNAs, prevalent leaderless mRNA transcripts, and antisense transcripts. When compared with other prokaryotes, we found that the number of antisense transcripts reversely correlated with genome size. The operational annotation consists of 1453 operons, 22% of which have multiple transcription start sites that use different RNA polymerase holoenzymes. Several operons with multiple transcription start sites encoded genes with essential functions, giving insight into the regulatory complexity of the genome. The experimentally determined structural and operational annotations can be combined with functional annotation, yielding a new three-level annotation that greatly expands our understanding of prokaryotic genomes.

  2. Optimal fatigue analysis of structures during complex loadings

    Directory of Open Access Journals (Sweden)

    Karaouni Habib


    Full Text Available A new framework for high cycle fatigue analysis of metallic structures under complex multi-parameter loadings was here developed. This allows to reduce the analysis on a 2-D window with a characterized one-parameter cyclic loading thanks to an equivalence rule relative to damage between any two loadings. The simplified inelastic analysis introduced by J. Zarka [J. Zarka et al. 1990. A new approach in inelastic analysis of structures. CADLM] was used to find the limit state of the structure. A new design rules for fatigue analysis by utilizing automatic learning systems was successfully performed. A database was built by coupling numerical simulations and experimental results on several welded specimens which are considered as a general structure in the proposed approach. This could be possible by the introduction of an intelligent description of a general fatigue case based on the actual theories and models. A software, FATPRO [M.I. Systems, FatPro, available at], based on this work has been developed at MZ Intelligent Systems.

  3. Brain structural complexity and life course cognitive change. (United States)

    Mustafa, Nazahah; Ahearn, Trevor S; Waiter, Gordon D; Murray, Alison D; Whalley, Lawrence J; Staff, Roger T


    Fractal measures such as fractal dimension (FD) can quantify the structural complexity of the brain. These have been used in clinical neuroscience to investigate brain development, ageing and in studies of psychiatric and neurological disorders. Here, we examined associations between the FD of white matter and cognitive changes across the life course in the absence of detectable brain disease. The FD was calculated from segmented cerebral white matter MR images in 217 subjects aged about 68years, in whom archived intelligence scores from age 11years were available. Cognitive test scores of fluid and crystallised intelligence were obtained at the time of MR imaging. Significant differences were found (intracranial volume, brain volume, white matter volume and Raven's Progressive Matrices score) between men and women at age 68years and novel associations were found between FD and measures of cognitive change over the life course from age 11 to 68years. Those with greater FD were found to have greater than expected fluid abilities at age 68years than predicted by their childhood intelligence and less cognitive decline from age 11 to 68years. These results are consistent with other reports that FD measures of cortical structural complexity increase across the early life course during maturation of the cerebral cortex and add new data to support an association between FD and cognitive ageing.

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

    Institute of Scientific and Technical Information of China (English)

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


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

  5. Perspective: Explicitly correlated electronic structure theory for complex systems (United States)

    Grüneis, Andreas; Hirata, So; Ohnishi, Yu-ya; Ten-no, Seiichiro


    The explicitly correlated approach is one of the most important breakthroughs in ab initio electronic structure theory, providing arguably the most compact, accurate, and efficient ansatz for describing the correlated motion of electrons. Since Hylleraas first used an explicitly correlated wave function for the He atom in 1929, numerous attempts have been made to tackle the significant challenges involved in constructing practical explicitly correlated methods that are applicable to larger systems. These include identifying suitable mathematical forms of a correlated wave function and an efficient evaluation of many-electron integrals. R12 theory, which employs the resolution of the identity approximation, emerged in 1985, followed by the introduction of novel correlation factors and wave function ansätze, leading to the establishment of F12 theory in the 2000s. Rapid progress in recent years has significantly extended the application range of explicitly correlated theory, offering the potential of an accurate wave-function treatment of complex systems such as photosystems and semiconductors. This perspective surveys explicitly correlated electronic structure theory, with an emphasis on recent stochastic and deterministic approaches that hold significant promise for applications to large and complex systems including solids.

  6. On the dimension of complex responses in nonlinear structural vibrations (United States)

    Wiebe, R.; Spottswood, S. M.


    The ability to accurately model engineering systems under extreme dynamic loads would prove a major breakthrough in many aspects of aerospace, mechanical, and civil engineering. Extreme loads frequently induce both nonlinearities and coupling which increase the complexity of the response and the computational cost of finite element models. Dimension reduction has recently gained traction and promises the ability to distill dynamic responses down to a minimal dimension without sacrificing accuracy. In this context, the dimensionality of a response is related to the number of modes needed in a reduced order model to accurately simulate the response. Thus, an important step is characterizing the dimensionality of complex nonlinear responses of structures. In this work, the dimensionality of the nonlinear response of a post-buckled beam is investigated. Significant detail is dedicated to carefully introducing the experiment, the verification of a finite element model, and the dimensionality estimation algorithm as it is hoped that this system may help serve as a benchmark test case. It is shown that with minor modifications, the method of false nearest neighbors can quantitatively distinguish between the response dimension of various snap-through, non-snap-through, random, and deterministic loads. The state-space dimension of the nonlinear system in question increased from 2-to-10 as the system response moved from simple, low-level harmonic to chaotic snap-through. Beyond the problem studied herein, the techniques developed will serve as a prescriptive guide in developing fast and accurate dimensionally reduced models of nonlinear systems, and eventually as a tool for adaptive dimension-reduction in numerical modeling. The results are especially relevant in the aerospace industry for the design of thin structures such as beams, panels, and shells, which are all capable of spatio-temporally complex dynamic responses that are difficult and computationally expensive to

  7. Bipyrimidine ruthenium(II) arene complexes: structure, reactivity and cytotoxicity. (United States)

    Betanzos-Lara, Soledad; Novakova, Olga; Deeth, Robert J; Pizarro, Ana M; Clarkson, Guy J; Liskova, Barbora; Brabec, Viktor; Sadler, Peter J; Habtemariam, Abraha


    The synthesis and characterization of complexes [(η(6)-arene)Ru(N,N')X][PF(6)], where arene is para-cymene (p-cym), biphenyl (bip), ethyl benzoate (etb), hexamethylbenzene (hmb), indane (ind) or 1,2,3,4-tetrahydronaphthalene (thn), N,N' is 2,2'-bipyrimidine (bpm) and X is Cl, Br or I, are reported, including the X-ray crystal structures of [(η(6)-p-cym)Ru(bpm)I][PF(6)], [(η(6)-bip)Ru(bpm)Cl][PF(6)], [(η(6)-bip)Ru(bpm)I][PF(6)] and [(η(6)-etb)Ru(bpm)Cl][PF(6)]. Complexes in which N,N' is 1,10-phenanthroline (phen), 1,10-phenanthroline-5,6-dione or 4,7-diphenyl-1,10-phenanthroline (bathophen) were studied for comparison. The Ru(II) arene complexes undergo ligand-exchange reactions in aqueous solution at 310 K; their half-lives for hydrolysis range from 14 to 715 min. Density functional theory calculations on [(η(6)-p-cym)Ru(bpm)Cl][PF(6)], [(η(6)-p-cym)Ru(bpm)Br][PF(6)], [(η(6)-p-cym)Ru(bpm)I][PF(6)], [(η(6)-bip)Ru(bpm)Cl][PF(6)], [(η(6)-bip)Ru(bpm)Br][PF(6)] and [(η(6)-bip)Ru(bpm)I][PF(6)] suggest that aquation occurs via an associative pathway and that the reaction is thermodynamically favourable when the leaving ligand is I > Br ≈ Cl. pK (a)* values for the aqua adducts of the complexes range from 6.9 to 7.32. A binding preference for 9-ethylguanine (9-EtG) compared with 9-ethyladenine (9-EtA) was observed for [(η(6)-p-cym)Ru(bpm)Cl][PF(6)], [(η(6)-hmb)Ru(bpm)Cl](+), [(η(6)-ind)Ru(bpm)Cl](+), [(η(6)-thn)Ru(bpm)Cl](+), [(η(6)-p-cym)Ru(phen)Cl](+) and [(η(6)-p-cym)Ru(bathophen)Cl](+) in aqueous solution at 310 K. The X-ray crystal structure of the guanine complex [(η(6)-p-cym)Ru(bpm)(9-EtG-N7)][PF(6)](2) shows multiple hydrogen bonding. Density functional theory calculations show that the 9-EtG adducts of all complexes are thermodynamically preferred compared with those of 9-EtA. However, the bmp complexes are inactive towards A2780 human ovarian cancer cells. Calf thymus DNA interactions for [(η(6)-p-cym)Ru(bpm)Cl][PF(6)] and [(η(6)-p

  8. Structure of Rare-earth/Alkali Halide Complexes (United States)

    Akdeniz, Z.; Önem, Z. Çiçek; Tosia, M. P.


    Vapour complex formation of rare-earth halides with alkali halides strongly increases the volatility of these compounds. We evaluate the structure taken by such complexes having the chemical formulas MRX4, M2RX5 and M3RX6, where X = F or Cl and typically M = Li or Na and R = La. The roles played by the two types of metal atom is investigated in MRX4 complexes by also taking M = K, Rb or Cs and R = Gd or Lu. The main predictions that emerge from our calculations are as follows: (i) in MRX4 a fourfold coordination of the rare-earth atom is accompanied by twofold or threefold coordination of the alkali atom, the energy difference in favour of the twofold-coordination state being about 0.3 eV in the case of the LiF complexing agent but even changing sign as the ionic radius of either the alkali or the halogen is increased; (ii) in M2RX5 a fivefold coordination of the rare-earth atom is energetically more stable than a fourfold one, by again not more than about 0.3 eV; (iii) in M3RX6 the fivefold and sixfold coordinations of the rare-earth atom are energetically competitive; and (iv) in both M2RX5 and M3RX6 each coordination state can be realized in various forms that differ in detail but are close in energy. Bond fluctuations and disorder around the rare-earth atom can be expected to be a general feature at elevated temperatures, both in the vapour and in liquid rare-earth/alkali halide mixtures.

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

    Energy Technology Data Exchange (ETDEWEB)

    Rossmann, Michael G., E-mail: [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Arisaka, Fumio [Graduate School and School of Bioscience and Biotechnology, Tokyo Institute of Technology, 5249 Nagatsuta-cho, Yokohama 226-8501-B39 (Japan); Battisti, Anthony J.; Bowman, Valorie D.; Chipman, Paul R.; Fokine, Andrei; Hafenstein, Susan [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Kanamaru, Shuji [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Graduate School and School of Bioscience and Biotechnology, Tokyo Institute of Technology, 5249 Nagatsuta-cho, Yokohama 226-8501-B39 (Japan); Kostyuchenko, Victor A. [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Mesyanzhinov, Vadim V.; Shneider, Mikhail M. [Laboratory of Molecular Bioengineering, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya Street, Moscow, 117997 (Russian Federation); Morais, Marc C.; Leiman, Petr G. [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Palermo, Laura M.; Parrish, Colin R. [James A. Baker Institute, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853 (United States); Xiao, Chuan [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States)


    The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy single-particle reconstructions. This paper concerns itself with the study of the macromolecular complexes that constitute viruses, using structural hybrid techniques. The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy (cryo-EM) single-particle reconstructions. Both techniques lean heavily on imposing icosahedral symmetry, thereby obscuring any deviation from the assumed symmetry. However, tailed bacteriophages have icosahedral or prolate icosahedral heads that have one obvious unique vertex where the genome can enter for DNA packaging and exit when infecting a host cell. The presence of the tail allows cryo-EM reconstructions in which the special vertex is used to orient the head in a unique manner. Some very large dsDNA icosahedral viruses also develop special vertices thought to be required for infecting host cells. Similarly, preliminary cryo-EM data for the small ssDNA canine parvovirus complexed with receptor suggests that these viruses, previously considered to be accurately icosahedral, might have some asymmetric properties that generate one preferred receptor-binding site on the viral surface. Comparisons are made between rhinoviruses that bind receptor molecules uniformly to all 60 equivalent binding sites, canine parvovirus, which appears to have a preferred receptor-binding site, and bacteriophage T4, which gains major biological advantages on account of its unique vertex and tail organelle.

  10. Thermodynamic and structural insights into CSL-DNA complexes

    Energy Technology Data Exchange (ETDEWEB)

    Friedmann, David R.; Kovall, Rhett A. (UCIN-MED)


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

  11. Light transport and lasing in complex photonic structures (United States)

    Liew, Seng Fatt

    Complex photonic structures refer to composite optical materials with dielectric constant varying on length scales comparable to optical wavelengths. Light propagation in such heterogeneous composites is greatly different from homogeneous media due to scattering of light in all directions. Interference of these scattered light waves gives rise to many fascinating phenomena and it has been a fast growing research area, both for its fundamental physics and for its practical applications. In this thesis, we have investigated the optical properties of photonic structures with different degree of order, ranging from periodic to random. The first part of this thesis consists of numerical studies of the photonic band gap (PBG) effect in structures from 1D to 3D. From these studies, we have observed that PBG effect in a 1D photonic crystal is robust against uncorrelated disorder due to preservation of long-range positional order. However, in higher dimensions, the short-range positional order alone is sufficient to form PBGs in 2D and 3D photonic amorphous structures (PASS). We have identified several parameters including dielectric filling fraction and degree of order that can be tuned to create a broad isotropic PBG. The largest PBG is produced by the dielectric networks due to local uniformity in their dielectric constant distribution. In addition, we also show that deterministic aperiodic structures (DASs) such as the golden-angle spiral and topological defect structures can support a wide PBG and their optical resonances contain unexpected features compared to those in photonic crystals. Another growing research field based on complex photonic structures is the study of structural color in animals and plants. Previous studies have shown that non-iridescent color can be generated from PASs via single or double scatterings. For better understanding of the coloration mechanisms, we have measured the wavelength-dependent scattering length from the biomimetic samples. Our

  12. Improved designs of Si-based quantum wells and Schottky diodes for IR detection

    Energy Technology Data Exchange (ETDEWEB)

    Moeen, M., E-mail: [School of Information and Communication Technology, KTH Royal Institute of Technology, Stockholm, 16640, Kista (Sweden); Kolahdouz, M. [School of Electrical and Computer Engineering, University of Tehran, Tehran (Iran, Islamic Republic of); Salemi, A.; Abedin, A.; Östling, M. [School of Information and Communication Technology, KTH Royal Institute of Technology, Stockholm, 16640, Kista (Sweden); Radamson, H.H., E-mail: [School of Information and Communication Technology, KTH Royal Institute of Technology, Stockholm, 16640, Kista (Sweden)


    Novel structures of intrinsic or carbon-doped multi quantum wells (MQWs) and intrinsic or carbon-doped Si Schottky diodes (SD), individually or in combination, have been manufactured to detect the infrared (IR) radiation. The carbon concentration in the structures was 5 × 10{sup 20} cm{sup −3} and the MQWs are located in the active part of the IR detector. A Schottky diode was designed and formed as one of the contacts (based on NiSi(C)/TiW) to MQWs where on the other side the structure had an Ohmic contact. The thermal response of the detectors is expressed in terms of temperature coefficient of resistance (TCR) and the quality of the electrical signal is quantified by the signal-to-noise ratio. The noise measurements provide the K{sub 1/f} parameter which is obtained from the power spectrum density. An excellent value of TCR = − 6%/K and K{sub 1/f} = 4.7 × 10{sup −14} was measured for the detectors which consist of the MQWs in series with the SD. These outstanding electrical results indicate a good opportunity to manufacture low cost Si-based IR detectors in the near future. - Highlights: • SiGe (C)/Si(C) multi quantum wells (MQWs) are evaluated to detect IR radiation. • Schottky diodes (SDs), individually or in series with MQWs are also fabricated. • Detectors consisted of MQWs in series with SD show excellent thermal sensing. • The noise values are also extremely low for MQWs in series with SD.

  13. Structure of the Rangel alkaline complex (Salta, NW Argentina) (United States)

    Vegas, Nestor; Hongn, Fernando; María Tubía, José; Menegatti, Nilda; Aranguren, Aitor; Rodriguez-Méndez, Lidia


    The alcaline complex of the Sierra de Rangel is a Cretaceous granitoid emplaced in the Puna Region, at the province of Salta (NW Argentina). This granitoid spreads over 9 km2 and is elongated following a NE-SW trend. The Rangel complex intrudes Quaternary sediments of the Salinas Grandes salt flat towards the east and Ordovician quartzites and metapelites to the west. There are three main facies in the Rangel granitoid: the easternmost part of the intrusion is composed by sienites that crop out in three hills isolated into the salt flat; the central part of the stock made of alkaline granites and quartz-sienites; and the westernmost side composed by alkaline granites. The available rubidium-strontium ages point out two magmatic pulses: 134±1,6Ma for the granites and quartz-sienites and the sienites of the central and eastern part and 122±1,5 Ma for the alkaline granites of the western border. The most common structure in the host quartzites and metapelites is N55oE-trending schistosity that dips around 60o to the SE. This schistosity is parallel to the axial surface of asymmetric folds with axes plunging to the east. The sharp western contact of the Rangel complex with the host rocks display a N30oE strike and dips around 40o to the SE. This contact is parallel to the intra-magmatic contact between the western and central facies and to the NE-SW elongation of the granitoid. The study of the magnetic fabrics carried on 52 sites of the Rangel complex outline the presence of two sets of tabular intrusions: a main group of overlapping NE-trending sheets that dip to the SE; and a minor group roughly perpendicular to the previous one. The integration of the magnetic fabrics results and the structural data suggest that the former set of intrusions are feeder dykes of the NE-trending sheeted intrusions. Moreover, the radiometric data suggest that the oldest pulse corresponds to the upper part of the granitoid. This fact would imply that the emplacement was controlled by

  14. A Structural Algorithm for Complex Natural Languages Parse Generation

    Directory of Open Access Journals (Sweden)

    Enikuomehin, A. O.


    Full Text Available In artificial intelligence, the study of how humans understand natural languages is cognitive based and such science is essential in the development of a modern day embedded robotic systems. Such systems should have the capability to process natural languages and generate meaningful output. As against machines, humans have the ability to understand a natural language sentence due to the in-born facility inherent in them and such is used to process it. Robotics requires appropriate PARSE systems to be developed in order to handle language based operations. In this paper, we present a new method of generating parse structures on complex natural language using algorithmic processes. The paper explores the process of generating meaning via parse structure and improves on the existing results using well established parsing scheme. The resulting algorithm was implemented in Java and a natural language interface for parse generation is presented. The result further shows that tokenizing sentences into their respective units affects the parse structure in the first instance and semantic representation in the larger scale. Efforts were made to limit the rules used in the generation of the grammar since natural language rules are almost infinite depending on the language set. (Abstract

  15. Bootstrap Percolation on Complex Networks with Community Structure

    CERN Document Server

    Chong, Wu; Rui, Zhang; Liujun, Chen; Jiawei, Chen; Xiaobin, Li; Yanqing, Hu


    Real complex networks usually involve community structure. How innovation and new products spread on social networks which have internal structure is a practically interesting and fundamental question. In this paper we study the bootstrap percolation on a single network with community structure, in which we initiate the bootstrap process by activating different fraction of nodes in each community. A previously inactive node transfers to active one if it detects at least $k$ active neighbors. The fraction of active nodes in community $i$ in the final state $S_i$ and its giant component size $S_{gci}$ are theoretically obtained as functions of the initial fractions of active nodes $f_i$. We show that such functions undergo multiple discontinuous transitions; The discontinuous jump of $S_i$ or $S_{gci}$ in one community may trigger a simultaneous jump of that in the other, which leads to multiple discontinuous transitions for the total fraction of active nodes $S$ and its associated giant component size $S_{gc}$...

  16. The complex impact structure Serra da Cangalha, Tocantins State, Brazil (United States)

    Kenkmann, Thomas; Vasconcelos, Marcos A. R.; Crósta, Alvaro P.; Reimold, Wolf U.


    Serra da Cangalha is a complex impact structure with a crater diameter of 13,700 m and a central uplift diameter of 5800 m. New findings of shatter cones, planar fractures, feather features, and possible planar deformation features are presented. Several ring-like features that are visible on remote sensing imagery are caused by selective erosion of tilted strata. The target at Serra da Cangalha is composed of Devonian to Permian sedimentary rocks, mainly sandstones that are interlayered with siltstone and claystones. NNE-SSW and WNW-ESE-striking joint sets were present prior to the impact and also overprinted the structure after its formation. As preferred zones of weakness, these joint sets partly controlled the shape of the outer perimeter of the structure and, in particular, affected the deformation within the central uplift. Joints in radial orientation to the impact center did not undergo a change in orientation during tilting of strata when the central uplift was formed. These planes were used as major displacement zones. The asymmetry of the central uplift, with preferred overturning of strata in the northern to western sector, may suggest a moderately oblique impact from a southerly direction. Buckle folding of tilted strata, as well as strata overturning, indicates that the central uplift became gravitationally unstable at the end of crater formation.

  17. 75 FR 77047 - Statement on Sound Practices Concerning Elevated Risk Complex Structured Finance Activities (United States)


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

  18. Metal induced crystallized poly-Si-based conductive bridge resistive switching memory device with one transistor and one resistor architecture (United States)

    Chand, Umesh; Huang, Chun-Yang; Kumar, Dayanand; Tseng, Tseung-Yuen


    In this letter, the metal induced crystallization (MIC) process is used in the Si-based conductive bridging resistive random access memory (CBRAM) application. The amorphous Si (a-Si) is transformed to crystallized poly-silicon (poly-Si) at a low temperature by using Ni metal for inducing poly-Si to provide the resistive switching. The MIC process can produce a highly preferred orientation poly-Si film, which can create the exact paths or grain boundaries through the top and down electrodes in the present CBRAM device. The grain boundary in MIC poly-Si layer can confine the conductive filament of metal bridging growth in it, which can improve the switching fluctuation behavior in the nonvolatile memory application. Compared with the a-Si based device, a significant improvement in terms of resistive switching parameters such as stability and resistance distribution is demonstrated in the MIC poly-Si CBRAM device. Moreover, the well-behaved memory performance, such as high ON/OFF resistance ratio (4 order), a large AC endurance (106), and good retention characteristics (104 s at 125 °C) are achieved in the Cu/poly-Si/n+-Si CMOS compatible cross bar structure.

  19. Decentralization of Decision Authority in Complex Task Structures DRUID

    DEFF Research Database (Denmark)

    Dobrajska, Magdalena; Billinger, Stephan; Karim, Samina

    We investigate tradeoffs associated with delegating authority over multiple interrelated decisions in a complex task structure. The empirical setting is a business process of a global Fortune 50 firm. The firm decentralized its organization and redefined decision authority across organizational......-relevant knowledge, the matching of required knowledge and manager?s expertise, and information processing intensity affect (a) the occurrence of delegation, and (b), if delegation occurs, how far down the organizational hierarchy authority is delegated. We discuss how these findings complement existing theories...... hierarchies between 2008 and 2011. We employ regression analysis of micro-level data on the organization design of 761 decision tasks and we investigate the allocation of decision authority at the level of all observable individual decision tasks. Our findings show how the specialization of decision...

  20. Experimental Investigation on Complex Structures Machining by Electrochemical Micromachining Technology

    Institute of Scientific and Technical Information of China (English)

    Liu Yong; Zhu Di; Zeng Yongbin; Huang Shaofu; Yu Hongbing


    Electrochemical micromachining(EMM)technology for fabricating micro structures is presented in this article.By applying ultra short pulses,dissolution of a workpiece can be restricted to the region very close to the electrode.First,an EMM system for meeting the requirements of the EMM process is established.Second,sets of experiments is carried out to investigate the influence of some of the predominant electrochemical process parameters such as electrical parameters,feed rate,electrode geometry features and electrolyte composition on machining quality,especially the influences of pulse on time on shape precision and working end shape of electrode on machined surface quality.Finally,after the preliminary experiments,a complex microstructure with good shape precision and surface quality is successfully obtained.

  1. Structure, complexity and cooperation in parallel external chat interactions

    DEFF Research Database (Denmark)

    Grønning, Anette


    This article examines structure, complexity and cooperation in external chat interactions at the workplace in which one of the participants is taking part in multiple parallel conversations. The investigation is based on an analysis of nine chat interactions in a work-related context......, with particular focus on the content of the parallel time spans of the chat interactions. The analysis was inspired by applied conversation analysis (CA). The empirical material has been placed at my disposal by Kristelig Fagbevægelse (Krifa), which is Denmark’s third-largest trade union. The article’s overall...... and cannot see, hear, or touch one another, it is possible to detect an informal, pleasant tone in their interactions. This challenges the basically asymmetrical relationship between employee and customer, and one can sense a further level of asymmetry. In terms of medium, chat interactions exist via various...


    Directory of Open Access Journals (Sweden)

    A. A. Smirnova


    Full Text Available The article presents results of back pain syndrome screening in a population of children according to the poll of 600 students of classes 1–11. The spread of dorsalgiae is 19%. According to the examination, nosological and clinical structure of dorsalgiae was determined in 35 children of 3–18 years of age hospitalized due to back pain. Lumbalgia was revealed in 55 (52% patients; cervicalgia — in 31 (30% patients; thoracalgia — in 19 (18% patients. Juvenile osteochondrosis of lumbosacral spine is the cause of lumbosacral pain syndrome in most patients. The authors analyzed complex treatment efficacy and demonstrated that affective disorders are a prognostically significant factor of back pain onset. 

  3. Encoding techniques for complex information structures in connectionist systems (United States)

    Barnden, John; Srinivas, Kankanahalli


    Two general information encoding techniques called relative position encoding and pattern similarity association are presented. They are claimed to be a convenient basis for the connectionist implementation of complex, short term information processing of the sort needed in common sense reasoning, semantic/pragmatic interpretation of natural language utterances, and other types of high level cognitive processing. The relationships of the techniques to other connectionist information-structuring methods, and also to methods used in computers, are discussed in detail. The rich inter-relationships of these other connectionist and computer methods are also clarified. The particular, simple forms are discussed that the relative position encoding and pattern similarity association techniques take in the author's own connectionist system, called Conposit, in order to clarify some issues and to provide evidence that the techniques are indeed useful in practice.

  4. The complex planetary synchronization structure of the solar system

    CERN Document Server

    Scafetta, Nicola


    The complex planetary synchronization structure of the solar system, which since Pythagoras of Samos (ca. 570-495 BC) is known as the music of the spheres, is briefly reviewed from the Renaissance up to contemporary research. Copernicus' heliocentric model from 1543 suggested that the planets of our solar system form a kind of mutually ordered and quasi-synchronized system. From 1596 to 1619 Kepler formulated preliminary mathematical relations of approximate commensurabilities among the planets, which were later reformulated in the Titius-Bode rule (1766-1772) that successfully predicted the orbital position of Ceres and Uranus. Following the discovery of the ~11 yr sunspot cycle, in 1859 Wolf suggested that the observed solar variability could be approximately synchronized with the orbital movements of Venus, Earth, Jupiter and Saturn. Modern research have further confirmed that: (1) the planetary orbital periods can be approximately deduced from a simple system of resonant frequencies; (2) the solar system ...

  5. Biological pattern formation: from basic mechanisms to complex structures (United States)

    Koch, A. J.; Meinhardt, H.


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

  6. Hybrid Direct Write Lithographic Strategies for Complex Hierarchical Structures (United States)

    Singer, Jonathan P.

    With the number of alternative lithographic techniques for high resolution and 3D patterning rapidly increasing, there is a need to identify a set of scalable techniques which balances the ability to arbitrarily control every detail of a target pattern and to produce these complex patterns at a high rate. It is in this way that metamaterial devices put forward on a lab scale for applications such as phononics, photonics, and plasmonics can be realized in the industrial scale. This thesis, in approaching this challenge, utilizes combinations of patterning techniques, leveraging the ability for "large" scale alternative lithographic techniques, such as interference lithography or self-assembly, to create the same nanostructured morphology over a large area combined with laser direct write. The process of drawing a single line or isolated voxel can result in a hierarchical pattern defined by the latent motif of the larger-scale technique. The net resuh is to shift the burden of high resolution patterning from the direct write to the large scale technique, effectively decoupling the correlation between the level of detail and the patterning speed and control. More specifically, the following combinations with laser direct writing were investigated: (1) proximity field nanopatterning for the predefinition of diffraction-order-defined 3D resonators which were applied as "stand-up" plasmodic microresonators, (2) dewetting to conduct development-free 2D patterning of isolated sub-micron lines, and, via overlap effects, nanoscale ( <1 00 nm) gratings, (3) block copolymer self-assembly to initiate the simultaneous annealing and alignment of near-equilibrium microdomains from a metastable starting morphology, and (4) interference lithography to fabricate 3D sub-micron periodic and quasiperiodic hierarchical structures with controllable positioning and tunable fill fraction that has potential for applications to microphotonics. In conjunction with the experimental components

  7. Structure of the guide-strand-containing argonaute silencing complex

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yanli; Sheng, Gang; Juranek, Stefan; Tuschl, Thomas; Patel, Dinshaw J. (MSKCC); (HHMI)


    The slicer activity of the RNA-induced silencing complex is associated with argonaute, the RNase H-like PIWI domain of which catalyses guide-strand-mediated sequence-specific cleavage of target messenger RNA. Here we report on the crystal structure of Thermus thermophilus argonaute bound to a 5'-phosphorylated 21-base DNA guide strand, thereby identifying the nucleic-acid-binding channel positioned between the PAZ- and PIWI-containing lobes, as well as the pivot-like conformational changes associated with complex formation. The bound guide strand is anchored at both of its ends, with the solvent-exposed Watson-Crick edges of stacked bases 2 to 6 positioned for nucleation with the mRNA target, whereas two critically positioned arginines lock bases 10 and 11 at the cleavage site into an unanticipated orthogonal alignment. Biochemical studies indicate that key amino acid residues at the active site and those lining the 5'-phosphate-binding pocket made up of the Mid domain are critical for cleavage activity, whereas alterations of residues lining the 2-nucleotide 3'-end-binding pocket made up of the PAZ domain show little effect.

  8. Controlling congestion on complex networks: fairness, efficiency and network structure. (United States)

    Buzna, Ľuboš; Carvalho, Rui


    We consider two elementary (max-flow and uniform-flow) and two realistic (max-min fairness and proportional fairness) congestion control schemes, and analyse how the algorithms and network structure affect throughput, the fairness of flow allocation, and the location of bottleneck edges. The more realistic proportional fairness and max-min fairness algorithms have similar throughput, but path flow allocations are more unequal in scale-free than in random regular networks. Scale-free networks have lower throughput than their random regular counterparts in the uniform-flow algorithm, which is favoured in the complex networks literature. We show, however, that this relation is reversed on all other congestion control algorithms for a region of the parameter space given by the degree exponent γ and average degree 〈k〉. Moreover, the uniform-flow algorithm severely underestimates the network throughput of congested networks, and a rich phenomenology of path flow allocations is only present in the more realistic α-fair family of algorithms. Finally, we show that the number of paths passing through an edge characterises the location of a wide range of bottleneck edges in these algorithms. Such identification of bottlenecks could provide a bridge between the two fields of complex networks and congestion control.

  9. The solution structure of the copper clioquinol complex. (United States)

    Pushie, M Jake; Nienaber, Kurt H; Summers, Kelly L; Cotelesage, Julien J H; Ponomarenko, Olena; Nichol, Helen K; Pickering, Ingrid J; George, Graham N


    Clioquinol (5-chloro-7-iodo-8-hydroxyquinoline) recently has shown promising results in the treatment of Alzheimer's disease and in cancer therapy, both of which also are thought to be due to clioquinol's ability as a lipophilic copper chelator. Previously, clioquinol was used as an anti-fungal and anti-protozoal drug that was responsible for an epidemic of subacute myelo-optic neuropathy (SMON) in Japan during the 1960s, probably a myeloneuropathy arising from a clioquinol-induced copper deficiency. Previous X-ray absorption spectroscopy of solutions of copper chelates of clioquinol suggested unusual coordination chemistry. Here we use a combination of electron paramagnetic, UV-visible and X-ray absorption spectroscopies to provide clarification of the chelation chemistry between clioquinol and copper. We find that the solution structures for the copper complexes formed with stoichiometric and excess clioquinol are conventional 8-hydroxyquinolate chelates. Thus, the promise of clioquinol in new treatments for Alzheimer's disease and in cancer therapy is not likely to be due to any novel chelation chemistry, but rather due to other factors including the high lipophilicity of the free ligand and chelate complexes.

  10. Computational studies of physical properties of Nb-Si based alloys

    Energy Technology Data Exchange (ETDEWEB)

    Ouyang, Lizhi [Middle Tennessee State Univ., Murfreesboro, TN (United States)


    The overall goal is to provide physical properties data supplementing experiments for thermodynamic modeling and other simulations such as phase filed simulation for microstructure and continuum simulations for mechanical properties. These predictive computational modeling and simulations may yield insights that can be used to guide materials design, processing, and manufacture. Ultimately, they may lead to usable Nb-Si based alloy which could play an important role in current plight towards greener energy. The main objectives of the proposed projects are: (1) developing a first principles method based supercell approach for calculating thermodynamic and mechanic properties of ordered crystals and disordered lattices including solid solution; (2) application of the supercell approach to Nb-Si base alloy to compute physical properties data that can be used for thermodynamic modeling and other simulations to guide the optimal design of Nb-Si based alloy.

  11. Paradigms of Complexity: Fractals and Structures in the Sciences (United States)

    Novak, Miroslav M.

    The Table of Contents for the book is as follows: * Preface * The Origin of Complexity (invited talk) * On the Existence of Spatially Uniform Scaling Laws in the Climate System * Multispectral Backscattering: A Fractal-Structure Probe * Small-Angle Multiple Scattering on a Fractal System of Point Scatterers * Symmetric Fractals Generated by Cellular Automata * Bispectra and Phase Correlations for Chaotic Dynamical Systems * Self-Organized Criticality Models of Neural Development * Altered Fractal and Irregular Heart Rate Behavior in Sick Fetuses * Extract Multiple Scaling in Long-Term Heart Rate Variability * A Semi-Continous Box Counting Method for Fractal Dimension Measurement of Short Single Dimension Temporal Signals - Preliminary Study * A Fractional Brownian Motion Model of Cracking * Self-Affine Scaling Studies on Fractography * Coarsening of Fractal Interfaces * A Fractal Model of Ocean Surface Superdiffusion * Stochastic Subsurface Flow and Transport in Fractal Fractal Conductivity Fields * Rendering Through Iterated Function Systems * The σ-Hull - The Hull Where Fractals Live - Calculating a Hull Bounded by Log Spirals to Solve the Inverse IFS-Problem by the Detected Orbits * On the Multifractal Properties of Passively Convected Scalar Fields * New Statistical Textural Transforms for Non-Stationary Signals: Application to Generalized Mutlifractal Analysis * Laplacian Growth of Parallel Needles: Their Mullins-Sekerka Instability * Entropy Dynamics Associated with Self-Organization * Fractal Properties in Economics (invited talk) * Fractal Approach to the Regional Seismic Event Discrimination Problem * Fractal and Topological Complexity of Radioactive Contamination * Pattern Selection: Nonsingular Saffman-Taylor Finger and Its Dynamic Evolution with Zero Surface Tension * A Family of Complex Wavelets for the Characterization of Singularities * Stabilization of Chaotic Amplitude Fluctuations in Multimode, Intracavity-Doubled Solid-State Lasers * Chaotic

  12. Si-based integrated optical and photonic microstructures (United States)

    Leppihalme, Matti J.; Aalto, Timo T.; Katila, Pekka; Heimala, Paeivi; Blomberg, Martti; Tammela, Simo K. T.


    The design, fabrication and properties of various types of optical waveguides on silicon substrates as well as Fabry- Perot devices accomplished mainly at the Microelectronics Center of VTT Electronics are introduced. Different waveguides, directional couplers, multimode interference couplers, switches and power splitters have been studied. For waveguide fabrication on silicon substrates principally three materials were used depending on the application: silicon oxynitride, silicon on insulator (SOI). Silicon waveguides with large Si-core and a thermo-optical switch have been fabricated by SOI technology. Silicon Fabry-Perot structures have been fabricated for wavelength scanning applications in instrumentation and to measure chirp properties of lasers used in optical communications.

  13. Thermal properties of composite materials with a complex fractal structure (United States)

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


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

  14. Motif structure and cooperation in real-world complex networks (United States)

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


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

  15. Analysis and representation of complex structures in separated flows (United States)

    Helman, James; Hesselink, Lambertus


    We discuss our recent work on extraction and visualization of topological information in separated fluid flow data sets. As with scene analysis, an abstract representation of a large data set can greatly facilitate the understanding of complex, high-level structures. When studying flow topology, such a representation can be produced by locating and characterizing critical points in the velocity field and generating the associated stream surfaces. In 3D flows, the surface topology serves as the starting point. The 2D tangential velocity field near the surface of the body is examined for critical points. The tangential velocity field is integrated out along the principal directions of certain classes of critical points to produce curves depicting the topology of the flow near the body. The points and curves are linked to form a skeleton representing the 2D vector field topology. This skeleton provides a basis for analyzing the 3D structures associated with the flow separation. The points along the separation curves in the skeleton are used to start tangent curve integrations. Integration origins are successively refined to produce stream surfaces. The map of the global topology is completed by generating those stream surfaces associated with 3D critical points.

  16. Complex structure of spatially resolved high-order-harmonic spectra (United States)

    Catoire, F.; Ferré, A.; Hort, O.; Dubrouil, A.; Quintard, L.; Descamps, D.; Petit, S.; Burgy, F.; Mével, E.; Mairesse, Y.; Constant, E.


    We investigate the spatiospectral coupling appearing in the spatially resolved high-order-harmonic spectra generated in gases. When ionization is weak, harmonic generation in the far field often exhibits rings surrounding a central spot centered on each odd harmonics in the spatiospectral domain. The nature of these structures is debated. They could stem from interferences between the emission of short and long trajectories, or could be the signature of the temporal and spatial dependence of the longitudinal phase matching of long trajectories (Maker fringes). We conducted spectrally and spatially resolved measurements of the harmonic spectra as a function of pressure, intensity, and ellipticity. In addition, we performed calculations where only a single emission plane is included (i.e., omitting deliberately the longitudinal phase matching), reproducing the features experimentally observed. This study has been completed by the spatiospectral coupling when strong ionization occurs leading to complex patterns which have been compared to calculations using the same model and also show good agreement. We conclude that many spatiospectral structures of the harmonic spectrum can be interpreted in terms of spatial and temporal transverse coherence of the emitting medium without resorting to longitudinal phase matching or quantum phase interference between short and long trajectories.

  17. Synthesis and Crystal Structure of a New Mononuclear Copper Complex

    Institute of Scientific and Technical Information of China (English)


    A new kind of Cu (Ⅱ) complex [Cu(tpmb)2Cl2]@CH3OH@H2O (tpmb = 1,3,5-tri(2- pyrimidinyl)sulfanylmethyl-2,4,6-trimethylbenzene) was synthesized, and its structure has been determined by X-ray single-crystal diffraction. It crystallizes in the triclinic, space group P ī with a = 8.8397(2), b = 13.327(3), c = 13.926(3) (A), ( = 63.27(3), ( = 86.96(3), ( = 80.68(3)°, V = 1445.6(5) (A)3, C49H51Cl2CuN12O2S6, Mr = 1166.82, Z = 1, F(000) = 604, Dc = 1.340 g/cm3, μ = 0.735 mm-1, R = 0.0545 and wR = 0.1575 for 4521 observed reflections (I > 2σ(I)). X-ray analysis reveals that the Cu (Ⅱ) ion is coordinated by two Cl- anions and two nitrogen atoms from different pyrimidine groups, forming a square structure.

  18. Complex Model Structure - SAHG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us SAHG Complex Model Structure Data detail Data name Complex Model Structure DOI 10.18908/lsdb...a.nbdc01193-007 Description of data contents Predicted protein compex structure (PDB format). Data file File name: File URL: sequence was related to a given subunit of a template complex in PQS database with >=80% sequence ident...ity by the BLAST search and all the other subunits were related to any target sequences, the complex model w

  19. Influence of the Hydrophobicity of Polyelectrolytes on Polyelectrolyte Complex Formation and Complex Particle Structure and Shape

    Directory of Open Access Journals (Sweden)

    Gudrun Petzold


    Full Text Available Polyelectrolyte complexes (PECs were prepared by structural uniform and strongly charged cationic and anionic modified alternating maleic anhydride copolymers. The hydrophobicity of the polyelectrolytes was changed by the comonomers (ethylene, isobutylene and styrene. Additionally, the n−/n+ ratio of the molar charges of the polyelectrolytes and the procedure of formation were varied. The colloidal stability of the systems and the size, shape, and structure of the PEC particles were investigated by turbidimetry, dynamic light scattering (DLS and atomic force microscopy (AFM. Dynamic light scattering indicates that beside large PEC particle aggregates distinct smaller particles were formed by the copolymers which have the highest hydrophobicity (styrene. These findings could be proved by AFM. Fractal dimension (D, root mean square (RMS roughness and the surface profiles of the PEC particles adsorbed on mica allow the following conclusions: the higher the hydrophobicity of the polyelectrolytes, the broader is the particle size distribution and the minor is the swelling of the PEC particles. Hence, the most compact particles are formed with the very hydrophobic copolymer.

  20. Complex central structures suggest complex evolutionary paths for barred S0 galaxies

    CERN Document Server

    Dullo, Bililign T; Knapen, Johan H


    We investigate three barred lenticular galaxies (NGC 2681, NGC 3945 and NGC 4371) which were previously reported to have complex central structures but without a detailed structural analysis of these galaxies' high-resolution data. We have therefore performed four- to six-component (pseudo-)bulge/disk/bar/ring/point source) decompositions of the composite (Hubble Space Telescope plus ground-based) surface brightness profiles. We find that NGC 2681 hosts three bars, while NGC 3945 and NGC 4371 are double- and single-barred galaxies, respectively, in agreement with past isophotal analysis. We find that the bulges in these galaxies are compact, and have S\\'ersic indices of $n\\sim 2.2 - 3.6$ and stellar masses of $M_{*}$ $\\sim 0.28\\times10^{10} - 1.1\\times10^{10} M_{\\sun}$. NGC 3945 and NGC 4371 have intermediate-scale `pseudo-bulges' that are well described by a S\\'ersic model with low $n \\la 0.5$ instead of an exponential ($n=1$) profile as done in the past. We measure emission line fluxes enclosed within 9 dif...

  1. Syntheses, reactions, and structures of dioxycarbene complexes of rhenium

    Energy Technology Data Exchange (ETDEWEB)

    Miessler, G.L.; Kim, S.; Jacobson, R.A.; Angelici, R.J.


    The cyclic dioxycarbene complex Re(CO)4Br(COCH2CH2O) (I) reacts with PPh3 to give initially fac-Re(CO)3(PPh3)Br(COCH2CH2O) (II) and upon further reaction Re(CO)2(PPh3)2Br(COCH2CH2O) (II). The reaction of I with the diphosphines Ph2P(CH2)/sub n/PPh2 (n = 1,2) gives the diphosphine-bridged complexes (Re(CO)3Br(COCH2CH2O))2(Ph2P(CH2)/sub n/PPh2) (IV, n = 1; V, n = 2). The structures of I and V were established by X-ray diffraction studies. The crystals of I are orthorhombic, space group Pbca, with a = 11.764 (2) A, b = 17.579 (4) A, c = 10.658 (2) A, and Z = 8, while those of V are triclinic, space group P anti I, with a = 11.160 (2) A, b = 11.369 (3) A, c = 10.090 (3) A, = 111.58 (3), US = 95.40 (2), el = 92.78 (2), Z = 1, and two acetones ((CH3)2CO) of crystallization. The dimethyldithiocarbamate ion, S2CN(CH3)2, reacts with I to remove in effect ethylene oxide form the carbene ligand, giving Gr(CO)5Br and HOCH2CH2SC(=S)N(CH3)2.

  2. Enhanced seismic depth imaging of complex fault-fold structures (United States)

    Kirtland Grech, Maria Graziella

    Synthetic seismic data were acquired over numerical and physical models, representing fault-fold structures encountered in the Canadian Rocky Mountain Foothills, to investigate which migration algorithm produces the best image in such complex environments. Results showed that pre-stack depth migration from topography with the known velocity model yielded the optimum migrated image. Errors in the positioning of a target underneath a dipping antisotropic overburden were also studied using multicomponent data. The largest error was observed on P-wave data where anisotropy was highest at 18%. For an overburden thickness of 1500 m, the target was imaged 300 m updip from the true location. Field data from a two-dimensional surface seismic line and a multioffset vertical seismic profile (VSP) from the Foothills of southern Alberta, Canada, were processed using a flow designed to yield an optimum depth image. Traveltime inversion of the first arrivals from all the shots from the multioffset VSP revealed that the Mesozoic shale strata in the area exhibit seismic velocity anisotropy. The anisotropy parameters, ε and delta, were calculated to be 0.1 and 0.05 respectively. Anisotropic pre-stack depth migration code for VSP and surface seismic data, which uses a modified version of a raytracer developed in this thesis for the computation of traveltime tables, was also developed. The algorithm was then used in a new method for integrated VSP and surface seismic depth imaging. Results from the migration of synthetic and field data show that the resulting integrated image is superior to that obtained from the migration of either data set alone or to that obtained from the conventional "splicing" approach. The combination of borehole and surface seismic data for anisotropy analysis, velocity model building, and depth migration, yielded a robust image even when the geology was complex, thus permitting a more accurate interpretation of the exploration target.

  3. Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.; Campbell, Elizabeth A.


    The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the αCTD may play a role in Mtb transcription regulation. Our results reveal the structure of an Actinobacteria-unique insert of the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σA, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.

  4. Biomineralization: Some complex crystallite-oriented skeletal structures

    Indian Academy of Sciences (India)

    Ashok Sahni


    The present review focuses on some specific aspects of biomineralization with regard to the evolution of the first focused visioning systems in trilobites, the formation of molluscan shell architecture, dental enamel and its biomechanical properties and the structure of the calcified amniote egg, both fossil and recent. As an interdisciplinary field, biomineralization deals with the formation, structure and mechanical strength of mineralized skeletonized tissue secreted by organisms. Mineral matter formed in this way occurs in all three domains of life and consists of several mineral varieties, of which carbonates, phosphates and opaline silica are the most common. Animals and plants need mechanical support to counteract gravitational forces on land and hydrostatic pressure in the deep ocean, which is provided by a skeletonized framework. Skeleton architecture mainly consists of basic elements represented by small usually micrometer- to nanometer-sized crystallites of calcite and aragonite for carbonate systems and apatite crystallites for phosphatic ones, and then these building blocks develop into structured more complex frameworks. As selective pressures work towards optimizing stress and response, the orientation, morphology and structural arrangement of the crystallites indicates the distribution of the stress field of the biomineralized tissue. Large animals such as the dinosaurs have to deal with large gravitational forces, but in much smaller skeletonized organism such as the coccoliths, a few micrometer in diameter made up of even smaller individual crystallites, van der Waals forces play an increasingly important role and are at present poorly understood. Skeleton formation is dependent upon many factors including ambient water chemistry, temperature and environment. Ocean chemistry has played a vital role in the origins of skeletonization, 500 to 600 million years (ma) ago with the dominance of calcium carbonate as the principal skeleton-forming tissue

  5. Structural characterization of core-bradavidin in complex with biotin (United States)

    Agrawal, Nitin; Määttä, Juha A. E.; Kulomaa, Markku S.; Hytönen, Vesa P.; Johnson, Mark S.; Airenne, Tomi T.


    Bradavidin is a tetrameric biotin-binding protein similar to chicken avidin and bacterial streptavidin, and was originally cloned from the nitrogen-fixing bacteria Bradyrhizobium diazoefficiens. We have previously reported the crystal structure of the full-length, wild-type (wt) bradavidin with 138 amino acids, where the C-terminal residues Gly129-Lys138 (“Brad-tag”) act as an intrinsic ligand (i.e. Gly129-Lys138 bind into the biotin-binding site of an adjacent subunit within the same tetramer) and has potential as an affinity tag for biotechnological purposes. Here, the X-ray structure of core-bradavidin lacking the C-terminal residues Gly114-Lys138, and hence missing the Brad-tag, was crystallized in complex with biotin at 1.60 Å resolution [PDB:4BBO]. We also report a homology model of rhodavidin, an avidin-like protein from Rhodopseudomonas palustris, and of an avidin-like protein from Bradyrhizobium sp. Ai1a-2, both of which have the Brad-tag sequence at their C-terminus. Moreover, core-bradavidin V1, an engineered variant of the original core-bradavidin, was also expressed at high levels in E. coli, as well as a double mutant (Cys39Ala and Cys69Ala) of core-bradavidin (CC mutant). Our data help us to further engineer the core-bradavidin–Brad-tag pair for biotechnological assays and chemical biology applications, and provide deeper insight into the biotin-binding mode of bradavidin. PMID:28426764

  6. Structural reorganization of the interleukin-7 signaling complex

    Energy Technology Data Exchange (ETDEWEB)

    McElroy, Craig A.; Holland, Paul J.; Zhao, Peng; Lim, Jae-Min; Wells, Lance; Eisenstein, Edward; Walsh, Scott T.R. (Maryland); (Battelle); (Georgia)


    We report here an unliganded receptor structure in the common gamma-chain ({gamma}{sub c}) family of receptors and cytokines. The crystal structure of the unliganded form of the interleukin-7 alpha receptor (IL-7R{alpha}) extracellular domain (ECD) at 2.15 {angstrom} resolution reveals a homodimer forming an 'X' geometry looking down onto the cell surface with the C termini of the two chains separated by 110 {angstrom} and the dimer interface comprising residues critical for IL-7 binding. Further biophysical studies indicate a weak association of the IL-7R{alpha} ECDs but a stronger association between the {gamma}{sub c}/IL-7R{alpha} ECDs, similar to previous studies of the full-length receptors on CD4{sup +} T cells. Based on these and previous results, we propose a molecular mechanism detailing the progression from the inactive IL-7R{alpha} homodimer and IL-7R{alpha}-{gamma}{sub c} heterodimer to the active IL-7-IL-7R{alpha}-{gamma}{sub c} ternary complex whereby the two receptors undergo at least a 90{sup o} rotation away from the cell surface, moving the C termini of IL-7R{alpha} and {gamma}{sub c} from a distance of 110 {angstrom} to less than 30 {angstrom} at the cell surface. This molecular mechanism can be used to explain recently discovered IL-7- and {gamma}{sub c}-independent gain-of-function mutations in IL-7R{alpha} from B- and T-cell acute lymphoblastic leukemia patients. The mechanism may also be applicable to other {gamma}{sub c} receptors that form inactive homodimers and heterodimers independent of their cytokines.

  7. Reactions of alkyl malonates with molybdenum and tungsten complexes. Syntheses and structure of hydrido-malonato complexes

    Energy Technology Data Exchange (ETDEWEB)

    Minato, Makoto; Kurishima, Susumu; Nagai, Ko-ichiro; Ito, Takashi [Yokohama National Univ. (Japan). Faculty of Engineering; Yamasaki, Mikio


    Molybdenum and tungsten hydrido-malonato complexes have been prepared by the photochemical or thermal reactions of [MoH{sub 4}(dppe){sub 2}] or trans-[W(N{sub 2}){sub 2}(dppe){sub 2}] with an excess of alkyl malonates. The structure of the complex is reported, and a possible mechanism is proposed for the reaction. (author).

  8. Structure, complexity and cooperation in parallel external chat interactions

    Directory of Open Access Journals (Sweden)

    Anette Grønning


    Full Text Available This article examines structure, complexity and cooperation in external chat interactions at the workplace in which one of the participants is taking part in multiple parallel conversations. The investigation is based on an analysis of nine chat interactions in a work-related context, with particular focus on the content of the parallel time spans of the chat interactions. The analysis was inspired by applied conversation analysis (CA. The empirical material has been placed at my disposal by Kristelig Fagbevægelse (Krifa, which is Denmark’s third-largest trade union. The article’s overall focus is on “turn-taking organisation as the fundamental and generic aspect of interaction organisation” (Drew & Heritage, 1992, p. 25, including the use of turn-taking rules, adjacency pairs, and the importance of pauses. Even though the employee and the union members do not know one another and cannot see, hear, or touch one another, it is possible to detect an informal, pleasant tone in their interactions. This challenges the basically asymmetrical relationship between employee and customer, and one can sense a further level of asymmetry. In terms of medium, chat interactions exist via various references to other media, including telephone calls and e-mails.

  9. Microstructure-based modelling of multiphase materials and complex structures (United States)

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


    Micromechanical approaches are frequently employed to monitor local and global field quantities and their evolution under varying mechanical and/or thermal loading scenarios. In this contribution, an overview on important methods is given that are currently used to gain insight into the deformational and failure behaviour of multiphase materials and complex structures. First, techniques to represent material microstructures are reviewed. It is common to either digitise images of real microstructures or generate virtual 2D or 3D microstructures using automated procedures (e.g. Voronoï tessellation) for grain generation and colouring algorithms for phase assignment. While the former method allows to capture exactly all features of the microstructure at hand with respect to its morphological and topological features, the latter method opens up the possibility for parametric studies with respect to the influence of individual microstructure features on the local and global stress and strain response. Several applications of these approaches are presented, comprising low and high strain behaviour of multiphase steels, failure and fracture behaviour of multiphase materials and the evolution of surface roughening of the aluminium top metallisation of semiconductor devices.

  10. Structural controllability of complex networks based on preferential matching. (United States)

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


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

  11. Collisional family structure within the Nysa-Polana complex

    CERN Document Server

    Dykhuis, Melissa


    The Nysa-Polana complex is a group of low-inclination asteroid families in the inner main belt, bounded in semimajor axis by the Mars-crossing region and the Jupiter 3:1 mean-motion resonance. This group is important as the most likely source region for the target of the OSIRIS-REx mission, (101955) Bennu; however, family membership in the region is complicated by the presence of several dynamically overlapping families with a range of surface properties. The large S-type structure in the region appears to be associated with the parent body (135) Hertha, and displays an ($e_\\text{P},a_\\text{P}$) correlation consistent with a collision event near true anomaly of ~180 degrees with ejecta velocity $v_\\text{ej} \\sim 285$ m/s. The ejecta distribution from a collision with these orbital properties is predicted to have a maximum semimajor axis dispersion of $\\delta a_{ej} = 0.005 \\pm 0.008$ AU, which constitutes only a small fraction (7\\%) of the observed semimajor axis dispersion, the rest of which is attributed to...

  12. Unsaturated platinum-rhenium cluster complexes. Synthesis, structures and reactivity. (United States)

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


    Two new compounds PtRe3(CO)12(PBut3)(micro-H)3, 9, and PtRe2(CO)9(PBut3)(micro-H)2, 10, were obtained from the reaction of Pt(PBut3)2 with Re3(CO)12(micro-H3), 8, at room temperature. Compound 9 contains a butterfly cluster of four metals formed by the insertion of the platinum atom from a Pt(PBut3) group into one of the hydride-bridged metal-metal bonds of 8. The three hydrido ligands are bridging ligands across each of three new Pt-Re bonds. Compound 10 contains a triangular PtRe2 cluster with two hydrido ligands; one bridges a Pt-Re bond, and the other bridges the Re-Re bond. The new compound Pt2Re2(CO)7(PBut3)2(micro-H)2, 11, was obtained from the reaction of 8 with Pt(PBut3)2 in hexane at reflux. Compound 11 was also obtained from 10 by reaction with an additional quantity of Pt(PBut3)2. Compound 11 contains a tetrahedral cluster of four metal atoms with two dynamically active hydrido ligands. A CO ligand on one of the two platinum atoms also exchanges between the two platinum atoms rapidly on the NMR time scale. Compound 11 is electronically unsaturated and was found to add hydrogen at room temperature to form the tetrahydrido cluster complex, Pt2Re2(CO)7(PBut3)2(micro-H)4, 12. Compound 12 has a structure similar to 11 but contains one triply bridging hydrido ligand, two edge bridging hydrido ligands, and one terminal hydrido ligand on one of the two platinum atoms. A kinetic isotope effect D/H of 1.5(1) was determined for the addition of H2 to 11. Hydrogen can be eliminated from 12 by heating to 97 degrees C or by the application of UV-vis irradiation at room temperature. Compound 12 adds CO at room temperature to yield the complex Pt2Re2(CO)8(PBut3)2(micro-H)4, 13, which contains a planar cluster of four metal atoms with a Pt-Pt bond and four edge bridging hydrido ligands. Compounds 11 and 12 react with Pt(PBut3)2 to yield the known five metal cluster complexes Pt3Re2(CO)6(PBut3)3(micro-H)2, 14, and Pt3Re2(CO)6(PBut3)3(micro-H)4, 15, respectively. Density

  13. Large recovery strain in Fe-Mn-Si-based shape memory steels obtained by engineering annealing twin boundaries. (United States)

    Wen, Y H; Peng, H B; Raabe, D; Gutierrez-Urrutia, I; Chen, J; Du, Y Y


    Shape memory alloys are a unique class of materials that can recover their original shape upon heating after a large deformation. Ti-Ni alloys with a large recovery strain are expensive, while low-cost conventional processed Fe-Mn-Si-based steels suffer from a low recovery strain (twin boundaries. Reducing the density of twin boundaries is thus a critical factor for obtaining a large recovery strain in these steels. By significantly suppressing the formation of twin boundaries, we attain a tensile recovery strain of 7.6% in an annealed cast polycrystalline Fe-20.2Mn-5.6Si-8.9Cr-5.0Ni steel (weight%). Further attractiveness of this material lies in its low-cost alloying components and simple synthesis-processing cycle consisting only of casting plus annealing. This enables these steels to be used at a large scale as structural materials with advanced functional properties.

  14. Evaluation of structural and functional properties of chitosan-chlorogenic acid complexes. (United States)

    Wei, Zihao; Gao, Yanxiang


    The objectives of the present study were to first synthesize chitosan-chlorogenic acid (CA) covalent complex and then compare structural and functional properties between chitosan-CA covalent complex and physical complex. First, chitosan-CA covalent complex was synthesized and its total phenolic content was as high as 276.5 ± 6.2 mg/g. Then structural and functional properties of chitosan-CA covalent and physical complexes were analyzed. The covalent reaction induced formation of both amide and ester bonds in chitosan. Data of X-ray diffraction (XRD) and scanning electron microscopy (SEM) indicated that the complexations of CA changed crystallinity and morphology of chitosan, and covalent complexation induced a larger change of physical structure than physical complexation. In terms of functional properties, chitosan-CA covalent complex exhibited better thermal stability than physical complex in terms of antioxidant activity, and the viscosity of chitosan was significantly increased by covalent modification.

  15. The Liaonan Metamorphic Core Complex: Constitution, Structure and Evolution

    Institute of Scientific and Technical Information of China (English)

    LIU Junlai; GUAN Huimei; JI Mo; CAO Shuyun; HU Ling


    The Liaonan metamorphic core complex (mcc) has a three-layer structure and is constituted by five parts, i.e. a detachment fault zone, an allochthonous upper plate and an supradetachment basin above the fault zone, and highly metamorphosed rocks and intrusive rocks in the lower plate. The allochthonous upper plate is mainly of Neoproterozoic and Paleozoic rocks weakly deformed and metamorphosed in pre-Indosinan stage. Above these rocks is a small-scale supradetachment basin of Cretaceous sedimentary and volcanic rocks. The lower plate is dominated by Archean TTG gneisses with minor amount of supracrustal rocks. The Archean rocks are intruded by late Mesozoic synkinematic monzogranitic and granitic plutons. Different types of fault rocks, providing clues to the evolution of the detachment fault zone, are well-preserved in the fault zone, e.g. mylonitic gneiss,mylonites, brecciated mylonites, microbreccias and pseudotachylites. Lineations in lower plate granitic intrusions have consistent orientation that indicate uniform top-to-NW shearing along the main detachment fault zone. This also provides evidence for the synkinematic characteristics of the granitic plutons in the lower plate. Structural analysis of the different parts in the mcc and isotopic dating of plutonic rocks from the lower plate and mylonitic rocks from detachment fault zone suggest that exhumation of the mcc started with regional crustal extension due to crustal block rotation and tangential shearing. The extension triggered magma formation, upwelling and emplacement. This event ended with appearance of pseudotachylite and fault gauges formed at the uppermost crustal level.U-Pb dating of single zircon grains from granitic rocks in the lower plate gives an age of 130±5 Ma, and biotite grains from the main detachment fault zone have 40Ar-39Ar ages of 108-119 Ma. Several aspects may provide constraints for the exhumation of the Liaonan mcc. These include regional extensional setting, cover

  16. Synthesis and structural characterization of pyrazole and pyrazole niobocene complexes

    Energy Technology Data Exchange (ETDEWEB)

    Carrillo-Hermosilla, F.; Jalon, F.A.; Otero, A.; Villasenor, E. [Departamento de Quimica Inorganica. Organica y Bioquimica, Facultad de Quimicas. Universidad de Castilla-La Mancha (Spain)


    The first pyrazolyl niobocene complexes were prepared by reacting the trihydride complex Nb/eta``5-C{sub 5}H{sub 4}(SiMe{sub 3}){sub 2}H{sub 3} with pyrazole. 3-methyl pyrazole and tetrafluoroborate salt of protonated bis (pyrazole-1-il)methane. (Author) 20 refs.

  17. Complex interfaces in food: Structure and mechanical properties

    NARCIS (Netherlands)

    Sagis, L.M.C.; Scholten, E.


    Multiphase food systems (emulsions, foam) often have interfaces with a complex microstructure, formed by interfacial self-assembly of proteins, lipids, or colloidal particles. The response of these interfaces to deformations tends to be highly nonlinear and far more complex than the response of inte

  18. The structure and singularities of quotient arc complexes

    DEFF Research Database (Denmark)

    Penner, Robert


    A well-known combinatorial fact is that the simplicial complex consisting of disjointly embedded chords in a convex planar polygon is a sphere. For any surface F with non-empty boundary, there is an analogous complex QA(F) consisting of equivalence classes of arcs in F connecting a given finite s...

  19. A holistic molecular docking approach for predicting protein-protein complex structure

    Institute of Scientific and Technical Information of China (English)


    A holistic protein-protein molecular docking approach,HoDock,was established,composed of such steps as binding site prediction,initial complex structure sampling,refined complex structure sampling,structure clustering,scoring and final structure selection.This article explains the detailed steps and applications for CAPRI Target 39.The CAPRI result showed that three predicted binding site residues,A191HIS,B512ARG and B531ARG,were correct,and there were five submitted structures with a high fraction of correct receptor-ligand interface residues,indicating that this docking approach may improve prediction accuracy for protein-protein complex structures.

  20. Architectural DNA: A genetic exploration of complex structures

    NARCIS (Netherlands)

    Van Embden Andres, M.V.; Turrin, M.; Von Buelow, P.


    The approach demonstrated in this paper uses Evolutionary Computation (EC) to enhance and modify structural form based on biological micro structures.The forms are modified to conform to new boundary conditions associated with architectural structures.The process is based on a Genetic Algorithm (GA)

  1. Architectural DNA: A genetic exploration of complex structures

    NARCIS (Netherlands)

    Van Embden Andres, M.V.; Turrin, M.; Von Buelow, P.


    The approach demonstrated in this paper uses Evolutionary Computation (EC) to enhance and modify structural form based on biological micro structures.The forms are modified to conform to new boundary conditions associated with architectural structures.The process is based on a Genetic Algorithm (GA)

  2. A unified perspective of complex band structure: interpretations, formulations, and applications (United States)

    Reuter, Matthew G.


    Complex band structure generalizes conventional band structure by also considering wavevectors with complex components. In this way, complex band structure describes both the bulk-propagating states from conventional band structure and the evanescent states that grow or decay from one unit cell to the next. Even though these latter states are excluded by translational symmetry, they become important when translational symmetry is broken via, for example, a surface or impurity. Many studies over the last 80 years have directly or indirectly developed complex band structure for an impressive range of applications, but very few discuss its fundamentals or compare its various results. In this work we build upon these previous efforts to expose the physical foundation of complex band structure, which mathematically implies its existence. We find that a material’s static and dynamic electronic structure are both completely described by complex band structure. Furthermore, we show that complex band structure reflects the minimal, intrinsic information contained in the material’s Hamiltonian. These realizations then provide a context for comparing and unifying the different formulations and applications of complex band structure that have been reported over the years. Ultimately, this discussion introduces the idea of examining the amount of information contained in a material’s Hamiltonian so that we can find and exploit the minimal information necessary for understanding a material’s properties.

  3. Research on design and firing performance of Si-based detonator

    Institute of Scientific and Technical Information of China (English)

    Rui-zhen XIE; Xiao-ming REN; Lan LIU; Yan XUE; Dong-xiao FU; Rui ZHANG


    For the chip integration of MEMS (micro-electromechanical system) safety and arming device, a miniature detonator needs to be developed to reduce the weight and volume of explosive train. A Si-based micro-detonator is designed and fabricated, which meets the requirement of MEMS safety and arming device. The firing sensitivity of micro-detonator is tested according to GJB/z377A-94 sensitivity test methods:Langlie. The function time of micro-detonator is measured using wire probe and photoelectric transducer. The result shows the average firing voltage is 6.4 V when the discharge capacitance of firing electro-circuit is 33 mF. And the average function time is 5.48 ms. The firing energy actually utilized by Si-based micro-detonator is explored.

  4. Structural investigation of amylose complexes with small ligands: helical conformation, crystalline structure and thermostability. (United States)

    Le Bail, P; Rondeau, C; Buléon, A


    Crystalline amylose complexes were prepared with decanal, 1-butanol, menthone and alpha-naphtol. Their crystalline structure and the related helical conformation, determined by wide angle X-ray diffraction (WAXD) and 13C CPMAS solid state NMR, were assigned to V6I, V6II, V6III and V8 types, respectively. It was possible to propose some hypotheses on the possible nature of interactions and especially intra-/inter-helical inclusion. Some shifts in the NMR C1 carbon signals were attributed to the presence of ligand in specific sites inside the structure for a same type of V6 helical conformation. Moreover, the crystallinity and polymorphic changes induced by desorption/rehydration were studied. A general increase of the carbon resonances sharpness upon rehydration has been observed, but also a V6II-V6I transition when decreasing the water content. Differential scanning calorimetry (DSC) experiments were also performed to approach the thermostability of the four types of complex and also the way they form again after melting/cooling sequences.

  5. Structural analysis of the human SYCE2-TEX12 complex provides molecular insights into synaptonemal complex assembly. (United States)

    Davies, Owen R; Maman, Joseph D; Pellegrini, Luca


    The successful completion of meiosis is essential for all sexually reproducing organisms. The synaptonemal complex (SC) is a large proteinaceous structure that holds together homologous chromosomes during meiosis, providing the structural framework for meiotic recombination and crossover formation. Errors in SC formation are associated with infertility, recurrent miscarriage and aneuploidy. The current lack of molecular information about the dynamic process of SC assembly severely restricts our understanding of its function in meiosis. Here, we provide the first biochemical and structural analysis of an SC protein component and propose a structural basis for its function in SC assembly. We show that human SC proteins SYCE2 and TEX12 form a highly stable, constitutive complex, and define the regions responsible for their homotypic and heterotypic interactions. Biophysical analysis reveals that the SYCE2-TEX12 complex is an equimolar hetero-octamer, formed from the association of an SYCE2 tetramer and two TEX12 dimers. Electron microscopy shows that biochemically reconstituted SYCE2-TEX12 complexes assemble spontaneously into filamentous structures that resemble the known physical features of the SC central element (CE). Our findings can be combined with existing biological data in a model of chromosome synapsis driven by growth of SYCE2-TEX12 higher-order structures within the CE of the SC.

  6. High efficiency thin film CdTe and a-Si based solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Compaan, A. D.; Deng, X.; Bohn, R. G.


    This report describes work done by the University of Toledo during the first year of this subcontract. During this time, the CdTe group constructed a second dual magnetron sputter deposition facility; optimized reactive sputtering for ZnTe:N films to achieve 10 ohm-cm resistivity and {approximately}9% efficiency cells with a copper-free ZnTe:N/Ni contact; identified Cu-related photoluminescence features and studied their correlation with cell performance including their dependence on temperature and E-fields; studied band-tail absorption in CdS{sub x}Te{sub 1{minus}x} films at 10 K and 300 K; collaborated with the National CdTe PV Team on (1) studies of high-resistivity tin oxide (HRT) layers from ITN Energy Systems, (2) fabrication of cells on the HRT layers with 0, 300, and 800-nm CdS, and (3) preparation of ZnTe:N-based contacts on First Solar materials for stress testing; and collaborated with Brooklyn College for ellipsometry studies of CdS{sub x}Te{sub 1{minus}x} alloy films, and with the University of Buffalo/Brookhaven NSLS for synchrotron X-ray fluorescence studies of interdiffusion in CdS/CdTe bilayers. The a-Si group established a baseline for fabricating a-Si-based solar cells with single, tandem, and triple-junction structures; fabricated a-Si/a-SiGe/a-SiGe triple-junction solar cells with an initial efficiency of 9.7% during the second quarter, and 10.6% during the fourth quarter (after 1166 hours of light-soaking under 1-sun light intensity at 50 C, the 10.6% solar cells stabilized at about 9%); fabricated wide-bandgap a-Si top cells, the highest Voc achieved for the single-junction top cell was 1.02 V, and top cells with high FF (up to 74%) were fabricated routinely; fabricated high-quality narrow-bandgap a-SiGe solar cells with 8.3% efficiency; found that bandgap-graded buffer layers improve the performance (Voc and FF) of the narrow-bandgap a-SiGe bottom cells; and found that a small amount of oxygen partial pressure ({approximately}2 {times} 10

  7. Structure of ristocetin A in complex with a bacterial cell-wall mimetic


    Nahoum, Virginie; Spector, Sherri; Loll, Patrick J.


    The crystal structure of the complex between ristocetin A and the cell-wall peptide mimetic N-acetyl-lysine-d-alanine-d-alanine has been solved. Structural details explaining the anticooperativity of the antibiotic have been identified.

  8. Structure of the Tuberous Sclerosis Complex 2 (TSC2) N Terminus Provides Insight into Complex Assembly and Tuberous Sclerosis Pathogenesis. (United States)

    Zech, Reinhard; Kiontke, Stephan; Mueller, Uwe; Oeckinghaus, Andrea; Kümmel, Daniel


    Tuberous sclerosis complex (TSC) is caused by mutations in the TSC1 and TSC2 tumor suppressor genes. The gene products hamartin and tuberin form the TSC complex that acts as GTPase-activating protein for Rheb and negatively regulates the mammalian target of rapamycin complex 1 (mTORC1). Tuberin contains a RapGAP homology domain responsible for inactivation of Rheb, but functions of other protein domains remain elusive. Here we show that the TSC2 N terminus interacts with the TSC1 C terminus to mediate complex formation. The structure of the TSC2 N-terminal domain from Chaetomium thermophilum and a homology model of the human tuberin N terminus are presented. We characterize the molecular requirements for TSC1-TSC2 interactions and analyze pathological point mutations in tuberin. Many mutations are structural and produce improperly folded protein, explaining their effect in pathology, but we identify one point mutant that abrogates complex formation without affecting protein structure. We provide the first structural information on TSC2/tuberin with novel insight into the molecular function.

  9. Complexing ability of (-)-cytisine--synthesis, spectroscopy and crystal structures of the new copper and zinc complexes. (United States)

    Przybył, Anna K; Kubicki, Maciej; Jastrzab, Renata


    For the first time the NMR spectra of quinolizidine alkaloid with Cu(II) are studied. Structures of new complexes of (-)-cytisine with Cu(+2) and Zn(+2) cations are visualized, discussed in detail and characterized by spectroscopic methods: ESI-MS, NMR, UV-vis, EPR and crystallographic methods. In solution metal coordinates through the protonated nitrogen atoms of secondary amino groups (in piperidine ring) of cytisine molecule. While in solid state the most stable structures of the complexes are those in which the coordination of Cu(II) and Zn(II) salts is realized solely through the lactam carbonyl oxygen atom.

  10. Epidemic spreading on complex networks with community structures

    CERN Document Server

    Stegehuis, Clara; van Leeuwaarden, Johan S H


    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 \\textit{enforce} as well as \\textit{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.

  11. Structural simplicity and complexity of compressed calcium: electronic origin. (United States)

    Degtyareva, Valentina F


    A simple cubic structure with one atom in the unit cell found in compressed calcium is counterintuitive to the traditional view of a tendency towards densely packed structures with an increase in pressure. To understand this unusual transformation it is necessary to assume electron transfer from the outer core band to the valence band, and an increase of valence electron number for calcium from 2 to ∼ 3.5. This assumption is supported by the Fermi sphere-Brillouin zone interaction model that increases under compression. The recently found structure of Ca-VII with a tetragonal cell containing 32 atoms (tI32) is similar to that in the intermetallic compound In5Bi3 with 3.75 valence electrons per atom. Structural relations are analyzed in terms of electronic structure resemblance. Correlations of structure and physical properties of Ca are discussed.

  12. Ring and Volcano Structures Formed by a Metal Dipyrromethene Complex

    Energy Technology Data Exchange (ETDEWEB)

    Son, Seung Bae; Hahn, Jae Ryang [Chonbuk National Univ., Jeonju (Korea, Republic of); Miao, Qing; Shin, Jiyoung; Dolphin, David [Univ. of British Columbia, Columbia (Canada)


    Dichloromethane liquid droplets containing a cobalt dipyrromethene trimer deposited on a graphite surface were found to form coffee ring, toroid ring, or volcano dot structures due to the redistribution of the solute during solvent evaporation. The shapes and size distributions of the ring structures depended on the drying temperature. The shape differences were attributed to the fact that the solvent evaporation rate controlled the self-assembly process that yielded the coffee stain and pinhole structures.

  13. Structure and thermal expansion of NbC complex carbides

    Energy Technology Data Exchange (ETDEWEB)

    Khatsinskaya, I.M.; Chaporova, I.N.; Cheburaeva, R.F.; Samojlov, A.I.; Logunov, A.V.; Ignatova, I.A.; Dodonova, L.P.


    Alloying dependences of the crystal lattice parameters at indoor temperature and coefficient of thermal linear expansion within a 373-1273 K range are determined for complex NbC-base carbides by the method of mathematical experimental design. It is shown that temperature changes in the linear expansion coefficient of certain complex carbides as distinct from NbC have an anomaly (minimum) within 773-973 K caused by occurring reversible phase transformations. An increase in the coefficient of thermal linear expansion and a decrease in hardness of NbC-base tungsten-, molybdenum-, vanadium- and hafnium-alloyed carbides show a weakening of a total chemical bond in the complex carbides during alloying.

  14. Predictive Modeling of Complex Contoured Composite Structures Project (United States)

    National Aeronautics and Space Administration — The existing HDWLT (pictured) contoured composite structure design, its analyses and manufacturing tools, will be used to validate key analyses inputs through...

  15. Generalized network structures: The configuration model and the canonical ensemble of simplicial complexes (United States)

    Courtney, Owen T.; Bianconi, Ginestra


    Simplicial complexes are generalized network structures able to encode interactions occurring between more than two nodes. Simplicial complexes describe a large variety of complex interacting systems ranging from brain networks to social and collaboration networks. Here we characterize the structure of simplicial complexes using their generalized degrees that capture fundamental properties of one, two, three, or more linked nodes. Moreover, we introduce the configuration model and the canonical ensemble of simplicial complexes, enforcing, respectively, the sequence of generalized degrees of the nodes and the sequence of the expected generalized degrees of the nodes. We evaluate the entropy of these ensembles, finding the asymptotic expression for the number of simplicial complexes in the configuration model. We provide the algorithms for the construction of simplicial complexes belonging to the configuration model and the canonical ensemble of simplicial complexes. We give an expression for the structural cutoff of simplicial complexes that for simplicial complexes of dimension d =1 reduces to the structural cutoff of simple networks. Finally, we provide a numerical analysis of the natural correlations emerging in the configuration model of simplicial complexes without structural cutoff.

  16. The structural linguistic complexity of lawyers' questions and children's responses in Scottish criminal courts. (United States)

    Andrews, Samantha J; Lamb, Michael E


    In the first study to systematically assess the structural linguistic complexity of lawyers' questions of children in Scotland, we examined 56 trial transcripts of 5- to 17-year-old children testifying as alleged victims of sexual abuse. Complexity was assessed using 8 quantitative measures of each utterance's components (number of questions, phrases, clauses, sentences, false starts, average word count, word length, and sentence length) and a composite measure was used in the analyses. Lawyers did not alter the complexity of questions when prompting children of different ages. Defense lawyers asked more structurally complex questions than prosecutors. Directive questions were the least structurally complex questions, followed by option-posing questions. Suggestive questions, followed by invitations, were the most structurally complex questions. Option-posing and suggestive questions were more complex when asked by defense lawyers than prosecutors. Of suggestive questions, confrontation and tagged questions were more complex than any other question type. Increased structural complexity led to more unresponsiveness, more expressions of uncertainty, and more self-contradictions regardless of which lawyer asked, the question type, or the children's ages. These findings highlight the additional risks associated with asking some types of questions in structurally complex ways and highlight the need for further innovations (e.g., the use of intermediaries) to facilitate the questioning of vulnerable witnesses in Scottish criminal courts. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Structures of dioxobipyridil-12-crown-4 and its complexes with silver (I) and copper (II) cations (United States)

    Starova, Galina L.; Denisova, Anna S.; Dem'yanchuk, Evgeniya M.


    The structures of dioxobipyridil-12-crown-4 ( bpy-CO-crown) and its complexes with copper (II) and silver (I) cations have been determined using single crystal X-ray-diffraction. The results have been compared with the literature data on the complexes of dcmbpy and its complex with silver (I) and copper (II) cations.

  18. Chaperonin Structure - The Large Multi-Subunit Protein Complex

    Directory of Open Access Journals (Sweden)

    Irena Roterman


    Full Text Available The multi sub-unit protein structure representing the chaperonins group is analyzed with respect to its hydrophobicity distribution. The proteins of this group assist protein folding supported by ATP. The specific axial symmetry GroEL structure (two rings of seven units stacked back to back - 524 aa each and the GroES (single ring of seven units - 97 aa each polypeptide chains are analyzed using the hydrophobicity distribution expressed as excess/deficiency all over the molecule to search for structure-to-function relationships. The empirically observed distribution of hydrophobic residues is confronted with the theoretical one representing the idealized hydrophobic core with hydrophilic residues exposure on the surface. The observed discrepancy between these two distributions seems to be aim-oriented, determining the structure-to-function relation. The hydrophobic force field structure generated by the chaperonin capsule is presented. Its possible influence on substrate folding is suggested.

  19. Fluctuation electron microscopy studies of complex structured materials (United States)

    Zhao, Gongpu; Rougée, Annick; Buseck, Peter; Treacy, Michael


    Fluctuation electron microscopy (FEM) is a hybrid imaging-diffraction technique. This technique is particularly sensitive to paracrystalline structures of dimension 0.5-2 nm, which are difficult to detect by either imaging or diffraction techniques alone. It has been successfully deployed to study paracrystalline structures in amorphous silicon, germanium thin film. This technique has also been used to study metallic glasses and oxide glasses. Until now, FEM has not been used to study disordered geological materials. In this talk we present our FEM studies of shungite, a naturally occurring disordered carbonaceous material, reveal that trace quantities of tightly curved graphene structures such as C60, or fragments of C60, is present in shungite. We also present results from our study of metamict zircon, whose crystal structure is destroyed by self-radiation during naturally occurring α decay events. Work is in progress to study the structural evolution during the metamictization process.

  20. Heterogeneous anisotropic complex structure gradual model and constitutive relation

    Institute of Scientific and Technical Information of China (English)

    李永; 宋健; 张志民


    Four new gradually delaminate models of the three-dimensional macro-/mesoscopic structure and delamination of the heterogeneous anisotropic composite (HAC) are set up by conducting research into its structure and performance. A general theory, which demonstrates the three-dimensional constitutive relation of the macro-/mesoscopic performance of this structure is further developed. The macroscopic expression of HAC is presented in terms of a Tanigawa delaminate homogeneous equivalent approach, the mesoscopic problems are analysed utilizing Eshelby-Mori-Tanaka theory, with the introduction of the representative volume elements of monolayer single unit cell and interlaminar double unit cells.According to the gradual continuity of the structure as a whole, great attention is given to the modelling and research of the interlaminar macroscopic and mesoscopic problems of HAC structure. Comparison with the existing solutions is made through calculation of typical cases.

  1. 75 FR 61857 - Statement on Sound Practices Concerning Elevated Risk Complex Structured Finance Activities (United States)


    ... Finance Activities AGENCY: Office of Thrift Supervision (OTS), Treasury. ACTION: Notice and request for... Elevated Risk Complex Structured Finance Activities. OMB Number: 1550-0111. Form Number: N/A. Description: Statement on Sound Practices Concerning Elevated Risk Complex Structured Finance Activities describes...

  2. Corrigendum: Structural diversity of target-specific homopyrimidine peptide nucleic acid-dsDNA complexes

    DEFF Research Database (Denmark)

    Bentin, T.; Hansen, G.I.; Nielsen, P.E.


    This corrects the article "Structural diversity of target-specific homopyrimidine peptide nucleic acid-dsDNA complexes" in volume 34 on page 5790.......This corrects the article "Structural diversity of target-specific homopyrimidine peptide nucleic acid-dsDNA complexes" in volume 34 on page 5790....

  3. Using Plants to Explore the Nature & Structural Complexity of Life (United States)

    Howard, Ava R.


    Use of real specimens brings the study of biology to life. This activity brings easily acquired plant specimens into the classroom to tackle common alternative conceptions regarding life, size, complexity, the nature of science, and plants as multicellular organisms. The activity occurs after a discussion of the characteristics of life and engages…

  4. Structural elucidation of low abundant metabolites in complex sample matrices

    NARCIS (Netherlands)

    Hooft, van der J.J.J.; Vos, de R.C.H.; Ridder, L.O.; Vervoort, J.; Bino, R.J.


    Identification of metabolites is a major challenge in biological studies and relies in principle on mass spectrometry (MS) and nuclear magnetic resonance (NMR) methods. The increased sensitivity and stability of both NMR and MS systems have made dereplication of complex biological samples feasible.

  5. Structure and stability of complex coacervate core micelles with lysozyme

    NARCIS (Netherlands)

    Lindhoud, Saskia; de Vries, Renko; Norde, Willem; Cohen Stuart, Martien A.

    Encapsulation of enzymes by polymers is a promising method to influence their activity and stability. Here, we explore the use of complex coacervate core micelles for encapsulation of enzymes. The core of the micelles consists of negatively charged blocks of the diblock copolymer PAA(42)PAAm(417)

  6. Structure and Stability of Complex Coacervate Core Micelles with Lysozyme

    NARCIS (Netherlands)

    Lindhoud, Saskia; de Vries, Renko; Norde, Willem; Cohen Stuart, Martinus Abraham


    Encapsulation of enzymes by polymers is a promising method to influence their activity and stability. Here, we explore the use of complex coacervate core micelles for encapsulation of enzymes. The core of the micelles consists of negatively charged blocks of the diblock copolymer PAA42PAAm417 and

  7. Structure and stability of complex coacervate core micelles with lysozyme

    NARCIS (Netherlands)

    Lindhoud, S.; Vries, de R.J.; Norde, W.; Cohen Stuart, M.A.


    Encapsulation of enzymes by polymers is a promising method to influence their activity and stability. Here, we explore the use of complex coacervate core micelles for encapsulation of enzymes. The core of the micelles consists of negatively charged blocks of the diblock copolymer PAA42PAAm417 and th

  8. Diene complexes of titanium, zirconium, and hafnium. Structure and reactivity

    NARCIS (Netherlands)

    Blenkers, Johannes


    This thesis describes a study of synthesis, characterization, and reactivity of novel n4-diene complexes of group IVB transition metals in low valence states. In the study of the reactivity, emphasus is put on reactions with simple substrate molecules, e.g. CO, H2, olefins, isocanides; in particular

  9. Structure and Stability of Complex Coacervate Core Micelles with Lysozyme

    NARCIS (Netherlands)

    Lindhoud, Saskia; Vries, de Renko; Norde, Willem; Cohen Stuart, Martien A.


    Encapsulation of enzymes by polymers is a promising method to influence their activity and stability. Here, we explore the use of complex coacervate core micelles for encapsulation of enzymes. The core of the micelles consists of negatively charged blocks of the diblock copolymer PAA42PAAm417 and th

  10. Structure and stability of complex coacervate core micelles with lysozyme

    NARCIS (Netherlands)

    Lindhoud, Saskia; de Vries, Renko; Norde, Willem; Cohen Stuart, Martien A.


    Encapsulation of enzymes by polymers is a promising method to influence their activity and stability. Here, we explore the use of complex coacervate core micelles for encapsulation of enzymes. The core of the micelles consists of negatively charged blocks of the diblock copolymer PAA(42)PAAm(417) an

  11. Shear wave velocity structure of the Bushveld Complex, South Africa

    CSIR Research Space (South Africa)

    Kgaswane, EM


    Full Text Available across the Bushveld Complex. Group velocities for 2–15 s periods were obtained from surface wave tomography using local and regional events, while group velocities for 20–60 s periods were taken from a published model. 1-D shear wave velocity models...

  12. Using Plants to Explore the Nature & Structural Complexity of Life (United States)

    Howard, Ava R.


    Use of real specimens brings the study of biology to life. This activity brings easily acquired plant specimens into the classroom to tackle common alternative conceptions regarding life, size, complexity, the nature of science, and plants as multicellular organisms. The activity occurs after a discussion of the characteristics of life and engages…

  13. Structural stability of complex hydrides LiBH4 revisited

    DEFF Research Database (Denmark)

    Lodziana, Zbigniew; Vegge, Tejs


    A systematic approach to study the phase stability of LiBH4 based on ab initio calculations is presented. Three thermodynamically stable phases are identified and a new phase of Cc symmetry is proposed for the first time for a complex hydride. The x-ray diffraction pattern and vibrational spectra...

  14. Cationic Dihydrogen/Dihydride Complexes of Osmium: Structure and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Egbert, Jonathan D.; Bullock, R. Morris; Heinekey, D. M.


    Reaction of Cp*Os(CO)2Cl with (Et3Si )(BArF4) under hydrogen gas affords the cationic hydrogen complex [Cp*Os(CO)2(H2)][BArF4] (1), (Cp* = C5Me5; ArF = C6F5). When this reaction is carried out with HD gas, complex 1-d1 results, with JHD = 24.5 Hz. When solutions of complex 1 are monitored by 1H NMR spectroscopy over several days, the gradual formation of a trans dihydride species is observed. Similarly, reaction of CpOs(dppm)Br with NaBArF*4 (ArF* = 3,5-(CF3)2C6H3) under hydrogen affords the cationic dihydride complex [CpOs(dppm)H2]BArF*4 (2). At 295 K, complex 2 exists as a 10:1 mixture of cis and trans isomers. The 1H NMR spectrum of the cis form in the hydride region exhibits a triplet with JHP = 6.5 Hz, due to rapid exchange of the hydrogen atoms. At low temperature, static spectra of the HH'PP' spin system can be obtained, revealing quantum mechanical exchange coupling between the two hydride ligands. The observed JHH' is temperature dependent, varying from 133 Hz at 141 K to 176 Hz at 198 K. This is the first report of detectable exchange coupling between pairs of chemically equivalent hydrogen atoms. Research at the University of Washington was supported by the National Science Foundation. Research at Brookhaven National Laboratory was carried out under contract DE-AC02-98CH10886 with the U.S. Department of Energy and was supported by its Division of Chemical Sciences, Office of Basic Energy Sciences. Research at Pacific Northwest National Laboratory (PNNL) was funded by LDRD funds. PNNL is operated by Battelle for the US Department of Energy.

  15. Structure and Function of SWI/SNF Chromatin Remodeling Complexes and Mechanistic Implications for Transcription


    Tang, Liling; Nogales, Eva; Ciferri, Claudio


    ATP-dependent chromatin remodeling complexes are specialized protein machinery able to restructure the nucleosome to make its DNA accessible during transcription, replication and DNA repair. During the past few years structural biologists have defined the architecture and dynamics of some of these complexes using electron microscopy, shedding light on the mechanisms of action of these important complexes. In this paper we review the existing structural information on the SWI/SNF family of the...

  16. A tetrairon(III)complex recognizing protein structures via a hydrolytic pathway

    Institute of Scientific and Technical Information of China (English)

    PAN Qunhui; JIANG Wei; WANG Ming; LIAO Zhanru; LIU Changlin


    There might be significant differences in the rate and efficiency in the metal complex-mediated hydrolytic reactions of proteins belonging to the different structural patterns. The tetrairon(III) complex [Fe4(NTB)4 (μ2-O)2(μ4- Suc)]6+, as a promoter in protein hydrolysis, is sensitive to α-helices in proteins, indicating that some metal complexes, as artificial proteolytic agents, could be used as a new hydrolytic probe of protein structures.

  17. Electronic structure and driving forces in {beta}-cyclodextrin: Diclofenac inclusion complexes

    Energy Technology Data Exchange (ETDEWEB)

    Bogdan, Diana [National Institute for Research and Development of Isotopic and Molecular Technologies, Donath street 71-103, 400293 Cluj-Napoca (Romania); Morari, C. [National Institute for Research and Development of Isotopic and Molecular Technologies, Donath street 71-103, 400293 Cluj-Napoca (Romania)]. E-mail:


    We investigate the geometry and electronic structure for complexes of {beta}-cyclodextrin with diclofenac using DFT calculations. The effect of solvent is explicitly taken into account. This investigation allows us to draw meaningful conclusions upon the stability of the complex and the nature of the driving forces leading to the complexation process. In particular we emphasize the role of the water, by pointing out the changes in the solvent's electronic structure for different docking geometries.

  18. Structure identification and adaptive synchronization of uncertain general complex dynamical networks

    Energy Technology Data Exchange (ETDEWEB)

    Xu Yuhua, E-mail: [College of Information Science and Technology, Donghua University, Shanghai 201620 (China) and Department of Maths, Yunyang Teacher' s College, Hubei 442000 (China); Zhou Wuneng, E-mail: [College of Information Science and Technology, Donghua University, Shanghai 201620 (China); Fang Jian' an [College of Information Science and Technology, Donghua University, Shanghai 201620 (China); Lu Hongqian [Shandong Institute of Light Industry, Shandong Jinan 250353 (China)


    This Letter proposes an approach to identify the topological structure and unknown parameters for uncertain general complex networks simultaneously. By designing effective adaptive controllers, we achieve synchronization between two complex networks. The unknown network topological structure and system parameters of uncertain general complex dynamical networks are identified simultaneously in the process of synchronization. Several useful criteria for synchronization are given. Finally, an illustrative example is presented to demonstrate the application of the theoretical results.

  19. Structural and thermal characterization of ternary complexes of piroxicam and alanine with transition metals: Uranyl binary and ternary complexes of piroxicam. Spectroscopic characterization and properties of metal complexes (United States)

    Mohamed, Gehad G.


    Ternary Fe(III), Co(II), Ni(II), Cu(II), Zn(II) and UO 2(II) complexes with piroxicam (Pir) drug (H 2L 1) and dl-alanine (Ala) (HL 2) and also the binary UO 2(II) complex with Pir were studied. The structures of the complexes were elucidated using elemental, IR, molar conductance, magnetic moment, diffused reflectance and thermal analyses. The UO 2(II) binary complex was isolated in 1:2 ratio with the formula [UO 2(H 2L) 2](NO 3) 2. The ternary complexes were isolated in 1:1:1 (M:H 2L 1:L 2) ratios. The solid complexes were isolated in the general formulae [M(H 2L)(L 2)(Cl) n(H 2O) m]· yH 2O (M = Fe(III) ( n = 2, m = 0, y = 1), Co(II) ( n = 1, m = 1, y = 2) and Ni(II) ( n = 1, m = 1, y = 0)); [M(H 2L)(L 2)](X) z· yH 2O (M = Cu(II) (X = AcO, z = 1, y = 0), Zn(II) (X = AcO, z = 1, y = 3) and UO 2(II) (X = NO 3, z = 1, y = 2)). Pir behaves as a neutral bidentate ligand coordinated to the metal ions via the pyridine-N and carbonyl-O groups, while Ala behaves as a uninegatively bidentate ligand coordinated to the metal ions via the deprotonated carboxylate-O and amino-N. The magnetic and reflectance spectral data show that the complexes have octahedral geometry except Cu(II) and Zn(II) complexes have tetrahedral structures. The thermal decomposition of the complexes was discussed in relation to structure, and the thermodynamic parameters of the decomposition stages were evaluated.

  20. Geophysical mapping of complex glaciogenic large-scale structures

    DEFF Research Database (Denmark)

    Høyer, Anne-Sophie


    is required to understand the structures. In practice, however, also the applicability and costs of the methods are crucial. The SkyTEM method is very cost-effective in providing dense data sets, and it is therefore recommendable to use this method initially in mapping campaigns. For more detailed structural...... by periglacial and postglacial erosion that formed the present-day terrain. Paleoglaciological calculations based on the observed thrust structures show that the deformation was caused by a very thick ice sheet with a steep ice profile, resting on permafrost....

  1. Characterization of Fe3Si-based coatings on low silicon steel by pulsed Nd:YAG laser cladding

    Institute of Scientific and Technical Information of China (English)

    Dan-yang Dong; Chang-sheng Liu; Sui-yuan Chen; Bin Zhang


    The Fe3Si based coating was produced on the Fe-lSi steel surface by a pulsed Nd:YAG (yttrium aluminum garnet) laser. Its phase constitution and microstructure were characterized by using X-ray diffraction (XRD), optical microscope (OM), and field emission scanning electron microscope (FESEM) with associated energy dispersive spectroscopy (EDS) and transmission electron microscopy (TEM). The hyperfine structure of the coating was studied by Mossbauer spectra (MS) and the magnetic property was also measured at room temperature by a vibrating sample magnetometer (VSM). The obtained coating is pore and crack-free with dense microstructure and high Si content. The metallurgical bonding between the coating and the substrate was realized. The micro-structure of the coating is typical fine dendrites. The major phase was confirmed by XRD and TEM to be the ordering DO3 structured Fe3Si phase. In addition, there were smaller amounts of the Fe5Si3 phase and the T-Fe phase in the coating. Compared with the sub-strate, the laser cladding coating has a lower saturation magnetization and a higher coercive force. The poor magnetic property might be because of rapid solidification microstructure and phase constitution in the coating.

  2. Crystal Structure of Mitochondrial Respiratory Membrane Protein Complex Ⅱ Determined

    Institute of Scientific and Technical Information of China (English)


    @@ Scientists at the CAS Institute of Biophysics (IBP) and Tsinghua University have gained new insights into the mechanism of mitochondria, the subcellular structures which generate energy for living cells.

  3. Study of the structure and dynamics of complex biological networks (United States)

    Samal, Areejit


    In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large scale metabolic networks inside three organisms, Escherichia coli, Saccharomyces cerevisiae and Staphylococcus aureus. We also study the dynamics of the large scale genetic network controlling E. coli metabolism. We have tried to explain the observed system level dynamical properties of these networks in terms of their underlying structure. Our studies of the system level dynamics of these large scale biological networks provide a different perspective on their functioning compared to that obtained from purely structural studies. Our study also leads to some new insights on features such as robustness, fragility and modularity of these large scale biological networks. We also shed light on how different networks inside the cell such as metabolic networks and genetic networks are interrelated to each other.

  4. Synthesis, spectroscopic characterization and electronic structure of some new Cu(I) carbene complexes

    Indian Academy of Sciences (India)

    Chinnappan Sivasankar; Christina Baskaran; Ashoka G Samuelson


    Reaction of oligomeric Cu(I) complexes [Cu{-S-C(=NR)(O-Ar-CH3)}] with Lewis acids gave Cu(I) carbene complexes, which were characterized by 1H and 13C NMR spectroscopy. Cu(I) carbene complexes could be directly generated from RNCS, Cu(I)-OAr and Lewis acids; this method can be used to prepare Cu(I) carbene complexes with different substitutents on the carbene carbon. The complexes were unreactive towards olefins and do not undergo cyclopropanation. Electronic structure calculations (DFT) show that the charge on the carbene carbon plays an important role in controlling the reactivity of the carbene complex.

  5. Computational Characterization of Electromagnetic Field Propagation in Complex Structures (United States)


    publication in the 1 August 1996 issue of Physical Review E. A patent disclosure baring the same title has also been filed jointly by MICOM and UAH...Surfaces: Applications to Photonic Band Gap Structures andSuperluminal Tunneling Times, Physical Review A 52, 726 (1995). (2) M. Tocci, M.J. Bloemer, M...dimensional photonic band gap structure. Physical Review A 53, 2799, (1996). (4) J. Bendickson, J.P. Dowling, and M. Scalora, Analytic Expression for Mode

  6. Modeling data irregularities and structural complexities in data envelopment analysis

    CERN Document Server

    Zhu, Joe


    In a relatively short period of time, Data Envelopment Analysis (DEA) has grown into a powerful quantitative, analytical tool for measuring and evaluating performance. It has been successfully applied to a whole variety of problems in many different contexts worldwide. This book deals with the micro aspects of handling and modeling data issues in modeling DEA problems. DEA's use has grown with its capability of dealing with complex "service industry" and the "public service domain" types of problems that require modeling of both qualitative and quantitative data. This handbook treatment deals with specific data problems including: imprecise or inaccurate data; missing data; qualitative data; outliers; undesirable outputs; quality data; statistical analysis; software and other data aspects of modeling complex DEA problems. In addition, the book will demonstrate how to visualize DEA results when the data is more than 3-dimensional, and how to identify efficiency units quickly and accurately.

  7. Structure Under the Bushveld Complex, South Africa from Receiver Functions (United States)

    Castillo, B. A.


    The Bushveld Igneous Complex (BIC) is the largest layered mafic intrusion on Earth and formed within Transvaal Basin in South Africa. The hypothesis that the limbs of the Rustenburg layer of the BIC are connected at depth is tested using teleseimic events of Mw > 5.5 to provide data under a seismic station (receiver) in the western limb of the BIC. Receiver functions have been computed from the data in order to image the layering under the Bushveld Complex. The receiver functions show discrete arrivals from the mafic layers, the Transvaal sediments under the BIC, and the Mohorovicic discontinuity at the base of the crust.. An interactive forward modeling method has been used to model the receiver functions in order to estimate the thickness of the BIC and the crust. Results show a BIC that is about 5-8 km thick and a Moho at ~40 km depth.

  8. Fundamentals of complex networks models, structures and dynamics

    CERN Document Server

    Chen, Guanrong; Li, Xiang


    Complex networks such as the Internet, WWW, transportationnetworks, power grids, biological neural networks, and scientificcooperation networks of all kinds provide challenges for futuretechnological development. In particular, advanced societies havebecome dependent on large infrastructural networks to an extentbeyond our capability to plan (modeling) and to operate (control).The recent spate of collapses in power grids and ongoing virusattacks on the Internet illustrate the need for knowledge aboutmodeling, analysis of behaviors, optimized planning and performancecontrol in such networks. F

  9. Pentamethylcyclopentadienyl Zirconium and Hafnium Polyhydride Complexes : Synthesis, Structure, and Reactivity

    NARCIS (Netherlands)

    Visser, Cindy; Hende, Johannes R. van den; Meetsma, Auke; Hessen, Bart; Teuben, Jan H.


    The half-sandwich zirconium and hafnium N,N-dimethylaminopropyl complexes Cp*M[(CH2)3NMe2]Cl2 (Cp* = η5-C5Me5, M = Zr, 1; Hf, 2) and Cp*M[(CH2)3NMe2]2Cl (M = Zr, 3; Hf, 4) were synthesized by mono- or dialkylation of Cp*MCl3 with the corresponding alkyllithium and Grignard reagents. Hydrogenolysis

  10. Modeling Complex Nesting Structures in International Business Research

    DEFF Research Database (Denmark)

    Nielsen, Bo Bernhard; Nielsen, Sabina


    International business (IB) phenomena often involve complex relationships between factors at different levels. Multinational corporations (MNCs) are influenced both by different country and industry environments which may have independent as well as interactive effects on MNC performance. While...... of analysis may yield novel insights to IB research. The results have implications for IB research in its pursuit of an integrative approach to understanding the multilevel determinants of firm internationalization and performance. The paper further illustrates the importance of adequately modeling crossed...

  11. Structure and dynamics of small van der Waals complexes

    Energy Technology Data Exchange (ETDEWEB)

    Loreau, J. [Service de Chimie Quantique et Photophysique, Université Libre de Bruxelles (ULB) CP 160/09, 1050 Brussels (Belgium)


    We illustrate computational aspects of the calculation of the potential energy surfaces of small (up to five atoms) van der Waals complexes with high-level quantum chemistry techniques such as the CCSD(T) method with extended basis sets. We discuss the compromise between the required accuracy and the computational time. Further, we show how these potential energy surfaces can be fitted and used in dynamical calculations such as non-reactive inelastic scattering.

  12. Musing on the structural organization of the exosome complex


    Mitchell, Philip; Tollervey, David


    The exosome complex of 3′→5′ exoribonucleases functions in both the precise processing of 3′ extended precursor molecules to mature stable RNAs and the complete degradation of other RNAs. Both processing and degradative activities of the exosome depend on additional cofactors, notably the putative RNA helicases Mtr4p and Ski2p. It is not known how these factors regulate exosome function or how the exosome distinguishes RNAs destined for processing events from substrates that are t...

  13. A graph theoretical approach for assessing bio-macromolecular complex structural stability. (United States)

    Del Carpio, Carlos Adriel; Iulian Florea, Mihai; Suzuki, Ai; Tsuboi, Hideyuki; Hatakeyama, Nozomu; Endou, Akira; Takaba, Hiromitsu; Ichiishi, Eiichiro; Miyamoto, Akira


    Fast and proper assessment of bio macro-molecular complex structural rigidity as a measure of structural stability can be useful in systematic studies to predict molecular function, and can also enable the design of rapid scoring functions to rank automatically generated bio-molecular complexes. Based on the graph theoretical approach of Jacobs et al. [Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF (2001) Protein flexibility predictions using graph theory. Proteins: Struct Funct Genet 44:150-165] for expressing molecular flexibility, we propose a new scheme to analyze the structural stability of bio-molecular complexes. This analysis is performed in terms of the identification in interacting subunits of clusters of flappy amino acids (those constituting regions of potential internal motion) that undergo an increase in rigidity at complex formation. Gains in structural rigidity of the interacting subunits upon bio-molecular complex formation can be evaluated by expansion of the network of intra-molecular inter-atomic interactions to include inter-molecular inter-atomic interaction terms. We propose two indices for quantifying this change: one local, which can express localized (at the amino acid level) structural rigidity, the other global to express overall structural stability for the complex. The new system is validated with a series of protein complex structures reported in the protein data bank. Finally, the indices are used as scoring coefficients to rank automatically generated protein complex decoys.

  14. Actinide-specific complexing agents: their structural and solution chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Raymond, K.N.; Freeman, G.E.; Kappel, M.J.


    The synthesis of a series of tetracatecholate ligands designed to be specific for Pu(IV) and other actinide(IV) ions has been achieved. Although these compounds are very effective as in vivo plutonium removal agents, potentiometric and voltammetric data indicate that at neutral pH full complexation of the Pu(IV) ion by all four catecholate groups does not occur. Spectroscopic results indicate that the tetracatecholates, 3,4,3-LICAMS and 3,4,3-LICAMC, complex Am(III). The Am(IV)/(III)-catecholate couple (where catecholate = 3,4,3-LICAMS or 3,4,3-LICAMC) is not observed, but may not be observable due to the large currents associated with ligand oxidation. However, within the potential range where ligand oxidation does not occur, these experiments indicate that the reduction potential of free Am(IV)/(III) is probably greater than or equal to + 2.6 V vs NHE or higher. Proof of the complexation of americium in the trivalent oxidation state by 3,4,3-LICAMS and 3,4,3-LICAMC elimates the possibility of tetracatholates stabilizing Am(IV) in vivo.

  15. Complexation thermodynamics and structural studies of trivalent actinide and lanthanide complexes with DTPA, MS-325 and HMDTPA

    Energy Technology Data Exchange (ETDEWEB)

    Thakur, P.; Choppin, G.R. [Florida State Univ., Tallahassee, FL (United States). Dept. of Chemistry and Biochemistry; Conca, J.L. [RJ Lee Group, Inc., Pasco, WA (United States). Center for Lab. Sciences; Dodge, C.J. [Brookhaven National Laboratory, Upton, NY (United States); Francis, A.J. [Brookhaven National Laboratory, Upton, NY (United States); Pohang Univ. of Science and Technology (Korea, Republic of). Div. of Advanced Nuclear Engineering


    The protonation constants of DTPA (diethylenetriaminepentaacetic acid) and two derivatives of DTPA, 1-R(4,4-diphenyl cyclohexyl-phosphonyl-methyl diethylenentriaminepentaacetic acid) (MS-325) and (R)-hydroxymethyl-diethylenentriaminepentaacetic acid (HMDTPA) were determined by potentiometric titration in 0.1 M NaClO{sub 4}. The formation of 1: 1 complexes of Am{sup 3+}, Cm{sup 3+} and Ln{sup 3+} cations with these three ligands were investigated by potentiometric titration with competition by ethylenediaminetetraacetic acid (EDTA) and the solvent extraction method in aqueous solutions of I=0.10 M NaClO{sub 4}. The thermodynamic data of complexation were determined by the temperature dependence of the stability constants and by calorimetry. The complexation is exothermic and becomes weaker with increase in temperature. The complexation strength of these ligands follows the order: DTPA {approx} HMDTPA > MS-325. Eu{sup 3+}/Cm{sup 3+} luminescence, EXAFS (Extended X-ray Absorption Fine Structure) and DFT (Density Functional Theory) calculations suggest that all three ligands are octadentate in the complex. In the complex, M(L){sup 2-} (L = DTPA, MS-325 and HMDTPA). The M{sup 3+} binds via five carboxylates oxygen atoms, three nitrogen atoms, and the complex contains one water of hydration. (orig.)

  16. InterEvol database: exploring the structure and evolution of protein complex interfaces


    Faure, Guilhem; Andreani, Jessica; Guerois, Raphaël


    Capturing how the structures of interacting partners evolved at their binding interfaces is a fundamental issue for understanding interactomes evolution. In that scope, the InterEvol database was designed for exploring 3D structures of homologous interfaces of protein complexes. For every chain forming a complex in the protein data bank (PDB), close and remote structural interologs were identified providing essential snapshots for studying interfaces evolution. The database provides tools to ...

  17. Structural Studies on Intact Clostridium Botulinum Neurotoxins Complexed with Inhibitors Leading to Drug Design (United States)


    structure1. Introduction Tetanus neurotoxin (TeNT) produced by Clostridium tetani and the seven antigenically distinct botulinum neurotoxins (BoNT/A-G...2-0011 TITLE: Structural Studies on Intact Clostridium Botulinum Neurotoxins Complexed with Inhibitors Leading to Drug...DATES COVERED (From - To) 28 Jan 2005 – 27 Jan 2006 4. TITLE AND SUBTITLE Structural Studies on Intact Clostridium Botulinum Neurotoxins Complexed

  18. Structures of trihydroxynaphthalene reductase-fungicide complexes: implications for structure-based design and catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Liao, D.-I.; Basarab, G.S.; Gatenby, A.A.; Valent, B.; Jordan, D.B. (DuPont)


    Trihydroxynaphthalene reductase catalyzes two intermediate steps in the fungal melanin biosynthetic pathway. The enzyme, a typical short-chain dehydrogenase, is the biochemical target of three commercial fungicides. The fungicides bind preferentially to the NADPH form of the enzyme. Three X-ray structures of the Magnaporthe grisea enzyme complexed with NADPH and two commercial and one experimental fungicide were determined at 1.7 {angstrom} (pyroquilon), 2.0 {angstrom} (2,3-dihydro-4-nitro-1H-inden-1-one, 1), and 2.1 {angstrom} (phthalide) resolutions. The chemically distinct inhibitors occupy similar space within the enzyme's active site. The three inhibitors share hydrogen bonds with the side chain hydroxyls of Ser-164 and Tyr-178 via a carbonyl oxygen (pyroquilon and 1) or via a carbonyl oxygen and a ring oxygen (phthalide). Active site residues occupy similar positions among the three structures. A buried water molecule that is hydrogen bonded to the NZ nitrogen of Lys-182 in each of the three structures likely serves to stabilize the cationic form of the residue for participation in catalysis. The pro S hydrogen of NADPH (which is transferred as a hydride to the enzyme's naphthol substrates) is directed toward the carbonyl carbon of the inhibitors that mimic an intermediate along the reaction coordinate. Modeling tetrahydroxynaphthalene and trihydroxynaphthalene in the active site shows steric and electrostatic repulsion between the extra hydroxyl oxygen of the former substrate and the sulfur atom of Met-283 (the C-terminal residue), which accounts, in part, for the 4-fold greater substrate specificity for trihydroxynaphthalene over tetrahydroxynaphthalene.

  19. Pinning controllability of complex networks with community structure. (United States)

    Miao, Qingying; Tang, Yang; Kurths, Jürgen; Fang, Jian-an; Wong, W K


    In this paper, we study the controllability of networks with different numbers of communities and various strengths of community structure. By means of simulations, we show that the degree descending pinning scheme performs best among several considered pinning schemes under a small number of pinned nodes, while the degree ascending pinning scheme is becoming more powerful by increasing the number of pinned nodes. It is found that increasing the number of communities or reducing the strength of community structure is beneficial for the enhancement of the controllability. Moreover, it is revealed that the pinning scheme with evenly distributed pinned nodes among communities outperforms other kinds of considered pinning schemes.

  20. Structural complexity and the time course of grammatical development. (United States)

    Frank, R


    One traditional view of the time course of language acquisition holds that a child's difficulties in learning her language are due to general processing, memory or conceptual limitations. As the child's cognitive capacities expand, so do her abilities to use her already-acquired grammar or to recognize additional properties of her soon-to-be native language. Recent work in the study of child language, however, has discovered the existence of a number of characteristic stages, transitions between which are best described in the terms of linguistic theory proper. These stages are surprising under a view of language acquisition according to which developmental delay derives from general cognitive limitations, which cannot characterize difficulties explicable only in language-specific terms. At the same time, current linguistic theories so severely restrict the variation among possible human grammars that there remains little reason why there should be any learning problem at all or characteristic developmental stages. In this paper, I propose that these two views can be reconciled. I show that children's difficulties with a wide range of syntactic constructions, which are indeed best defined in linguistic terms, should nonetheless be derived from limitations on the child's ability to deal with processing load and formal representational complexity. I suggest however that this can be done only in the context of a particular view of syntactic representation, one which is articulated in the terms of the formal system of tree adjoining grammar (TAG). I demonstrate how precisely those difficulties that children experience in the acquisition of relative clauses, adjectival modification, control constructions, raising, wh-questions and the obligatoriness of finite inflection can be traced to the complexity associated with one of the TAG combinatory operations, adjoining. This proposal relates this apparently disparate set of constructions in a novel way and provides us with

  1. The evolution of cerebellum structure correlates with nest complexity


    Hall, Zachary Jonas; Street, Sally; Healy, Susan Denise


    This article was made open access through RCUK OA block grant funds. The work was financially supported by the BBSRC (BB/I019502/1), NSERC (PGSD3-409582-2011 to Z.J.H.) and ERC (232823 to S.E.S.). Across the brains of different bird species, the cerebellum varies greatly in the amount of surface folding (foliation). The degree of cerebellar foliation is thought to correlate positively with the processing capacity of the cerebellum, supporting complex motor abilities, particularly manipulat...

  2. Finding instabilities in the community structure of complex networks (United States)

    Gfeller, David; Chappelier, Jean-Cédric; de Los Rios, Paolo


    The problem of finding clusters in complex networks has been studied by mathematicians, computer scientists, and, more recently, by physicists. Many of the existing algorithms partition a network into clear clusters without overlap. Here we introduce a method to identify the nodes lying “between clusters,” allowing for a general measure of the stability of the clusters. This is done by adding noise over the edge weights. Our method can in principle be used with almost any clustering algorithm able to deal with weighted networks. We present several applications on real-world networks using two different clustering algorithms.

  3. Designing a Simple Folder Structure for a Complex Domain

    DEFF Research Database (Denmark)

    Clemmensen, Torkil


    In this paper I explore a case of designing a simple folder structure for a new e-learning software program for a university study program. The aim is to contribute to the theoretical base for human work interaction design (HWID) by identifying the type of relations connecting design artifacts...

  4. Complex modes and frequencies in damped structural vibrations

    DEFF Research Database (Denmark)

    Krenk, Steen


    It is demonstrated that the state space formulation of the equation of motion of damped structural elements like cables and beams leads to a symmetric eigenvalue problem if the stiffness and damping operators are self-adjoint, and that this is typically the case in the absence of gyroscopic force...

  5. Total neutron scattering: The key to the local and medium range structure of complex materials

    Indian Academy of Sciences (India)

    Th Proffen


    Structural characterization is mainly based on the measurement of Bragg intensities and yields the average structure of crystalline materials. The total scattering pattern, however, contains structural information over all length scales, and it can be used to obtain a complete structural picture of complex materials. Suddenly one has access to a new parameter, the real-space range of the refinement and structures can be analysed as a function of length scale straightforwardly.

  6. Temperature Sensitive Nanocapsule of Complex Structural Form for Methane Storage

    Directory of Open Access Journals (Sweden)

    Suyetin MV


    Full Text Available Abstract The processes of methane adsorption, storage and desorption by the nanocapsule are investigated with molecular-dynamic modeling method. The specific nanocapsule shape defines its functioning uniqueness: methane is adsorbed under 40 MPa and at normal temperature with further blocking of methane molecules the K@C601+ endohedral complex in the nanocapsule by external electric field, the storage is performed under normal external conditions, and methane desorption is performed at 350 K. The methane content in the nanocapsule during storage reaches 11.09 mass%. The nanocapsule consists of tree parts: storage chamber, junction and blocking chamber. The storage chamber comprises the nanotube (20,20. The blocking chamber is a short nanotube (20,20 with three holes. The junction consists of the nanotube (10,10 and nanotube (8,8; moreover, the nanotube (8,8 is connected with the storage chamber and nanotube (10,10 with the blocking chamber. The blocking chamber is opened and closed by the transfer of the K@C60 1+ endohedral complex under electrostatic field action.

  7. Complex molecular gas structure in the Medusa merger

    CERN Document Server

    Aalto, S


    High resolution OVRO aperture synthesis maps of the 12CO 1-0 emission in the `Medusa' galaxy merger (NGC4194) reveal the molecular emission being surprisingly extended. It is distributed on a total scale of 25$''$ (4.7 kpc) - despite the apparent advanced stage of the merger. The complex, striking CO morphology occupies mainly the center and the north-eastern part of the main optical body. The extended 12CO flux is tracing two prominent dust lanes: one which is crossing the central region at right angle and a second which curves to the north-east and then into the beginning of the northern tidal tail. The bulk of the 12CO emission (67%) can be found in a complex starburst region encompassing the central 2kpc. The molecular gas is distributed in five major emission regions of typical size 300pc. About 15% of the total 12CO flux is found in a bright region 1.5'' south of the radio continuum nucleus. We suggest that this region together with the kpc sized central starburst is being fueled by gas flows along the ...

  8. Tear Film Dynamics: the roles of complex structure and rheology (United States)

    Dey, Mohar; Feng, James; Vivek, Atul S.; Dixit, Harish N.; Richhariya, Ashutosh


    Ocular surface infections such as microbial and fungal keratitis are among leading causes of blindness in the world. A thorough understanding of the pre-corneal tear film dynamics is essential to comprehend the role of various tear layer components in the escalation of such ocular infections. The pre-corneal tear film comprises of three layers of complex fluids, viz. the innermost mucin layer, a hydrophilic protective cover over the sensitive corneal epithelium, the intermediate aqueous layer that forms the bulk of the tear film and is often embedded with large number of bio-polymers either in the form of soluble mucins or pathogens, and finally the outermost lipid layer that stabilizes the film by decreasing the air/tear film interfacial tension. We have developed a comprehensive mathematical model to describe such a film by incorporating the effects of the non-uniform mucin distribution along with the complex rheology of the aqueous layer with/without pathogens, Marangoni effects from the lipid layer and the slip effects at the base of the tear film. A detailed linear stability analysis and a fully non-linear solution determine the break up time (BUT) of such a tear film. We also probe the role of the various components of the pre-corneal tear film in the dynamics of rupture.

  9. Structural investigations of sodium caseinate micelles in complex environments

    Energy Technology Data Exchange (ETDEWEB)

    Huck Iriart, C.; Herrera, M.L.; Candal, R. [Universidad de Buenos Aires, Buenos Aires (Argentina); Oliveira, C.L.P. [Universidade de Sao Paulo (USP), Sao Paulo, SP (Brazil); Torriani, I. [Laboratorio Nacional de Luz Sincrotron (LNLS), Campinas, SP (Brazil)


    Full text: The most frequent destabilization mechanisms in Sodium Caseinate (NaCas) emulsions are creaming and flocculation. Coarse or fine emulsions with low protein con- tent destabilize mainly by creaming. If migration mechanism is suppressed, flocculation may become the main mechanism of destabilization. Small Angle X-Ray Scattering (SAXS) technique was applied to investigate sodium caseinate micelles structure in different environments. As many natural products, Sodium Caseinate samples have large polydisperse size distribution. The experimental data was analyzed using advanced modeling approaches. The Form Factor for the Caseinate micelle subunits was described by an ellipsoidal core shell model and the structure factor was split into two contributions, one corresponding to the particle-particle interactions and another one for the long range correlation of the subunits in the supramolecular structure. For the first term the hard sphere structure factor using the Percus-Yevick approximation for closure relation was used and for the second term a fractal model was applied. Three concentrations of sodium Caseinate (2, 5 and 7.5 %wt.) were measured in pure water, sugar solutions (20 %wt.) and in three different lipid phase emulsions containing 10 %wt. sunflower seed, olive and fish oils. Data analysis provided an average casein subunit radius of 4 nm, an average distance between the subunits of around 20nm and a fractal dimension value of around 3 for all samples. As indicated by the values of the correlation lengths for the set of studied samples, the casein aggregation is strongly affected by simple sugar additions and it is enhanced by emulsion droplets hydrophobic interaction. As will be presented, these nanoscale structural results provided by scattering experiments is consistent with macroscopic results obtained from several techniques, providing a new understanding of NaCas emulsions. (author)

  10. Complex network perspective on structure and function of Staphylococcus aureus metabolic network

    Indian Academy of Sciences (India)

    L Ying; D W Ding


    With remarkable advances in reconstruction of genome-scale metabolic networks, uncovering complex network structure and function from these networks is becoming one of the most important topics in system biology. This work aims at studying the structure and function of Staphylococcus aureus (S. aureus) metabolic network by complex network methods. We first generated a metabolite graph from the recently reconstructed high-quality S. aureus metabolic network model. Then, based on `bow tie' structure character, we explain and discuss the global structure of S. aureus metabolic network. The functional significance, global structural properties, modularity and centrality analysis of giant strong component in S. aureus metabolic networks are studied.

  11. K-capture by Al-Si based Additives in an Entrained Flow Reactor

    DEFF Research Database (Denmark)

    Wang, Guoliang; Jensen, Peter Arendt; Wu, Hao


    A water slurry, consisting of KCl and Al-Si based additives (kaolin and coal fly ash) was fed into an entrained flow reactor (EFR) to study the K-capturing reaction of the additives at suspension-fired conditions. Solid products collected from the reactor were analysed with respect to total...... and water-soluble K content to quantify the extent of the K-capturing reaction. The results showed that under suspension-fired conditions (1100 °C-1450 °C), kaolin and coal fly ash can effectively capture gaseous KCl. When increasing the mass ratio of KCl to Al-Si additives in the reactants, the conversion...

  12. Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes

    Directory of Open Access Journals (Sweden)

    Selvaraj S


    Full Text Available Abstract Background Protein-protein interactions are important for several cellular processes. Understanding the mechanism of protein-protein recognition and predicting the binding sites in protein-protein complexes are long standing goals in molecular and computational biology. Methods We have developed an energy based approach for identifying the binding site residues in protein–protein complexes. The binding site residues have been analyzed with sequence and structure based parameters such as binding propensity, neighboring residues in the vicinity of binding sites, conservation score and conformational switching. Results We observed that the binding propensities of amino acid residues are specific for protein-protein complexes. Further, typical dipeptides and tripeptides showed high preference for binding, which is unique to protein-protein complexes. Most of the binding site residues are highly conserved among homologous sequences. Our analysis showed that 7% of residues changed their conformations upon protein-protein complex formation and it is 9.2% and 6.6% in the binding and non-binding sites, respectively. Specifically, the residues Glu, Lys, Leu and Ser changed their conformation from coil to helix/strand and from helix to coil/strand. Leu, Ser, Thr and Val prefer to change their conformation from strand to coil/helix. Conclusions The results obtained in this study will be helpful for understanding and predicting the binding sites in protein-protein complexes.

  13. Determination of channeling perspectives for complex crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Allen, W.R.


    Specification of the atomic arrangement for axes and planes of high symmetry is essential for crystal alignment using Rutherford backscattering and for studies of the lattice location of impurities in single crystals. By rotation of an inscribed orthogonal coordinate system, a visual image for a given perspective of a crystal structure can be specified. Knowledge of the atomic arrangement permits qualitative channeling perspectives to be visualized and calculation of continuum potentials for channeling. Channeling angular-yield profiles can then be analytically modeled and, subsequently, shadowing by host atoms of positions within the unit cell predicted. Software to calculate transformed atom positions for a channeling perspective in a single crystal are described and illustrated for the spinel crystal structure.

  14. The Cell Probe Complexity of Succinct Data Structures

    DEFF Research Database (Denmark)

    Gal, Anna; Miltersen, Peter Bro


    In the cell probe model with word size 1 (the bit probe model), a static data structure problem is given by a map , where is a set of possible data to be stored, is a set of possible queries (for natural problems, we have ) and is the answer to question about data . A solution is given by a repre......In the cell probe model with word size 1 (the bit probe model), a static data structure problem is given by a map , where is a set of possible data to be stored, is a set of possible queries (for natural problems, we have ) and is the answer to question about data . A solution is given...

  15. Maps of random walks on complex networks reveal community structure. (United States)

    Rosvall, Martin; Bergstrom, Carl T


    To comprehend the multipartite organization of large-scale biological and social systems, we introduce an information theoretic approach that reveals community structure in weighted and directed networks. We use the probability flow of random walks on a network as a proxy for information flows in the real system and decompose the network into modules by compressing a description of the probability flow. The result is a map that both simplifies and highlights the regularities in the structure and their relationships. We illustrate the method by making a map of scientific communication as captured in the citation patterns of >6,000 journals. We discover a multicentric organization with fields that vary dramatically in size and degree of integration into the network of science. Along the backbone of the network-including physics, chemistry, molecular biology, and medicine-information flows bidirectionally, but the map reveals a directional pattern of citation from the applied fields to the basic sciences.

  16. Comparison and validation of community structures in complex networks (United States)

    Gustafsson, Mika; Hörnquist, Michael; Lombardi, Anna


    The issue of partitioning a network into communities has attracted a great deal of attention recently. Most authors seem to equate this issue with the one of finding the maximum value of the modularity, as defined by Newman. Since the problem formulated this way is believed to be NP-hard, most effort has gone into the construction of search algorithms, and less to the question of other measures of community structures, similarities between various partitionings and the validation with respect to external information. Here we concentrate on a class of computer generated networks and on three well-studied real networks which constitute a bench-mark for network studies; the karate club, the US college football teams and a gene network of yeast. We utilize some standard ways of clustering data (originally not designed for finding community structures in networks) and show that these classical methods sometimes outperform the newer ones. We discuss various measures of the strength of the modular structure, and show by examples features and drawbacks. Further, we compare different partitions by applying some graph-theoretic concepts of distance, which indicate that one of the quality measures of the degree of modularity corresponds quite well with the distance from the true partition. Finally, we introduce a way to validate the partitionings with respect to external data when the nodes are classified but the network structure is unknown. This is here possible since we know everything of the computer generated networks, as well as the historical answer to how the karate club and the football teams are partitioned in reality. The partitioning of the gene network is validated by use of the Gene Ontology database, where we show that a community in general corresponds to a biological process.

  17. Nanoparticle Controlled Soft Complex Structures with Topological Defects (United States)


    4) Soft Matter 9, 3956-3964 (2013); 5) Adv. Cond. Matter Phys. 2013, 505219-1-505219-10 (2013); 6) J. Phys.: Condens. Matter, Special Issue on...Curvature control of valence on nematic shells, Soft Matter 7, 670 (2011). [14] F.C. MacKintosh, T.C. Lubensky, Orientational order, topology, and...Zidansek, Different modulated structures of topological defects stabilized by adaptive targeting nanoparticles, Soft Matter 9, 3956 (2013). [20

  18. Multiscale Reduced Order Modeling of Complex Multi-Bay Structures (United States)


    indeed achieved with both enrichments. Manuscript Click here to download Manuscript: ROM_Notch_final2.pdf Click here to view linked References 1... brick elements (CHEXA in NX/Nastran), and 14 such elements were used along the width of the beam. Along the length, the notched beam was divided in...not a long body problem. Therefore, the structure was discretized throughout its entire domain with 8-node brick elements (CHEXA in NX/Nastran

  19. Electrocyclization of oxatrienes in the construction of structurally complex pyranopyridones. (United States)

    Fotiadou, Anna D; Zografos, Alexandros L


    Application of a tandem Knoevenagel/6π-electrocyclization sequence is able to produce highly substituted pyranopyridones from moderate to high yields in a one-step reaction. High diasteroselectivity is observed in some cases and was rationalized on the basis of the thermodynamic control of the evidenced reversibility of a 6π-electrocyclization reaction. Numerous examples are provided establishing a novel entry in natural product-like structures of pyranopyridone alkaloids.

  20. A System for Social Network Extraction of Web Complex Structures


    Amir Ansari; Mehrdad Jalali


    A social network is social structure composed of nodes which generally are individually or organizationally and are connected based on several common traits. Currently, social networks are applied in wide parts of the web. Its popularity is due to discovery of connections hidden in the web and its representation in a visual manner. Social networks are used in many levels from households to nations. They play an important role in finding solutions to problems, management of organizations and i...

  1. Guiding of Plasmons and Phonons in Complex Three Dimensional Structures (United States)


    photovoltaic conversion efficiency of copper phthalocyanine thin film devices by incorporation of metal clusters. Solar Energy Materials and Solar Cells 37...Atwater, H. A. & Polman, A. Plasmonics for improved photovoltaic devices (vol 9, pg 205, 2010). Nat Mater 9, 865-865 (2010). 59 Tegart, W. J., The...108 The corresponding porosity of the inverse opal structure is 1-86%*(1-0.74)=78% 109 King, J. S., Graugnard, E. & Summers, C. J. TiO2 Inverse

  2. The Hume-Rothery Rules for Structurally Complex Alloy Phases (United States)

    Mizutani, Uichiro

    The underlying physics behind the Hume-Rothery rules, which have earned great reputations over the past century in the field of materials science in designing new alloys, is reviewed. The discussion is developed following several key themes: (a) what is the critical depth and width of the pseudo-gap to stabilize a complex metallic alloy?, (b) what does the Hume-Rothery stabilization mechanism mean?, (c) the existence of FsBz-induced and orbital hybridization-induced pseudo-gaps, (d) the need of distinguishing two different electron concentrations e/a and VEC, (e) are most quasicrystals really scaled in terms of e/a and stabilized via the FsBz-induced pseudo-gap mechanism? The answer is "no".

  3. Semantic Annotation of Complex Text Structures in Problem Reports (United States)

    Malin, Jane T.; Throop, David R.; Fleming, Land D.


    Text analysis is important for effective information retrieval from databases where the critical information is embedded in text fields. Aerospace safety depends on effective retrieval of relevant and related problem reports for the purpose of trend analysis. The complex text syntax in problem descriptions has limited statistical text mining of problem reports. The presentation describes an intelligent tagging approach that applies syntactic and then semantic analysis to overcome this problem. The tags identify types of problems and equipment that are embedded in the text descriptions. The power of these tags is illustrated in a faceted searching and browsing interface for problem report trending that combines automatically generated tags with database code fields and temporal information.

  4. Complex transition to cooperative behavior in a structured population model.

    Directory of Open Access Journals (Sweden)

    Luciano Miranda

    Full Text Available Cooperation plays an important role in the evolution of species and human societies. The understanding of the emergence and persistence of cooperation in those systems is a fascinating and fundamental question. Many mechanisms were extensively studied and proposed as supporting cooperation. The current work addresses the role of migration for the maintenance of cooperation in structured populations. This problem is investigated in an evolutionary perspective through the prisoner's dilemma game paradigm. It is found that migration and structure play an essential role in the evolution of the cooperative behavior. The possible outcomes of the model are extinction of the entire population, dominance of the cooperative strategy and coexistence between cooperators and defectors. The coexistence phase is obtained in the range of large migration rates. It is also verified the existence of a critical level of structuring beyond that cooperation is always likely. In resume, we conclude that the increase in the number of demes as well as in the migration rate favor the fixation of the cooperative behavior.

  5. Validation of Superelement Modelling of Complex Offshore Support Structures

    DEFF Research Database (Denmark)

    Wang, Shaofeng; Larsen, Torben J.; Hansen, Anders Melchior


    Modern large MW wind turbines today are installed at larger water depth than applicable for traditional monopile substructure. It appears that foundation types such as jacket and tripod are gaining more popularity for these locations. For certification purposes, a full set of design load calculat......Modern large MW wind turbines today are installed at larger water depth than applicable for traditional monopile substructure. It appears that foundation types such as jacket and tripod are gaining more popularity for these locations. For certification purposes, a full set of design load...... calculations consisting of up to thousands design load cases needs to be evaluated. However, even the simplest aero-elastic model of such structures has many more DOFs than monopile, resulting in excessive computation burden. In order to deal with this problem, the superelement method has been introduced...... for modelling such structures. One superelement method has been proven very promising in the previous project of Wave Loads [1] and a fundamental question in such DOFs reduction methods is which modes that are essential and which modes can be neglected. For the jacket structure, the introduction of a gravity...

  6. Comparison and validation of community structures in complex networks

    CERN Document Server

    Gustafsson, M; Lombardi, A; Gustafsson, Mika; Hornquist, Michael; Lombardi, Anna


    The issue of partitioning a network into communities has attracted a great deal of attention recently. Most authors seem to equate this issue with the one of finding the maximum value of the modularity, as defined by Newman. Since the problem formulated this way is NP-hard, most effort has gone into the construction of search algorithms, and less to the question of other measures of community structures, similarities between various partitionings and the validation with respect to external information. Here we concentrate on a class of computer generated networks and on three well-studied real networks which constitute a bench-mark for network studies; the karate club, the US college football teams and a gene network of yeast. We utilize some standard ways of clustering data (originally not designed for finding community structures in networks) and show that these classical methods sometimes outperform the newer ones. We discuss various measures of the strength of the modular structure, and show by examples f...

  7. Structural Studies of Complex Carbohydrates of Plant Cell Walls

    Energy Technology Data Exchange (ETDEWEB)

    Darvill, Alan [Univ. of Georgia, Athens, GA (United States); Hahn, Michael G. [Univ. of Georgia, Athens, GA (United States); O' Neill, Malcolm A. [Univ. of Georgia, Athens, GA (United States); York, William S. [Univ. of Georgia, Athens, GA (United States)


    Most of the solar energy captured by land plants is converted into the polysaccharides (cellulose, hemicellulose, and pectin) that are the predominant components of the cell wall. These walls, which account for the bulk of plant biomass, have numerous roles in the growth and development of plants. Moreover, these walls have a major impact on human life as they are a renewable source of biomass, a source of diverse commercially useful polymers, a major component of wood, and a source of nutrition for humans and livestock. Thus, understanding the molecular mechanisms that lead to wall assembly and how cell walls and their component polysaccharides contribute to plant growth and development is essential to improve and extend the productivity and value of plant materials. The proposed research will develop and apply advanced analytical and immunological techniques to study specific changes in the structures and interactions of the hemicellulosic and pectic polysaccharides that occur during differentiation and in response to genetic modification and chemical treatments that affect wall biosynthesis. These new techniques will make it possible to accurately characterize minute amounts of cell wall polysaccharides so that subtle changes in structure that occur in individual cell types can be identified and correlated to the physiological or developmental state of the plant. Successful implementation of this research will reveal fundamental relationships between polysaccharide structure, cell wall architecture, and cell wall functions.

  8. Modular Structures, Robustness and Protection of Complex Networks: Theory, Complexity and Algorithms

    NARCIS (Netherlands)

    Trajanovski, S.


    Community structure is observed in many real-world networks, such as (online) social networks, where groups of friends of a certain person are often also friends of each other. Newman's modularity has been explored as an important quantitative metric for communities and clusters detection in network

  9. Modular Structures, Robustness and Protection of Complex Networks: Theory, Complexity and Algorithms

    NARCIS (Netherlands)

    Trajanovski, S.


    Community structure is observed in many real-world networks, such as (online) social networks, where groups of friends of a certain person are often also friends of each other. Newman's modularity has been explored as an important quantitative metric for communities and clusters detection in network

  10. Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements

    KAUST Repository

    Guturu, H.


    Mapping the DNA-binding preferences of transcription factor (TF) complexes is critical for deciphering the functions of cis-regulatory elements. Here, we developed a computational method that compares co-occurring motif spacings in conserved versus unconserved regions of the human genome to detect evolutionarily constrained binding sites of rigid TF complexes. Structural data were used to estimate TF complex physical plausibility, explore overlapping motif arrangements seldom tackled by non-structure-aware methods, and generate and analyse three-dimensional models of the predicted complexes bound to DNA. Using this approach, we predicted 422 physically realistic TF complex motifs at 18% false discovery rate, the majority of which (326, 77%) contain some sequence overlap between binding sites. The set of mostly novel complexes is enriched in known composite motifs, predictive of binding site configurations in TF-TF-DNA crystal structures, and supported by ChIP-seq datasets. Structural modelling revealed three cooperativity mechanisms: direct protein-protein interactions, potentially indirect interactions and \\'through-DNA\\' interactions. Indeed, 38% of the predicted complexes were found to contain four or more bases in which TF pairs appear to synergize through overlapping binding to the same DNA base pairs in opposite grooves or strands. Our TF complex and associated binding site predictions are available as a web resource at

  11. Synthesis, structural characterization and thermal properties of copper and silver silyl complexes. (United States)

    Sgro, Michael J; Piers, Warren E; Romero, Patricio E


    The synthesis of copper and silver silyl complexes containing either N-heterocyclic carbenes or nitrogen donors is described. Alterations made to both the neutral donor ligands as well as the silyl group provided access to a number of different compounds. Many of the complexes synthesized were studied in the solid state and the effect of the donor ligand on the final structure of the complexes was examined. The thermal properties of the complexes were explored using thermogravimetric analysis, differential scanning calorimetry and sublimations. Some of the complexes synthesized were demonstrated to be promising volatile metal precursors.

  12. Structure of a eukaryotic SWEET transporter in a homotrimeric complex. (United States)

    Tao, Yuyong; Cheung, Lily S; Li, Shuo; Eom, Joon-Seob; Chen, Li-Qing; Xu, Yan; Perry, Kay; Frommer, Wolf B; Feng, Liang


    Eukaryotes rely on efficient distribution of energy and carbon skeletons between organs in the form of sugars. Glucose in animals and sucrose in plants serve as the dominant distribution forms. Cellular sugar uptake and release require vesicular and/or plasma membrane transport proteins. Humans and plants use proteins from three superfamilies for sugar translocation: the major facilitator superfamily (MFS), the sodium solute symporter family (SSF; only in the animal kingdom), and SWEETs. SWEETs carry mono- and disaccharides across vacuolar or plasma membranes. Plant SWEETs play key roles in sugar translocation between compartments, cells, and organs, notably in nectar secretion, phloem loading for long distance translocation, pollen nutrition, and seed filling. Plant SWEETs cause pathogen susceptibility possibly by sugar leakage from infected cells. The vacuolar Arabidopsis thaliana AtSWEET2 sequesters sugars in root vacuoles; loss-of-function mutants show increased susceptibility to Pythium infection. Here we show that its orthologue, the vacuolar glucose transporter OsSWEET2b from rice (Oryza sativa), consists of an asymmetrical pair of triple-helix bundles, connected by an inversion linker transmembrane helix (TM4) to create the translocation pathway. Structural and biochemical analyses show OsSWEET2b in an apparent inward (cytosolic) open state forming homomeric trimers. TM4 tightly interacts with the first triple-helix bundle within a protomer and mediates key contacts among protomers. Structure-guided mutagenesis of the close paralogue SWEET1 from Arabidopsis identified key residues in substrate translocation and protomer crosstalk. Insights into the structure-function relationship of SWEETs are valuable for understanding the transport mechanism of eukaryotic SWEETs and may be useful for engineering sugar flux.

  13. Advanced ultrasonic testing of complex shaped composite structures (United States)

    Dolmatov, D.; Zhvyrblya, V.; Filippov, G.; Salchak, Y.; Sedanova, E.


    Due to the wide application of composite materials it is necessary to develop unconventional quality control techniques. One of the methods that can be used for this purpose is ultrasonic tomography. In this article an application of a robotic ultrasonic system is considered. Precise positioning of the robotic scanner and path generating are defined as ones of the most important aspects. This study proposes a non-contact calibration method of a robotic ultrasonic system. Path of the scanner requires a 3D model of controlled objects which are created in accordance with the proposed algorithm. The suggested techniques are based on implementation of structured light method.

  14. Diversity and Phylogenetic Structure of Two Complex Marine Microbial Communities (United States)


    Du, Y., et al. (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron...C.A., Newell, S.Y., and Paerl, H.W. (1995) The role References of standing dead Spartina alternfflora and benthic microal- gae in salt marsh food webs ...q Ja 1,4 1 S., 47. 145-1 156 (19r . lntiutoide Geologia’ Mineria , Universidad Nactonalde Jujuy, Avenida Bolwiva . V~a. C 3. j kLmnnnaommntal

  15. Structural and dielectric properties of a complex tungsten bronze ferroelectric (United States)

    Padhee, R.; Das, P. R.; Parida, B. N.; Choudhary, R. N. P.


    The polycrystalline sample of K2Pb2Y2W2Ti4Nb4O30 was synthesized by a mixed-oxide method at high temperature. The compound formation was checked by preliminary X-ray structural analysis. The SEM micrograph exhibits uniform plate and rod-like grain distribution. Detailed studies of variation of dielectric parameters with temperature and frequency, and polarization confirmed the existence of ferroelectricity in the material, with phase transition at 390°C. The ac conductivity follows the Arrhenius equation.

  16. Analysis on complex structure stability under different bar angle with BIM technology

    Directory of Open Access Journals (Sweden)

    Wang Xiongjue


    Full Text Available Sun Valley, the landmark building of World Expo in Shanghai, which has free surface with single-layer reticulated shell structure, is a typical complex structure. CAD/CAM integrated information system to design is used for the complex structure; however, it is a very rigorous process to be used widely. The relevant technology of the Sun Valley is not open to the public at present, so we try to use BIM technology to model the Sun Valley, including architecture modelling and structure analysis. By analysis of the Sun Valley structure using this method, it is proved that the problems in modelling may be solved by writing some script codes in Rhino software and the stability of the model can also be analyzed. The new approach is viable and effective in combination with different softwares such as Rhino, Revit, and Midas in solution of the complex shaped surfaces’ structure for modelling and calculation.

  17. Crystallographic structure of ubiquitin in complex with cadmium ions

    Directory of Open Access Journals (Sweden)

    Cheung Peter


    Full Text Available Abstract Background Ubiquitination plays a critical role in regulating many cellular processes, from DNA repair and gene transcription to cell cycle and apoptosis. It is catalyzed by a specific enzymatic cascade ultimately leading to the conjugation of ubiquitin to lysine residues of the target protein that can be the ubiquitin molecule itself and to the formation of poly-ubiquitin chains. Findings We present the crystal structure at 3.0 Å resolution of bovine ubiquitin crystallized in presence of cadmium ions. Two molecules of ubiquitin are present in the asymmetric unit. Interestingly this non-covalent dimeric arrangement brings Lys-6 and Lys-63 of each crystallographically-independent monomer in close contact with the C-terminal ends of the other monomer. Residues Leu-8, Ile-44 and Val-70 that form a hydrophobic patch at the surface of the Ub monomer are trapped at the dimer interface. Conclusions The structural basis for signalling by poly-Ub chains relies on a visualization of conformations of alternatively linked poly-Ub chains. This arrangement of ubiquitin could illustrate how linkages involving Lys-6 or Lys-63 of ubiquitin are produced in the cell. It also details how ubiquitin molecules can specifically chelate cadmium ions.

  18. Syntheses and Structures of Lanthanide Complexes with Isonicotinate

    Institute of Scientific and Technical Information of China (English)

    ZHANG Man-Bo; ZHENG Shou-Tian; YANG Guo-Yu


    The crystal structures of two coordination polymers [Ln(IN)3(H2O)2]n (Ln = Nd 1, Gd 2; IN = isonicotinate) were determined by single-crystal X-ray diffraction and further chara- cterized by IR, elemental analysis and thermogravimetric analysis. Crystal data for 1: monoclinic, space group P21/c, a = 9.6636(5), b = 19.7532(10), c = 11.6183(6) (A), β = 112.032(1)°, V = 2055.83(18) (A)3, Z = 4, Dc = 1.766 g/cm3, F(000) = 1076, μ = 2.575 mm-1 and R = 0.0493; Crystal data for 2: monoclinic, space group C2/c, a = 20.251(2), b = 11.6199(11), c = 9.8240(9) (A), β = 115.505(3)°, V = 2086.4(3) (A)3, Z = 4, Dc = 1.781 g/cm3, F(000) = 1092, μ = 3.228 mm-1 and R = 0.0695. In the title compounds, the center atoms Ln(III) are in a distorted square antiprismatic geometry and linked by bridging isonicotinate to form an infinite chain. The intermolecular hydro- gen bonds lead to the formation of three-dimensional supramolecular structures.

  19. Optimal pinning controllability of complex networks: dependence on network structure. (United States)

    Jalili, Mahdi; Askari Sichani, Omid; Yu, Xinghuo


    Controlling networked structures has many applications in science and engineering. In this paper, we consider the problem of pinning control (pinning the dynamics into the reference state), and optimally placing the driver nodes, i.e., the nodes to which the control signal is fed. Considering the local controllability concept, a metric based on the eigenvalues of the Laplacian matrix is taken into account as a measure of controllability. We show that the proposed optimal placement strategy considerably outperforms heuristic methods including choosing hub nodes with high degree or betweenness centrality as drivers. We also study properties of optimal drivers in terms of various centrality measures including degree, betweenness, closeness, and clustering coefficient. The profile of these centrality values depends on the network structure. For homogeneous networks such as random small-world networks, the optimal driver nodes have almost the mean centrality value of the population (much lower than the centrality value of hub nodes), whereas the centrality value of optimal drivers in heterogeneous networks such as scale-free ones is much higher than the average and close to that of hub nodes. However, as the degree of heterogeneity decreases in such networks, the profile of centrality approaches the population mean.

  20. Structural biology. Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target. (United States)

    Mulepati, Sabin; Héroux, Annie; Bailey, Scott


    In prokaryotes, RNA derived from type I and type III CRISPR loci direct large ribonucleoprotein complexes to destroy invading bacteriophage and plasmids. In Escherichia coli, this 405-kilodalton complex is called Cascade. We report the crystal structure of Cascade bound to a single-stranded DNA (ssDNA) target at a resolution of 3.03 angstroms. The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. This noncanonical structure is facilitated by rotation of every sixth nucleotide out of the RNA-DNA hybrid and is stabilized by the highly interlocked organization of protein subunits. These studies provide insight into both the assembly and the activity of this complex and suggest a mechanism to enforce fidelity of target binding.

  1. Synthesis, characterization, and structure of reduced tungsten chalcogenide cluster complexes

    Energy Technology Data Exchange (ETDEWEB)

    Xiaobing, Xie


    Over the previous twenty years, ternary molybdenum chalcogenides of the general formula M{sub x}Mo{sub 6}Y{sub 8} (M = ternary metal cation; Y = chalcogenide), known as Chevrel phases, have been extensively studied. Many of these compounds have been found to have superconductivity, catalytic activity and ionic conductivity. The rich chemistry of the Chevrel phases raises considerable interest in finding the tungsten analogues of these phases. However, no such analogue has ever been synthesized, although the Chevrel phases are usually prepared directly from elements at high temperatures above 1000{degrees}C. The absence of the tungsten analogues may be caused by their thermodynamic instability at such high temperatures. Thus it might be necessary to avoid high-temperature synthetic procedures in order to establish the ternary and binary tungsten chalcogenides. A major focus of the McCarley research group has been on the preparation of M{sub 6}Y{sub 8}L{sub 6} (M = Mo, W; Y = S, Se, Te) cluster complexes as low temperature pathways to the Chevrel phases.

  2. Common neighbour structure and similarity intensity in complex networks (United States)

    Hou, Lei; Liu, Kecheng


    Complex systems as networks always exhibit strong regularities, implying underlying mechanisms governing their evolution. In addition to the degree preference, the similarity has been argued to be another driver for networks. Assuming a network is randomly organised without similarity preference, the present paper studies the expected number of common neighbours between vertices. A symmetrical similarity index is accordingly developed by removing such expected number from the observed common neighbours. The developed index can not only describe the similarities between vertices, but also the dissimilarities. We further apply the proposed index to measure of the influence of similarity on the wring patterns of networks. Fifteen empirical networks as well as artificial networks are examined in terms of similarity intensity and degree heterogeneity. Results on real networks indicate that, social networks are strongly governed by the similarity as well as the degree preference, while the biological networks and infrastructure networks show no apparent similarity governance. Particularly, classical network models, such as the Barabási-Albert model, the Erdös-Rényi model and the Ring Lattice, cannot well describe the social networks in terms of the degree heterogeneity and similarity intensity. The findings may shed some light on the modelling and link prediction of different classes of networks.

  3. Complex structure of a bacterial class 2 histone deacetylase homologue with a trifluoromethylketone inhibitor

    Energy Technology Data Exchange (ETDEWEB)

    Nielsen, Tine Kragh [Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik and GZMB, Justus-von-Liebig Weg 11, 37077 Göttingen (Germany); Hildmann, Christian; Riester, Daniel; Wegener, Dennis; Schwienhorst, Andreas [Abteilung für Molekulare Genetik und Präparative Molekularbiologie, Institut für Mikrobiologie und Genetik, Grisebachstrasse 8, 37077 Göttingen (Germany); Ficner, Ralf, E-mail: [Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik and GZMB, Justus-von-Liebig Weg 11, 37077 Göttingen (Germany)


    The crystal structure of HDAH FB188 in complex with a trifluoromethylketone at 2.2 Å resolution is reported and compared to a previously determined inhibitor complex. Histone deacetylases (HDACs) have emerged as attractive targets in anticancer drug development. To date, a number of HDAC inhibitors have been developed and most of them are hydroxamic acid derivatives, typified by suberoylanilide hydroxamic acid (SAHA). Not surprisingly, structural information that can greatly enhance the design of novel HDAC inhibitors is so far only available for hydroxamic acids in complex with HDAC or HDAC-like enzymes. Here, the first structure of an enzyme complex with a nonhydroxamate HDAC inhibitor is presented. The structure of the trifluoromethyl ketone inhibitor 9,9,9-trifluoro-8-oxo-N-phenylnonanamide in complex with bacterial FB188 HDAH (histone deacetylase-like amidohydrolase from Bordetella/Alcaligenes strain FB188) has been determined. HDAH reveals high sequential and functional homology to human class 2 HDACs and a high structural homology to human class 1 HDACs. Comparison with the structure of HDAH in complex with SAHA reveals that the two inhibitors superimpose well. However, significant differences in binding to the active site of HDAH were observed. In the presented structure the O atom of the trifluoromethyl ketone moiety is within binding distance of the Zn atom of the enzyme and the F atoms participate in interactions with the enzyme, thereby involving more amino acids in enzyme–inhibitor binding.

  4. Structure and Bonding Investigation of Plutonium Peroxocarbonate Complexes Using Cerium Surrogates and Electronic Structure Modeling

    Energy Technology Data Exchange (ETDEWEB)

    Sweet, Lucas E.; Corbey, Jordan F.; Gendron, Frédéric; Autschbach, Jochen; McNamara, Bruce K.; Ziegelgruber, Kate L.; Arrigo, Leah M.; Peper, Shane M.; Schwantes, Jon M.


    Herein, we report the synthesis and structural characterization of K8[(CO3)3Pu]2(µ-η2-η2-O2)2•12H2O. This is the second plutonium-containing addition to the previously studied alkali metal peroxo-carbonate series M8[(CO3)3A]2(µ-η2-η2-O2)2•xH2O (M = alkali metal; A = Ce or Pu; x = 8, 10, 12 or 18), for which only the M = Na analog has been previously reported when A = Pu. The previously reported crystal structure for Na8[(CO3)3Pu]2(µ-η2-η2-O2)2•12H2O is not isomorphous with its known Ce analogue. However, a new synthetic route to these M8[(CO3)3A]2(µ-η2-η2-O2)2•12H2O complexes, described below, has produced crystals of Na8[(CO3)3Ce]2(µ-η2-η2-O2)2•12H2O that are isomorphous with the previously reported Pu analogue. Via this synthetic method, the M = Na, K, Rb, and Cs salts of M8[(CO3)3Ce]2(µ-η2-η2-O2)2•xH2O have also been synthesized for systematic structural comparison with each other and the available Pu analogues using single-crystal X-ray diffraction, Raman spectroscopy and density functional theory (DFT) calculations. The cerium salts in particular demonstrate subtle differences in the peroxide bond lengths which correlate to Raman shifts for the peroxide Op–Op stretch (Op = the oxygen atoms of the peroxide bridges) with each of the cations studied: Na+ (1.492(3) Å /847 cm-1), Rb+ (1.471(1) Å /854 cm-1), Cs+ (1.474(1) Å /859 cm-1), and K+ (1.468(6) Å, 870 cm-1). The trends observed in the M–Op and Op–Op bond distances appear to relate to supermolecular interactions between the neighboring cations.

  5. Two organoantimony (V) coordination complexes modulated by isomers of trifluoromethylbenzoate ligands: Syntheses, crystal structure, photodegradation properties (United States)

    Zhang, Xiao-Yin; Cui, Lian-sheng; Zhang, Xia; Jin, Fan; Fan, Yu-Hua


    Two organoantimony (V) coordination complexes, namely Ph3Sb(2-tmbc) (1) and Ph3Sb(3-tmbc) (2) (2-tmbc = 2-(trifluoromethyl)benzoic carboxyl, 3-tmbc = 3-(trifluoromethyl)benzoic carboxyl) have been synthesized and characterized by IR spectra, elemental analysis, powder X-ray diffraction (PXRD) and single-crystal X-ray diffraction. Single-crystal X-ray diffraction analysis reveals that complexes 1 and 2 show different architectures by the intermolecular hydrogen bonds (Csbnd H⋯F), complex 1 displays an 1D straight chain structure, while complex 2 shows an 1D zigzag chain structure. The photodegradation properties of complexes 1 and 2 has been investigated in organic dyes (RhB, MV, MB) the results indicated that the two complexes are good candidates for the photocatalytic degradation of three dyes. The tentative photocatalytic degradations mechanism is discussed.

  6. n +-Microcrystalline-Silicon Tunnel Layer in Tandem Si-Based Thin Film Solar Cells (United States)

    Lee, Ching-Ting; Lee, Hsin-Ying; Chen, Kuan-Hao


    In this study, the p-SiC/ i-Si/ n-Si cell and the p-SiC/ i-SiGe/ n-Si cell deposited using plasma-enhanced chemical vapor deposition were cascaded for forming the tandem Si-based thin film solar cells to absorb the wide solar spectrum. To further improve the performances of the tandem Si-based thin film solar cells, a 5-nm-thick n +-microcrystalline-Si ( n +-μc-Si) tunnel layer deposited using the laser-assisted plasma-enhanced chemical vapor deposition was inserted between the p-SiC/ i-Si/ n-Si cell and the p-SiC/ i-SiGe/ n-Si cell. Since both the plasma and the CO2 laser were simultaneously utilized to efficiently decompose the reactant and doping gases, the carrier concentration and the carrier mobility of the n +-μc-Si tunnel layer were significantly improved. The ohmic contact formed between the p-SiC layer and the n +-μc-Si tunnel layer with low resistance was beneficial to the generated current transportation and the carrier recombination rate. Therefore, the conversion efficiency of the tandem solar cells was promoted from 8.57% and 8.82% to 9.91% compared to that without tunnel layer and with 5-nm-thick n +-amorphous-Si tunnel layer.

  7. Enhanced photocurrent density in graphene/Si based solar cell (GSSC) by optimizing active layer thickness

    Energy Technology Data Exchange (ETDEWEB)

    Rosikhin, Ahmad, E-mail:; Hidayat, Aulia Fikri; Syuhada, Ibnu; Winata, Toto, E-mail: [Department of physics, physics of electronic materials research division Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung Jl. Ganesha 10, Bandung 40132, Jawa Barat – Indonesia (Indonesia)


    Thickness dependent photocurrent density in active layer of graphene/Si based solar cell has been investigated via analytical – simulation study. This report is a preliminary comparison of experimental and analytical investigation of graphene/Si based solar cell. Graphene sheet was interfaced with Si thin film forming heterojunction solar cell that was treated as a device model for photocurrent generator. Such current can be enhanced by optimizing active layer thickness and involving metal oxide as supporting layer to shift photons absorption. In this case there are two type of devices model with and without TiO{sub 2} in which the silicon thickness varied at 20 – 100 nm. All of them have examined and also compared with each other to obtain an optimum value. From this calculation it found that generated currents almost linear with thickness but there are saturated conditions that no more enhancements will be achieved. Furthermore TiO{sub 2} layer is effectively increases photon absorption but reducing device stability, maximum current is fluctuates enough. This may caused by the disturbance of excitons diffusion and resistivity inside each layer. Finally by controlling active layer thickness, it is quite useful to estimate optimization in order to develop the next solar cell devices.

  8. Two-Dimensional Cavity Resonant Modes of Si Based Bragg Reflection Ridge Waveguide

    Institute of Scientific and Technical Information of China (English)

    CHEN San; Lu Hong-Yan; CHEN Kun-Ji; XU Jun; MA Zhong-Yuan; LI Wei; HUANG Xin-Fan


    @@ Si-based ridge-waveguides with Bragg reflectors are fabricated based on our method.Three resonant peaks could be obviously identified from the photoluminescence spectra, and field patterns of these resonant peaks, simulated by the finite difference time domain (FDTD) method, confirm that these peaks originate from cavity resonances.The resonant wavelengths and spatial angular distribution are given by the resonant models, which agree well with the experimental data.Experimentally, a simple method is proposed to testify the experimental and theoretical results.Such devices based on Bragg reflectors may have potential applications in light-emitting diodes, lasers and integrated photonic circuits.%Si-based ridge-waveguides with Bragg reflectors are fabricated based on our method. Three resonant peaks could be obviously identified from the photoluminescence spectra, and field patterns of these resonant peaks, simulated by the finite difference time domain (FDTD) method, confirm that these peaks originate from cavity resonances. The resonant wavelengths and spatial angular distribution are given by the resonant models, which agree well with the experimental data. Experimentally, a simple method is proposed to testify the experimental and theoretical results. Such devices based on Bragg reflectors may have potential applications in light-emitting diodes, lasers and integrated photonic circuits.

  9. Diffuse scattering and partial disorder in complex structures

    Directory of Open Access Journals (Sweden)

    T. R. Welberry


    Full Text Available The study of single-crystal diffuse scattering (SCDS goes back almost to the beginnings of X-ray crystallography. Because SCDS arises from two-body correlations, it contains information about local (short-range ordering in the sample, information which is often crucial in the attempt to relate structure to function. This review discusses the state of the field, including detectors and data collection and the modelling of SCDS using Monte Carlo and ab initio techniques. High-quality, three-dimensional volumes of SCDS data can now be collected at synchrotron light sources, allowing ever more detailed and quantitative analyses to be undertaken, and opening the way to approaches such as three-dimensional pair distribution function studies (3D-PDF and automated refinement of a disorder model, powerful techniques that require large volumes of low-noise data.

  10. Exploiting Structural Complexity for Robust and Rapid Hyperspectral Imaging

    CERN Document Server

    Ely, Gregory; Miller, Eric L


    This paper presents several strategies for spectral de-noising of hyperspectral images and hypercube reconstruction from a limited number of tomographic measurements. In particular we show that the non-noisy spectral data, when stacked across the spectral dimension, exhibits low-rank. On the other hand, under the same representation, the spectral noise exhibits a banded structure. Motivated by this we show that the de-noised spectral data and the unknown spectral noise and the respective bands can be simultaneously estimated through the use of a low-rank and simultaneous sparse minimization operation without prior knowledge of the noisy bands. This result is novel for for hyperspectral imaging applications. In addition, we show that imaging for the Computed Tomography Imaging Systems (CTIS) can be improved under limited angle tomography by using low-rank penalization. For both of these cases we exploit the recent results in the theory of low-rank matrix completion using nuclear norm minimization.

  11. Designing A Simple Folder Structure For A Complex Domain

    Directory of Open Access Journals (Sweden)

    Torkil Clemmensen


    Full Text Available In this paper I explore a case of designing a simple folder structure for a new e-learning software program for a university study program. The aim is to contribute to the theoretical base for human work interaction design (HWID by identifying the type of relations connecting design artifacts with work analysis and interaction design processes. The action research method was used, with the author in a double role as university researcher and project manager of a developer group within the university. Analysis was conducted through grounded theory, inspired by the HWID framework. The findings support the use of a holistic framework with asymmetrical relations between work analysis and design artifacts, and between design artifacts and interaction design. The paper concludes with suggestions for modifying the general framework, and recommendations for a HWID approach to design artifacts.

  12. Modelling nutrient reduction targets - model structure complexity vs. data availability (United States)

    Capell, Rene; Lausten Hansen, Anne; Donnelly, Chantal; Refsgaard, Jens Christian; Arheimer, Berit


    In most parts of Europe, macronutrient concentrations and loads in surface water are currently affected by human land use and land management choices. Moreover, current macronutrient concentration and load levels often violate European Water Framework Directive (WFD) targets and effective measures to reduce these levels are sought after by water managers. Identifying such effective measures in specific target catchments should consider the four key processes release, transport, retention, and removal, and thus physical catchment characteristics as e.g. soils and geomorphology, but also management data such as crop distribution and fertilizer application regimes. The BONUS funded research project Soils2Sea evaluates new, differentiated regulation strategies to cost-efficiently reduce nutrient loads to the Baltic Sea based on new knowledge of nutrient transport and retention processes between soils and the coast. Within the Soils2Sea framework, we here examine the capability of two integrated hydrological and nutrient transfer models, HYPE and Mike SHE, to model runoff and nitrate flux responses in the 100 km2 Norsminde catchment, Denmark, comparing different model structures and data bases. We focus on comparing modelled nitrate reductions within and below the root zone, and evaluate model performances as function of available model structures (process representation within the model) and available data bases (temporal forcing data and spatial information). This model evaluation is performed to aid in the development of model tools which will be used to estimate the effect of new nutrient reduction measures on the catchment to regional scale, where available data - both climate forcing and land management - typically are increasingly limited with the targeted spatial scale and may act as a bottleneck for process conceptualizations and thus the value of a model as tool to provide decision support for differentiated regulation strategies.

  13. Multi-Path Guided Wave Imaging for Inspection and Monitoring of Large, Complex Structures Project (United States)

    National Aeronautics and Space Administration — There is a well-recognized need within NASA and the aerospace community at large for rapid and reliable methods for inspection of large, complex structures. This...

  14. Cleave to Leave : Structural Insights into the Dynamic Organization of the Nuclear Pore Complex

    NARCIS (Netherlands)

    Dokudovskaya, Svetlana; Veenhoff, Liesbeth M.; Rout, Michael P.


    A detailed understanding of the fine structure of the nuclear pore complex has remained elusive. Now, studies on a small protein domain have shed light on the dynamic organization of this massive assembly.

  15. 3D Printing Complex Unitized Instrument Optical Benches and Metering Structures Project (United States)

    National Aeronautics and Space Administration — The objective of this project is to determine the engineering techniques required to manufacture complex, thin-shelled instrument structures. These techniques will...

  16. Microstructure and High Temperature Plastic Deformation Behavior of Al-12Si Based Alloy Fabricated by an Electromagnetic Casting and Stirring Process

    Energy Technology Data Exchange (ETDEWEB)

    Jeon, Kyung-Soo; Roh, Heung-Ryeol; Kim, Mok-Soon [Inha University, Incheon (Korea, Republic of); Kim, Jong-Ho; Park, Joon-Pyo [Research Institute of Industrial Science and Technology, Pohang (Korea, Republic of)


    An as-received EMC/S (electromagnetic casting and stirring)-processed Al-12Si based alloy billet was homogenized to examine its microstructure and high temperature plastic deformation behavior, using compressive tests over the temperature range from 623 to 743 K and a strain rate range from 1.0×10{sup -3} to 1.0×10{sup 0}s{sup -1}. The results were compared with samples processed by the direct chill casting (DC) method. The fraction of equiaxed structure for the as-received EMC/S billet(41%) was much higher than that of the as-received DC billet(6 %). All true stress – true strain curves acquired from the compressive tests exhibited a peak stress at the initial stage of plastic deformation. Flow stress showed a steady state region after the appearance of peak stress with increasing strain. The peak stress decreased with increasing temperature at a given strain rate and a decreasing strain rate at a given temperature. A constitutive equation was made for each alloy, which could be used to predict the peak stress. A recrystallized grain structure was observed in all the deformed specimens, indicating that dynamic recrystallization is the predominant mechanism during high temperature plastic deformation of both the homogenized EMC/S and DC-processed Al-12Si based alloys.

  17. Surface Structures Formed by a Copper(II Complex of Alkyl-Derivatized Indigo

    Directory of Open Access Journals (Sweden)

    Akinori Honda


    Full Text Available Assembled structures of dyes have great influence on their coloring function. For example, metal ions added in the dyeing process are known to prevent fading of color. Thus, we have investigated the influence of an addition of copper(II ion on the surface structure of alkyl-derivatized indigo. Scanning tunneling microscope (STM analysis revealed that the copper(II complexes of indigo formed orderly lamellar structures on a HOPG substrate. These lamellar structures of the complexes are found to be more stable than those of alkyl-derivatized indigos alone. Furthermore, 2D chirality was observed.

  18. Uncertainty Quantification for Complex RF-structures Using the State-space Concatenation Approach

    CERN Document Server

    Heller, Johann; Schmidt, Christian; Van Rienen, Ursula


    as well as to employ robust optimizations, a so-called uncertainty quantification (UQ) is applied. For large and complex structures such computations are heavily demanding and cannot be carried out using standard brute-force approaches. In this paper, we propose a combination of established techniques to perform UQ for long and complex structures, where the uncertainty is located only in parts of the structure. As exemplary structure, we investigate the third-harmonic cavity, which is being used at the FLASH accelerator at DESY, assuming an uncertain...

  19. Structural and functional characterization of protein complexes in the blood coagulation cascade

    DEFF Research Database (Denmark)

    Madsen, Jesper Jonasson

    In this dissertation, components of coagulation factor (F)X-activating (tenase; fXase) complexes are studied using computational biophysics and the molecular dynamics (MD) method. The main focus is on structure-function relationships of the two central tenase complexes with respect to activation...

  20. Structural Study of Inclusion Complex of Andrographolide with β-Cyclodextrin Prepared under Microwave Irradiation

    Institute of Scientific and Technical Information of China (English)


    An inclusion complex of β-cyclodextrin with andrographolide (Andro) was prepared by using a convenient method of microwave irradiation. The structure of the inclusion complex was determined by the 1H NMR, 2D NMR spectroscopy as well as the elemental analysis.

  1. Diamino-ligated platinum(II) and platinum(IV) phenoxide complexes; syntheses and crystal structures

    NARCIS (Netherlands)

    Koten, G. van; Kapteijn, G.M.; Meijer, M.D.; Grove, D.M.; Veldman, N.; Spek, A.L.


    The reaction of the diamino-ligated dimethylplatinum(II) complex [Pt(Me){2}(bpy)] (bpy=2, 2'-bipyridyl) with phenol affords the new complex [Pt(Me)(OPh)(bpy)] (1). The X-ray crystal structure of square-planar 1 is reported: orthorhombic, space group P2{1}2{1}2{1} (No. 19), a = 9.1625(12), b =

  2. Cryo-EM structure of respiratory complex I reveals a link to mitochondrial sulfur metabolism. (United States)

    D'Imprima, Edoardo; Mills, Deryck J; Parey, Kristian; Brandt, Ulrich; Kühlbrandt, Werner; Zickermann, Volker; Vonck, Janet


    Mitochondrial complex I is a 1MDa membrane protein complex with a central role in aerobic energy metabolism. The bioenergetic core functions are executed by 14 central subunits that are conserved from bacteria to man. Despite recent progress in structure determination, our understanding of the function of the ~30 accessory subunits associated with the mitochondrial complex is still limited. We have investigated the structure of complex I from the aerobic yeast Yarrowia lipolytica by cryo-electron microscopy. Our density map at 7.9Å resolution closely matches the 3.6-3.9Å X-ray structure of the Yarrowia lipolytica complex. However, the cryo-EM map indicated an additional subunit on the side of the matrix arm above the membrane surface, pointing away from the membrane arm. The density, which is not present in any previously described complex I structure and occurs in about 20 % of the particles, was identified as the accessory sulfur transferase subunit ST1. The Yarrowia lipolytica complex I preparation is active in generating H2S from the cysteine derivative 3-mercaptopyruvate, catalyzed by ST1. We thus provide evidence for a link between respiratory complex I and mitochondrial sulfur metabolism.

  3. Electronic structure and luminescence of tellurium (IV) halide complexes with guanidine and caesium cations (United States)

    Dotsenko, A. A.; Shcheka, O. L.; Vovna, V. I.; Korochentsev, V. V.; Mirochnik, A. G.; Sedakova, T. V.


    The present paper continues a series of publications on the investigation of complex compounds of s2 ions and their properties. The structure of the valence levels of Cs2TeX6, (HGu)2TeCl6 complexes (where X = Cl, Br; HGu+ - guanidinium) is examined, the orbital nature of luminescence excitation is established, and the relationship of properties with the electronic structure is determined by means of X-ray photoelectron spectroscopy (XPS) and density functional theory (DFT).

  4. Spectroscopic and structural study of the newly synthesized heteroligand complex of copper with creatinine and urea (United States)

    Gangopadhyay, Debraj; Singh, Sachin Kumar; Sharma, Poornima; Mishra, Hirdyesh; Unnikrishnan, V. K.; Singh, Bachcha; Singh, Ranjan K.


    Study of copper complex of creatinine and urea is very important in life science and medicine. In this paper, spectroscopic and structural study of a newly synthesized heteroligand complex of copper with creatinine and urea has been discussed. Structural studies have been carried out using DFT calculations and spectroscopic analyses were carried out by FT-IR, Raman, UV-vis absorption and fluorescence techniques. The copper complex of creatinine and the heteroligand complex were found to have much increased water solubility as compared to pure creatinine. The analysis of FT-IR and Raman spectra helps to understand the coordination properties of the two ligands and to determine the probable structure of the heteroligand complex. The LIBS spectra of the heteroligand complex reveal that the complex is free from other metal impurities. UV-visible absorption spectra and the fluorescence emission spectra of the aqueous solution of Cu-Crn-urea heteroligand complex at different solute concentrations have been analyzed and the complex is found to be rigid and stable in its monomeric form at very low concentrations.

  5. Spectroscopic and structural study of the newly synthesized heteroligand complex of copper with creatinine and urea. (United States)

    Gangopadhyay, Debraj; Singh, Sachin Kumar; Sharma, Poornima; Mishra, Hirdyesh; Unnikrishnan, V K; Singh, Bachcha; Singh, Ranjan K


    Study of copper complex of creatinine and urea is very important in life science and medicine. In this paper, spectroscopic and structural study of a newly synthesized heteroligand complex of copper with creatinine and urea has been discussed. Structural studies have been carried out using DFT calculations and spectroscopic analyses were carried out by FT-IR, Raman, UV-vis absorption and fluorescence techniques. The copper complex of creatinine and the heteroligand complex were found to have much increased water solubility as compared to pure creatinine. The analysis of FT-IR and Raman spectra helps to understand the coordination properties of the two ligands and to determine the probable structure of the heteroligand complex. The LIBS spectra of the heteroligand complex reveal that the complex is free from other metal impurities. UV-visible absorption spectra and the fluorescence emission spectra of the aqueous solution of Cu-Crn-urea heteroligand complex at different solute concentrations have been analyzed and the complex is found to be rigid and stable in its monomeric form at very low concentrations.

  6. Infant food applications of complex carbohydrates: Structure, synthesis, and function. (United States)

    Ackerman, Dorothy L; Craft, Kelly M; Townsend, Steven D


    Professional health bodies such as the World Health Organization (WHO), the American Academy of Pediatrics (AAP), and the U.S. Department of Health and Human Services (HHS) recommend breast milk as the sole source of food during the first year of life. This position recognizes human milk as being uniquely suited for infant nutrition. Nonetheless, most neonates in the West are fed alternatives by 6 months of age. Although inferior to human milk in most aspects, infant formulas are able to promote effective growth and development. However, while breast-fed infants feature a microbiota dominated by bifidobacteria, the bacterial flora of formula-fed infants is usually heterogeneous with comparatively lower levels of bifidobacteria. Thus, the objective of any infant food manufacturer is to prepare a product that results in a formula-fed infant developing a breast-fed infant-like microbiota. The goal of this focused review is to discuss the structure, synthesis, and function of carbohydrate additives that play a role in governing the composition of the infant microbiome and have other health benefits.

  7. Searching and optimizing structure ensembles for complex flexible sugars. (United States)

    Xia, Junchao; Margulis, Claudio J; Case, David A


    NMR restrictions are suitable to specify the geometry of a molecule when a single well-defined global free energy minimum exists that is significantly lower than other local minima. Carbohydrates are quite flexible, and therefore, NMR observables do not always correlate with a single conformer but instead with an ensemble of low free energy conformers that can be accessed by thermal fluctuations. In this communication, we describe a novel procedure to identify and weight the contribution to the ensemble of local minima conformers based on comparison to residual dipolar couplings (RDCs) or other NMR observables, such as scalar couplings. A genetic algorithm is implemented to globally minimize the R factor comparing calculated RDCs to experiment. This is done by optimizing the weights of different conformers derived from the exhaustive local minima conformational search program, fast sugar structure prediction software (FSPS). We apply this framework to six human milk sugars, LND-1, LNF-1, LNF-2, LNF-3, LNnT, and LNT, and are able to determine corresponding population weights for the ensemble of conformers. Interestingly, our results indicate that in all cases the RDCs can be well represented by only a few most important conformers. This confirms that several, but not all of the glycosidic linkages in histo-blood group "epitopes" are quite rigid.

  8. The similitude research on underwater complex shell-structure based on SEA

    Institute of Scientific and Technical Information of China (English)

    WANG San-de; YANG De-sen; SHI Sheng-guo; FANG Er-zheng


    In this paper, the vibration and sound radiation of the underwater complex shell-structure which is the cylindrical shell with hemi-spherical shell on the ends are studied by statistical energy analysis (SEA). The whole shell-structure is divided into the four subsystems, and the SEA physical model and power flow balance equations among these subsystems are established. The similitude relations of input power, coupling loss factor and modal density of the subsystems between the complex shell-structure and its scaled-down model are analyzed. According to the similitude theory and power flow balance equations, when the immerged shell-structures are excited, the similar relations of spatially averaged vibration response and underwater radiating sound power are established for the complex shell-structure and its scaled-down model.

  9. A structural model of the E. coli PhoB Dimer in the transcription initiation complex

    Directory of Open Access Journals (Sweden)

    Tung Chang-Shung


    Full Text Available Abstract Background There exist > 78,000 proteins and/or nucleic acids structures that were determined experimentally. Only a small portion of these structures corresponds to those of protein complexes. While homology modeling is able to exploit knowledge-based potentials of side-chain rotomers and backbone motifs to infer structures for new proteins, no such general method exists to extend our understanding of protein interaction motifs to novel protein complexes. Results We use a Motif Binding Geometries (MBG approach, to infer the structure of a protein complex from the database of complexes of homologous proteins taken from other contexts (such as the helix-turn-helix motif binding double stranded DNA, and demonstrate its utility on one of the more important regulatory complexes in biology, that of the RNA polymerase initiating transcription under conditions of phosphate starvation. The modeled PhoB/RNAP/σ-factor/DNA complex is stereo-chemically reasonable, has sufficient interfacial Solvent Excluded Surface Areas (SESAs to provide adequate binding strength, is physically meaningful for transcription regulation, and is consistent with a variety of known experimental constraints. Conclusions Based on a straightforward and easy to comprehend concept, "proteins and protein domains that fold similarly could interact similarly", a structural model of the PhoB dimer in the transcription initiation complex has been developed. This approach could be extended to enable structural modeling and prediction of other bio-molecular complexes. Just as models of individual proteins provide insight into molecular recognition, catalytic mechanism, and substrate specificity, models of protein complexes will provide understanding into the combinatorial rules of cellular regulation and signaling.

  10. Toward the atomic structure of the nuclear pore complex: when top down meets bottom up. (United States)

    Hoelz, André; Glavy, Joseph S; Beck, Martin


    Elucidating the structure of the nuclear pore complex (NPC) is a prerequisite for understanding the molecular mechanism of nucleocytoplasmic transport. However, owing to its sheer size and flexibility, the NPC is unapproachable by classical structure determination techniques and requires a joint effort of complementary methods. Whereas bottom-up approaches rely on biochemical interaction studies and crystal-structure determination of NPC components, top-down approaches attempt to determine the structure of the intact NPC in situ. Recently, both approaches have converged, thereby bridging the resolution gap from the higher-order scaffold structure to near-atomic resolution and opening the door for structure-guided experimental interrogations of NPC function.

  11. Building Structural Complexity in Semiconductor Nanocrystals through Chemical Transformations

    Energy Technology Data Exchange (ETDEWEB)

    Sadtler, Bryce F [Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)


    Ag2S lattices were used to calculate interface formation energies. The formation energies indicate the favorability for interface nucleation at different facets of the nanorod and the stability of the interfaces during growth of the secondary material (Cu2S or Ag2S) within the CdS nanocrystal. The physical properties of the CdS-Ag2S and CdS-Cu2S binary nanorods are discussed in terms of the electronic structure of their components and the heterostructure morphology.

  12. Synthesis and Crystal Structure of Binuclear Ytterbium Complex with Isonicotinoyl Hydrazone

    Institute of Scientific and Technical Information of China (English)

    卜显和; 鹿守亮; 陈巍; 张若桦


    The ytterbium complex of isonicotinoyl hydrazone was synthesized and the structure was determined by X-ray diffraction analysis. The crystal and molecular structure of the title complex [Yb2(L)3](OH)3 shows that the complex has two identical nine-coordinated ytterbium ions with each surrounded by N3O6 donor set. Two ytterbium ions are bridged by three phenolate oxygen atoms. The geometry around each ytterbium ions can be considered as a three-capped trigonal prism.

  13. Structural plasticity: how intermetallics deform themselves in response to chemical pressure, and the complex structures that result. (United States)

    Berns, Veronica M; Fredrickson, Daniel C


    Interfaces between periodic domains play a crucial role in the properties of metallic materials, as is vividly illustrated by the way in which the familiar malleability of many metals arises from the formation and migration of dislocations. In complex intermetallics, such interfaces can occur as an integral part of the ground-state crystal structure, rather than as defects, resulting in such marvels as the NaCd2 structure (whose giant cubic unit cell contains more than 1000 atoms). However, the sources of the periodic interfaces in intermetallics remain mysterious, unlike the dislocations in simple metals, which can be associated with the exertion of physical stresses. In this Article, we propose and explore the concept of structural plasticity, the hypothesis that interfaces in complex intermetallic structures similarly result from stresses, but ones that are inherent in a defect-free parent structure, rather than being externally applied. Using DFT-chemical pressure analysis, we show how the complex structures of Ca2Ag7 (Yb2Ag7 type), Ca14Cd51 (Gd14Ag51 type), and the 1/1 Tsai-type quasicrystal approximant CaCd6 (YCd6 type) can all be traced to large negative pressures around the Ca atoms of a common progenitor structure, the CaCu5 type with its simple hexagonal 6-atom unit cell. Two structural paths are found by which the compounds provide relief to the Ca atoms' negative pressures: a Ca-rich pathway, where lower coordination numbers are achieved through defects eliminating transition metal (TM) atoms from the structure; and a TM-rich path, along which the addition of spacer Cd atoms provides the Ca coordination environments greater independence from each other as they contract. The common origins of these structures in the presence of stresses within a single parent structure highlights the diverse paths by which intermetallics can cope with competing interactions, and the role that structural plasticity may play in navigating this diversity.

  14. Determining Complex Structures using Docking Method with Single Particle Scattering Data

    Directory of Open Access Journals (Sweden)

    Haiguang Liu


    Full Text Available Protein complexes are critical for many molecular functions. Due to intrinsic flexibility and dynamics of complexes, their structures are more difficult to determine using conventional experimental methods, in contrast to individual subunits. One of the major challenges is the crystallization of protein complexes. Using X-ray free electron lasers (XFELs, it is possible to collect scattering signals from non-crystalline protein complexes, but data interpretation is more difficult because of unknown orientations. Here, we propose a hybrid approach to determine protein complex structures by combining XFEL single particle scattering data with computational docking methods. Using simulations data, we demonstrate that a small set of single particle scattering data collected at random orientations can be used to distinguish the native complex structure from the decoys generated using docking algorithms. The results also indicate that a small set of single particle scattering data is superior to spherically averaged intensity profile in distinguishing complex structures. Given the fact that XFEL experimental data are difficult to acquire and at low abundance, this hybrid approach should find wide applications in data interpretations.

  15. Palladium and platinum complexes of 2-(2'-carboxyphenylazo)-4 methylphenol: Synthesis, structure and spectral properties

    Indian Academy of Sciences (India)

    Sarmistha Halder; Michael G B Drew; Samaresh Bhattacharya


    Reaction of 2-(2'-carboxyphenylazo)-4-methylphenol (H2L) with [M(PPh3)2Cl2] (M = Pd, Pt) affords mixed-ligand complexes of type [M(PPh3)(L)]. Structures of both the complexes have been determined by X-ray crystallography. Both the complexes are square planar, where the 2-(2'-carboxyphenylazo)-4-methylphenol is coordinated to the metal center, via dissociation of the two acidic protons, as a dianionic tridentate O,N,O-donor, and the fourth position is occupied by the triphenylphosphine. These complexes show intense MLCT transitions in the visible region.

  16. Synthesis, Structure and Catalytic Activity of NHC-AgICarboxylate Complexes

    KAUST Repository

    Wong, Valerie H. L.


    A general synthetic route was used to prepare 15 new N-heterocyclic carbene (NHC)–AgI complexes bearing anionic carboxylate ligands [Ag(NHC)(O2CR)], including a homologous series of complexes of sterically flexible ITent ligands, which permit a systematic spectroscopic and theoretical study of the structural and electronic features of these compounds. The complexes displayed a significant ligand-accelerated effect in the intramolecular cyclisation of propargylic amides to oxazolidines. The substrate scope is highly complementary to that previously achieved by NHC–Au and pyridyl–AgI complexes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

  17. Structure, luminescence and antimicrobial properties of mononuclear silver(I) complexes of pyridine 2-carboxamide

    Indian Academy of Sciences (India)

    Sutapa Joardar; Shounak Roy; Suvendu Samanta; Amit Kumar Dutta


    Two Ag(I) complexes, [Ag(HL)2]ClO4 (1) and [Ag(HL)2]NO3·H2O (2), where HL is pyridine 2– carboxamide, have been synthesized and characterized by various spectroscopic techniques. The X-ray crystal structural analyses indicate that both the complexes consist of slightly distorted square planar silver(I) ions and ligand-supported weak Ag⋯Ag metallophilic interactions. Both the complexes show photoluminescence in solid state and acetonitrile solution at room temperature. Antimicrobial studies have been performed with these silver(I) complexes against various gram +ve, gram −ve bacterial and fungal species.

  18. Modifying the DPClus algorithm for identifying protein complexes based on new topological structures

    Directory of Open Access Journals (Sweden)

    Wang Jian-xin


    Full Text Available Abstract Background Identification of protein complexes is crucial for understanding principles of cellular organization and functions. As the size of protein-protein interaction set increases, a general trend is to represent the interactions as a network and to develop effective algorithms to detect significant complexes in such networks. Results Based on the study of known complexes in protein networks, this paper proposes a new topological structure for protein complexes, which is a combination of subgraph diameter (or average vertex distance and subgraph density. Following the approach of that of the previously proposed clustering algorithm DPClus which expands clusters starting from seeded vertices, we present a clustering algorithm IPCA based on the new topological structure for identifying complexes in large protein interaction networks. The algorithm IPCA is applied to the protein interaction network of Sacchromyces cerevisiae and identifies many well known complexes. Experimental results show that the algorithm IPCA recalls more known complexes than previously proposed clustering algorithms, including DPClus, CFinder, LCMA, MCODE, RNSC and STM. Conclusion The proposed algorithm based on the new topological structure makes it possible to identify dense subgraphs in protein interaction networks, many of which correspond to known protein complexes. The algorithm is robust to the known high rate of false positives and false negatives in data from high-throughout interaction techniques. The program is available at

  19. Three-Dimentional Structures of Autophosphorylation Complexes in Crystals of Protein Kinases

    KAUST Repository

    Dumbrack, Roland


    Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Several autophosphorylation complexes have been identified in crystals of protein kinases, with a known serine, threonine, or tyrosine autophosphorylation site of one kinase monomer sitting in the active site of another monomer of the same protein in the crystal. We utilized a structural bioinformatics method to identify all such autophosphorylation complexes in X-ray crystallographic structures in the Protein Data Bank (PDB) by generating all unique kinase/kinase interfaces within and between asymmetric units of each crystal and measuring the distance between the hydroxyl oxygen of potential autophosphorylation sites and the oxygen atoms of the active site aspartic acid residue side chain. We have identified 15 unique autophosphorylation complexes in the PDB, of which 5 complexes have not previously been described in the relevant publications on the crystal structures (N-terminal juxtamembrane regions of CSF1R and EPHA2, activation loop tyrosines of LCK and IGF1R, and a serine in a nuclear localization signal region of CLK2. Mutation of residues in the autophosphorylation complex interface of LCK either severely impaired autophosphorylation or increased it. Taking the autophosphorylation complexes as a whole and comparing them with peptide-substrate/kinase complexes, we observe a number of important features among them. The novel and previously observed autophosphorylation sites are conserved in many kinases, indicating that by homology we can extend the relevance of these complexes to many other clinically relevant drug targets.

  20. Novel polymeric potassium complex: Its synthesis, structural characterization, photoluminescence and electrochemical properties

    Energy Technology Data Exchange (ETDEWEB)

    Ceyhan, Goekhan [Chemistry Department, K.Maras Suetcue Imam University, 46100 K.Maras (Turkey); Tuemer, Mehmet, E-mail: [Chemistry Department, K.Maras Suetcue Imam University, 46100 K.Maras (Turkey); Koese, Muhammet; McKee, Vickie [Chemistry Department, Loughborough University, LE11 3TU Leicestershire (United Kingdom)


    In this paper, we obtained a novel poly(vanillinato potassium) complex (PVP) as a single crystal and characterized by analytical and spectroscopic methods. A single crystal of the PVP was obtained from the acetone solution. X-ray structural data show that crystals contain polymeric K{sup +} complex of vanillin. Each potassium ion in the polymeric structure is identical and seven-coordinate, bonded to two methoxy, two phenoxy and three aldehyde oxygen atoms from four vaniline molecules. Two aldehyde oxygen atoms are bridging between potassium ions. It crystallizes in the monoclinic system, space group P2{sub 1}/c, with lattice parameters a=9.6215(10) A, b=17.4139(19) A, c=9.6119(10) A, {beta}=100.457(2) Degree-Sign and Z=4. Thermal properties of the PVP were investigated by TGA, DTA and DSC methods. The electrochemical properties of the complex were studied in different solvents and at various scan rates. The luminescence properties of the complex in different solvents and at different pH values have been investigated. The results show that the complex exhibits more efficient luminescence property in CH{sub 3}CN and n-butanol. - Highlights: Black-Right-Pointing-Pointer Novel polymeric potassium complex was prepared and fully characterized. Black-Right-Pointing-Pointer X-ray crystal structure of complex was reported. Black-Right-Pointing-Pointer Electrochemical properties of compound were investigated. Black-Right-Pointing-Pointer Thermal and DSC measurements of complex were examined.

  1. Structural, magnetic and luminescent properties of lanthanide complexes with N-salicylideneglycine. (United States)

    Vančo, Ján; Trávníček, Zdeněk; Kozák, Ondřej; Boča, Roman


    A series of anionic heavy lanthanide complexes, involving the N-salicylideneglycinato(2-) Schiff base ligand (salgly) and having the general formula K[Ln(salgly)₂(H₂O)₂]∙H₂O (1-6), where Ln stands for Gd, Tb, Dy, Ho, Er and Tm, was prepared using the one-pot template synthesis. The complexes were thoroughly characterized by elemental and Thermogravimetric/Differential Thermal Analyses (TG/DTA), Fourier Transform Infrared Spectroscopy (FT-IR), and photoluminescence spectroscopies, electrospray-ionization mass spectrometry, and their magnetic properties were studied by temperature-dependent dc magnetic measurements using the superconducting quantum interference device (SQUID). The X-ray structure of the terbium(III) complex (2), representing the unique structure between the lanthanide complexes of N-salicylideneamino acids, was determined. The results of spectral and structural studies revealed the isostructural nature of the prepared complexes, in which the lanthanide ion is octacoordinated by two O,N,O-donor salgly ligands and two aqua ligands. The analysis of magnetic data confirmed that the complexes behave as paramagnets obeying the Curie law. The results of photoluminescence spectral studies of the complexes showed the different origin in their luminescent properties between the solid state and solution. An antenna effect of the Schiff base ligand was observed in a powder form of the complex only, while it acts as a fluorophore in a solution.

  2. RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

    Directory of Open Access Journals (Sweden)

    Chen Chun


    Full Text Available Abstract Background With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. Results RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1 present a robust and effective way for RNA structural data compression; (2 design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. Conclusion A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool

  3. Structure of ruthenium(II) complexes with coproporphyrin I tetraethyl ester (United States)

    Zverev, S. A.; Andreev, S. V.; Zamilatskov, I. A.; Kurochkina, N. M.; Tyurin, V. S.; Senchikhin, I. N.; Ponomarev, G. V.; Erzina, D. R.; Chernyshev, V. V.


    The reaction between coproporphyrin I tetraethyl ester and ruthenium(II) dodecacarbonyl in toluene is investigated. The formation of two different products, complexes 2 and 3 of ruthenium(II) with coproporphyrin I tetraethyl ester, studied by means of mass spectrometry, electronic absorption spectroscopy, NMR, X-ray diffraction, and thermogravimetric analysis, is revealed. Structures are proposed for the products, of which ( 2) is a monocarbonyl complex of ruthenium(II) porphyrin that exists as a coordination polymer formed owing to intermolecular axial bonding between the oxygen atoms of carboethoxyl groups and ruthenium(II). The structure proposed for second product ( 3) is in the form of the corresponding monomer of a monocarbonyl complex of ruthenium(II) porphyrin. It is established that polymeric complex 2 transforms into monomeric complex 3 when it is heating in pyridine.

  4. Electronic structures of ruthenium complexes encircling non-innocent ligand assembly

    Indian Academy of Sciences (India)

    Amit Das; Dipanwita Das; Tanaya Kundu; Goutam Kumar Lahiri


    Electronic structural forms of selected mononuclear and dinuclear ruthenium complexes encompassing redox non-innocent terminal as well as bridging ligands have been addressed. The sensitive valence and spin situations of the complexes have been established in the native and accessible redox states via detailed analysis of their crystal structures, electrochemistry, UV/VIS/NIR spectroelectrochemistry, EPR signatures at the paramagnetic states and DFT calculations. Mononuclear complexes exhibit significant variations in valence and spin distribution processes based on the simple modification of the non-innocent ligand frameworks as well as electronic nature of the co-ligands, -donating or -accepting. Dinuclear complexes with modified pyrazine, -quinone and azo-derived redox-active bridging ligands show complex features including redoxinduced electron-transfer (RIET), remote metal to metal spin-interaction in a three-spin metal-bridge-metal arrangement as well as electron-transfer driven chemical transformation (EC).

  5. Complexity

    CERN Document Server

    Gershenson, Carlos


    The term complexity derives etymologically from the Latin plexus, which means interwoven. Intuitively, this implies that something complex is composed by elements that are difficult to separate. This difficulty arises from the relevant interactions that take place between components. This lack of separability is at odds with the classical scientific method - which has been used since the times of Galileo, Newton, Descartes, and Laplace - and has also influenced philosophy and engineering. In recent decades, the scientific study of complexity and complex systems has proposed a paradigm shift in science and philosophy, proposing novel methods that take into account relevant interactions.

  6. RNA polymerase II/TFIIF structure and conserved organization of the initiation complex. (United States)

    Chung, Wen-Hsiang; Craighead, John L; Chang, Wei-Hau; Ezeokonkwo, Chukwudi; Bareket-Samish, Avital; Kornberg, Roger D; Asturias, Francisco J


    The structure of an RNA polymerase II/general transcription factor TFIIF complex was determined by cryo-electron microscopy and single particle analysis. Density due to TFIIF was not concentrated in one area but rather was widely distributed across the surface of the polymerase. The largest subunit of TFIIF interacted with the dissociable Rpb4/Rpb7 polymerase subunit complex and with the mobile "clamp." The distribution of the second largest subunit of TFIIF was very similar to that previously reported for the sigma subunit in the bacterial RNA polymerase holoenzyme, consisting of a series of globular domains extending along the polymerase active site cleft. This result indicates that the second TFIIF subunit is a true structural homolog of the bacterial sigma factor and reveals an important similarity of the transcription initiation mechanism between bacteria and eukaryotes. The structure of the RNAPII/TFIIF complex suggests a model for the organization of a minimal transcription initiation complex.

  7. Significantly elevated dielectric permittivity of Si-based semiconductor/polymer 2-2 composites induced by high polarity polymers (United States)

    Feng, Yefeng; Gong, Honghong; Xie, Yunchuan; Wei, Xiaoyong; Zhang, Zhicheng


    To disclose the essential influence of polymer polarity on dielectric properties of polymer composites filled with semiconductive fillers, a series of Si-based semiconductor/polymer 2-2 composites in a series model was fabricated. The dielectric permittivity of composites is highly dependant on the polarity of polymer layers as well as the electron mobility in Si-based semiconductive sheets. The huge dielectric permittivity achieved in Si-based semiconductive sheets after being coated with high polarity polymer layers is inferred to originate from the strong induction of high polarity polymers. The increased mobility of the electrons in Si-based semiconductive sheets coated by high polarity polymer layers should be responsible for the significantly enhanced dielectric properties of composites. This could be facilely achieved by either increasing the polarity of polymer layers or reducing the percolative electric field of Si-based semiconductive sheets. The most promising 2-2 dielectric composite was found to be made of α-SiC with strong electron mobility and poly(vinyl alcohol) (PVA) with high polarity, and its highest permittivity was obtained as 372 at 100 Hz although the permittivity of α-SiC and PVA is 3-5 and 15, respectively. This work may help in the fabrication of high dielectric constant (high-k) composites by tailoring the induction effect of high polarity polymers to semiconductors.

  8. Complex dynamic and static structures in interconnected particle systems

    Energy Technology Data Exchange (ETDEWEB)

    Kristiansen, Kai de Lange


    -Mandelbrot relation is not fully understood, and may also be a subject. for future studies. The diffusive behaviour of a cluster of a semi-large number spheres in a soft potential undergoes transitions in length scale from super diffusion via normal diffusion to sub diffusion. This analysis follows the motion of one sphere over a large time span. Knot theory can be used to get other measures of the collective behaviour, e.g. the linking number seems to be a promising measure and would be worth studying. This quantity represents the number of times the world lines from two spheres cross each other in a preferred direction of rotation. Random dense packing of spheres is a useful model for disordered and granular media. The monolayer of non-magnetic spheres in a ferro fluid is used to simulate this packing in 2D. Our experiments show packing structures similar to previous results. In 3D we have used a mechanical contraction method, paper 5, to simulate rapid sedimentation of binary mixture of spherical colloidal particles. The densities as function of sphere composition were found to be similar to results from the experiments. For a random dense packing it would be interesting to follow the idea of the excluded volume argument to explain quantitatively the density as function of size- and shape distributions. The mechanical contraction method seems to be ideal for doing these kinds of numerical calculations. The coordination number < C > is difficult to find in a real system of colloidal particles, but is easily obtained in numerical simulations. Nucleation of a colloidal monolayer in all alternating electric field has been studied recently. The magnetic hole system may be used to show a similar behaviour in a magnetic field. With this system we can study the nucleation process from the beginning and also to investigate the nucleation rate. Preliminary experiments have also been done that show large differences in the behaviour in systems with only free spheres and systems with some

  9. Complex dynamic and static structures in interconnected particle systems

    Energy Technology Data Exchange (ETDEWEB)

    Kristiansen, Kai de Lange


    -Mandelbrot relation is not fully understood, and may also be a subject. for future studies. The diffusive behaviour of a cluster of a semi-large number spheres in a soft potential undergoes transitions in length scale from super diffusion via normal diffusion to sub diffusion. This analysis follows the motion of one sphere over a large time span. Knot theory can be used to get other measures of the collective behaviour, e.g. the linking number seems to be a promising measure and would be worth studying. This quantity represents the number of times the world lines from two spheres cross each other in a preferred direction of rotation. Random dense packing of spheres is a useful model for disordered and granular media. The monolayer of non-magnetic spheres in a ferro fluid is used to simulate this packing in 2D. Our experiments show packing structures similar to previous results. In 3D we have used a mechanical contraction method, paper 5, to simulate rapid sedimentation of binary mixture of spherical colloidal particles. The densities as function of sphere composition were found to be similar to results from the experiments. For a random dense packing it would be interesting to follow the idea of the excluded volume argument to explain quantitatively the density as function of size- and shape distributions. The mechanical contraction method seems to be ideal for doing these kinds of numerical calculations. The coordination number < C > is difficult to find in a real system of colloidal particles, but is easily obtained in numerical simulations. Nucleation of a colloidal monolayer in all alternating electric field has been studied recently. The magnetic hole system may be used to show a similar behaviour in a magnetic field. With this system we can study the nucleation process from the beginning and also to investigate the nucleation rate. Preliminary experiments have also been done that show large differences in the behaviour in systems with only free spheres and systems with some

  10. Understanding Complex Natural Systems by Articulating Structure-Behavior-Function Models (United States)

    Vattam, Swaroop S.; Goel, Ashok K.; Rugaber, Spencer; Hmelo-Silver, Cindy E.; Jordan, Rebecca; Gray, Steven; Sinha, Suparna


    Artificial intelligence research on creative design has led to Structure-Behavior-Function (SBF) models that emphasize functions as abstractions for organizing understanding of physical systems. Empirical studies on understanding complex systems suggest that novice understanding is shallow, typically focusing on their visible structures and…

  11. 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles. (United States)

    Fantino, Erika; Chiappone, Annalisa; Roppolo, Ignazio; Manfredi, Diego; Bongiovanni, Roberta; Pirri, Candido Fabrizio; Calignano, Flaviana


    Coupling the photoreduction of a metal precursor with 3D-printing technology is shown to allow the fabrication of conductive 3D hybrid structures consisting of metal nanoparticles and organic polymers shaped in complex multilayered architectures. 3D conductive structures are fabricated incorporating silver nitrate into a photocurable oligomer in the presence of suitable photoinitiators and exposing them to a digital light system.

  12. Complex Network Structure Influences Processing in Long-Term and Short-Term Memory (United States)

    Vitevitch, Michael S.; Chan, Kit Ying; Roodenrys, Steven


    Complex networks describe how entities in systems interact; the structure of such networks is argued to influence processing. One measure of network structure, clustering coefficient, C, measures the extent to which neighbors of a node are also neighbors of each other. Previous psycholinguistic experiments found that the C of phonological…

  13. The relation between structural and functional connectivity patterns in complex brain networks

    NARCIS (Netherlands)

    Stam, C. J.; van Straaten, E. C W; Van Dellen, E.; Tewarie, P.; Gong, G.; Hillebrand, A.; Meier, J.; Van Mieghem, P.


    Objective An important problem in systems neuroscience is the relation between complex structural and functional brain networks. Here we use simulations of a simple dynamic process based upon the susceptible–infected–susceptible (SIS) model of infection dynamics on an empirical structural brain netw

  14. Complex Network Structure Influences Processing in Long-Term and Short-Term Memory (United States)

    Vitevitch, Michael S.; Chan, Kit Ying; Roodenrys, Steven


    Complex networks describe how entities in systems interact; the structure of such networks is argued to influence processing. One measure of network structure, clustering coefficient, C, measures the extent to which neighbors of a node are also neighbors of each other. Previous psycholinguistic experiments found that the C of phonological…

  15. Bilberry xyloglucan - novel building blocks containing ß-xylose within a complex structure

    NARCIS (Netherlands)

    Hilz, H.; Jong, de L.E.; Kabel, M.A.; Verhoef, R.P.; Schols, H.A.; Voragen, A.G.J.


    Bilberries are known to have one of the most complex xyloglucan structures described in the plant kingdom until now. To characterise this structure, xyloglucans were enzymatically degraded and the oligosaccharides obtained were analysed. More than 20 different building blocks were found to make up t

  16. Design, synthesis, structural elucidation, pharmacological evaluation of metal complexes with pyrazoline derivatives. (United States)

    Muneera, M Sirajul; Joseph, J


    A bioactive pyrazoline derivatives have been synthesized by the base-catalyzed Claisen-Schmidt condensation of imidazole-2-carboxaldehyde with 1-acetyl-2-hydroxynaphthalene followed by cyclization with phenylhydrazine (L(1))/2,3-dimethylphenylhydrazine (L(2)) and 3-nitrophenylhydrazine (L(3)). The metal(II) complexes [Ni(II), Co(II), Cu(II) and Zn(II)] were formed by reacting the corresponding metal acetates with the ligands. All complexes were characterized by elemental analyses, electronic, IR, NMR, mass and ESR spectroscopic techniques. The synthesized metal complexes of pyrazoline compounds showed significant antibacterial activity against the organisms Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Proteus mirabilis and Salmonella typhii when compared with the standard antibiotic (Streptomycin). The ligands and their metal complexes were screened for antioxidant activity using DPPH radical scavenging and superoxide radical scavenging assay methods. All the complexes showed good free radical scavenging activity which is comparable to that of the standards. Among the metal complexes, the copper complex has showed higher activity. The results were indicated that 2-pyrazoline (structural core) and copper ion could be responsible for the potential candidate eliciting antioxidant activity. All compounds were evaluated for their in vitro antimycobacterial activity against Mycobacterium tuberculosis. The ligands and metal complexes were subjected to fluorescence properties and exhibited that the variable fluorescence emission behavior of complexes. It can be attributed to the combined effect of the substituents and naphthyl structural core present in the ligands.

  17. Preparation and structural characterization of corn starch-aroma compound inclusion complexes. (United States)

    Zhang, Shu; Zhou, Yibin; Jin, Shanshan; Meng, Xin; Yang, Liping; Wang, Haisong


    Six corn starch inclusion complexes were synthesized using small nonpolar or weak polar aroma compounds (heptanolide, carvone and menthone) and small polar aroma compounds (linalool, heptanol and menthol). The objectives of this study were to (a) investigate the ability of corn starch to form inclusion complexes with these aroma compounds and (b) characterize the structure of the corn starch inclusion complexes. The resulting inclusion ratios were 75.6, 36.9, 43.8, 91.9, 67.2 and 54.7% for heptanolide, carvone, menthone, linalool, heptanol and menthol respectively. The inclusion complexes had laminated structures with a certain amount of holes or blocky constructions. Compared with gelatinized corn starch, the transition temperatures, peak temperatures and enthalpies of the inclusion complexes were significantly different. The major peak of CO at 1771 cm(-1) and significant peak shifts revealed the formation of inclusion complexes. X-ray diffractometry (XRD) analyses revealed that the crystallinity of corn starch-polar aroma compound inclusion complexes increased. Based on cross-polarization magic angle spinning (13) C nuclear magnetic resonance (CP-MAS (13) C NMR) results, novel peaks and chemical shifts were attributed to the presence of small aroma compounds, thereby confirming the formation of corn starch inclusion complexes. Small nonpolar and polar aroma compounds can be complexed to corn starch. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  18. Analysis of information gain and Kolmogorov complexity for structural evaluation of cellular automata configurations (United States)

    Javaheri Javid, Mohammad Ali; Blackwell, Tim; Zimmer, Robert; Majid al-Rifaie, Mohammad


    Shannon entropy fails to discriminate structurally different patterns in two-dimensional images. We have adapted information gain measure and Kolmogorov complexity to overcome the shortcomings of entropy as a measure of image structure. The measures are customised to robustly quantify the complexity of images resulting from multi-state cellular automata (CA). Experiments with a two-dimensional multi-state cellular automaton demonstrate that these measures are able to predict some of the structural characteristics, symmetry and orientation of CA generated patterns.

  19. A formalism for scattering of complex composite structures. I. Applications to branched structures of asymmetric sub-units. (United States)

    Svaneborg, Carsten; Pedersen, Jan Skov


    We present a formalism for the scattering of an arbitrary linear or acyclic branched structure build by joining mutually non-interacting arbitrary functional sub-units. The formalism consists of three equations expressing the structural scattering in terms of three equations expressing the sub-unit scattering. The structural scattering expressions allow composite structures to be used as sub-units within the formalism itself. This allows the scattering expressions for complex hierarchical structures to be derived with great ease. The formalism is generic in the sense that the scattering due to structural connectivity is completely decoupled from internal structure of the sub-units. This allows sub-units to be replaced by more complex structures. We illustrate the physical interpretation of the formalism diagrammatically. By applying a self-consistency requirement, we derive the pair distributions of an ideal flexible polymer sub-unit. We illustrate the formalism by deriving generic scattering expressions for branched structures such as stars, pom-poms, bottle-brushes, and dendrimers build out of asymmetric two-functional sub-units.

  20. Application of Nuclear Magnetic Resonance and Hybrid Methods to Structure Determination of Complex Systems. (United States)

    Prischi, Filippo; Pastore, Annalisa


    The current main challenge of Structural Biology is to undertake the structure determination of increasingly complex systems in the attempt to better understand their biological function. As systems become more challenging, however, there is an increasing demand for the parallel use of more than one independent technique to allow pushing the frontiers of structure determination and, at the same time, obtaining independent structural validation. The combination of different Structural Biology methods has been named hybrid approaches. The aim of this review is to critically discuss the most recent examples and new developments that have allowed structure determination or experimentally-based modelling of various molecular complexes selecting them among those that combine the use of nuclear magnetic resonance and small angle scattering techniques. We provide a selective but focused account of some of the most exciting recent approaches and discuss their possible further developments.

  1. Atomic Resolution Imaging of Nanoscale Structural Ordering in a Complex Metal Oxide Catalyst

    KAUST Repository

    Zhu, Yihan


    The determination of the atomic structure of a functional material is crucial to understanding its "structure-to-property" relationship (e.g., the active sites in a catalyst), which is however challenging if the structure possesses complex inhomogeneities. Here, we report an atomic structure study of an important MoVTeO complex metal oxide catalyst that is potentially useful for the industrially relevant propane-based BP/SOHIO process. We combined aberration-corrected scanning transmission electron microscopy with synchrotron powder X-ray crystallography to explore the structure at both nanoscopic and macroscopic scales. At the nanoscopic scale, this material exhibits structural and compositional order within nanosized "domains", while the domains show disordered distribution at the macroscopic scale. We proposed that the intradomain compositional ordering and the interdomain electric dipolar interaction synergistically induce the displacement of Te atoms in the Mo-V-O channels, which determines the geometry of the multifunctional metal oxo-active sites.

  2. Imaging and structural studies of DNA–protein complexes and membrane ion channels

    KAUST Repository

    Marini, M.


    In bio-imaging by electron microscopy, damage of the sample and limited contrast are the two main hurdles for reaching high image quality. We extend a new preparation method based on nanofabrication and super-hydrophobicity to the imaging and structural studies of nucleic acids, nucleic acid-protein complexes (DNA/Rad51 repair protein complex) and neuronal ion channels (gap-junction, K+ and GABA(A) channels) as paradigms of biological significance and increasing complexity. The preparation method is based on the liquid phase and is compatible with physiological conditions. Only in the very last stage, samples are dried for TEM analysis. Conventional TEM and high-resolution TEM (HRTEM) were used to achieve a resolution of 3.3 and 1.5 angstrom, respectively. The EM dataset quality allows the determination of relevant structural and metrological information on the DNA structure, DNA-protein interactions and ion channels, allowing the identification of specific macromolecules and their structure.

  3. Fritjof Capra’s holism and the structures of philosophical conceptualisation: The logosemantics of complexity

    Directory of Open Access Journals (Sweden)

    P.J. Visagie


    Full Text Available This article explores a field of study that I call logosemantics: the theory of conceptual structures that determine philosophical expressions of ultimate insight. The kind of structures that logosemantics postulates are described with reference to the holistic philosophy of Capra. In particular the conceptualisation of holistic complexity in relation to reductionistic simplicity is thematised. In the course of this analysis the logosemantic place of complexity in the conceptual structure of philosophically foundational expressions is identified, with reference not only to Capra, but also to various philosophical "languages" in the history of Western thought, from Greek metaphysics to systems philosophy and post-structuralism. Attention is also given to some Eastern philosophies. After a purely descriptive analysis of logosemantic form, the possibility of logosemantic criticism is considered. The relation of simplicity and complexity is reviewed again, and an alternative interpretation to the one seemingly favoured by Capra is suggested.

  4. HCF-1 self-association via an interdigitated Fn3 structure facilitates transcriptional regulatory complex formation. (United States)

    Park, Jihye; Lammers, Fabienne; Herr, Winship; Song, Ji-Joon


    Host-cell factor 1 (HCF-1) is an unusual transcriptional regulator that undergoes a process of proteolytic maturation to generate N- (HCF-1(N)) and C- (HCF-1(C)) terminal subunits noncovalently associated via self-association sequence elements. Here, we present the crystal structure of the self-association sequence 1 (SAS1) including the adjacent C-terminal HCF-1 nuclear localization signal (NLS). SAS1 elements from each of the HCF-1(N) and HCF-1(C) subunits form an interdigitated fibronectin type 3 (Fn3) tandem repeat structure. We show that the C-terminal NLS recruited by the interdigitated SAS1 structure is required for effective formation of a transcriptional regulatory complex: the herpes simplex virus VP16-induced complex. Thus, HCF-1(N)-HCF-1(C) association via an integrated Fn3 structure permits an NLS to facilitate formation of a transcriptional regulatory complex.

  5. Complexes of uranyl nitrate with 2,6-pyridinedicarboxamides: synthesis, crystal structure, and DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Alyapyshev, Mikhail; Babain, Vasiliy [ITMO University, 49, Kronverksky pr., 197101, St. Petersburg (Russian Federation); ThreeArc Mining Ltd., 5, Stary Tolmachevskiy per., 115184, Moscow (Russian Federation); Tkachenko, Lyudmila; Lumpov, Alexander [Khlopin Radium Institute, 28, 2nd Murinskiy pr., 194021, St. Petersburg (Russian Federation); Gurzhiy, Vladislav; Zolotarev, Andrey; Dar' in, Dmitriy [St. Petersburg State University, 7-9, Universitetskaya nab., 199034, St. Petersburg (Russian Federation); Ustynyuk, Yuriy; Gloriozov, Igor [M.V. Lomonosov Moscow State University, 119991, Moscow (Russian Federation); Paulenova, Alena [Department of Nuclear Engineering, Oregon State University, Corvallis, OR (United States)


    Two complexes of uranyl nitrate with N,N,N',N'-tetrabutyl-2,6-pyridinedicarboxamide (TBuDPA) and N,N'-diethyl-N,N'-diphenyl-2,6-pyridinedicarboxamide (EtPhDPA) were synthesized and studied. The complex of tetraalkyl-2,6-pyridinedicarboxamide with metal nitrate was synthesized for the first time. XRD analysis revealed the different type of complexation: a 1:1 metal:ligand complex for EtPhDPA and complex with polymeric structure for TBuDPA. The quantum chemical calculations (DFT) confirm that both ligands form the most stable complexes that match the minimal values pre-organization energy of the ligands. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  6. Electrocatalytic activity of Pt grown by ALD on carbon nanotubes for Si-based DMFC applications

    DEFF Research Database (Denmark)

    Johansson, Alicia Charlotte; Dalslet, Bjarke Thomas; Yang, R.B.


    We present an anode design for silicon-based direct methanol fuel cell (DMFC) applications. Platinum was deposited conformally by atomic layer deposition (ALD) onto vertically aligned, nitrogendoped multi-walled carbon nanotubes (MWCNTs) grown on porous silicon. The deposition was carried out...... that ALD could be a MEMS compatible deposition technique for Si-based fuel cell applications. © The Electrochemical Society....... in a top-flow ALD reactor at 250°C, using MeCpPtMe3 and O2 as precursors. The anode was tested for the methanol oxidation reaction (MOR) in a three-electrode electrochemical set-up and it showed improved catalytic activity compared to a reference sample of Pt deposited on flat Si. It is demonstrated...

  7. Scintillation induced response in passively-quenched Si-based single photon counting avalanche diode arrays. (United States)

    Spanoudaki, Virginia Ch; Levin, Craig S


    An optical electrical model which studies the response of Si-based single photon counting arrays, specifically silicon photomultipliers (SiPMs), to scintillation light has been developed and validated with analytically derived and experimental data. The scintillator-photodetector response in terms of relative pulse height, 10%-90% rise/decay times to light stimuli of different rise times (ranging from 0.1 to 5 ns) and decay times (ranging from 1 to 50 ns), as well as for different decay times of the photodetector are compared in theory and simulation. A measured detector response is used as a reference to further validate the model and the results show a mean deviation of simulated over measured values of 1%.

  8. BCB-Si Based Wide Band Millimeter Wave Antenna Fed by Substrate Integrated Waveguide

    Directory of Open Access Journals (Sweden)

    Hamsakutty Vettikalladi


    Full Text Available A benzocyclobutene (BCB silicon (Si based wideband antenna for millimeter wave applications is presented. The antenna consists of multilayer with one layer of BCB and the remaining three layers of Si. A patch is etched on the Si substrate above the air gap, which is excited through a slot. This architecture of slot, air gap, and patch will produce wide bandwidth by merging each one of resonances. The simulated results show that the antenna provides an S11<-10 dB bandwidth of 9.7 GHz (17% starting from 51.5 GHz to 61.2 GHz around 57 GHz central frequency. The antenna provides a maximum gain of 8.9 dBi with an efficiency of 70%.

  9. Functional metal-insulator-metal top contacts for Si-based color photodetectors (United States)

    Butun, Serkan; Aydin, Koray


    Here, we report on Si-based color photodetectors using monolithically integrated metal-insulator-metal Fabry-Perot cavity top contacts. Contacts were formed by depositing Ag/SiO2/Ag layers with different oxide thicknesses for each color. This allowed controlling the transmission band position and width while maintaining the high conductivity. We have obtained over 55% external quantum efficiency for different colors both numerically and experimentally. The FWHM was less than 50 nm and the rejection ratio was an order of magnitude for each color. The total transmission through these top contacts exceeded that of dye filters used in conventional color CCDs and CMOS imaging arrays. In addition, these contacts performed similarly to recently proposed plasmonic hole array filters without the necessity of complicated fabrication steps like FIB milling and e-beam lithography. This type of top contacts can serve as a cheap alternative to dye filters used in contemporary devices without making the fabrication complicated.

  10. Internal transmission coefficient in charges carrier generation layer of graphene/Si based solar cell device

    Energy Technology Data Exchange (ETDEWEB)

    Rosikhin, Ahmad, E-mail:; Winata, Toto, E-mail: [Department of physics, physics of electronic materials research division Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung Jl. Ganesha 10, Bandung 40132, Jawa Barat – Indonesia (Indonesia)


    Internal transmission profile in charges carrier generation layer of graphene/Si based solar cell has been explored theoretically. Photovoltaic device was constructed from graphene/Si heterojunction forming a multilayer stuck with Si as generation layer. The graphene/Si sheet was layered on ITO/glass wafer then coated by Al forming Ohmic contact with Si. Photon incident propagate from glass substrate to metal electrode and assumed that there is no transmission in Al layer. The wavelength range spectra used in this calculation was 200 – 1000 nm. It found that transmission intensity in the generation layer show non-linear behavior and partitioned by few areas which related with excitation process. According to this information, it may to optimize the photons absorption to create more excitation process by inserting appropriate material to enhance optical properties in certain wavelength spectra because of the exciton generation is strongly influenced by photon absorption.

  11. Wave propagation in one-dimension: Methods and applications to complex and fractal structures

    CERN Document Server

    Akkermans, Eric; Levy, Eli


    This chapter is a pedagogical review of methods and results for studying wave propagation in one-dimensional complex structures. We describe and compare the tight-binding, scattering matrix, transfer matrix and Riccati formalisms. We present examples for transport through finite-sized layered dielectric systems with periodic, quasi-periodic, fractal, disordered, and random structure, illustrating how can spatial structure affect the spectrum of modes as well as the local mode intensity.

  12. The Gd{sub 14}Ag{sub 51} structure type and its relation to some complex amalgam structures

    Energy Technology Data Exchange (ETDEWEB)

    Tambornino, Frank; Sappl, Jonathan; Hoch, Constantin, E-mail:


    Highlights: • The Gd{sub 14}Ag{sub 51} structure type has been revisited on the basis of single crystal diffraction data. • Symmetry analysis from electron density and TEM shows the space group P6/m to be true. • Gd{sub 14}Ag{sub 51} shows good metallic behaviour. • Structure relations to alkali, alkaline-earth and rare-earth metal amalgams can be established. • Complexity values for the RE{sub 14}Ag{sub 51} structure family were calculated. - Abstract: A plethora of binary and ternary intermetallic compounds has been assigned to the Gd{sub 14}Ag{sub 51} structure type, crystallising in the hexagonal system (space group P6/m, a = 1264.30(18) pm, c = 933.58(11) pm for Gd{sub 14}Ag{sub 51}). Starting in the late 1960s, much work has been invested in the structural elucidation of these crystal structures. However, reliable single crystal data are scarce, and most structure type assignments have been performed merely on the basis of powder data. We have redetermined four representatives of the binary RE{sub 14}Ag{sub 51} structure type (RE = Y, Ce, Gd, Tb) with modern high-precision single crystal X-ray methods. The assignment of the Gd{sub 14}Ag{sub 51} structure type to space group P6/m was additionally verified by careful analysis of high resolution transmission electron micrographs. We emphasise the close relation of the Gd{sub 14}Ag{sub 51} structure type to the structures of some recently described amalgams of similar composition focussing on disorder phenomena and structural complexity. Furthermore, we provide detailed information on synthesis as well as electrical and magnetic properties for Gd{sub 14}Ag{sub 51}, the parent compound of this structure family.

  13. Using crystallographic water properties for the analysis and prediction of lectin-carbohydrate complex structures. (United States)

    Modenutti, C; Gauto, D; Radusky, L; Blanco, J; Turjanski, A; Hajos, S; Marti, Ma


    Understanding protein-ligand interactions is a fundamental question in basic biochemistry, and the role played by the solvent along this process is not yet fully understood. This fact is particularly relevant in lectins, proteins that mediate a large variety of biological processes through the recognition of specific carbohydrates. In the present work, we have thoroughly analyzed a nonredundant and well-curated set of lectin structures looking for a potential relationship between the structural water properties in the apo-structures and the corresponding protein-ligand complex structures. Our results show that solvent structure adjacent to the binding sites mimics the ligand oxygen structural framework in the resulting protein-ligand complex, allowing us to develop a predictive method using a Naive Bayes classifier. We also show how these properties can be used to improve docking predictions of lectin-carbohydrate complex structures in terms of both accuracy and precision, thus developing a solid strategy for the rational design of glycomimetic drugs. Overall our results not only contribute to the understanding of protein-ligand complexes, but also underscore the role of the water solvent in the ligand recognition process. Finally, we discuss our findings in the context of lectin specificity and ligand recognition properties.

  14. An ab initio quantum chemical investigation of the structure and stability of ozone-water complexes

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Pradeep [Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016 (India); Sathyamurthy, N., E-mail: [Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016 (India); Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli 140306 (India)


    Highlights: ► Eclipse geometry most stable for the 1:1 ozone-water complex. ► Cyclic structure most stable for the 1:2 complex. ► Shift in the vertical electronic excitation energy of ozone due to hydration. - Abstract: Ab initio quantum chemical calculations have been carried out to investigate the structure and stability of 1:1 and 1:2 ozone-water complexes. All the geometries have been optimized at the CCSD level of theory using aug-cc-pVDZ and aug-cc-pVTZ basis sets. The importance of correlation-consistent basis sets in deciding the nature of critical points on these complexes is emphasized. An analysis based on the dipole moment of the complexes and the charge distribution on atoms follows. The effect of ozone molecule on the structure and properties of water dimer is also investigated. Values of the vertical electronic excitation energy and the corresponding transition dipole moment have been calculated for the ozone-water complexes using the multi-reference-configuration-interaction method and the aug-cc-pVTZ basis set. The calculated shift in vibrational frequencies due to complex formation is compared with the earlier reported experimental and theoretical values.

  15. Synthesis, structures, and luminescent properties of lanthanide complexes with triphenylphospine oxide

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Yan; Xu, Shan; Wang, Xin; Li, Yue-Xue; Jin, Qiong-Hua [Department of Chemistry, Capital Normal University, Beijing (China); Liu, Min [The College of Materials Science and Engineering, Beijing University of Technology (China); Xin, Xiu-Lan [School of Food and Chemical Engineering, Beijing Technology and Business University (China)


    Seven lanthanide complexes [Ln(OPPh{sub 3}){sub 3}(NO{sub 3}){sub 3}] (1-3) (OPPh{sub 3} = triphenylphosphine oxide, Ln = Nd, Sm, Gd), [Dy(OPPh{sub 3}){sub 4}(NO{sub 3}){sub 2}](NO{sub 3}) (4), [Ln(OPPh{sub 3}){sub 3}(NO{sub 3}){sub 3}]{sub 2} (5-7) (Ln = Pr, Eu, Gd) were synthesized by the reactions of different lanthanide salts and OPPh{sub 3} ligand in the air. These complexes were characterized by single-crystal X-ray diffraction analysis, elemental analysis, IR and fluorescence spectra. Structure analysis shows that complexes 1-4 are mononuclear complexes formed by OPPh{sub 3} ligands and nitrates. The asymmetric units of complexes 5-7 consist of two crystallographic-separate molecules. Complex 1 is self-assembled to construct a 2D layer-structure of (4,4) net topology by hydrogen bond interactions. The other complexes show a 1D chain-like structure that was assembled by OPPh{sub 3} ligands and nitrate ions through C-H..O interactions. Solid emission spectra of compounds 4 and 6 are assigned to the characteristic fluorescence of Tb{sup 3+} (λ{sub em} = 480, 574 nm) and Eu{sup 3+} (λ{sub em} = 552, 593, 619, 668 nm). (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  16. Magnetic, structural and computational studies on transition metal complexes of a neurotransmitter, histamine (United States)

    Kaştaş, Gökhan; Paşaoğlu, Hümeyra; Karabulut, Bünyamin


    In this study, the transition metal complexes of histamine (His) prepared with oxalate (Ox), that is, [Cu(His)(Ox)(H 2O)], [Zn(His)(Ox)(H 2O)] (or [Zn(His)(Ox)]·(H 2O)), [Cd(His)(Ox)(H 2O) 2] and [Co(His)(Ox)(H 2O)], are investigated experimentally and computationally as part of ongoing studies on the mode of complexation, the tautomeric form and non-covalent interactions of histamine in supramolecular structures. The structural properties of prepared complexes are experimentally studied by X-ray diffraction (XRD) technique and Fourier transform infrared (FT-IR) spectroscopy and computationally by density functional theory (DFT). The magnetic properties of the complexes are investigated by electron paramagnetic resonance (EPR) technique. The [Cu(His)(Ox)(H 2O)] complex has a supramolecular structure constructed by two different non-covalent interactions as hydrogen bond and C-H⋯π interactions. EPR studies on [Cu(His)(Ox)(H 2O)], Cu 2+-doped [Zn(His)(Ox)(H 2O)] and [Cd(His)(Ox)(H 2O) 2] complexes show that the paramagnetic centers have axially symmetric g values. It is also found that the ground state of the unpaired electrons in the complexes is dominantly d and unpaired electrons' life time is spent over this orbital.

  17. Syntheses, structures and magnetic properties of four-spin Mn-Imino nitroxide radical complexes (United States)

    Lv, Xue-Hui; Yang, Shuai-Liang; Li, Yuan-Xia; Zhang, Chen-Xi; Wang, Qing-Lun


    Based on the nitroxide radicals, four-spin complexes [Mn(hfac)2(IMpPhCl)]2·NITpPhCl (1) and [Mn(hfac)2(IMmPhCl)]2·NITmPhCl (2) (IMpPhCl = 2-(4'-chlorophenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl, IMmPhCl = 2-(3'-chlorophenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl, hfac = hexafluoroacetylacetonate) have been synthesized and characterized by single-crystal X-ray diffraction. The X-ray crystal structure analyses show that the structures of the two compounds are similar and the imino nitroxide radical ligand acts as a bridge ligand linking two Mn(II) ions through the oxygen atom of the N-O group to form a four-spin system. Two kinds of nitroxide radicals: nitronyl nitroxide and imino nitroxide radicals coexist in the cyclic Mn(II) complexes. The magnetic studies show that there exists an antiferromagnetic interaction between Mn(II) ions and the imino nitroxide radical ligands, which is explained by spin polarization mechanism. The antiferromagnetic interaction of Mn-Rad in complex 2 (J1 = -9.36 cm-1) is stronger than that in complex 1 (J1 = -9.19 cm-1), which is consistent with crystal structure of complexes (The bond length of the shortest Mn-O in complex 2 (2.1625 Å) is smaller than complex 1 (2.1898 Å)).

  18. One-dimensional chiral copper (II) complexes with novel nano-structures and superior antitumor activity. (United States)

    Zhang, Wei Chuan; Tang, Xue; Lu, Xiaoming


    Three novel copper(II) compounds of formulas {[Cu(Phen)(Ala)]·NO3·H2O}n (1), {[Cu(Phen)(Ala)]·NO3}n (2) and [Cu(Ala)2]n (3) have been synthesized and determined by X-ray diffraction. 1 and 2 are shown in one dimensional long-chain chiral structures, and 3 is a two dimensional checkerboard-type structure. Both 1 and 2 displayed a higher anticancer activity than 3 against various cancer cells, even higher than the similar mononuclear complexes and clinical anticancer drug 5-fluorouracil. The noncancerous cell lines (CCC-HEL-1) have showed that complexes 1-3 have hardly any cytotoxicity. Transmission electron microscopy was studied to show the nano-structure and π function of two complexes. The ligand 1,10-phenanthroline inserted into its enantiomer lead complex 1 stable, and the π-π interaction outside the chain made complex 2 active, which is easy to crack and pile up together. In addition, the energy gaps, UV-vis, luminescent and cyclic voltammetry were experimented to show the stable one dimensional long-chain chiral structure and the π function of two complexes.

  19. Methodology for Simulation and Analysis of Complex Adaptive Supply Network Structure and Dynamics Using Information Theory

    Directory of Open Access Journals (Sweden)

    Joshua Rodewald


    Full Text Available Supply networks existing today in many industries can behave as complex adaptive systems making them more difficult to analyze and assess. Being able to fully understand both the complex static and dynamic structures of a complex adaptive supply network (CASN are key to being able to make more informed management decisions and prioritize resources and production throughout the network. Previous efforts to model and analyze CASN have been impeded by the complex, dynamic nature of the systems. However, drawing from other complex adaptive systems sciences, information theory provides a model-free methodology removing many of those barriers, especially concerning complex network structure and dynamics. With minimal information about the network nodes, transfer entropy can be used to reverse engineer the network structure while local transfer entropy can be used to analyze the network structure’s dynamics. Both simulated and real-world networks were analyzed using this methodology. Applying the methodology to CASNs allows the practitioner to capitalize on observations from the highly multidisciplinary field of information theory which provides insights into CASN’s self-organization, emergence, stability/instability, and distributed computation. This not only provides managers with a more thorough understanding of a system’s structure and dynamics for management purposes, but also opens up research opportunities into eventual strategies to monitor and manage emergence and adaption within the environment.

  20. Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights. (United States)

    Shimizu, Masahiro; Noguchi, Yasunori; Sakiyama, Yukari; Kawakami, Hironori; Katayama, Tsutomu; Takada, Shoji


    Upon DNA replication initiation in Escherichia coli, the initiator protein DnaA forms higher-order complexes with the chromosomal origin oriC and a DNA-bending protein IHF. Although tertiary structures of DnaA and IHF have previously been elucidated, dynamic structures of oriC-DnaA-IHF complexes remain unknown. Here, combining computer simulations with biochemical assays, we obtained models at almost-atomic resolution for the central part of the oriC-DnaA-IHF complex. This complex can be divided into three subcomplexes; the left and right subcomplexes include pentameric DnaA bound in a head-to-tail manner and the middle subcomplex contains only a single DnaA. In the left and right subcomplexes, DnaA ATPases associated with various cellular activities (AAA+) domain III formed helices with specific structural differences in interdomain orientations, provoking a bend in the bound DNA. In the left subcomplex a continuous DnaA chain exists, including insertion of IHF into the DNA looping, consistent with the DNA unwinding function of the complex. The intervening spaces in those subcomplexes are crucial for DNA unwinding and loading of DnaB helicases. Taken together, this model provides a reasonable near-atomic level structural solution of the initiation complex, including the dynamic conformations and spatial arrangements of DnaA subcomplexes.

  1. Paradigms in the structural biology of the mitogenic ternary complex FGF:FGFR:heparin. (United States)

    Pomin, Vitor H


    The main achievements regarding the molecular interaction involving fibroblast growth factors (FGFs), canonical receptors (FGFRs) and the glycosaminoglycans (GAGs) heparan sulfate (HS)/heparin (Hp) are overviewed. Despite the recent works concerning the subject, conflicting paradigms in the structural biology of the resultant ternary complex FGF:FGFR:HS/Hp seem to persist up to these days. The principal dilemma, centered on the functional intermolecular complex of mitogenesis and angiogenesis, has been lasting for approximately a decade and a half since the publications of the two contradicting crystal structures, the asymmetric 2:2:1 versus the symmetric 2:2:2 complex model. When the principal results regarding this ternary complex are analyzed as a whole and through an impartial manner, conclusion heavily and reliably supports the existence and activity of both complex models. Selection of each complex is driven by multiple factors of different degrees of impact. Specificity in protein-binding motifs in ligands (although the minimal binding sequences are yet controversial), slight differences on the structure of the GAG-binding sites of FGF and of FGFR isoforms as well as on the possible ligand-induced conformational changes of FGFR are examples of these factors. Here, the structural biology of the mitogenic FGF:FGFR:HS/Hp ternary complex is revisited. Discussion is focused on the major attributes of this intermolecular complex including the existing conflicts about the righter biologically active model and information regarding ligand structure, conformation and minimal length required for binding to the growth factors and receptors. This review is very timely in light of the 100(th) anniversary of the discovery of Hp.

  2. Structural elucidation and physicochemical properties of mononuclear Uranyl(VI) complexes incorporating dianionic units (United States)

    Azam, Mohammad; Velmurugan, Gunasekaran; Wabaidur, Saikh Mohammad; Trzesowska-Kruszynska, Agata; Kruszynski, Rafal; Al-Resayes, Saud I.; Al-Othman, Zeid A.; Venuvanalingam, Ponnambalam


    Two derivatives of organouranyl mononuclear complexes [UO2(L)THF] (1) and [UO2(L)Alc] (2), where L = (2,2′-(1E,1′E)-(2,2-dimethylpropane-1,3-dyl)bis(azanylylidene, THF = Tetrahydrofuran, Alc = Alcohol), have been prepared. These complexes have been determined by elemental analyses, single crystal X-ray crystallography and various spectroscopic studies. Moreover, the structure of these complexes have also been studied by DFT and time dependent DFT measurements showing that both the complexes have distorted pentagonal bipyramidal environment around uranyl ion. TD-DFT results indicate that the complex 1 displays an intense band at 458.7 nm which is mainly associated to the uranyl centered LMCT, where complex 2 shows a band at 461.8 nm that have significant LMCT character. The bonding has been further analyzed by EDA and NBO. The photocatalytic activity of complexes 1 and 2 for the degradation of rhodamine-B (RhB) and methylene blue (MB) under the irradiation of 500W Xe lamp has been explored, and found more efficient in presence of complex 1 than complex 2 for both dyes. In addition, dye adsorption and photoluminescence properties have also been discussed for both complexes. PMID:27595801

  3. Structural elucidation and physicochemical properties of mononuclear Uranyl(VI) complexes incorporating dianionic units (United States)

    Azam, Mohammad; Velmurugan, Gunasekaran; Wabaidur, Saikh Mohammad; Trzesowska-Kruszynska, Agata; Kruszynski, Rafal; Al-Resayes, Saud I.; Al-Othman, Zeid A.; Venuvanalingam, Ponnambalam


    Two derivatives of organouranyl mononuclear complexes [UO2(L)THF] (1) and [UO2(L)Alc] (2), where L = (2,2‧-(1E,1‧E)-(2,2-dimethylpropane-1,3-dyl)bis(azanylylidene, THF = Tetrahydrofuran, Alc = Alcohol), have been prepared. These complexes have been determined by elemental analyses, single crystal X-ray crystallography and various spectroscopic studies. Moreover, the structure of these complexes have also been studied by DFT and time dependent DFT measurements showing that both the complexes have distorted pentagonal bipyramidal environment around uranyl ion. TD-DFT results indicate that the complex 1 displays an intense band at 458.7 nm which is mainly associated to the uranyl centered LMCT, where complex 2 shows a band at 461.8 nm that have significant LMCT character. The bonding has been further analyzed by EDA and NBO. The photocatalytic activity of complexes 1 and 2 for the degradation of rhodamine-B (RhB) and methylene blue (MB) under the irradiation of 500W Xe lamp has been explored, and found more efficient in presence of complex 1 than complex 2 for both dyes. In addition, dye adsorption and photoluminescence properties have also been discussed for both complexes.

  4. Structural insights into Saccharomyces cerevisiae Msh4-Msh5 complex function using homology modeling.

    Directory of Open Access Journals (Sweden)

    Ramaswamy Rakshambikai

    Full Text Available The Msh4-Msh5 protein complex in eukaryotes is involved in stabilizing Holliday junctions and its progenitors to facilitate crossing over during Meiosis I. These functions of the Msh4-Msh5 complex are essential for proper chromosomal segregation during the first meiotic division. The Msh4/5 proteins are homologous to the bacterial mismatch repair protein MutS and other MutS homologs (Msh2, Msh3, Msh6. Saccharomyces cerevisiae msh4/5 point mutants were identified recently that show two fold reduction in crossing over, compared to wild-type without affecting chromosome segregation. Three distinct classes of msh4/5 point mutations could be sorted based on their meiotic phenotypes. These include msh4/5 mutations that have a crossover and viability defects similar to msh4/5 null mutants; b intermediate defects in crossing over and viability and c defects only in crossing over. The absence of a crystal structure for the Msh4-Msh5 complex has hindered an understanding of the structural aspects of Msh4-Msh5 function as well as molecular explanation for the meiotic defects observed in msh4/5 mutations. To address this problem, we generated a structural model of the S. cerevisiae Msh4-Msh5 complex using homology modeling. Further, structural analysis tailored with evolutionary information is used to predict sites with potentially critical roles in Msh4-Msh5 complex formation, DNA binding and to explain asymmetry within the Msh4-Msh5 complex. We also provide a structural rationale for the meiotic defects observed in the msh4/5 point mutations. The mutations are likely to affect stability of the Msh4/5 proteins and/or interactions with DNA. The Msh4-Msh5 model will facilitate the design and interpretation of new mutational data as well as structural studies of this important complex involved in meiotic chromosome segregation.

  5. Boron carbide: Consistency of components, lattice parameters, fine structure and chemical composition makes the complex structure reasonable (United States)

    Werheit, Helmut


    The complex, highly distorted structure of boron carbide is composed of B12 and B11C icosahedra and CBC, CBB and B□B linear elements, whose concentration depends on the chemical composition each. These concentrations are shown to be consistent with lattice parameters, fine structure data and chemical composition. The respective impacts on lattice parameters are estimated and discussed. Considering the contributions of the different structural components to the energy of the overall structure makes the structure and its variation within the homogeneity range reasonable; in particular that of B4.3C representing the carbon-rich limit of the homogeneity range. Replacing in B4.3C virtually the B□B components by CBC yields the hypothetical moderately distorted B4.0C (structure formula (B11C)CBC). The reduction of lattice parameters related is compatible with recently reported uncommonly prepared single crystals, whose compositions deviate from B4.3C.

  6. Ab initio study of the structural and electronic properties of the complex structures of RuO 2 (United States)

    Benyahia, K.; Nabi, Z.; Tadjer, A.; Khalfi, A.


    We have studied structural and electronic properties of RuO 2 in the two complex structures (rutile and orthorhombic) by means of accurate first principle total energy calculations using the full potential linearized augmented plane wave (FP-LAPW). The calculations are presented within the local-density approximation and the generalized gradient approximation. The orthorhombic (CaCl 2-type Pnnm) structure is just a deformation of the rutile (P4 2/mnm). Until now, considerable work has been performed on the rutile structure; however, no work has been performed on the orthorhombic structure. The structural properties are in good agreement with experiment. Our calculations of the electronic properties have been compared with experiment and previous calculations and a good agreement is found.

  7. Ab initio study of the structural and electronic properties of the complex structures of RuO{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Benyahia, K.; Nabi, Z.; Tadjer, A.; Khalfi, A


    We have studied structural and electronic properties of RuO{sub 2} in the two complex structures (rutile and orthorhombic) by means of accurate first principle total energy calculations using the full potential linearized augmented plane wave (FP-LAPW). The calculations are presented within the local-density approximation and the generalized gradient approximation. The orthorhombic (CaCl{sub 2}-type Pnnm) structure is just a deformation of the rutile (P4{sub 2}/mnm). Until now, considerable work has been performed on the rutile structure; however, no work has been performed on the orthorhombic structure. The structural properties are in good agreement with experiment. Our calculations of the electronic properties have been compared with experiment and previous calculations and a good agreement is found.

  8. Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution. (United States)

    von der Ecken, Julian; Heissler, Sarah M; Pathan-Chhatbar, Salma; Manstein, Dietmar J; Raunser, Stefan


    The interaction of myosin with actin filaments is the central feature of muscle contraction and cargo movement along actin filaments of the cytoskeleton. The energy for these movements is generated during a complex mechanochemical reaction cycle. Crystal structures of myosin in different states have provided important structural insights into the myosin motor cycle when myosin is detached from F-actin. The difficulty of obtaining diffracting crystals, however, has prevented structure determination by crystallography of actomyosin complexes. Thus, although structural models exist of F-actin in complex with various myosins, a high-resolution structure of the F-actin–myosin complex is missing. Here, using electron cryomicroscopy, we present the structure of a human rigor actomyosin complex at an average resolution of 3.9 Å. The structure reveals details of the actomyosin interface, which is mainly stabilized by hydrophobic interactions. The negatively charged amino (N) terminus of actin interacts with a conserved basic motif in loop 2 of myosin, promoting cleft closure in myosin. Surprisingly, the overall structure of myosin is similar to rigor-like myosin structures in the absence of F-actin, indicating that F-actin binding induces only minimal conformational changes in myosin. A comparison with pre-powerstroke and intermediate (Pi-release) states of myosin allows us to discuss the general mechanism of myosin binding to F-actin. Our results serve as a strong foundation for the molecular understanding of cytoskeletal diseases, such as autosomal dominant hearing loss and diseases affecting skeletal and cardiac muscles, in particular nemaline myopathy and hypertrophic cardiomyopathy.

  9. PRI-Modeler: extracting RNA structural elements from PDB files of protein-RNA complexes. (United States)

    Han, Kyungsook; Nepal, Chirag


    A complete understanding of protein and RNA structures and their interactions is important for determining the binding sites in protein-RNA complexes. Computational approaches exist for identifying secondary structural elements in proteins from atomic coordinates. However, similar methods have not been developed for RNA, due in part to the very limited structural data so far available. We have developed a set of algorithms for extracting and visualizing secondary and tertiary structures of RNA and for analyzing protein-RNA complexes. These algorithms have been implemented in a web-based program called PRI-Modeler (protein-RNA interaction modeler). Given one or more protein data bank files of protein-RNA complexes, PRI-Modeler analyzes the conformation of the RNA, calculates the hydrogen bond (H bond) and van der Waals interactions between amino acids and nucleotides, extracts secondary and tertiary RNA structure elements, and identifies the patterns of interactions between the proteins and RNAs. This paper presents PRI-Modeler and its application to the hydrogen bond and van der Waals interactions in the most representative set of protein-RNA complexes. The analysis reveals several interesting interaction patterns at various levels. The information provided by PRI-Modeler should prove useful for determining the binding sites in protein-RNA complexes. PRI-Modeler is accessible at, and supplementary materials are available in the analysis results section at

  10. Estimating the complexity of 3D structural models using machine learning methods (United States)

    Mejía-Herrera, Pablo; Kakurina, Maria; Royer, Jean-Jacques


    Quantifying the complexity of 3D geological structural models can play a major role in natural resources exploration surveys, for predicting environmental hazards or for forecasting fossil resources. This paper proposes a structural complexity index which can be used to help in defining the degree of effort necessary to build a 3D model for a given degree of confidence, and also to identify locations where addition efforts are required to meet a given acceptable risk of uncertainty. In this work, it is considered that the structural complexity index can be estimated using machine learning methods on raw geo-data. More precisely, the metrics for measuring the complexity can be approximated as the difficulty degree associated to the prediction of the geological objects distribution calculated based on partial information on the actual structural distribution of materials. The proposed methodology is tested on a set of 3D synthetic structural models for which the degree of effort during their building is assessed using various parameters (such as number of faults, number of part in a surface object, number of borders, ...), the rank of geological elements contained in each model, and, finally, their level of deformation (folding and faulting). The results show how the estimated complexity in a 3D model can be approximated by the quantity of partial data necessaries to simulated at a given precision the actual 3D model without error using machine learning algorithms.

  11. Quantifying Multiscale Habitat Structural Complexity: A Cost-Effective Framework for Underwater 3D Modelling

    Directory of Open Access Journals (Sweden)

    Renata Ferrari


    Full Text Available Coral reef habitat structural complexity influences key ecological processes, ecosystem biodiversity, and resilience. Measuring structural complexity underwater is not trivial and researchers have been searching for accurate and cost-effective methods that can be applied across spatial extents for over 50 years. This study integrated a set of existing multi-view, image-processing algorithms, to accurately compute metrics of structural complexity (e.g., ratio of surface to planar area underwater solely from images. This framework resulted in accurate, high-speed 3D habitat reconstructions at scales ranging from small corals to reef-scapes (10s km2. Structural complexity was accurately quantified from both contemporary and historical image datasets across three spatial scales: (i branching coral colony (Acropora spp.; (ii reef area (400 m2; and (iii reef transect (2 km. At small scales, our method delivered models with <1 mm error over 90% of the surface area, while the accuracy at transect scale was 85.3% ± 6% (CI. Advantages are: no need for an a priori requirement for image size or resolution, no invasive techniques, cost-effectiveness, and utilization of existing imagery taken from off-the-shelf cameras (both monocular or stereo. This remote sensing method can be integrated to reef monitoring and improve our knowledge of key aspects of coral reef dynamics, from reef accretion to habitat provisioning and productivity, by measuring and up-scaling estimates of structural complexity.

  12. Structure function relationship in complex brain networks expressed by hierarchical synchronization (United States)

    Zhou, Changsong; Zemanová, Lucia; Zamora-López, Gorka; Hilgetag, Claus C.; Kurths, Jürgen


    The brain is one of the most complex systems in nature, with a structured complex connectivity. Recently, large-scale corticocortical connectivities, both structural and functional, have received a great deal of research attention, especially using the approach of complex network analysis. Understanding the relationship between structural and functional connectivity is of crucial importance in neuroscience. Here we try to illuminate this relationship by studying synchronization dynamics in a realistic anatomical network of cat cortical connectivity. We model the nodes (cortical areas) by a neural mass model (population model) or by a subnetwork of interacting excitable neurons (multilevel model). We show that if the dynamics is characterized by well-defined oscillations (neural mass model and subnetworks with strong couplings), the synchronization patterns are mainly determined by the node intensity (total input strengths of a node) and the detailed network topology is rather irrelevant. On the other hand, the multilevel model with weak couplings displays more irregular, biologically plausible dynamics, and the synchronization patterns reveal a hierarchical cluster organization in the network structure. The relationship between structural and functional connectivity at different levels of synchronization is explored. Thus, the study of synchronization in a multilevel complex network model of cortex can provide insights into the relationship between network topology and functional organization of complex brain networks.

  13. Si-based thin film coating on Y-TZP: Influence of deposition parameters on adhesion of resin cement

    Energy Technology Data Exchange (ETDEWEB)

    Queiroz, José Renato Cavalcanti, E-mail: [Potiguar University, Department of Biotechnology, Natal (Brazil); Nogueira Junior, Lafayette [São Paulo State University, Department of Prosthodontics and Dental Materials, São José dos Campos (Brazil); Massi, Marcos [Federal University of São Paulo, Institute of Science and Technology, São José dos Campos (Brazil); Silva, Alecssandro de Moura; Bottino, Marco Antonio [São Paulo State University, Department of Prosthodontics and Dental Materials, São José dos Campos (Brazil); Sobrinho, Argemiro Soares da Silva [Technological Institute of Aeronautics, Department of Physics, São José dos Campos (Brazil); Özcan, Mutlu [University of Zurich, Dental Materials Unit, Center for Dental and Oral Medicine, Clinic for Fixed and Removable Prosthodontics and Dental Materials Science, Zurich (Switzerland)


    This study evaluated the influence of deposition parameters for Si-based thin films using magnetron sputtering for coating zirconia and subsequent adhesion of resin cement. Zirconia ceramic blocks were randomly divided into 8 groups and specimens were either ground finished and polished or conditioned using air-abrasion with alumina particles coated with silica. In the remaining groups, the polished specimens were coated with Si-based film coating with argon/oxygen magnetron discharge at 8:1 or 20:1 flux. In one group, Si-based film coating was performed on air-abraded surfaces. After application of bonding agent, resin cement was bonded. Profilometry, goniometry, Energy Dispersive X-ray Spectroscopy and Rutherford Backscattering Spectroscopy analysis were performed on the conditioned zirconia surfaces. Adhesion of resin cement to zirconia was tested using shear bond test and debonded surfaces were examined using Scanning Electron Microscopy. Si-based film coating applied on air-abraded rough zirconia surfaces increased the adhesion of the resin cement (22.78 ± 5.2 MPa) compared to those of other methods (0–14.62 MPa) (p = 0.05). Mixed type of failures were more frequent in Si film coated groups on either polished or air-abraded groups. Si-based thin films increased wettability compared to the control group but did not change the roughness, considering the parameters evaluated. Deposition parameters of Si-based thin film and after application of air-abrasion influenced the initial adhesion of resin cement to zirconia.

  14. Complex

    African Journals Online (AJOL)


    Schiff bases and their complex compounds have been studied for their .... establishing coordination of the N–(2 – hydroxybenzyl) - L - α - valine Schiff base ..... (1967); “Spectrophotometric Identification of Organic Compounds”, Willey, New.

  15. Analysis of PL spectrum shape of Si-based materials as a tool for determination of Si crystallites' distribution

    Energy Technology Data Exchange (ETDEWEB)

    Khomenkova, L., E-mail:


    This paper represents the analysis of the shape of photoluminescence spectra of Si-based nano-materials vs. energy of excitation light and temperature of measurements as a tool for the estimation of Si nanocrystallites' distribution. The samples fabricated by electrochemical etching (allowed different termination of Si nanocrystallites to be obtained) were used as modeling material. Bright emission at room temperature was observed for oxygen-terminated Si nanocrytallites, whereas hydrogen-terminated samples emit at low temperatures only. For most samples the photoluminescence spectrum was found to be complex, demonstrating competitive emission from Si crystallites and oxide defects. In latter case to separate the contribution of each recombination channel and to obtain information about crystallite distribution, low-temperature measurements of photoluminescence spectra under different excitation light energy were performed.

  16. Rate-prediction structure complexity analysis for multi-view video coding using hybrid genetic algorithms (United States)

    Liu, Yebin; Dai, Qionghai; You, Zhixiang; Xu, Wenli


    Efficient exploitation of the temporal and inter-view correlation is critical to multi-view video coding (MVC), and the key to it relies on the design of prediction chain structure according to the various pattern of correlations. In this paper, we propose a novel prediction structure model to design optimal MVC coding schemes along with tradeoff analysis in depth between compression efficiency and prediction structure complexity for certain standard functionalities. Focusing on the representation of the entire set of possible chain structures rather than certain typical ones, the proposed model can given efficient MVC schemes that adaptively vary with the requirements of structure complexity and video source characteristics (the number of views, the degrees of temporal and interview correlations). To handle large scale problem in model optimization, we deploy a hybrid genetic algorithm which yields satisfactory results shown in the simulations.

  17. The Crystal Structure and Behavior of Fenamic Acid-Acridine Complex Under High Pressure. (United States)

    Jerzykiewicz, Lucjan; Sroka, Adam; Majerz, Irena


    The crystal structure of fenamic acid-acridine complex is determined by X-ray diffraction. The strong OHN hydrogen bond linking the complex components and other interactions responsible for packing of the molecules into a crystal are investigated within the Quantum Theory of Atom in Molecule theory. The crystal structure is compared with the structure optimized at B3LYP/6-311++G** level and with the theoretical structures optimized under systematically changed pressure. Analysis of the lattice constants, hydrogen bond lengths, and angles of the inter- and intramolecular hydrogen bond under compression is performed. The structural transformation observed at 5 GPa is connected with a change in the intermolecular OHN hydrogen bond. The proton shifts to acceptor and a new interaction in the crystal appears.

  18. Model updating of complex structures using the combination of component mode synthesis and Kriging predictor. (United States)

    Liu, Yang; Li, Yan; Wang, Dejun; Zhang, Shaoyi


    Updating the structural model of complex structures is time-consuming due to the large size of the finite element model (FEM). Using conventional methods for these cases is computationally expensive or even impossible. A two-level method, which combined the Kriging predictor and the component mode synthesis (CMS) technique, was proposed to ensure the successful implementing of FEM updating of large-scale structures. In the first level, the CMS was applied to build a reasonable condensed FEM of complex structures. In the second level, the Kriging predictor that was deemed as a surrogate FEM in structural dynamics was generated based on the condensed FEM. Some key issues of the application of the metamodel (surrogate FEM) to FEM updating were also discussed. Finally, the effectiveness of the proposed method was demonstrated by updating the FEM of a real arch bridge with the measured modal parameters.

  19. Model Updating of Complex Structures Using the Combination of Component Mode Synthesis and Kriging Predictor

    Directory of Open Access Journals (Sweden)

    Yang Liu


    Full Text Available Updating the structural model of complex structures is time-consuming due to the large size of the finite element model (FEM. Using conventional methods for these cases is computationally expensive or even impossible. A two-level method, which combined the Kriging predictor and the component mode synthesis (CMS technique, was proposed to ensure the successful implementing of FEM updating of large-scale structures. In the first level, the CMS was applied to build a reasonable condensed FEM of complex structures. In the second level, the Kriging predictor that was deemed as a surrogate FEM in structural dynamics was generated based on the condensed FEM. Some key issues of the application of the metamodel (surrogate FEM to FEM updating were also discussed. Finally, the effectiveness of the proposed method was demonstrated by updating the FEM of a real arch bridge with the measured modal parameters.

  20. Structural systematics of some metal complexes with 4,5-diazafluoren-9-one

    Indian Academy of Sciences (India)

    Abhijit Pal; Bhaskar Biswas; Merry Mitra; Chandra Shekhar Purohit; Chia-Her Lind; Rajarshi Ghosh


    Synthesis and X-ray structural characterization of three complexes of type cis-[M(dafone)2(NCS)2] (M = Co(II), 1; Ni(II), 2; Zn(II), 3; dafone = 4,5-diazafluoren-9-one) and a polymer cis-[Cd(dafone)(NCS)2]n (4) have been reported. Each of the four complexes is crystallized in orthorhombic crystal system. Structural study reveals that each metal(II) centre in the four complexes adopts distorted octahedral geometry with MN6 chromophore in 1-3 and MN4S2 chromophore in 4. The room temperature steady-state fluorescent intensity of dafone in dimethyl formamide at 402 nm is found to be quenched in these reported dafone complexes (1-4).

  1. Structural basis for MOF and MSL3 recruitment into the dosage compensation complex by MSL1. (United States)

    Kadlec, Jan; Hallacli, Erinc; Lipp, Michael; Holz, Herbert; Sanchez-Weatherby, Juan; Cusack, Stephen; Akhtar, Asifa


    The male-specific lethal (MSL) complex is required for dosage compensation in Drosophila melanogaster, and analogous complexes exist in mammals. We report structures of binary complexes of mammalian MSL3 and the histone acetyltransferase (HAT) MOF with consecutive segments of MSL1. MSL1 interacts with MSL3 as an extended chain forming an extensive hydrophobic interface, whereas the MSL1-MOF interface involves electrostatic interactions between the HAT domain and a long helix of MSL1. This structure provides insights into the catalytic mechanism of MOF and enables us to show analogous interactions of MOF with NSL1. In Drosophila, selective disruption of Msl1 interactions with Msl3 or Mof severely affects Msl1 targeting to the body of dosage-compensated genes and several high-affinity sites, without affecting promoter binding. We propose that Msl1 acts as a scaffold for MSL complex assembly to achieve specific targeting to the X chromosome.

  2. Theoretical Studies on Docking Dynamics and Electronic Structure in Metalloprotein Complexes (United States)

    Sugiyama, Ayumu; Nishikawa, Keigo; Yamamoto, Tetsunori; Purqon, Acep; Nishikawa, Kiyoshi; Nagao, Hidemi


    An investigating of docking structure and dynamics between metalloprotein is interested from the viewpoint of searching the function of protein. We investigate the cytochrome c551 and azurin complexes by three computational methods, quantum mechanical calculation, docking searching algorism and molecular dynamics simulation. At first we present the docking structure of the cytochrome c551-azurin complexes expected by ZDOCK searching algorism. Quantum chemical calculation is tools to estimate the charge distrubution around the active site for each protein and force field parameters. From these parameters, we reproduce the protein docking dynamics by molecular dynamics simulation. We analyze some physical properties of complex system such as binding free energy, dynamical cross correlation map, and so on. We discuss the docking stability and dynamical effect of the cytochrome c551-azurin complexes.

  3. Atomic and molecular complex resonances from real eigenvalues using standard (hermitian) electronic structure calculations

    CERN Document Server

    Landau, Arie; Kaprálová-Žďánská, Petra Ruth; Moiseyev, Nimrod


    Complex eigenvalues, resonances, play an important role in large variety of fields in physics and chemistry. For example, in cold molecular collision experiments and electron scattering experiments, autoionizing and pre-dissociative metastable resonances are generated. However, the computation of complex resonance eigenvalues is difficult, since it requires severe modifications of standard electronic structure codes and methods. Here we show how resonance eigenvalues, positions and widths, can be calculated using the standard, widely used, electronic-structure packages. Our method enables the calculations of the complex resonance eigenvalues by using analytical continuation procedures (such as Pad\\'{e}). The key point in our approach is the existence of narrow analytical passages from the real axis to the complex energy plane. In fact, the existence of these analytical passages relies on using finite basis sets. These passages become narrower as the basis set becomes more complete, whereas in the exact limit,...

  4. The gross structure of the respiratory complex I: a Lego System. (United States)

    Friedrich, Thorsten; Böttcher, Bettina


    The proton-pumping NADH:ubiquinone oxidoreductase, also called complex I, is the entry point for electrons into the respiratory chains of many bacteria and mitochondria of most eucaryotes. It couples electron transfer with the translocation of protons across the membrane, thus providing the proton motive force essential for energy-consuming processes. Electron microscopy revealed the 'L'-shaped structure of the bacterial and mitochondrial complex with two arms arranged perpendicular to each other. Recently, we showed that the Escherichia coli complex I takes on another stable conformation with the two arms arranged side by side resulting in a horseshoe-shaped structure. This model reflects the evolution of complex I from pre-existing modules for electron transfer and proton translocation.

  5. Structure of the FANCI-FANCD2 Complex: Insights into the Fanconi Anemia DNA Repair Pathway

    Energy Technology Data Exchange (ETDEWEB)

    Joo, Woo; Xu, Guozhou; Persky, Nicole S.; Smogorzewska, Agata; Rudge, Derek G.; Buzovetsky, Olga; Elledge, Stephen J.; Pavletich, Nikola P. (Harvard-Med); (Cornell); (MSKCC)


    Fanconi anemia is a cancer predisposition syndrome caused by defects in the repair of DNA interstrand cross-links (ICLs). Central to this pathway is the Fanconi anemia I-Fanconi anemia D2 (FANCI-FANCD2) (ID) complex, which is activated by DNA damage-induced phosphorylation and monoubiquitination. The 3.4 angstrom crystal structure of the {approx}300 kilodalton ID complex reveals that monoubiquitination and regulatory phosphorylation sites map to the I-D interface, suggesting that they occur on monomeric proteins or an opened-up complex and that they may serve to stabilize I-D heterodimerization. The 7.8 angstrom electron-density map of FANCI-DNA crystals and in vitro data show that each protein has binding sites for both single- and double-stranded DNA, suggesting that the ID complex recognizes DNA structures that result from the encounter of replication forks with an ICL.

  6. Structure of the FANCI-FANCD2 Complex: Insights into the Fanconi Anemia DNA Repair Pathway

    Energy Technology Data Exchange (ETDEWEB)

    W Joo; G Xu; n Persky; A Smogorzewska; D Rudge; O Buzovetsky; S Elledge; N Pavletich


    Fanconi anemia is a cancer predisposition syndrome caused by defects in the repair of DNA interstrand cross-links (ICLs). Central to this pathway is the Fanconi anemia I-Fanconi anemia D2 (FANCI-FANCD2) (ID) complex, which is activated by DNA damage-induced phosphorylation and monoubiquitination. The 3.4 angstrom crystal structure of the {approx}300 kilodalton ID complex reveals that monoubiquitination and regulatory phosphorylation sites map to the I-D interface, suggesting that they occur on monomeric proteins or an opened-up complex and that they may serve to stabilize I-D heterodimerization. The 7.8 angstrom electron-density map of FANCI-DNA crystals and in vitro data show that each protein has binding sites for both single- and double-stranded DNA, suggesting that the ID complex recognizes DNA structures that result from the encounter of replication forks with an ICL.

  7. Characterization of local complex structures in a recurrence plot to improve nonlinear dynamic discriminant analysis. (United States)

    Ding, Hang


    Structures in recurrence plots (RPs), preserving the rich information of nonlinear invariants and trajectory characteristics, have been increasingly analyzed in dynamic discrimination studies. The conventional analysis of RPs is mainly focused on quantifying the overall diagonal and vertical line structures through a method, called recurrence quantification analysis (RQA). This study extensively explores the information in RPs by quantifying local complex RP structures. To do this, an approach was developed to analyze the combination of three major RQA variables: determinism, laminarity, and recurrence rate (DLR) in a metawindow moving over a RP. It was then evaluated in two experiments discriminating (1) ideal nonlinear dynamic series emulated from the Lorenz system with different control parameters and (2) data sets of human heart rate regulations with normal sinus rhythms (n = 18) and congestive heart failure (n = 29). Finally, the DLR was compared with seven major RQA variables in terms of discriminatory power, measured by standardized mean difference (DSMD). In the two experiments, DLR resulted in the highest discriminatory power with DSMD = 2.53 and 0.98, respectively, which were 7.41 and 2.09 times the best performance from RQA. The study also revealed that the optimal RP structures for the discriminations were neither typical diagonal structures nor vertical structures. These findings indicate that local complex RP structures contain some rich information unexploited by RQA. Therefore, future research to extensively analyze complex RP structures would potentially improve the effectiveness of the RP analysis in dynamic discrimination studies.

  8. Characterization of local complex structures in a recurrence plot to improve nonlinear dynamic discriminant analysis (United States)

    Ding, Hang


    Structures in recurrence plots (RPs), preserving the rich information of nonlinear invariants and trajectory characteristics, have been increasingly analyzed in dynamic discrimination studies. The conventional analysis of RPs is mainly focused on quantifying the overall diagonal and vertical line structures through a method, called recurrence quantification analysis (RQA). This study extensively explores the information in RPs by quantifying local complex RP structures. To do this, an approach was developed to analyze the combination of three major RQA variables: determinism, laminarity, and recurrence rate (DLR) in a metawindow moving over a RP. It was then evaluated in two experiments discriminating (1) ideal nonlinear dynamic series emulated from the Lorenz system with different control parameters and (2) data sets of human heart rate regulations with normal sinus rhythms (n = 18) and congestive heart failure (n = 29). Finally, the DLR was compared with seven major RQA variables in terms of discriminatory power, measured by standardized mean difference (DSMD). In the two experiments, DLR resulted in the highest discriminatory power with DSMD = 2.53 and 0.98, respectively, which were 7.41 and 2.09 times the best performance from RQA. The study also revealed that the optimal RP structures for the discriminations were neither typical diagonal structures nor vertical structures. These findings indicate that local complex RP structures contain some rich information unexploited by RQA. Therefore, future research to extensively analyze complex RP structures would potentially improve the effectiveness of the RP analysis in dynamic discrimination studies.

  9. Slalom in complex time: Emergence of low-energy structures in tunnel ionization via complex-time contours (United States)

    Pisanty, Emilio; Ivanov, Misha


    The ionization of atoms by strong, low-frequency fields can generally be described well by assuming that the photoelectron is, after the ionization step, completely at the mercy of the laser field. However, certain phenomena, like the recent discovery of low-energy structures (LESs) in the long-wavelength regime, require the inclusion of the Coulomb interaction with the ion once the electron is in the continuum. We explore the first-principles inclusion of this interaction, known as analytical R -matrix theory, and its consequences on the corresponding quantum orbits. We show that the trajectory must have an imaginary component, and that this causes branch cuts in the complex time plane when the real trajectory revisits the neighborhood of the ionic core. We provide a framework for consistently navigating these branch cuts based on closest-approach times, which satisfy the equation r (t ).v (t )=0 in the complex plane. We explore the geometry of these roots and describe the geometrical structures underlying the emergence of LESs in both the classical and quantum domains.

  10. Crystal structure of TAZ-TEAD complex reveals a distinct interaction mode from that of YAP-TEAD complex. (United States)

    Kaan, Hung Yi Kristal; Chan, Siew Wee; Tan, Siew Kim Joyce; Guo, Fusheng; Lim, Chun Jye; Hong, Wanjin; Song, Haiwei


    The Hippo pathway is a tumor suppressor pathway that is implicated in the regulation of organ size. The pathway has three components: the upstream regulatory factors, the kinase core, and the downstream transcriptional machinery, which consists of YAP, TAZ (transcription co-activators) and TEAD (transcription factor). Formation of YAP/TAZ-TEAD complexes leads to the transcription of growth-promoting genes. Herein, we report the crystal structure of TAZ-TEAD4 complex, which reveals two binding modes. The first is similar to the published YAP-TEAD structure. The second is a unique binding mode, whereby two molecules of TAZ bind to and bridge two molecules of TEAD4. We validated the latter using cross-linking and multi-angle light scattering. Using siRNA, we showed that TAZ knockdown leads to a decrease in TEAD4 dimerization. Lastly, results from luciferase assays, using YAP/TAZ transfected or knockdown cells, give support to the non-redundancy of YAP/TAZ co-activators in regulating gene expression in the Hippo pathway.

  11. Hybrid local FEM/global LISA modeling of damped guided wave propagation in complex composite structures (United States)

    Shen, Yanfeng; Cesnik, Carlos E. S.


    This paper presents a new hybrid modeling technique for the efficient simulation of guided wave generation, propagation, and interaction with damage in complex composite structures. A local finite element model is deployed to capture the piezoelectric effects and actuation dynamics of the transmitter, while the global domain wave propagation and interaction with structural complexity (structure features and damage) are solved utilizing a local interaction simulation approach (LISA). This hybrid approach allows the accurate modeling of the local dynamics of the transducers and keeping the LISA formulation in an explicit format, which facilitates its readiness for parallel computing. The global LISA framework was extended through the 3D Kelvin-Voigt viscoelasticity theory to include anisotropic damping effects for composite structures, as an improvement over the existing LISA formulation. The global LISA framework was implemented using the compute unified device architecture running on graphic processing units. A commercial preprocessor is integrated seamlessly with the computational framework for grid generation and material property allocation to handle complex structures. The excitability and damping effects are successfully captured by this hybrid model, with experimental validation using the scanning laser doppler vibrometry. To demonstrate the capability of our hybrid approach for complex structures, guided wave propagation and interaction with a delamination in a composite panel with stiffeners is presented.

  12. Colony geometry and structural complexity of the endangered species Acropora cervicornis partly explains the structure of their associated fish assemblage

    Directory of Open Access Journals (Sweden)

    Esteban A. Agudo-Adriani


    Full Text Available In the past decade, significant efforts have been made to describe fish-habitat associations. However, most studies have oversimplified actual connections between fish assemblages and their habitats by using univariate correlations. The purpose of this study was to identify the features of habitat forming corals that facilitate and influences assemblages of associated species such as fishes. For this we developed three-dimensional models of colonies of Acropora cervicornis to estimate geometry (length and height, structural complexity (i.e., volume, density of branches, etc. and biological features of the colonies (i.e., live coral tissue, algae. We then correlated these colony characteristics with the associated fish assemblage using multivariate analyses. We found that geometry and complexity were better predictors of the structure of fish community, compared to other variables such as percentage of live coral tissue or algae. Combined, the geometry of each colony explained 40% of the variability of the fish assemblage structure associated with this coral species; 61% of the abundance and 69% of fish richness, respectively. Our study shows that three-dimensional reconstructions of discrete colonies of Acropora cervicornis provides a useful description of the colonial structural complexity and may explain a great deal of the variance in the structure of the associated coral reef fish community. This demonstration of the strongly trait-dependent ecosystem role of this threatened species has important implications for restoration and conservation efforts.

  13. Colony geometry and structural complexity of the endangered species Acropora cervicornis partly explains the structure of their associated fish assemblage. (United States)

    Agudo-Adriani, Esteban A; Cappelletto, Jose; Cavada-Blanco, Francoise; Croquer, Aldo


    In the past decade, significant efforts have been made to describe fish-habitat associations. However, most studies have oversimplified actual connections between fish assemblages and their habitats by using univariate correlations. The purpose of this study was to identify the features of habitat forming corals that facilitate and influences assemblages of associated species such as fishes. For this we developed three-dimensional models of colonies of Acropora cervicornis to estimate geometry (length and height), structural complexity (i.e., volume, density of branches, etc.) and biological features of the colonies (i.e., live coral tissue, algae). We then correlated these colony characteristics with the associated fish assemblage using multivariate analyses. We found that geometry and complexity were better predictors of the structure of fish community, compared to other variables such as percentage of live coral tissue or algae. Combined, the geometry of each colony explained 40% of the variability of the fish assemblage structure associated with this coral species; 61% of the abundance and 69% of fish richness, respectively. Our study shows that three-dimensional reconstructions of discrete colonies of Acropora cervicornis provides a useful description of the colonial structural complexity and may explain a great deal of the variance in the structure of the associated coral reef fish community. This demonstration of the strongly trait-dependent ecosystem role of this threatened species has important implications for restoration and conservation efforts.

  14. Spatiotemporal Chaos, Localized Structures and Synchronization in the Vector Complex Ginzburg-Landau Equation

    CERN Document Server

    Hernández-García, E; Colet, P; Montagne, R; Miguel, M S; Hernandez-Garcia, Emilio; Hoyuelos, Miguel; Colet, Pere; Montagne, Raul; Miguel, Maxi San


    We study the spatiotemporal dynamics, in one and two spatial dimensions, of two complex fields which are the two components of a vector field satisfying a vector form of the complex Ginzburg-Landau equation. We find synchronization and generalized synchronization of the spatiotemporally chaotic dynamics. The two kinds of synchronization can coexist simultaneously in different regions of the space, and they are mediated by localized structures. A quantitative characterization of the degree of synchronization is given in terms of mutual information measures.

  15. Iron complexes of chiral phenol-oxazoline ligands: Structural studies and oxidation catalysis

    NARCIS (Netherlands)

    Godbole, M.D.; Prat Puig, M.; Tanase, S.; Kooijman, H.; Spek, A.L.; Bouwman, E.


    Iron complexes of two ligands, HphoxCOOH and HphoxiPr, have been synthesized and characterized by crystal structure analyses. The complexes (HNEt3)2[Fe(phoxCOO)2](ClO4) and [Fe(phoxiPr)3] are reported. Reactions of the ligands rac-HphoxCOOH and rac- HphoxiPr with iron(II) or iron(III) perchlorate re

  16. A new stepped tetranuclear copper(II) complex: synthesis, crystal structure and photoluminescence properties. (United States)

    Gungor, Elif


    Binuclear and tetranuclear copper(II) complexes are of interest because of their structural, magnetic and photoluminescence properties. Of the several important configurations of tetranuclear copper(II) complexes, there are limited reports on the crystal structures and solid-state photoluminescence properties of `stepped' tetranuclear copper(II) complexes. A new Cu(II) complex, namely bis{μ3-3-[(4-methoxy-2-oxidobenzylidene)amino]propanolato}bis{μ2-3-[(4-methoxy-2-oxidobenzylidene)amino]propanolato}tetracopper(II), [Cu4(C11H13NO3)4], has been synthesized and characterized using elemental analysis, FT-IR, solid-state UV-Vis spectroscopy and single-crystal X-ray diffraction. The crystal structure determination shows that the complex is a stepped tetranuclear structure consisting of two dinuclear [Cu2(L)2] units {L is 3-[(4-methoxy-2-oxidobenzylidene)amino]propanolate}. The two terminal Cu(II) atoms are four-coordinated in square-planar environments, while the two central Cu(II) atoms are five-coordinated in square-pyramidal environments. The solid-state photoluminescence properties of both the complex and 3-[(2-hydroxy-4-methoxybenzylidene)amino]propanol (H2L) have been investigated at room temperature in the visible region. When the complex and H2L are excited under UV light at 349 nm, the complex displays a strong blue emission at 469 nm and H2L displays a green emission at 515 nm.

  17. CTCF-cohesin complex: architect of chromatin structure regulates V(D)J rearrangement

    Institute of Scientific and Technical Information of China (English)

    Ann J Feeney; Jiyoti Verma-Gaur


    The CTCF/cohesin complex regulates higher order chromatin structure by creating long-range chromatin loops and by insulating neighboring genes from each other.The lymphocyte antigen receptor loci have large numbers of CTCF/cohesin binding sites,and recent studies demonstrate that the CTCF/cohesin complex plays several important roles in regulating the process of V(D)J recombination at these megabase-sized receptor loci.

  18. Diamino-ligated platinum(II) and platinum(IV) phenoxide complexes; syntheses and crystal structures

    NARCIS (Netherlands)

    Koten, G. van; Kapteijn, G.M.; Meijer, M.D.; Grove, D.M.; Veldman, N.; Spek, A.L.


    The reaction of the diamino-ligated dimethylplatinum(II) complex [Pt(Me){2}(bpy)] (bpy=2, 2'-bipyridyl) with phenol affords the new complex [Pt(Me)(OPh)(bpy)] (1). The X-ray crystal structure of square-planar 1 is reported: orthorhombic, space group P2{1}2{1}2{1} (No. 19), a = 9.1625(12), b = 12.392

  19. Crystal structure of a PCP/Sfp complex reveals the structural basis for carrier protein posttranslational modification. (United States)

    Tufar, Peter; Rahighi, Simin; Kraas, Femke I; Kirchner, Donata K; Löhr, Frank; Henrich, Erik; Köpke, Jürgen; Dikic, Ivan; Güntert, Peter; Marahiel, Mohamed A; Dötsch, Volker


    Phosphopantetheine transferases represent a class of enzymes found throughout all forms of life. From a structural point of view, they are subdivided into three groups, with transferases from group II being the most widespread. They are required for the posttranslational modification of carrier proteins involved in diverse metabolic pathways. We determined the crystal structure of the group II phosphopantetheine transferase Sfp from Bacillus in complex with a substrate carrier protein in the presence of coenzyme A and magnesium, and observed two protein-protein interaction sites. Mutational analysis showed that only the hydrophobic contacts between the carrier protein's second helix and the C-terminal domain of Sfp are essential for their productive interaction. Comparison with a similar structure of a complex of human proteins suggests that the mode of interaction is highly conserved in all domains of life.

  20. Local kernel nonparametric discriminant analysis for adaptive extraction of complex structures (United States)

    Li, Quanbao; Wei, Fajie; Zhou, Shenghan


    The linear discriminant analysis (LDA) is one of popular means for linear feature extraction. It usually performs well when the global data structure is consistent with the local data structure. Other frequently-used approaches of feature extraction usually require linear, independence, or large sample condition. However, in real world applications, these assumptions are not always satisfied or cannot be tested. In this paper, we introduce an adaptive method, local kernel nonparametric discriminant analysis (LKNDA), which integrates conventional discriminant analysis with nonparametric statistics. LKNDA is adept in identifying both complex nonlinear structures and the ad hoc rule. Six simulation cases demonstrate that LKNDA have both parametric and nonparametric algorithm advantages and higher classification accuracy. Quartic unilateral kernel function may provide better robustness of prediction than other functions. LKNDA gives an alternative solution for discriminant cases of complex nonlinear feature extraction or unknown feature extraction. At last, the application of LKNDA in the complex feature extraction of financial market activities is proposed.