WorldWideScience

Sample records for nanoscale domain structures

  1. Self-assembled domain structures: From micro- to nanoscale

    Directory of Open Access Journals (Sweden)

    Vladimir Shur

    2015-06-01

    Full Text Available The recent achievements in studying the self-assembled evolution of micro- and nanoscale domain structures in uniaxial single crystalline ferroelectrics lithium niobate and lithium tantalate have been reviewed. The results obtained by visualization of static domain patterns and kinetics of the domain structure by different methods from common optical microscopy to more sophisticated scanning probe microscopy, scanning electron microscopy and confocal Raman microscopy, have been discussed. The kinetic approach based on various nucleation processes similar to the first-order phase transition was used for explanation of the domain structure evolution scenarios. The main mechanisms of self-assembling for nonequilibrium switching conditions caused by screening ineffectiveness including correlated nucleation, domain growth anisotropy, and domain–domain interaction have been considered. The formation of variety of self-assembled domain patterns such as fractal-type, finger and web structures, broad domain boundaries, and dendrites have been revealed at each of all five stages of domain structure evolution during polarization reversal. The possible applications of self-assembling for micro- and nanodomain engineering were reviewed briefly. The review covers mostly the results published by our research group.

  2. Direct nanoscale imaging of evolving electric field domains in quantum structures.

    Science.gov (United States)

    Dhar, Rudra Sankar; Razavipour, Seyed Ghasem; Dupont, Emmanuel; Xu, Chao; Laframboise, Sylvain; Wasilewski, Zbig; Hu, Qing; Ban, Dayan

    2014-11-28

    The external performance of quantum optoelectronic devices is governed by the spatial profiles of electrons and potentials within the active regions of these devices. For example, in quantum cascade lasers (QCLs), the electric field domain (EFD) hypothesis posits that the potential distribution might be simultaneously spatially nonuniform and temporally unstable. Unfortunately, there exists no prior means of probing the inner potential profile directly. Here we report the nanoscale measured electric potential distribution inside operating QCLs by using scanning voltage microscopy at a cryogenic temperature. We prove that, per the EFD hypothesis, the multi-quantum-well active region is indeed divided into multiple sections having distinctly different electric fields. The electric field across these serially-stacked quantum cascade modules does not continuously increase in proportion to gradual increases in the applied device bias, but rather hops between discrete values that are related to tunneling resonances. We also report the evolution of EFDs, finding that an incremental change in device bias leads to a hopping-style shift in the EFD boundary--the higher electric field domain expands at least one module each step at the expense of the lower field domain within the active region.

  3. Nanoscale Turing structures

    DEFF Research Database (Denmark)

    Dziekan, Piotr; Hansen, Jesper Schmidt; Nowakowski, Bogdan

    2014-01-01

    Formation of Turing patterns of nanoscopic length scale is simulated using molecular dynamics. Based on Fourier spectra of the concentrations of species, we compare stabilities of the structures of different wavelengths and for different intermolecular potentials. Long range attraction is shown...... to oppose the formation of structures. Our simulations suggest that Turing patterns can be a method of self-organization at a length scale of down to 20 molecular diameters...

  4. Nanoscale Membrane Domain Formation Driven by Cholesterol

    DEFF Research Database (Denmark)

    Javanainen, Matti; Martinez-Seara, Hector; Vattulainen, Ilpo

    2017-01-01

    Biological membranes generate specific functions through compartmentalized regions such as cholesterol-enriched membrane nanodomains that host selected proteins. Despite the biological significance of nanodomains, details on their structure remain elusive. They cannot be observed via microscopic...... dipalmitoylphosphatidylcholine and cholesterol - the "minimal standard" for nanodomain formation. The simulations reveal how cholesterol drives the formation of fluid cholesterol-rich nanodomains hosting hexagonally packed cholesterol-poor lipid nanoclusters, both of which show registration between the membrane leaflets....... The complex nanodomain substructure forms when cholesterol positions itself in the domain boundary region. Here cholesterol can also readily flip-flop across the membrane. Most importantly, replacing cholesterol with a sterol characterized by a less asymmetric ring region impairs the emergence of nanodomains...

  5. Dynamic structural disorder in supported nanoscale catalysts

    International Nuclear Information System (INIS)

    Rehr, J. J.; Vila, F. D.

    2014-01-01

    We investigate the origin and physical effects of “dynamic structural disorder” (DSD) in supported nano-scale catalysts. DSD refers to the intrinsic fluctuating, inhomogeneous structure of such nano-scale systems. In contrast to bulk materials, nano-scale systems exhibit substantial fluctuations in structure, charge, temperature, and other quantities, as well as large surface effects. The DSD is driven largely by the stochastic librational motion of the center of mass and fluxional bonding at the nanoparticle surface due to thermal coupling with the substrate. Our approach for calculating and understanding DSD is based on a combination of real-time density functional theory/molecular dynamics simulations, transient coupled-oscillator models, and statistical mechanics. This approach treats thermal and dynamic effects over multiple time-scales, and includes bond-stretching and -bending vibrations, and transient tethering to the substrate at longer ps time-scales. Potential effects on the catalytic properties of these clusters are briefly explored. Model calculations of molecule-cluster interactions and molecular dissociation reaction paths are presented in which the reactant molecules are adsorbed on the surface of dynamically sampled clusters. This model suggests that DSD can affect both the prefactors and distribution of energy barriers in reaction rates, and thus can significantly affect catalytic activity at the nano-scale

  6. Dynamic structural disorder in supported nanoscale catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Rehr, J. J.; Vila, F. D. [Department of Physics, University of Washington, Seattle, Washington 98195 (United States)

    2014-04-07

    We investigate the origin and physical effects of “dynamic structural disorder” (DSD) in supported nano-scale catalysts. DSD refers to the intrinsic fluctuating, inhomogeneous structure of such nano-scale systems. In contrast to bulk materials, nano-scale systems exhibit substantial fluctuations in structure, charge, temperature, and other quantities, as well as large surface effects. The DSD is driven largely by the stochastic librational motion of the center of mass and fluxional bonding at the nanoparticle surface due to thermal coupling with the substrate. Our approach for calculating and understanding DSD is based on a combination of real-time density functional theory/molecular dynamics simulations, transient coupled-oscillator models, and statistical mechanics. This approach treats thermal and dynamic effects over multiple time-scales, and includes bond-stretching and -bending vibrations, and transient tethering to the substrate at longer ps time-scales. Potential effects on the catalytic properties of these clusters are briefly explored. Model calculations of molecule-cluster interactions and molecular dissociation reaction paths are presented in which the reactant molecules are adsorbed on the surface of dynamically sampled clusters. This model suggests that DSD can affect both the prefactors and distribution of energy barriers in reaction rates, and thus can significantly affect catalytic activity at the nano-scale.

  7. Programmed assembly of nanoscale structures using peptoids.

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Jianhua (University of the Pacific, Stockton, CA); Russell, Scott (California State University, Stanislaus, Turlock, CA); Morishetti, Kiran (University of the Pacific, Stockton, CA); Robinson, David B.; Zuckermann, Ronald N. (Lawrence Berkeley National Laboratory, Berkeley, CA); Buffleben, George M.; Hjelm, Rex P. (Los Alamos National Laboratory, Los Alamos, NM); Kent, Michael Stuart (Sandia National Laboratories, Albuquerque, NM)

    2011-02-01

    Sequence-specific polymers are the basis of the most promising approaches to bottom-up programmed assembly of nanoscale materials. Examples include artificial peptides and nucleic acids. Another class is oligo(N-functional glycine)s, also known as peptoids, which permit greater sidegroup diversity and conformational control, and can be easier to synthesize and purify. We have developed a set of peptoids that can be used to make inorganic nanoparticles more compatible with biological sequence-specific polymers so that they can be incorporated into nucleic acid or other biologically based nanostructures. Peptoids offer degrees of modularity, versatility, and predictability that equal or exceed other sequence-specific polymers, allowing for rational design of oligomers for a specific purpose. This degree of control will be essential to the development of arbitrarily designed nanoscale structures.

  8. Static electric field enhancement in nanoscale structures

    Energy Technology Data Exchange (ETDEWEB)

    Lepetit, Bruno, E-mail: bruno.lepetit@irsamc.ups-tlse.fr; Lemoine, Didier, E-mail: didier.lemoine@irsamc.ups-tlse.fr [Université de Toulouse, UPS, Laboratoire Collisions Agrégats Réactivité, IRSAMC, F-31062 Toulouse (France); CNRS, UMR 5589, F-31062 Toulouse (France); Márquez-Mijares, Maykel, E-mail: mmarquez@instec.cu [Université de Toulouse, UPS, Laboratoire Collisions Agrégats Réactivité, IRSAMC, F-31062 Toulouse (France); CNRS, UMR 5589, F-31062 Toulouse (France); Instituto Superior de Tecnologías y Ciencias Aplicadas, Avenida Salvador Allende 1110, Quinta de los Molinos, La Habana (Cuba)

    2016-08-28

    We study the effect of local atomic- and nano-scale protrusions on field emission and, in particular, on the local field enhancement which plays a key role as known from the Fowler-Nordheim model of electronic emission. We study atomic size defects which consist of right angle steps forming an infinite length staircase on a tungsten surface. This structure is embedded in a 1 GV/m ambient electrostatic field. We perform calculations based upon density functional theory in order to characterize the total and induced electronic densities as well as the local electrostatic fields taking into account the detailed atomic structure of the metal. We show how the results must be processed to become comparable with those of a simple homogeneous tungsten sheet electrostatic model. We also describe an innovative procedure to extrapolate our results to nanoscale defects of larger sizes, which relies on the microscopic findings to guide, tune, and improve the homogeneous metal model, thus gaining predictive power. Furthermore, we evidence analytical power laws for the field enhancement characterization. The main physics-wise outcome of this analysis is that limited field enhancement is to be expected from atomic- and nano-scale defects.

  9. Nanoscale array structures suitable for surface enhanced raman scattering and methods related thereto

    Science.gov (United States)

    Bond, Tiziana C.; Miles, Robin; Davidson, James C.; Liu, Gang Logan

    2014-07-22

    Methods for fabricating nanoscale array structures suitable for surface enhanced Raman scattering, structures thus obtained, and methods to characterize the nanoscale array structures suitable for surface enhanced Raman scattering. Nanoscale array structures may comprise nanotrees, nanorecesses and tapered nanopillars.

  10. Nanoscale array structures suitable for surface enhanced raman scattering and methods related thereto

    Science.gov (United States)

    Bond, Tiziana C; Miles, Robin; Davidson, James; Liu, Gang Logan

    2015-11-03

    Methods for fabricating nanoscale array structures suitable for surface enhanced Raman scattering, structures thus obtained, and methods to characterize the nanoscale array structures suitable for surface enhanced Raman scattering. Nanoscale array structures may comprise nanotrees, nanorecesses and tapered nanopillars.

  11. Nanoscale array structures suitable for surface enhanced raman scattering and methods related thereto

    Science.gov (United States)

    Bond, Tiziana C.; Miles, Robin; Davidson, James C.; Liu, Gang Logan

    2015-07-14

    Methods for fabricating nanoscale array structures suitable for surface enhanced Raman scattering, structures thus obtained, and methods to characterize the nanoscale array structures suitable for surface enhanced Raman scattering. Nanoscale array structures may comprise nanotrees, nanorecesses and tapered nanopillars.

  12. Structural domain walls in polar hexagonal manganites

    Science.gov (United States)

    Kumagai, Yu

    2014-03-01

    The domain structure in the multiferroic hexagonal manganites is currently intensely investigated, motivated by the observation of intriguing sixfold topological defects at their meeting points [Choi, T. et al,. Nature Mater. 9, 253 (2010).] and nanoscale electrical conductivity at the domain walls [Wu, W. et al., Phys. Rev. Lett. 108, 077203 (2012).; Meier, D. et al., Nature Mater. 11, 284 (2012).], as well as reports of coupling between ferroelectricity, magnetism and structural antiphase domains [Geng, Y. et al., Nano Lett. 12, 6055 (2012).]. The detailed structure of the domain walls, as well as the origin of such couplings, however, was previously not fully understood. In the present study, we have used first-principles density functional theory to calculate the structure and properties of the low-energy structural domain walls in the hexagonal manganites [Kumagai, Y. and Spaldin, N. A., Nature Commun. 4, 1540 (2013).]. We find that the lowest energy domain walls are atomically sharp, with {210}orientation, explaining the orientation of recently observed stripe domains and suggesting their topological protection [Chae, S. C. et al., Phys. Rev. Lett. 108, 167603 (2012).]. We also explain why ferroelectric domain walls are always simultaneously antiphase walls, propose a mechanism for ferroelectric switching through domain-wall motion, and suggest an atomistic structure for the cores of the sixfold topological defects. This work was supported by ETH Zurich, the European Research Council FP7 Advanced Grants program me (grant number 291151), the JSPS Postdoctoral Fellowships for Research Abroad, and the MEXT Elements Strategy Initiative to Form Core Research Center TIES.

  13. Current-induced domain wall motion in nanoscale ferromagnetic elements

    Energy Technology Data Exchange (ETDEWEB)

    Malinowski, G [Laboratoire de Physique des Solides, CNRS, Universite Paris-sud 11, 91405 Orsay Cedex (France); Boulle, O [SPINTEC, CEA/CNRS/UJF/GINP, INAC, 38054 Grenoble Cedex 9 (France); Klaeui, M, E-mail: Klaeui@uni-mainz.de [SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI (Switzerland); Laboratory of Nanomagnetism and Spin Dynamics, Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne (Switzerland)

    2011-09-28

    We review the details of domain wall (DW) propagation due to spin-polarized currents that could potentially be used in magnetic data storage devices based on domains and DWs. We discuss briefly the basics of the underlying spin torque effect and show how the two torques arising from the interaction between the spin-polarized charge carriers and the magnetization lead to complex dynamics of a spin texture such as a DW. By direct imaging we show how confined DWs in nanowires can be displaced using currents in in-plane soft-magnetic materials, and that when using short pulses, fast velocities can be attained. For high-anisotropy out-of-plane magnetized wires with narrow DWs we present approaches to deducing the torque terms and show that in these materials potentially more efficient domain wall motion could be achieved.

  14. Predictive modeling of nanoscale domain morphology in solution-processed organic thin films

    Science.gov (United States)

    Schaaf, Cyrus; Jenkins, Michael; Morehouse, Robell; Stanfield, Dane; McDowall, Stephen; Johnson, Brad L.; Patrick, David L.

    2017-09-01

    The electronic and optoelectronic properties of molecular semiconductor thin films are directly linked to their extrinsic nanoscale structural characteristics such as domain size and spatial distributions. In films prepared by common solution-phase deposition techniques such as spin casting and solvent-based printing, morphology is governed by a complex interrelated set of thermodynamic and kinetic factors that classical models fail to adequately capture, leaving them unable to provide much insight, let alone predictive design guidance for tailoring films with specific nanostructural characteristics. Here we introduce a comprehensive treatment of solution-based film formation enabling quantitative prediction of domain formation rates, coverage, and spacing statistics based on a small number of experimentally measureable parameters. The model combines a mean-field rate equation treatment of monomer aggregation kinetics with classical nucleation theory and a supersaturation-dependent critical nucleus size to solve for the quasi-two-dimensional temporally and spatially varying monomer concentration, nucleation rate, and other properties. Excellent agreement is observed with measured nucleation densities and interdomain radial distribution functions in polycrystalline tetracene films. Numerical solutions lead to a set of general design rules enabling predictive morphological control in solution-processed molecular crystalline films.

  15. Study of nanoscale structural biology using advanced particle beam microscopy

    Science.gov (United States)

    Boseman, Adam J.

    This work investigates developmental and structural biology at the nanoscale using current advancements in particle beam microscopy. Typically the examination of micro- and nanoscale features is performed using scanning electron microscopy (SEM), but in order to decrease surface charging, and increase resolution, an obscuring conductive layer is applied to the sample surface. As magnification increases, this layer begins to limit the ability to identify nanoscale surface structures. A new technology, Helium Ion Microscopy (HIM), is used to examine uncoated surface structures on the cuticle of wild type and mutant fruit flies. Corneal nanostructures observed with HIM are further investigated by FIB/SEM to provide detailed three dimensional information about internal events occurring during early structural development. These techniques are also used to reconstruct a mosquito germarium in order to characterize unknown events in early oogenesis. Findings from these studies, and many more like them, will soon unravel many of the mysteries surrounding the world of developmental biology.

  16. Introduction of Functional Structures in Nano-Scales into Engineering Polymer Films Using Radiation Technique

    Energy Technology Data Exchange (ETDEWEB)

    Maekawa, Y., E-mail: maekawa.yasunari@jaea.go.jp [Japan Atomic Energy Agency (JAEA), Quantum Beam Science Directorate, High Performance Polymer Group, 1233 Watanuki-Machi, Takasaki, Gunma-ken 370-1292 (Japan)

    2010-07-01

    Introduction of functional regions in nanometer scale in polymeric films using γ-rays, EB, and ion beams are proposed. Two approaches to build nano-scale functional domains in polymer substrates are proposed: 1) Radiation-induced grafting to transfer nano-scale polymer crystalline structures (morphology), acting as a nano-template, to nano-scale graft polymer regions. The obtained polymers with nano structures can be applied to high performance polymer membranes. 2) Fabrication of nanopores and functional domains in engineering plastic films using ion beams, which deposit the energy in very narrow region of polymer films. Hydrophilic grafting polymers are introduced into hydrophobic fluorinated polymers, cross-linked PTFE (cPTFE) and aromatic hydrocarbon polymer, poly(ether ether ketone (PEEK), which is known to have lamella and crystallite in the polymer films. Then, the hierarchical structures of graft domains are analyzed by a small angle neutron scattering (SANS) experiment. From these analyses, the different structures and the different formation of graft domains were observed in fluorinated and hydrocarbon polymer substrates. the grafted domains in the cPTFE film, working as an ion channel, grew as covering the crystallite and the size of domain seems to be similar to that of crystallite. On the other hand, the PEEK-based PEM has a smaller domain size and it seems to grow independently on the crystallites of PEEK substrate. For nano-fabrication of polymer films using heavy ion beams, the energy distribution in radial direction, which is perpendicular to ion trajectory, is mainly concerned. For penumbra, we re-estimated effective radius of penumbra, in which radiation induced grafting took place, for several different ion beams. We observed the different diameters of the ion channels consisting of graft polymers. The channel sizes were quite in good agreement with the effective penumbra which possess the absorption doses more than 1 kGy. (author)

  17. Introduction of Functional Structures in Nano-Scales into Engineering Polymer Films Using Radiation Technique

    International Nuclear Information System (INIS)

    Maekawa, Y.

    2010-01-01

    Introduction of functional regions in nanometer scale in polymeric films using γ-rays, EB, and ion beams are proposed. Two approaches to build nano-scale functional domains in polymer substrates are proposed: 1) Radiation-induced grafting to transfer nano-scale polymer crystalline structures (morphology), acting as a nano-template, to nano-scale graft polymer regions. The obtained polymers with nano structures can be applied to high performance polymer membranes. 2) Fabrication of nanopores and functional domains in engineering plastic films using ion beams, which deposit the energy in very narrow region of polymer films. Hydrophilic grafting polymers are introduced into hydrophobic fluorinated polymers, cross-linked PTFE (cPTFE) and aromatic hydrocarbon polymer, poly(ether ether ketone (PEEK), which is known to have lamella and crystallite in the polymer films. Then, the hierarchical structures of graft domains are analyzed by a small angle neutron scattering (SANS) experiment. From these analyses, the different structures and the different formation of graft domains were observed in fluorinated and hydrocarbon polymer substrates. the grafted domains in the cPTFE film, working as an ion channel, grew as covering the crystallite and the size of domain seems to be similar to that of crystallite. On the other hand, the PEEK-based PEM has a smaller domain size and it seems to grow independently on the crystallites of PEEK substrate. For nano-fabrication of polymer films using heavy ion beams, the energy distribution in radial direction, which is perpendicular to ion trajectory, is mainly concerned. For penumbra, we re-estimated effective radius of penumbra, in which radiation induced grafting took place, for several different ion beams. We observed the different diameters of the ion channels consisting of graft polymers. The channel sizes were quite in good agreement with the effective penumbra which possess the absorption doses more than 1 kGy. (author)

  18. Structures composing protein domains.

    Science.gov (United States)

    Kubrycht, Jaroslav; Sigler, Karel; Souček, Pavel; Hudeček, Jiří

    2013-08-01

    This review summarizes available data concerning intradomain structures (IS) such as functionally important amino acid residues, short linear motifs, conserved or disordered regions, peptide repeats, broadly occurring secondary structures or folds, etc. IS form structural features (units or elements) necessary for interactions with proteins or non-peptidic ligands, enzyme reactions and some structural properties of proteins. These features have often been related to a single structural level (e.g. primary structure) mostly requiring certain structural context of other levels (e.g. secondary structures or supersecondary folds) as follows also from some examples reported or demonstrated here. In addition, we deal with some functionally important dynamic properties of IS (e.g. flexibility and different forms of accessibility), and more special dynamic changes of IS during enzyme reactions and allosteric regulation. Selected notes concern also some experimental methods, still more necessary tools of bioinformatic processing and clinically interesting relationships. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  19. Nanoscale nuclear architecture for cancer diagnosis by spatial-domain low-coherence quantitative phase microscopy

    Science.gov (United States)

    Wang, Pin; Bista, Rajan K.; Khalbuss, Walid E.; Qiu, Wei; Staton, Kevin D.; Zhang, Lin; Brentnall, Teresa A.; Brand, Randall E.; Liu, Yang

    2011-03-01

    Alterations in nuclear architecture are the hallmark diagnostic characteristic of cancer cells. In this work, we show that the nuclear architectural characteristics quantified by spatial-domain low-coherence quantitative phase microscopy (SL-QPM), is more sensitive for the identification of cancer cells than conventional cytopathology. We demonstrated the importance of nuclear architectural characteristics in both an animal model of intestinal carcinogenesis - APC/Min mouse model and human cytology specimens with colorectal cancer by identifying cancer from cytologically noncancerous appearing cells. The determination of nanoscale nuclear architecture using this simple and practical optical instrument is a significant advance towards cancer diagnosis.

  20. Nanoscale surface topographies for structural colors

    DEFF Research Database (Denmark)

    Clausen, Jeppe Sandvik

    The thesis describes and demonstrates the possibilities for utilization of structural colors in mass fabricated plastic products as replacement for or in combination with pigments and inks. The motivation is the possible advantages related to re-cycling and re-use of plastic by limiting the number......-polymer interface is suppressed. This improves the ability to see through a clear plastic in the presence of specular reflection. The tapered nanostructures are also utilized to enhance the chroma of pigmented polymers. Larger tapered structures fabricated in a similar manor are shown to work as color filters....... Through an experimental study is the color of the transmitted light linked directly to the random topography of the surface by use of diffraction theory. The color effects from periodic structures and how these might be employed to create bright colors are investigated. This is done both for opaque...

  1. Probing defect and magnetic structures on the nanoscale

    OpenAIRE

    Kallis, Alexis

    2010-01-01

    This thesis reports on experimental research on structural defects and magnetic species on the nanoscale. The latter project involved considerable development work on the production of a spin-polarised mono-energetic positron beam. The construction of the system is described through various trial steps with emphasis on the methods of maximum practical polarization of the positron beam and of electrons in the sample with the smallest possible loss of beam intensity. A new sodium-22 source caps...

  2. Imaging the Nanoscale Band Structure of Topological Sb

    OpenAIRE

    Soumyanarayanan, Anjan; Yee, Michael M.; He, Yang; Lin, Hsin; Gardner, Dillon R.; Bansil, Arun; Lee, Young S.; Hoffman, Jennifer E.

    2013-01-01

    Many promising building blocks of future electronic technology - including non-stoichiometric compounds, strongly correlated oxides, and strained or patterned films - are inhomogeneous on the nanometer length scale. Exploiting the inhomogeneity of such materials to design next-generation nanodevices requires a band structure probe with nanoscale spatial resolution. To address this demand, we report the first simultaneous observation and quantitative reconciliation of two candidate probes - La...

  3. Infrared photoconductivity and photovoltaic response from nanoscale domains of PbS alloyed with thorium and oxygen

    Science.gov (United States)

    Arad-Vosk, N.; Beach, R.; Ron, A.; Templeman, T.; Golan, Y.; Sarusi, G.; Sa'ar, A.

    2018-03-01

    Thin films of lead sulfide alloyed with thorium and oxygen were deposited on GaAs substrates and processed to produce a photo-diode structure. Structural, optical and electrical characterizations indicate the presence of small nanoscale domains (NDs) that are characterized by dense packaging, high quality interfaces and a blue-shift of the energy bandgap toward the short wavelength infrared range of the spectrum. Photocurrent spectroscopy revealed a considerable photoconductivity that is correlated with excitation of carriers in the NDs of lead sulfide alloyed with thorium and oxygen. Furthermore, the appearance of a photovoltaic effect under near infrared illumination indicates a quasi-type II band alignment at the interface of the GaAs and the film of NDs.

  4. Methods and devices for fabricating three-dimensional nanoscale structures

    Science.gov (United States)

    Rogers, John A.; Jeon, Seokwoo; Park, Jangung

    2010-04-27

    The present invention provides methods and devices for fabricating 3D structures and patterns of 3D structures on substrate surfaces, including symmetrical and asymmetrical patterns of 3D structures. Methods of the present invention provide a means of fabricating 3D structures having accurately selected physical dimensions, including lateral and vertical dimensions ranging from 10s of nanometers to 1000s of nanometers. In one aspect, methods are provided using a mask element comprising a conformable, elastomeric phase mask capable of establishing conformal contact with a radiation sensitive material undergoing photoprocessing. In another aspect, the temporal and/or spatial coherence of electromagnetic radiation using for photoprocessing is selected to fabricate complex structures having nanoscale features that do not extend entirely through the thickness of the structure fabricated.

  5. Organisation and Control of Nanoscale Structures on Au(111)

    DEFF Research Database (Denmark)

    Zhang, Jingdong; Chi, Qijin; Andersen, Jens Enevold Thaulov

    2001-01-01

    system is IDe arnino acid cystine in the adsorbed state. Af ter dissociation of its disulfide band cystine farms a highly ordered pattem controlled by adsorption via IDe liberated sulfur atoms and intermolecular hydrogen bonding. Further organisation at three different leveis by lateral interactions can...... constitutes a new case for the lise of in situ STM as a tool for manufacturing nanoscale pit structures on IDe Au(lll) surface at small bias voltage. Individually and in combination these data hold perspectives for preparation of atornically planar electrochernical surfaces willi controlled functionalisation...

  6. Fabrication of complex nanoscale structures on various substrates

    Science.gov (United States)

    Han, Kang-Soo; Hong, Sung-Hoon; Lee, Heon

    2007-09-01

    Polymer based complex nanoscale structures were fabricated and transferred to various substrates using reverse nanoimprint lithography. To facilitate the fabrication and transference of the large area of the nanostructured layer to the substrates, a water-soluble polyvinyl alcohol mold was used. After generation and transference of the nanostructured layer, the polyvinyl alcohol mold was removed by dissolving in water. A residue-free, UV-curable, glue layer was formulated and used to bond the nanostructured layer onto the substrates. As a result, nanometer scale patterned polymer layers were bonded to various substrates and three-dimensional nanostructures were also fabricated by stacking of the layers.

  7. Nanoscale domain formation of phosphatidylinositol 4-phosphate in the plasma and vacuolar membranes of living yeast cells.

    Science.gov (United States)

    Tomioku, Kan-Na; Shigekuni, Mikiko; Hayashi, Hiroki; Yoshida, Akane; Futagami, Taiki; Tamaki, Hisanori; Tanabe, Kenji; Fujita, Akikazu

    2018-05-01

    In budding yeast Saccharomyces cerevisiae, PtdIns(4)P serves as an essential signalling molecule in the Golgi complex, endosomal system, and plasma membrane, where it is involved in the control of multiple cellular functions via direct interactions with PtdIns(4)P-binding proteins. To analyse the distribution of PtdIns(4)P in yeast cells at a nanoscale level, we employed an electron microscopy technique that specifically labels PtdIns(4)P on the freeze-fracture replica of the yeast membrane. This method minimizes the possibility of artificial perturbation, because molecules in the membrane are physically immobilised in situ. We observed that PtdIns(4)P is localised on the cytoplasmic leaflet, but not the exoplasmic leaflet, of the plasma membrane, Golgi body, vacuole, and vesicular structure membranes. PtdIns(4)P labelling was not observed in the membrane of the endoplasmic reticulum, and in the outer and inner membranes of the nuclear envelope or mitochondria. PtdIns(4)P forms clusters of plasma membrane and vacuolar membrane according to point pattern analysis of immunogold labelling. There are three kinds of compartments in the cytoplasmic leaflet of the plasma membrane. In the present study, we showed that PtdIns(4)P is specifically localised in the flat undifferentiated plasma membrane compartment. In the vacuolar membrane, PtdIns(4)P was concentrated in intramembrane particle (IMP)-deficient raft-like domains, which are tightly bound to lipid droplets, but not surrounding IMP-rich non-raft domains in geometrical IMP-distributed patterns in the stationary phase. This is the first report showing microdomain formations of PtdIns(4)P in the plasma membrane and vacuolar membrane of budding yeast cells at a nanoscale level, which will illuminate the functionality of PtdIns(4)P in each membrane. Copyright © 2018 Elsevier GmbH. All rights reserved.

  8. Nanoscale assembly of lanthanum silica with dense and porous interfacial structures.

    Science.gov (United States)

    Ballinger, Benjamin; Motuzas, Julius; Miller, Christopher R; Smart, Simon; Diniz da Costa, João C

    2015-02-03

    This work reports on the nanoscale assembly of hybrid lanthanum oxide and silica structures, which form patterns of interfacial dense and porous networks. It was found that increasing the molar ratio of lanthanum nitrate to tetraethyl orthosilicate (TEOS) in an acid catalysed sol-gel process alters the expected microporous metal oxide silica structure to a predominantly mesoporous structure above a critical lanthanum concentration. This change manifests itself by the formation of a lanthanum silicate phase, which results from the reaction of lanthanum oxide nanoparticles with the silica matrix. This process converts the microporous silica into the denser silicate phase. Above a lanthanum to silica ratio of 0.15, the combination of growth and microporous silica consumption results in the formation of nanoscale hybrid lanthanum oxides, with the inter-nano-domain spacing forming mesoporous volume. As the size of these nano-domains increases with concentration, so does the mesoporous volume. The absence of lanthanum hydroxide (La(OH)3) suggests the formation of La2O3 surrounded by lanthanum silicate.

  9. Phase transitions and domain structures in multiferroics

    Science.gov (United States)

    Vlahos, Eftihia

    2011-12-01

    Thin film ferroelectrics and multiferroics are two important classes of materials interesting both from a scientific and a technological prospective. The volatility of lead and bismuth as well as environmental issues regarding the toxicity of lead are two disadvantages of the most commonly used ferroelectric random access memory (FeRAM) materials such as Pb(Zr,Ti)O3 and SrBi2Ta2O9. Therefore lead-free thin film ferroelectrics are promising substitutes as long as (a) they can be grown on technologically important substrates such as silicon, and (b) their T c and Pr become comparable to that of well established ferroelectrics. On the other hand, the development of functional room temperature ferroelectric ferromagnetic multiferroics could lead to very interesting phenomena such as control of magnetism with electric fields and control of electrical polarization with magnetic fields. This thesis focuses on the understanding of material structure-property relations using nonlinear optical spectroscopy. Nonlinear spectroscopy is an excellent tool for probing the onset of ferroelectricity, and domain dynamics in strained ferroelectrics and multiferroics. Second harmonic generation was used to detect ferroelectricity and the antiferrodistortive phase transition in thin film SrTiO3. Incipient ferroelectric CaTiO3 has been shown to become ferroelectric when strained with a combination of SHG and dielectric measurements. The tensorial nature of the induced nonlinear polarization allows for probing of the BaTiO3 and SrTiO3 polarization contributions in nanoscale BaTiO3/SrTiO3 superlattices. In addition, nonlinear optics was used to demonstrate ferroelectricity in multiferroic EuTiO3. Finally, confocal SHG and Raman microscopy were utilized to visualize polar domains in incipient ferroelectric and ferroelastic CaTiO3.

  10. Nanoscale organization of {beta}{sub 2}-adrenergic receptor-Venus fusion protein domains on the surface of mammalian cells

    Energy Technology Data Exchange (ETDEWEB)

    Vobornik, Dusan; Rouleau, Yanouchka; Haley, Jennifer [Steacie Institute for Molecular Sciences, National Research Council Canada, Ottawa, ON, Canada K1A 0R6 (Canada); Bani-Yaghoub, Mahmud [Institute for Biological Sciences, National Research Council Canada, Ottawa, ON, Canada K1A 0R6 (Canada); Taylor, Rod [Steacie Institute for Molecular Sciences, National Research Council Canada, Ottawa, ON, Canada K1A 0R6 (Canada); Johnston, Linda J., E-mail: Linda.Johnston@nrc-cnrc.gc.ca [Steacie Institute for Molecular Sciences, National Research Council Canada, Ottawa, ON, Canada K1A 0R6 (Canada); Pezacki, John Paul, E-mail: John.Pezacki@nrc-cnrc.gc.ca [Steacie Institute for Molecular Sciences, National Research Council Canada, Ottawa, ON, Canada K1A 0R6 (Canada)

    2009-04-24

    Adrenergic receptors are a key component of nanoscale multiprotein complexes that are responsible for controlling the beat rate in a mammalian heart. We demonstrate the ability of near-field scanning optical microscopy (NSOM) to visualize {beta}{sub 2}-adrenergic receptors ({beta}{sub 2}AR) fused to the GFP analogue Venus at the nanoscale on HEK293 cells. The expression of the {beta}{sub 2}AR-Venus fusion protein was tightly controlled using a tetracycline-induced promoter. Both the size and density of the observed nanoscale domains are dependent on the level of induction and thus the level of protein expression. At concentrations between 100 and 700 ng/ml of inducer doxycycline, the size of domains containing the {beta}{sub 2}AR-Venus fusion protein appears to remain roughly constant, but the number of domains per cell increase. At 700 ng/ml doxycycline the functional receptors are organized into domains with an average diameter of 150 nm with a density similar to that observed for the native protein on primary murine cells. By contrast, larger micron-sized domains of {beta}{sub 2}AR are observed in the membrane of the HEK293 cells that stably overexpress {beta}{sub 2}AR-GFP and {beta}{sub 2}AR-eYFP. We conclude that precise chemical control of gene expression is highly advantageous for the use {beta}{sub 2}AR-Venus fusion proteins as models for {beta}{sub 2}AR function. These observations are critical for designing future cell models and assays based on {beta}{sub 2}AR, since the receptor biology is consistent with a relatively low density of nanoscale receptor domains.

  11. Toward a Blended Ontology: Applying Knowledge Systems to Compare Therapeutic and Toxicological Nanoscale Domains

    Directory of Open Access Journals (Sweden)

    Christopher M. Grulke

    2012-01-01

    Full Text Available Bionanomedicine and environmental research share need common terms and ontologies. This study applied knowledge systems, data mining, and bibliometrics used in nano-scale ADME research from 1991 to 2011. The prominence of nano-ADME in environmental research began to exceed the publication rate in medical research in 2006. That trend appears to continue as a result of the growing products in commerce using nanotechnology, that is, 5-fold growth in number of countries with nanomaterials research centers. Funding for this research virtually did not exist prior to 2002, whereas today both medical and environmental research is funded globally. Key nanoparticle research began with pharmacology and therapeutic drug-delivery and contrasting agents, but the advances have found utility in the environmental research community. As evidence ultrafine aerosols and aquatic colloids research increased 6-fold, indicating a new emphasis on environmental nanotoxicology. User-directed expert elicitation from the engineering and chemical/ADME domains can be combined with appropriate Boolean logic and queries to define the corpus of nanoparticle interest. The study combined pharmacological expertise and informatics to identify the corpus by building logical conclusions and observations. Publication records informatics can lead to an enhanced understanding the connectivity between fields, as well as overcoming the differences in ontology between the fields.

  12. Nano-scale structure in membranes in relation to enzyme action - computer simulation vs. experiment

    DEFF Research Database (Denmark)

    Høyrup, P.; Jørgensen, Kent; Mouritsen, O.G.

    2002-01-01

    There is increasing theoretical and experimental evidence indicating that small-scale domain structure and dynamical heterogeneity develop in lipid membranes as a consequence of the the underlying phase transitions and the associated density and composition fluctuations. The relevant coherence...... lengths are in the nano-meter range. The nano-scale structure is believed to be important for controlling the activity of enzymes, specifically phospholipases, which act at bilayer membranes. We propose here a lattice-gas statistical mechanical model with appropriate dynamics to account for the non......-equilibrium action of the enzyme phospholipase A(2) which hydrolyses lipid-bilayer substrates. The resulting product molecules are assumed to induce local variations in the membrane interfacial pressure. Monte Carlo simulations of the non-equilibrium properties of the model for one-component as well as binary lipid...

  13. Effects of structural modification on reliability of nanoscale nitride HEMTs

    Science.gov (United States)

    Gaddipati, Vamsi Mohan

    AlGaN based nanoscale high-electron-mobility transistors (HEMTs) are the next generation of transistor technology that features the unique combination of higher power, wider bandwidth, low noise, higher efficiency, and temperature/radiation hardness than conventional AlGaAs and Si based technologies. However, as evidenced by recent stress tests, reliability of these devices (characterized by a gradual decrease in the output current/power leading to failure of the device in just tens of hours of operation) remains a major concern. Although, in these tests, physical damages were clearly visible in the device, the root cause and nature of these damages have not yet been fully assessed experimentally. Therefore, a comprehensive theoretical study of the physical mechanisms responsible for degradation of AlGaN HEMTs is essential before these devices are deployed in targeted applications. The main objective of the proposed research is to computationally investigate how degradation of state-of-the-art nanoscale AlGaN HEMTs is governed by an intricate and dynamical coupling of thermo-electromechanical processes at different length (atoms-to-transistor) and time (femtosecondto- hours) scales while operating in high voltage, large mechanical, and high temperature/radiation stresses. This work centers around a novel hypotheses as follows: High voltage applied to AlGaN HEMT causes excessive internal heat dissipation, which triggers gate metal diffusion into the semiconducting barrier layer and structural modifications (defect ii formation) leading to diminished polarization induced charge density and output current. Since the dynamical system to be studied is complex, chaotic (where the evolution rule is guided by atomicity of the underlying material), and involve coupled physical processes, an in-house multiscale simulator (QuADS 3-D) has been employed and augmented, where material parameters are obtained atomistically using firstprinciples, structural relaxation and defect

  14. Charge transport in nanoscale "all-inorganic" networks of semiconductor nanorods linked by metal domains.

    Science.gov (United States)

    Lavieville, Romain; Zhang, Yang; Casu, Alberto; Genovese, Alessandro; Manna, Liberato; Di Fabrizio, Enzo; Krahne, Roman

    2012-04-24

    Charge transport across metal-semiconductor interfaces at the nanoscale is a crucial issue in nanoelectronics. Chains of semiconductor nanorods linked by Au particles represent an ideal model system in this respect, because the metal-semiconductor interface is an intrinsic feature of the nanosystem and does not manifest solely as the contact to the macroscopic external electrodes. Here we investigate charge transport mechanisms in all-inorganic hybrid metal-semiconductor networks fabricated via self-assembly in solution, in which CdSe nanorods were linked to each other by Au nanoparticles. Thermal annealing of our devices changed the morphology of the networks and resulted in the removal of small Au domains that were present on the lateral nanorod facets, and in ripening of the Au nanoparticles in the nanorod junctions with more homogeneous metal-semiconductor interfaces. In such thermally annealed devices the voltage dependence of the current at room temperature can be well described by a Schottky barrier lowering at a metal semiconductor contact under reverse bias, if the spherical shape of the gold nanoparticles is considered. In this case the natural logarithm of the current does not follow the square-root dependence of the voltage as in the bulk, but that of V(2/3). From our fitting with this model we extract the effective permittivity that agrees well with theoretical predictions for the permittivity near the surface of CdSe nanorods. Furthermore, the annealing improved the network conductance at cryogenic temperatures, which could be related to the reduction of the number of trap states.

  15. Monolithic integration of nanoscale tensile specimens and MEMS structures

    International Nuclear Information System (INIS)

    Yilmaz, Mehmet; Kysar, Jeffrey W

    2013-01-01

    Nanoscale materials often have stochastic material properties due to a random distribution of material defects and an insufficient number of defects to ensure a consistent average mechanical response. Current methods to measure the mechanical properties employ MEMS-based actuators. The nanoscale specimens are typically mounted manually onto the load platform, so the boundary conditions have random variations, complicating the experimental measurement of the intrinsic stochasticity of the material properties. Here we show methods for monolithic integration of a nanoscale specimen co-fabricated with the loading platform. The nanoscale specimen is gold with dimensions of ∼40 nm thickness, 350 ± 50 nm width, and 7 μm length and the loading platform is an interdigitated electrode electrostatic actuator. The experiment is performed in a scanning electron microscope and digital image correlation is employed to measure displacements to determine stress and strain. The ultimate tensile strength of the nanocrystalline nanoscale specimen approaches 1 GPa, consistent with measurements made by other nanometer scale sample characterization methods on other material samples at the nanometer scale, as well as gold samples at the nanometer scale. The batch-compatible microfabrication method can be used to create nominally identical nanoscale specimens and boundary conditions for a broad range of materials. (paper)

  16. A micromagnetic study of domain structure modeling

    International Nuclear Information System (INIS)

    Matsuo, Tetsuji; Mimuro, Naoki; Shimasaki, Masaaki

    2008-01-01

    To develop a mesoscopic model for magnetic-domain behavior, a domain structure model (DSM) was examined and compared with a micromagnetic simulation. The domain structure of this model is given by several domains with uniform magnetization vectors and domain walls. The directions of magnetization vectors and the locations of domain walls are determined so as to minimize the magnetic total energy of the magnetic material. The DSM was modified to improve its representation capability for domain behavior. The domain wall energy is multiplied by a vanishing factor to represent the disappearance of magnetic domain. The sequential quadratic programming procedure is divided into two steps to improve an energy minimization process. A comparison with micromagnetic simulation shows that the modified DSM improves the representation accuracy of the magnetization process

  17. Potential of silicon nanowires structures as nanoscale piezoresistors in mechanical sensors

    International Nuclear Information System (INIS)

    Messina, M; Njuguna, J

    2012-01-01

    This paper presents the design of a single square millimeter 3-axial accelerometer for bio-mechanics measurements that exploit the potential of silicon nanowires structures as nanoscale piezoresistors. The main requirements of this application are miniaturization and high measurement accuracy. Nanowires as nanoscale piezoresistive devices have been chosen as sensing element, due to their high sensitivity and miniaturization achievable. By exploiting the electro-mechanical features of nanowires as nanoscale piezoresistors, the nominal sensor sensitivity is overall boosted by more than 30 times. This approach allows significant higher accuracy and resolution with smaller sensing element in comparison with conventional devices without the need of signal amplification.

  18. Investigation of Short Channel Effect on Vertical Structures in Nanoscale MOSFET

    Directory of Open Access Journals (Sweden)

    Munawar A. Riyadi

    2009-12-01

    Full Text Available The recent development of MOSFET demands innovative approach to maintain the scaling into nanoscale dimension. This paper focuses on the physical nature of vertical MOSFET in nanoscale regime. Vertical structure is one of the promising devices in further scaling, with relaxed-lithography feature in the manufacture. The comparison of vertical and lateral MOSFET performance for nanoscale channel length (Lch is demonstrated with the help of numerical tools. The evaluation of short channel effect (SCE parameters, i.e. threshold voltage roll-off, subthreshold swing (SS, drain induced barrier lowering (DIBL and leakage current shows the considerable advantages as well as its thread-off in implementing the structure, in particular for nanoscale regime.

  19. Toward a Blended Ontology: Applying Knowledge Systems to Compare Therapeutic and Toxicological Nanoscale Domains

    Science.gov (United States)

    Bionanomedicine and environmental research share need common terms and ontologies. This study applied knowledge systems, data mining, and bibliometrics used in nano-scale ADME research from 1991 to 2011. The prominence of nano-ADME in environmental research began to exceed the pu...

  20. On the structure of order domains

    DEFF Research Database (Denmark)

    Geil, Olav; Pellikaan, Ruud

    2002-01-01

    The notion of an order domain is generalized. The behaviour of an order domain by taking a subalgebra, the extension of scalars, and the tensor product is studied. The relation of an order domain with valuation theory, Gröbner algebras, and graded structures is given. The theory of Gröbner bases...... for order domains is developed and used to show that the factor ring theorem and its converse, the presentation theorem, hold. The dimension of an order domain is related to the rank of its value semigroup....

  1. Structuring very large domain models

    DEFF Research Database (Denmark)

    Störrle, Harald

    2010-01-01

    View/Viewpoint approaches like IEEE 1471-2000, or Kruchten's 4+1-view model are used to structure software architectures at a high level of granularity. While research has focused on architectural languages and with consistency between multiple views, practical questions such as the structuring a...

  2. Investigation of nanoscale structures by small-angle X-ray scattering in a radiochromic dosimeter

    DEFF Research Database (Denmark)

    Skyt, Peter Sandegaard; Jensen, Grethe Vestergaard; Wahlstedt, Isak Hannes

    2014-01-01

    This study examines the nanoscale structures in a radiochromic dosimeter that was based on leuco-malachite-green dye and the surfactant sodium dodecyl sulfate (SDS) suspended in a gelatin matrix. Small-angle X-ray scattering was used to investigate the structures of a range of compositions...

  3. On ripples and rafts: Curvature induced nanoscale structures in lipid membranes

    International Nuclear Information System (INIS)

    Schmid, Friederike; Dolezel, Stefan; Meinhardt, Sebastian; Lenz, Olaf

    2014-01-01

    We develop an elastic theory that predicts the spontaneous formation of nanoscale structures in lipid bilayers which locally phase separate between two phases with different spontaneous monolayer curvature. The theory rationalizes in a unified manner the observation of a variety of nanoscale structures in lipid membranes: Rippled states in one-component membranes, lipid rafts in multicomponent membranes. Furthermore, we report on recent observations of rippled states and rafts in simulations of a simple coarse-grained model for lipid bilayers, which are compatible with experimental observations and with our elastic model

  4. Nanoscale spin-dependent transport of electrons and holes in Si-ferromagnet structures

    NARCIS (Netherlands)

    Ul Haq, E.

    Given the rapid development of magnetic data storage and spin-electronics into the realm of nanotechnology, the understanding of the spin-dependent electronic transport and switching behavior of magnetic structures at the nanoscale is an important issue. We have developed spin-sensitive techniques

  5. Subcritical switching dynamics and humidity effects in nanoscale studies of domain growth in ferroelectric thin films

    International Nuclear Information System (INIS)

    Blaser, Cédric; Paruch, Patrycja

    2015-01-01

    Ferroelectric domain switching in c-axis-oriented epitaxial Pb(Zr 0.2 Ti 0.8 )O 3 thin films was studied using biased scanning probe microscopy tips. While linear and logarithmic dependence of domain size on tip bias and writing time, respectively, are well known, we report an additional linear dependence on relative humidity in the 28–65% range. We map out the switched domain size as a function of both the tip bias and the applied pulse time and describe a growth-limited regime for very short pulses and a nucleation-limited regime for very low tip bias. Using ‘interrupted-switching’ measurements, we probe the nucleation regime with subcritical pulses and identify a surprisingly long relaxation time on the order of 100 ms, which we relate to ionic redistribution both on the surface and within the thin film itself. (paper)

  6. Structural Time Domain Identification Toolbox User's Guide

    DEFF Research Database (Denmark)

    Andersen, P.; Kirkegaard, Poul Henning; Brincker, Rune

    This manual describes the Structural Time Domain Identification toolbox for use with MA TLAB. This version of the tool box has been developed using the PC-based MA TLAB version 4.2c, but is compatible with prior versions of MATLAB and UNIX-based versions. The routines of the toolbox are the so...

  7. Investigations on a nano-scale periodical waveguide structure taking surface plasmon polaritons into consideration

    International Nuclear Information System (INIS)

    Liu Weihao; Zhong Renbin; Zhou Jun; Zhang Yaxin; Hu Min; Liu Shenggang

    2012-01-01

    Detailed theoretical analysis and computer simulations on the electromagnetic characteristics of a nano-scale periodical waveguide structure, taking surface plasmon polaritons (SPPs) into consideration, are carried out in this paper. The results show that SPPs will significantly influence the electromagnetic characteristics of the structure. When the operation frequency is in a certain band—the ‘radial confinement band’, neither radial surface plasmon waves nor guided waves, which both will lead to radial energy loss, can be excited in the structure. And the electromagnetic waves are completely confined within the longitudinal waveguide and propagate along it with little attenuation. The radial energy loss is then significantly reduced. These results are of great significance not only for increasing the efficiency of the radiation sources based on the nano-scale periodical waveguide structure but also for the development of high-efficiency waveguides and wide-band filters in the infrared and visible light regimes. (paper)

  8. Multilevel domain decomposition for electronic structure calculations

    International Nuclear Information System (INIS)

    Barrault, M.; Cances, E.; Hager, W.W.; Le Bris, C.

    2007-01-01

    We introduce a new multilevel domain decomposition method (MDD) for electronic structure calculations within semi-empirical and density functional theory (DFT) frameworks. This method iterates between local fine solvers and global coarse solvers, in the spirit of domain decomposition methods. Using this approach, calculations have been successfully performed on several linear polymer chains containing up to 40,000 atoms and 200,000 atomic orbitals. Both the computational cost and the memory requirement scale linearly with the number of atoms. Additional speed-up can easily be obtained by parallelization. We show that this domain decomposition method outperforms the density matrix minimization (DMM) method for poor initial guesses. Our method provides an efficient preconditioner for DMM and other linear scaling methods, variational in nature, such as the orbital minimization (OM) procedure

  9. Polyamide membranes with nanoscale Turing structures for water purification

    Science.gov (United States)

    Tan, Zhe; Chen, Shengfu; Peng, Xinsheng; Zhang, Lin; Gao, Congjie

    2018-05-01

    The emergence of Turing structures is of fundamental importance, and designing these structures and developing their applications have practical effects in chemistry and biology. We use a facile route based on interfacial polymerization to generate Turing-type polyamide membranes for water purification. Manipulation of shapes by control of reaction conditions enabled the creation of membranes with bubble or tube structures. These membranes exhibit excellent water-salt separation performance that surpasses the upper-bound line of traditional desalination membranes. Furthermore, we show the existence of high water permeability sites in the Turing structures, where water transport through the membranes is enhanced.

  10. Controlling Non-Equilibrium Structure Formation on the Nanoscale.

    Science.gov (United States)

    Buchmann, Benedikt; Hecht, Fabian Manfred; Pernpeintner, Carla; Lohmueller, Theobald; Bausch, Andreas R

    2017-12-06

    Controlling the structure formation of gold nanoparticle aggregates is a promising approach towards novel applications in many fields, ranging from (bio)sensing to (bio)imaging to medical diagnostics and therapeutics. To steer structure formation, the DNA-DNA interactions of DNA strands that are coated on the surface of the particles have become a valuable tool to achieve precise control over the interparticle potentials. In equilibrium approaches, this technique is commonly used to study particle crystallization and ligand binding. However, regulating the structural growth processes from the nano- to the micro- and mesoscale remains elusive. Here, we show that the non-equilibrium structure formation of gold nanoparticles can be stirred in a binary heterocoagulation process to generate nanoparticle clusters of different sizes. The gold nanoparticles are coated with sticky single stranded DNA and mixed at different stoichiometries and sizes. This not only allows for structural control but also yields access to the optical properties of the nanoparticle suspensions. As a result, we were able to reliably control the kinetic structure formation process to produce cluster sizes between tens of nanometers up to micrometers. Consequently, the intricate optical properties of the gold nanoparticles could be utilized to control the maximum of the nanoparticle suspension extinction spectra between 525 nm and 600 nm. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. On the relationship between the dynamic behavior and nanoscale staggered structure of the bone

    Science.gov (United States)

    Qwamizadeh, Mahan; Zhang, Zuoqi; Zhou, Kun; Zhang, Yong Wei

    2015-05-01

    Bone, a typical load-bearing biological material, composed of ordinary base materials such as organic protein and inorganic mineral arranged in a hierarchical architecture, exhibits extraordinary mechanical properties. Up to now, most of previous studies focused on its mechanical properties under static loading. However, failure of the bone occurs often under dynamic loading. An interesting question is: Are the structural sizes and layouts of the bone related or even adapted to the functionalities demanded by its dynamic performance? In the present work, systematic finite element analysis was performed on the dynamic response of nanoscale bone structures under dynamic loading. It was found that for a fixed mineral volume fraction and unit cell area, there exists a nanoscale staggered structure at some specific feature size and layout which exhibits the fastest attenuation of stress waves. Remarkably, these specific feature sizes and layouts are in excellent agreement with those experimentally observed in the bone at the same scale, indicating that the structural size and layout of the bone at the nanoscale are evolutionarily adapted to its dynamic behavior. The present work points out the importance of dynamic effect on the biological evolution of load-bearing biological materials.

  12. Formation of nanoscale tungsten oxide structures and colouration ...

    Indian Academy of Sciences (India)

    The X-ray diffraction, together with transmission electron microscopic studies have revealed formation of regular polyhedral nanocrystalline ..... For molecular structure and orientation determination, the ... self-similarity within a complicated system. ..... Hummel R I 1997 Handbook of optical properties: Optics of small particles ...

  13. Structural and mechanical properties of glassy water in nanoscale confinement.

    Science.gov (United States)

    Lombardo, Thomas G; Giovambattista, Nicolás; Debenedetti, Pablo G

    2009-01-01

    We investigate the structure and mechanical properties of glassy water confined between silica-based surfaces with continuously tunable hydrophobicity and hydrophilicity by computing and analyzing minimum energy, mechanically stable configurations (inherent structures). The structured silica substrate imposes long-range order on the first layer of water molecules under hydrophobic confinement at high density (p > or = 1.0 g cm(-3)). This proximal layer is also structured in hydrophilic confinement at very low density (p approximately 0.4 g cm(-3)). The ordering of water next to the hydrophobic surface greatly enhances the mechanical strength of thin films (0.8 nm). This leads to a substantial stress anisotropy; the transverse strength of the film exceeds the normal strength by 500 MPa. The large transverse strength results in a minimum in the equation of state of the energy landscape that does not correspond to a mechanical instability, but represents disruption of the ordered layer of water next to the wall. In addition, we find that the mode of mechanical failure is dependent on the type of confinement. Under large lateral strain, water confined by hydrophilic surfaces preferentially forms voids in the middle of the film and fails cohesively. In contrast, water under hydrophobic confinement tends to form voids near the walls and fails by loss of adhesion.

  14. A poly(vinyl alcohol)/sodium alginate blend monolith with nanoscale porous structure

    OpenAIRE

    Sun, Xiaoxia; Uyama, Hiroshi

    2013-01-01

    A stimuli-responsive poly(vinyl alcohol) (PVA)/sodium alginate (SA) blend monolith with nanoscale porous (mesoporous) structure is successfully fabricated by thermally impacted non-solvent induced phase separation (TINIPS) method. The PVA/SA blend monolith with different SA contents is conveniently fabricated in an aqueous methanol without any templates. The solvent suitable for the fabrication of the present blend monolith by TINIPS is different with that of the PVA monolith. The nanostructu...

  15. Role of Acoustoelectric Interaction in the Formation of Nanoscale Periodic Structures of Adsorbed Atoms

    Energy Technology Data Exchange (ETDEWEB)

    Peleshchak, R. M., E-mail: peleshchak@rambler.ru; Lazurchak, I. I.; Kuzyk, O. V.; Dan’kiv, O. O. [Ivan Franko Drohobych State Pedagogical University (Ukraine); Zegrya, G. G. [Russian Academy of Sciences, Ioffe Physical–Technical Institute (Russian Federation)

    2016-03-15

    The role of acoustoelectric effects in the formation of nanoscale structures of adatoms, resulting from the self-consistent interaction of adatoms with a surface acoustic wave and the electronic subsystem, is studied for the case of charged and uncharged adatoms. It is shown that an increase in the doping level of a semiconductor with donor impurities at a fixed average adatom concentration results in an increase in the critical temperature below which self-organization processes occur.

  16. A poly(vinyl alcohol)/sodium alginate blend monolith with nanoscale porous structure.

    Science.gov (United States)

    Sun, Xiaoxia; Uyama, Hiroshi

    2013-10-04

    A stimuli-responsive poly(vinyl alcohol) (PVA)/sodium alginate (SA) blend monolith with nanoscale porous (mesoporous) structure is successfully fabricated by thermally impacted non-solvent induced phase separation (TINIPS) method. The PVA/SA blend monolith with different SA contents is conveniently fabricated in an aqueous methanol without any templates. The solvent suitable for the fabrication of the present blend monolith by TINIPS is different with that of the PVA monolith. The nanostructural control of the blend monolith is readily achieved by optimizing the fabrication conditions. Brunauer Emmett Teller measurement shows that the obtained blend monolith has a large surface area. Pore size distribution plot for the blend monolith obtained by the non-local density functional theory method reveals the existence of the nanoscale porous structure. Fourier transform infrared analysis reveals the strong interactions between PVA and SA. The pH-responsive property of the blend monolith is investigated on the basis of swelling ratio in different pH solutions. The present blend monolith of biocompatible and biodegradable PVA and SA with nanoscale porous structure has large potential for applications in biomedical and environmental fields.

  17. Structure Transformation and Coherent Interface in Large Lattice-Mismatched Nanoscale Multilayers

    Directory of Open Access Journals (Sweden)

    J. Y. Xie

    2013-01-01

    Full Text Available Nanoscale Al/W multilayers were fabricated by DC magnetron sputtering and characterized by transmission electron microscopy and high-resolution electron microscopy. Despite the large lattice mismatch and significantly different lattice structures between Al and W, a structural transition from face-centered cubic to body-centered cubic in Al layers was observed when the individual layer thickness was reduced from 5 nm to 1 nm, forming coherent Al/W interfaces. For potential mechanisms underlying the observed structure transition and forming of coherent interfaces, it was suggested that the reduction of interfacial energy and high stresses induced by large lattice-mismatch play a crucial role.

  18. Nanoscale structure and atomic disorder in the iron-based chalcogenides

    Directory of Open Access Journals (Sweden)

    Naurang Lal Saini

    2013-01-01

    Full Text Available The multiband iron-based superconductors have layered structure with a phase diagram characterized by a complex interplay of charge, spin and lattice excitations, with nanoscale atomic structure playing a key role in their fundamental electronic properties. In this paper, we briefly review nanoscale structure and atomic disorder in iron-based chalcogenide superconductors. We focus on the Fe(Se,S1−xTex (11-type and K0.8Fe1.6Se2 (122-type systems, discussing their local structure obtained by extended x-ray absorption fine structure. Local structure studies on the Fe(Se,S1−xTex system reveal clear nanoscale phase separation characterized by coexisting components of different atomic configurations, similar to the case of random alloys. In fact, the Fe–Se/S and Fe–Te distances in the ternary Fe(Se,S1−xTex are found to be closer to the respective distances in the binary FeSe/FeS and FeTe systems, showing significant divergence of the local structure from the average one. The observed features are characteristic of ternary random alloys, indicating breaking of the local symmetry in these materials. On the other hand, K0.8Fe1.6Se2 is known for phase separation in an iron-vacancy ordered phase and an in-plane compressed lattice phase. The local structure of these 122-type chalcogenides shows that this system is characterized by a large local disorder. Indeed, the experiments suggest a nanoscale glassy phase in K0.8Fe1.6Se2, with the superconductivity being similar to the granular materials. While the 11-type structure has no spacer layer, the 122-type structure contains intercalated atoms unlike the 1111-type REFeAsO (RE = rare earth oxypnictides, having well-defined REO spacer layers. It is clear that the interlayer atomic correlations in these iron-based superconducting structures play an important role in structural stability as well as superconductivity and magnetism.

  19. Nanoscale structural order from the atomic pair distribution function (PDF): There's plenty of room in the middle

    International Nuclear Information System (INIS)

    Billinge, Simon J.L.

    2008-01-01

    Emerging materials of scientific and technological interest are generally complex and often nanostructured: they have atomic orderings that extend on nanometer length-scales. These can be discrete nanoparticles; bulk crystals with nanoscale chemical or displacive order within them; mesoporous materials that are bulk materials containing nanoscale holes; and nanocomposites that are intimate heterogeneous mixtures of nano-sized constituents. As always, a quantitative knowledge of the atomic structure within these materials is a prerequisite to understanding and engineering their properties. Traditional crystallographic methods for obtaining this information break down at the nanoscale, sometimes referred to as 'the nanostructure problem'. We describe here some emerging methods for studying nanoscale structure. We present some examples of recent successes. Finally, we discuss future directions and opportunities and draw attention to limitations and potential problems. -

  20. Insights into function of PSI domains from structure of the Met receptor PSI domain

    International Nuclear Information System (INIS)

    Kozlov, Guennadi; Perreault, Audrey; Schrag, Joseph D.; Park, Morag; Cygler, Miroslaw; Gehring, Kalle; Ekiel, Irena

    2004-01-01

    PSI domains are cysteine-rich modules found in extracellular fragments of hundreds of signaling proteins, including plexins, semaphorins, integrins, and attractins. Here, we report the solution structure of the PSI domain from the human Met receptor, a receptor tyrosine kinase critical for proliferation, motility, and differentiation. The structure represents a cysteine knot with short regions of secondary structure including a three-stranded antiparallel β-sheet and two α-helices. All eight cysteines are involved in disulfide bonds with the pattern consistent with that for the PSI domain from Sema4D. Comparison with the Sema4D structure identifies a structurally conserved core comprising the N-terminal half of the PSI domain. Interestingly, this part links adjacent SEMA and immunoglobulin domains in the Sema4D structure, suggesting that the PSI domain serves as a wedge between propeller and immunoglobulin domains and is responsible for the correct positioning of the ligand-binding site of the receptor

  1. The Structure and Transport of Water and Hydrated Ions Within Hydrophobic, Nanoscale Channels

    International Nuclear Information System (INIS)

    Holt, J.K.; Herberg, J.L.; Wu, Y.; Schwegler, E.; Mehta, A.

    2009-01-01

    The purpose of this project includes an experimental and modeling investigation into water and hydrated ion structure and transport at nanomaterials interfaces. This is a topic relevant to understanding the function of many biological systems such as aquaporins that efficiently shuttle water and ion channels that permit selective transport of specific ions across cell membranes. Carbon nanotubes (CNT) are model nanoscale, hydrophobic channels that can be functionalized, making them artificial analogs for these biological channels. This project investigates the microscopic properties of water such as water density distributions and dynamics within CNTs using Nuclear Magnetic Resonance (NMR) and the structure of hydrated ions at CNT interfaces via X-ray Absorption Spectroscopy (XAS). Another component of this work is molecular simulation, which can predict experimental measurables such as the proton relaxation times, chemical shifts, and can compute the electronic structure of CNTs. Some of the fundamental questions this work is addressing are: (1) what is the length scale below which nanoscale effects such as molecular ordering become important, (2) is there a relationship between molecular ordering and transport?, and (3) how do ions interact with CNT interfaces? These are questions of interest to the scientific community, but they also impact the future generation of sensors, filters, and other devices that operate on the nanometer length scale. To enable some of the proposed applications of CNTs as ion filtration media and electrolytic supercapacitors, a detailed knowledge of water and ion structure at CNT interfaces is critical.

  2. Possible Diamond-Like Nanoscale Structures Induced by Slow Highly-Charged Ions on Graphite (HOPG)

    Energy Technology Data Exchange (ETDEWEB)

    Sideras-Haddad, E.; Schenkel, T.; Shrivastava, S.; Makgato, T.; Batra, A.; Weis, C. D.; Persaud, A.; Erasmus, R.; Mwakikunga, B.

    2009-01-06

    The interaction between slow highly-charged ions (SHCI) of different charge states from an electron-beam ion trap and highly oriented pyrolytic graphite (HOPG) surfaces is studied in terms of modification of electronic states at single-ion impact nanosizeareas. Results are presented from AFM/STM analysis of the induced-surface topological features combined with Raman spectroscopy. I-V characteristics for a number of different impact regions were measured with STM and the results argue for possible formation of diamond-like nanoscale structures at the impact sites.

  3. Numerical analysis of micro-/nanoscale gas-film lubrication of sliding surface with complicated structure

    International Nuclear Information System (INIS)

    Kawagoe, Yoshiaki; Isono, Susumu; Takeno, Takanori; Yonemura, Shigeru; Takagi, Toshiyuki; Miki, Hiroyuki

    2014-01-01

    It has been reported that the friction between a partially polished diamond-coated surface and a metal surface was drastically reduced to zero when they are slid at a few m/s. Since the sliding was noiseless, it seems that the diamond-coated surface was levitated over the counter surface and the sliding mechanism was the gas film lubrication. Recently, the mechanism of levitation of a slider with a micro/nanoscale surface structure on a rotating disk was theoretically clarified [S. Yonemura et al., Tribol. Lett., (2014), doi:10.1007/s11249-014-0368-2]. Probably, the partially polished diamond-coated surface may be levitated by high gas pressure generated by the micro/nanoscale surface structure on it. In this study, in order to verify our deduction, we performed numerical simulations of sliding of partially polished diamond-coated surface by reproducing its complicated surface structure using the data measured by an atomic force microscope (AFM). As a result, we obtained the lift force which is large enough to levitate the slider used in the experiment

  4. Numerical analysis of micro-/nanoscale gas-film lubrication of sliding surface with complicated structure

    Energy Technology Data Exchange (ETDEWEB)

    Kawagoe, Yoshiaki; Isono, Susumu; Takeno, Takanori [Department of Nanomechanics, Graduate School of Engineering, Tohoku University, 6-6-01 Aoba, Aramaki, Aoba-ku, Sendai 980-8579 (Japan); Yonemura, Shigeru; Takagi, Toshiyuki [Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Miki, Hiroyuki [Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578 (Japan)

    2014-12-09

    It has been reported that the friction between a partially polished diamond-coated surface and a metal surface was drastically reduced to zero when they are slid at a few m/s. Since the sliding was noiseless, it seems that the diamond-coated surface was levitated over the counter surface and the sliding mechanism was the gas film lubrication. Recently, the mechanism of levitation of a slider with a micro/nanoscale surface structure on a rotating disk was theoretically clarified [S. Yonemura et al., Tribol. Lett., (2014), doi:10.1007/s11249-014-0368-2]. Probably, the partially polished diamond-coated surface may be levitated by high gas pressure generated by the micro/nanoscale surface structure on it. In this study, in order to verify our deduction, we performed numerical simulations of sliding of partially polished diamond-coated surface by reproducing its complicated surface structure using the data measured by an atomic force microscope (AFM). As a result, we obtained the lift force which is large enough to levitate the slider used in the experiment.

  5. Assembly and structural analysis of a covalently closed nano-scale DNA cage

    DEFF Research Database (Denmark)

    Andersen, Félicie Faucon; Knudsen, Bjarne; Oliveira, Cristiano Luis Pinto De

    2008-01-01

    for investigations of DNA-interacting enzymes. More recently, strategies for synthesis of more complex two-dimensional (2D) and 3D DNA structures have emerged. However, the building of such structures is still in progress and more experiences from different research groups and different fields of expertise...... be described as a nano-scale DNA cage, Hence, in theory it could hold proteins or other bio-molecules to enable their investigation in certain harmful environments or even allow their organization into higher order structures...... The inherent properties of DNA as a stable polymer with unique affinity for partner molecules determined by the specific Watson-Crick base pairing makes it an ideal component in self-assembling structures. This has been exploited for decades in the design of a variety of artificial substrates...

  6. An assessment of the contributing factors to the nanoscale structural refinement of advanced bainitic steels

    International Nuclear Information System (INIS)

    Cornide, J.; Garcia-Mateo, C.; Capdevila, C.; Caballero, F.G.

    2013-01-01

    A new generation of steels has been designed, which on transformation at low temperature (200–350 °C), leads to a nano-scale microstructure, known as NANOBAIN. The microstructure consists of slender crystals of ferrite, whose controlling scale compares well with that of carbon nanotubes (20–40 nm). These advanced steels present the highest strength/toughness combinations ever recorded in bainitic steels. Their properties are mainly a consequence of the formation of nanoscale bainitic ferrite plates at very low temperatures. Transmission electron microscopy observations have shown that plastic relaxation in the austenite adjacent to the bainite plates may control the final size of the bainitic ferrite plates. The dislocation debris generated in this process resists the advance of the bainitic ferrite–austenite interface, the resistance being greatest for strong austenite. The yield strength of the austenite must then feature in any assessment of plate size. In this scenario, the plates are expected to become thicker at high temperatures because the yield strength of the austenite will then be lower. The goal of this study is to evaluate the influence of yield strength of austenite to the nanoscale structural refinement of advanced bainitic steels. In this sense, in situ measurements of austenite strength before bainite formation using a deformation dilatometer Bähr 805D have been performed in a medium carbon high silicon steel transforming at intermediate temperatures (325–400 °C) to a submicron structure of bainite and in a high carbon high silicon steel transforming at low temperatures (200–350 °C) to nanostructured bainite. The role of the transformation driving force on the bainite plate thickness will be also discussed

  7. An assessment of the contributing factors to the nanoscale structural refinement of advanced bainitic steels

    Energy Technology Data Exchange (ETDEWEB)

    Cornide, J., E-mail: jca@cenim.csic.es [Centro Nacional de Investigaciones Metalúrgicas (CENIM-CSIC), Avda Gregorio del Amo 8, Madrid E-28040 (Spain); Garcia-Mateo, C., E-mail: cgm@cenim.csic.es [Centro Nacional de Investigaciones Metalúrgicas (CENIM-CSIC), Avda Gregorio del Amo 8, Madrid E-28040 (Spain); Capdevila, C., E-mail: ccm@cenim.csic.es [Centro Nacional de Investigaciones Metalúrgicas (CENIM-CSIC), Avda Gregorio del Amo 8, Madrid E-28040 (Spain); Caballero, F.G., E-mail: fgc@cenim.csic.es [Centro Nacional de Investigaciones Metalúrgicas (CENIM-CSIC), Avda Gregorio del Amo 8, Madrid E-28040 (Spain)

    2013-11-15

    A new generation of steels has been designed, which on transformation at low temperature (200–350 °C), leads to a nano-scale microstructure, known as NANOBAIN. The microstructure consists of slender crystals of ferrite, whose controlling scale compares well with that of carbon nanotubes (20–40 nm). These advanced steels present the highest strength/toughness combinations ever recorded in bainitic steels. Their properties are mainly a consequence of the formation of nanoscale bainitic ferrite plates at very low temperatures. Transmission electron microscopy observations have shown that plastic relaxation in the austenite adjacent to the bainite plates may control the final size of the bainitic ferrite plates. The dislocation debris generated in this process resists the advance of the bainitic ferrite–austenite interface, the resistance being greatest for strong austenite. The yield strength of the austenite must then feature in any assessment of plate size. In this scenario, the plates are expected to become thicker at high temperatures because the yield strength of the austenite will then be lower. The goal of this study is to evaluate the influence of yield strength of austenite to the nanoscale structural refinement of advanced bainitic steels. In this sense, in situ measurements of austenite strength before bainite formation using a deformation dilatometer Bähr 805D have been performed in a medium carbon high silicon steel transforming at intermediate temperatures (325–400 °C) to a submicron structure of bainite and in a high carbon high silicon steel transforming at low temperatures (200–350 °C) to nanostructured bainite. The role of the transformation driving force on the bainite plate thickness will be also discussed.

  8. Identification of structural domains in proteins by a graph heuristic

    NARCIS (Netherlands)

    Wernisch, Lorenz; Hunting, M.M.G.; Wodak, Shoshana J.

    1999-01-01

    A novel automatic procedure for identifying domains from protein atomic coordinates is presented. The procedure, termed STRUDL (STRUctural Domain Limits), does not take into account information on secondary structures and handles any number of domains made up of contiguous or non-contiguous chain

  9. Partial wave spectroscopy based nanoscale structural disorder analysis for cancer diagnosis and treatment

    Science.gov (United States)

    Almabadi, Huda; Sahay, Peeyush; Nagesh, Prashanth K. B.; Yallapu, Murali M.; Jaggi, Meena; Chauhan, Subhash C.; Pradhan, Prabhakar

    Mesoscopic physics based partial wave spectroscopy (PWS) was recently introduced to quantify nanoscale structural disorder in weakly disordered optical media such as biological cells. The degree of structural disorder (Ld) , defined as Ld = 〈 dn2 〉 ×lc is quantified in terms of strength of refractive index fluctuation (〈 dn2 〉) in the system and its correlation length (lc) .With nanoscale sensitivity,Ldhas been shown to have potential to be used in cancer diagnostics. In this work, we analyze the hierarchy of different stages of prostate cancer cells by quantifying their intracellular refractive index fluctuations in terms of Ld parameter. We observe that the increase in tumorigenicity levels inside these prostate cancer cells results in proportionally higherLdvalues. For a weakly disordered optical media like biological cells, this result suggests that the progression of carcinogenesis or the increase in the tumorigenicity level is associated with increased 〈 dn2 〉 and/or lcvalues for the samples. Furthermore, we also examined the applicability of Ld parameter in analyzing the effect of drug on these prostate cancer cells. In accordance with the hypothesis that the cancer cells which survives the drug, becomes more aggressive, we found increased Ldvalues for all the drug resistant prostate cells studied.

  10. Probing Structural and Catalytic Characteristics of Galactose Oxidase Confined in Nanoscale Chemical Environments

    DEFF Research Database (Denmark)

    Ikemoto, Hideki; Mossin, Susanne; Ulstrup, Jens

    2014-01-01

    Galactose oxidase (GAOX) is a special metalloenzyme in terms of its active site structure and catalytic mechanisms. This work reports a study where the enzyme confined in a nanoscale chemical environment provided by mesoporous silicas (MPS) is probed. Two types of MPS, i.e. SBA-15 and MCF, were...... synthesized and used to accommodate GAOX. SBA-15-ROD is rod-shaped particles with periodically ordered nanopores (9.5 nm), while MCF has a mesocellular foam-like structure with randomly distributed pores (23 nm) interconnected by smaller windows (8.8 nm). GAOX is non-covalently confined in SBA-15- ROD, while...... it is covalently immobilized in MCF. Relatively high loadings in the range of 50–60 mg g1 are achieved. Electron spin resonance (ESR) spectroscopy is used to probe the active site structures of the enzyme. The similar ESR spectra observed for GAOX in the free and immobilized states support that the electronic...

  11. Structural and Histone Binding Ability Characterizations of Human PWWP Domains

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Hong; Zeng, Hong; Lam, Robert; Tempel, Wolfram; Amaya, Maria F.; Xu, Chao; Dombrovski, Ludmila; Qiu, Wei; Wang, Yanming; Min, Jinrong (Toronto); (Penn)

    2013-09-25

    The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently. The PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other 'Royal Family' members, implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3. PWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical {beta}-barrel core, an insertion motif between the second and third {beta}-strands and a C-terminal {alpha}-helix bundle. Both the canonical {beta}-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones.

  12. Shell and membrane theories in mechanics and biology from macro- to nanoscale structures

    CERN Document Server

    Mikhasev, Gennadi

    2015-01-01

    This book presents the latest results related to shells  characterize and design shells, plates, membranes and other thin-walled structures, a multidisciplinary approach from macro- to nanoscale is required which involves the classical disciplines of mechanical/civil/materials engineering (design, analysis, and properties) and physics/biology/medicine among others. The book contains contributions of a meeting of specialists (mechanical engineers, mathematicians, physicists and others) in such areas as classical and non-classical shell theories. New trends with respect to applications in mechanical, civil and aero-space engineering, as well as in new branches like medicine and biology are presented which demand improvements of the theoretical foundations of these theories and a deeper understanding of the material behavior used in such structures.

  13. Experimental Study of Electron and Phonon Dynamics in Nanoscale Materials by Ultrafast Laser Time-Domain Spectroscopy

    Science.gov (United States)

    Shen, Xiaohan

    With the rapid advances in the development of nanotechnology, nowadays, the sizes of elementary unit, i.e. transistor, of micro- and nanoelectronic devices are well deep into nanoscale. For the pursuit of cheaper and faster nanoscale electronic devices, the size of transistors keeps scaling down. As the miniaturization of the nanoelectronic devices, the electrical resistivity increases dramatically, resulting rapid growth in the heat generation. The heat generation and limited thermal dissipation in nanoscale materials have become a critical problem in the development of the next generation nanoelectronic devices. Copper (Cu) is widely used conducting material in nanoelectronic devices, and the electron-phonon scattering is the dominant contributor to the resistivity in Cu nanowires at room temperature. Meanwhile, phonons are the main carriers of heat in insulators, intrinsic and lightly doped semiconductors. The thermal transport is an ensemble of phonon transport, which strongly depends on the phonon frequency. In addition, the phonon transport in nanoscale materials can behave fundamentally different than in bulk materials, because of the spatial confinement. However, the size effect on electron-phonon scattering and frequency dependent phonon transport in nanoscale materials remain largely unexplored, due to the lack of suitable experimental techniques. This thesis is mainly focusing on the study of carrier dynamics and acoustic phonon transport in nanoscale materials. The weak photothermal interaction in Cu makes thermoreflectance measurement difficult, we rather measured the reflectivity change of Cu induced by absorption variation. We have developed a method to separately measure the processes of electron-electron scattering and electron-phonon scattering in epitaxial Cu films by monitoring the transient reflectivity signal using the resonant probe with particular wavelengths. The enhancement on electron-phonon scattering in epitaxial Cu films with thickness

  14. Electron Microscopy and Analytical X-ray Characterization of Compositional and Nanoscale Structural Changes in Fossil Bone

    Science.gov (United States)

    Boatman, Elizabeth Marie

    The nanoscale structure of compact bone contains several features that are direct indicators of bulk tissue mechanical properties. Fossil bone tissues represent unique opportunities to understand the compact bone structure/property relationships from a deep time perspective, offering a possible array of new insights into bone diseases, biomimicry of composite materials, and basic knowledge of bioapatite composition and nanoscale bone structure. To date, most work with fossil bone has employed microscale techniques and has counter-indicated the survival of bioapatite and other nanoscale structural features. The obvious disconnect between the use of microscale techniques and the discernment of nanoscale structure has prompted this work. The goal of this study was to characterize the nanoscale constituents of fossil compact bone by applying a suite of diffraction, microscopy, and spectrometry techniques, representing the highest levels of spatial and energy resolution available today, and capable of complementary structural and compositional characterization from the micro- to the nanoscale. Fossil dinosaur and crocodile long bone specimens, as well as modern ratite and crocodile femurs, were acquired from the UC Museum of Paleontology. Preserved physiological features of significance were documented with scanning electron microscopy back-scattered imaging. Electron microprobe wavelength-dispersive X-ray spectroscopy (WDS) revealed fossil bone compositions enriched in fluorine with a complementary loss of oxygen. X-ray diffraction analyses demonstrated that all specimens were composed of apatite. Transmission electron microscopy (TEM) imaging revealed preserved nanocrystallinity in the fossil bones and electron diffraction studies further identified these nanocrystallites as apatite. Tomographic analyses of nanoscale elements imaged by TEM and small angle X-ray scattering were performed, with the results of each analysis further indicating that nanoscale structure is

  15. Solution structure of leptospiral LigA4 Big domain

    Energy Technology Data Exchange (ETDEWEB)

    Mei, Song; Zhang, Jiahai [Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026 (China); Zhang, Xuecheng [School of Life Sciences, Anhui University, Hefei, Anhui 230039 (China); Tu, Xiaoming, E-mail: xmtu@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026 (China)

    2015-11-13

    Pathogenic Leptospiraspecies express immunoglobulin-like proteins which serve as adhesins to bind to the extracellular matrices of host cells. Leptospiral immunoglobulin-like protein A (LigA), a surface exposed protein containing tandem repeats of bacterial immunoglobulin-like (Big) domains, has been proved to be involved in the interaction of pathogenic Leptospira with mammalian host. In this study, the solution structure of the fourth Big domain of LigA (LigA4 Big domain) from Leptospira interrogans was solved by nuclear magnetic resonance (NMR). The structure of LigA4 Big domain displays a similar bacterial immunoglobulin-like fold compared with other Big domains, implying some common structural aspects of Big domain family. On the other hand, it displays some structural characteristics significantly different from classic Ig-like domain. Furthermore, Stains-all assay and NMR chemical shift perturbation revealed the Ca{sup 2+} binding property of LigA4 Big domain. - Highlights: • Determining the solution structure of a bacterial immunoglobulin-like domain from a surface protein of Leptospira. • The solution structure shows some structural characteristics significantly different from the classic Ig-like domains. • A potential Ca{sup 2+}-binding site was identified by strains-all and NMR chemical shift perturbation.

  16. Solution structure of leptospiral LigA4 Big domain

    International Nuclear Information System (INIS)

    Mei, Song; Zhang, Jiahai; Zhang, Xuecheng; Tu, Xiaoming

    2015-01-01

    Pathogenic Leptospiraspecies express immunoglobulin-like proteins which serve as adhesins to bind to the extracellular matrices of host cells. Leptospiral immunoglobulin-like protein A (LigA), a surface exposed protein containing tandem repeats of bacterial immunoglobulin-like (Big) domains, has been proved to be involved in the interaction of pathogenic Leptospira with mammalian host. In this study, the solution structure of the fourth Big domain of LigA (LigA4 Big domain) from Leptospira interrogans was solved by nuclear magnetic resonance (NMR). The structure of LigA4 Big domain displays a similar bacterial immunoglobulin-like fold compared with other Big domains, implying some common structural aspects of Big domain family. On the other hand, it displays some structural characteristics significantly different from classic Ig-like domain. Furthermore, Stains-all assay and NMR chemical shift perturbation revealed the Ca"2"+ binding property of LigA4 Big domain. - Highlights: • Determining the solution structure of a bacterial immunoglobulin-like domain from a surface protein of Leptospira. • The solution structure shows some structural characteristics significantly different from the classic Ig-like domains. • A potential Ca"2"+-binding site was identified by strains-all and NMR chemical shift perturbation.

  17. Nanoscale monoclinic domains in epitaxial SrRuO3 thin films deposited by pulsed laser deposition

    Science.gov (United States)

    Ghica, C.; Negrea, R. F.; Nistor, L. C.; Chirila, C. F.; Pintilie, L.

    2014-07-01

    In this paper, we analyze the structural distortions observed by transmission electron microscopy in thin epitaxial SrRuO3 layers used as bottom electrodes in multiferroic coatings onto SrTiO3 substrates for future multiferroic devices. Regardless of the nature and architecture of the multilayer oxides deposited on the top of the SrRuO3 thin films, selected area electron diffraction patterns systematically revealed the presence of faint diffraction spots appearing in forbidden positions for the SrRuO3 orthorhombic structure. High-resolution transmission electron microscopy (HRTEM) combined with Geometric Phase Analysis (GPA) evidenced the origin of these forbidden diffraction spots in the presence of structurally disordered nanometric domains in the SrRuO3 bottom layers, resulting from a strain-driven phase transformation. The local high compressive strain (-4% ÷ -5%) measured by GPA in the HRTEM images induces a local orthorhombic to monoclinic phase transition by a cooperative rotation of the RuO6 octahedra. A further confirmation of the origin of the forbidden diffraction spots comes from the simulated diffraction patterns obtained from a monoclinic disordered SrRuO3 structure.

  18. Fabrication of two-dimensional visible wavelength nanoscale plasmonic structures using hydrogen silsesquioxane based resist

    Science.gov (United States)

    Smith, Kyle Z.; Gadde, Akshitha; Kadiyala, Anand; Dawson, Jeremy M.

    2016-03-01

    In recent years, the global market for biosensors has continued to increase in combination with their expanding use in areas such as biodefense/detection, home diagnostics, biometric identification, etc. A constant necessity for inexpensive, portable bio-sensing methods, while still remaining simple to understand and operate, is the motivation behind novel concepts and designs. Labeled visible spectrum bio-sensing systems provide instant feedback that is both simple and easy to work with, but are limited by the light intensity thresholds required by the imaging systems. In comparison, label-free bio-sensing systems and other detection modalities like electrochemical, frequency resonance, thermal change, etc., can require additional technical processing steps to convey the final result, increasing the system's complexity and possibly the time required for analysis. Further decrease in the detection limit can be achieved through the addition of plasmonic structures into labeled bio-sensing systems. Nano-structures that operate in the visible spectrum have feature sizes typically in the order of the operating wavelength, calling for high aspect ratio nanoscale fabrication capabilities. In order to achieve these dimensions, electron beam lithography (EBL) is used due to its accurate feature production. Hydrogen silsesquioxane (HSQ) based electron beam resist is chosen for one of its benefits, which is after exposure to oxygen plasma, the patterned resist cures into silicon dioxide (SiO2). These cured features in conjunction with nanoscale gold particles help in producing a high electric field through dipole generation. In this work, a detailed process flow of the fabrication of square lattice of plasmonic structures comprising of gold coated silicon dioxide pillars designed to operate at 560 nm wavelength and produce an intensity increase of roughly 100 percent will be presented.

  19. Nanoscale control of stripe-ordered magnetic domain walls by vertical spin transfer torque in La0.67Sr0.33MnO3 film

    Science.gov (United States)

    Wang, Jing; Wu, Shizhe; Ma, Ji; Xie, Lishan; Wang, Chuanshou; Malik, Iftikhar Ahmed; Zhang, Yuelin; Xia, Ke; Nan, Ce-Wen; Zhang, Jinxing

    2018-02-01

    Stripe-ordered domains with perpendicular magnetic anisotropy have been intensively investigated due to their potential applications in high-density magnetic data-storage devices. However, the conventional control methods (e.g., epitaxial strain, local heating, magnetic field, and magnetoelectric effect) of the stripe-ordered domain walls either cannot meet the demands for miniaturization and low power consumption of spintronic devices or require high strength of the electric field due to the small value of the magnetoelectric effect at room temperature. Here, a domain-wall resistive effect of 0.1% was clarified in La0.67Sr0.33MnO3 thin films between the configurations of current in the plane and perpendicular to the plane of walls. Furthermore, a reversible nanoscale control of the domain-wall re-orientation by vertical spin transfer torque across the probe/film interface was achieved, where a probe voltage of 0.1 V was applied on a manganite-based capacitor. We also demonstrated that the stripe-ordered magnetic domain-wall re-orientation strongly depends on the AC frequency of the scanning probe voltage which was applied on the capacitor.

  20. Nano-scale patterns of polymers and their structural phase transitions

    Energy Technology Data Exchange (ETDEWEB)

    Matsushita, Yushu [Tokyo Univ. (Japan). Inst. for Solid State Physics

    1998-03-01

    Nano-scale patterns formed by polymers and their related soft materials were investigated by measuring neutron scattering from them. Two apparatuses installed at cold neutron guides in JRR-3M, a small angle neutron scattering (SANS) apparatus and a neutron reflectometer, which give out elastic scattering intensities, were used. Chain dimensions of polystyrenes diluted with low molecular weight homologous polystyrenes, orientation behaviour of microphase-separated block copolymer in concentrated solutions under shear, shrinkage and recovery of polyvinylalcohol gel with temperature and structural phase transition of microemulsion under high-pressure and so on were measured by SANS, while microphase-separated polystyrene(S)/poly(2-vinylpyridine)(P) interfaces of a PSP triblock copolymer was observed by specular neutron reflectivity measurements. (author)

  1. Dynamics at the nanoscale

    International Nuclear Information System (INIS)

    Stoneham, A.M.; Gavartin, J.L.

    2007-01-01

    However fascinating structures may be at the nanoscale, time-dependent behaviour at the nanoscale has far greater importance. Some of the dynamics is random, with fluctuations controlling rate processes and making thermal ratchets possible. Some of the dynamics causes the transfer of energy, of signals, or of charge. Such transfers are especially efficiently controlled in biological systems. Other dynamical processes occur when we wish to control the nanoscale, e.g., to avoid local failures of gate dielectrics, or to manipulate structures by electronic excitation, to use spin manipulation in quantum information processing. Our prime purpose is to make clear the enormous range and variety of time-dependent nanoscale phenomena

  2. Structure and switching of in-plane ferroelectric nano-domains in strained PbxSr1-xTiO3 thin films

    Energy Technology Data Exchange (ETDEWEB)

    Matzen, Sylivia [University of Groningen, The Netherlands; Nesterov, Okeksiy [ORNL; Rispens, Gregory [University of Groningen, The Netherlands; Heuver, J. A. [University of Groningen, The Netherlands; Bark, C [University of Wisconsin, Madison; Biegalski, Michael D [ORNL; Christen, Hans M [ORNL; Noheda, Beatriz [University of Groningen, The Netherlands

    2014-01-01

    Nanoscale ferroelectrics, the active elements of a variety of nanoelectronic devices, develop denser and richer domain structures than the bulk counterparts. With shrinking device sizes understanding and controlling domain formation in nanoferroelectrics is being intensely studied. Here we show that a precise control of the epitaxy and the strain allows stabilizing a hierarchical domain architecture in PbxSr1-xTiO3 thin films, showing periodic, purely in-plane polarized, ferroelectric nano-domains that can be switched by a scanning probe.

  3. Quantitative FLIM-FRET Microscopy to Monitor Nanoscale Chromatin Compaction In Vivo Reveals Structural Roles of Condensin Complexes

    Directory of Open Access Journals (Sweden)

    David Llères

    2017-02-01

    Full Text Available How metazoan genomes are structured at the nanoscale in living cells and tissues remains unknown. Here, we adapted a quantitative FRET (Förster resonance energy transfer-based fluorescence lifetime imaging microscopy (FLIM approach to assay nanoscale chromatin compaction in living organisms. Caenorhabditis elegans was chosen as a model system. By measuring FRET between histone-tagged fluorescent proteins, we visualized distinct chromosomal regions and quantified the different levels of nanoscale compaction in meiotic cells. Using RNAi and repetitive extrachromosomal array approaches, we defined the heterochromatin state and showed that its architecture presents a nanoscale-compacted organization controlled by Heterochromatin Protein-1 (HP1 and SETDB1 H3-lysine-9 methyltransferase homologs in vivo. Next, we functionally explored condensin complexes. We found that condensin I and condensin II are essential for heterochromatin compaction and that condensin I additionally controls lowly compacted regions. Our data show that, in living animals, nanoscale chromatin compaction is controlled not only by histone modifiers and readers but also by condensin complexes.

  4. Atomic Resolution Imaging of Nanoscale Structural Ordering in a Complex Metal Oxide Catalyst

    KAUST Repository

    Zhu, Yihan

    2012-08-28

    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.

  5. Nanoscale characterization of martensite structures in copper based shape memory alloys

    Energy Technology Data Exchange (ETDEWEB)

    Adiguzel, O, E-mail: oadiguzel@firat.edu.t [Firat University Department of Physics, 23169 Elazig (Turkey)

    2010-11-01

    Martensitic transformations are first order displacive transitions and occur in the materials on cooling from high temperature. Shape memory effect is an unusual property exhibited by certain alloy systems, and leads to martensitic transition. Copper-based alloys exhibit this property in beta phase field which possess simple bcc- structures, austenite structure at high-temperatures. As temperature is lowered the austenite undergoes martensitic transition following two ordering reactions, and structural changes in nanoscale govern this transition. Atomic movements are also confined to interatomic lengths in sub-{mu}m or angstrom scale in martensitic transformation. The formation of the layered structures in copper based alloys consists of shears and shear mechanism. Martensitic transformations occur in a few steps with the cooperative movement of atoms less than interatomic distances by means of lattice invariant shears on a {l_brace}110{r_brace} - type plane of austenite matrix which is basal plane or stacking plane of martensite. The lattice invariant shears occurs, in two opposite directions, <110> -type directions on the {l_brace}110{r_brace}-type plane. These shears gives rise to the formation of layered structure.

  6. Real time nanoscale structural evaluation of gold structures on Si (100) surface using in-situ transmission electron microscopy

    International Nuclear Information System (INIS)

    Rath, A.; Juluri, R. R.; Satyam, P. V.

    2014-01-01

    Transport behavior of gold nanostructures on Si(100) substrate during annealing under high vacuum has been investigated using in-situ real time transmission electron microscopy (TEM). A comparative study has been done on the morphological changes due to annealing under different vacuum environments. Au thin films of thickness ∼2.0 nm were deposited on native oxide covered silicon substrate by using thermal evaporation system. In-situ real time TEM measurements at 850 °C showed the isotropic growth of rectangular/square shaped gold-silicon alloy structures. During the growth, it is observed that the alloying occurs in liquid phase followed by transformation into the rectangular shapes. For similar system, ex-situ annealing in low vacuum (10 −2 millibars) at 850 °C showed the spherical gold nanostructures with no Au-Si alloy formation. Under low vacuum annealing conditions, the rate of formation of the oxide layer dominates the oxide desorption rate, resulting in the creation of a barrier layer between Au and Si, which restricts the inter diffusion of Au in to Si. This work demonstrates the important role of interfacial oxide layer on the growth of nanoscale Au-Si alloy structures during the initial growth. The time dependent TEM images are presented to offer a direct insight into the fundamental dynamics of the sintering process at the nanoscale

  7. Nanoscale thermal transport

    Science.gov (United States)

    Cahill, David G.; Ford, Wayne K.; Goodson, Kenneth E.; Mahan, Gerald D.; Majumdar, Arun; Maris, Humphrey J.; Merlin, Roberto; Phillpot, Simon R.

    2003-01-01

    promise of improved thermoelectric materials and problems of thermal management of optoelectronic devices have stimulated extensive studies of semiconductor superlattices; agreement between experiment and theory is generally poor. Advances in measurement methods, e.g., the 3ω method, time-domain thermoreflectance, sources of coherent phonons, microfabricated test structures, and the scanning thermal microscope, are enabling new capabilities for nanoscale thermal metrology.

  8. Nanoscale stiffness topography reveals structure and mechanics of the transport barrier in intact nuclear pore complexes

    Science.gov (United States)

    Bestembayeva, Aizhan; Kramer, Armin; Labokha, Aksana A.; Osmanović, Dino; Liashkovich, Ivan; Orlova, Elena V.; Ford, Ian J.; Charras, Guillaume; Fassati, Ariberto; Hoogenboom, Bart W.

    2015-01-01

    The nuclear pore complex (NPC) is the gate for transport between the cell nucleus and the cytoplasm. Small molecules cross the NPC by passive diffusion, but molecules larger than ∼5 nm must bind to nuclear transport receptors to overcome a selective barrier within the NPC. Although the structure and shape of the cytoplasmic ring of the NPC are relatively well characterized, the selective barrier is situated deep within the central channel of the NPC and depends critically on unstructured nuclear pore proteins, and is therefore not well understood. Here, we show that stiffness topography with sharp atomic force microscopy tips can generate nanoscale cross-sections of the NPC. The cross-sections reveal two distinct structures, a cytoplasmic ring and a central plug structure, which are consistent with the three-dimensional NPC structure derived from electron microscopy. The central plug persists after reactivation of the transport cycle and resultant cargo release, indicating that the plug is an intrinsic part of the NPC barrier. Added nuclear transport receptors accumulate on the intact transport barrier and lead to a homogenization of the barrier stiffness. The observed nanomechanical properties in the NPC indicate the presence of a cohesive barrier to transport and are quantitatively consistent with the presence of a central condensate of nuclear pore proteins in the NPC channel.

  9. Structure of an isolated unglycosylated antibody CH2 domain

    International Nuclear Information System (INIS)

    Prabakaran, Ponraj; Vu, Bang K.; Gan, Jianhua; Feng, Yang; Dimitrov, Dimiter S.; Ji, Xinhua

    2008-01-01

    The crystal structure of an isolated unglycosylated antibody C H 2 domain has been determined at 1.7 Å resolution. The C H 2 (C H 3 for IgM and IgE) domain of an antibody plays an important role in mediating effector functions and preserving antibody stability. It is the only domain in human immunoglobulins (Igs) which is involved in weak interchain protein–protein interactions with another C H 2 domain solely through sugar moieties. The N-linked glycosylation at Asn297 is conserved in mammalian IgGs as well as in homologous regions of other antibody isotypes. To examine the structural details of the C H 2 domain in the absence of glycosylation and other antibody domains, the crystal structure of an isolated unglycosylated antibody γ1 C H 2 domain was determined at 1.7 Å resolution and compared with corresponding C H 2 structures from intact Fc, IgG and Fc receptor complexes. Furthermore, the oligomeric state of the protein in solution was studied using size-exclusion chromatography. The results suggested that the unglycosylated human antibody C H 2 domain is a monomer and that its structure is similar to that found in the intact Fc, IgG and Fc receptor complex structures. However, certain structural variations were observed in the Fc receptor-binding sites. Owing to its small size, stability and non-immunogenic Ig template, the C H 2-domain structure could be useful for the development by protein design of antibody domains exerting effector functions and/or antigen specificity and as a robust scaffold in protein-engineering applications

  10. Study of domain structure in segmented polyether polyurethaneureas by PAT

    International Nuclear Information System (INIS)

    Yin Chuanyuan; Xu Weizheng; Gu Qingchao

    1990-01-01

    The domain structure of segmented polyether polyurethaneureas is investigated by means of positron annihilation technique, small angle X-ray scattering and differential scanning calorimetry. The experimental results show that the decrease of domain volume and free volume results from the increase of hard segment contents, and that the increase of domain volume and free volume results from the increase of molecular weight of soft segments

  11. Structural and functional analysis of multi-interface domains.

    Directory of Open Access Journals (Sweden)

    Liang Zhao

    Full Text Available A multi-interface domain is a domain that can shape multiple and distinctive binding sites to contact with many other domains, forming a hub in domain-domain interaction networks. The functions played by the multiple interfaces are usually different, but there is no strict bijection between the functions and interfaces as some subsets of the interfaces play the same function. This work applies graph theory and algorithms to discover fingerprints for the multiple interfaces of a domain and to establish associations between the interfaces and functions, based on a huge set of multi-interface proteins from PDB. We found that about 40% of proteins have the multi-interface property, however the involved multi-interface domains account for only a tiny fraction (1.8% of the total number of domains. The interfaces of these domains are distinguishable in terms of their fingerprints, indicating the functional specificity of the multiple interfaces in a domain. Furthermore, we observed that both cooperative and distinctive structural patterns, which will be useful for protein engineering, exist in the multiple interfaces of a domain.

  12. Structure of synaptophysin: a hexameric MARVEL-domain channel protein.

    Science.gov (United States)

    Arthur, Christopher P; Stowell, Michael H B

    2007-06-01

    Synaptophysin I (SypI) is an archetypal member of the MARVEL-domain family of integral membrane proteins and one of the first synaptic vesicle proteins to be identified and cloned. Most all MARVEL-domain proteins are involved in membrane apposition and vesicle-trafficking events, but their precise role in these processes is unclear. We have purified mammalian SypI and determined its three-dimensional (3D) structure by using electron microscopy and single-particle 3D reconstruction. The hexameric structure resembles an open basket with a large pore and tenuous interactions within the cytosolic domain. The structure suggests a model for Synaptophysin's role in fusion and recycling that is regulated by known interactions with the SNARE machinery. This 3D structure of a MARVEL-domain protein provides a structural foundation for understanding the role of these important proteins in a variety of biological processes.

  13. Molecular Structure and Dynamics of Water on Pristine and Strained Phosphorene: Wetting and Diffusion at Nanoscale.

    Science.gov (United States)

    Zhang, Wei; Ye, Chao; Hong, Linbi; Yang, Zaixing; Zhou, Ruhong

    2016-12-06

    Phosphorene, a newly fabricated two-dimensional (2D) nanomaterial, has emerged as a promising material for biomedical applications with great potential. Nonetheless, understanding the wetting and diffusive properties of bio-fluids on phosphorene which are of fundamental importance to these applications remains elusive. In this work, using molecular dynamics (MD) simulations, we investigated the structural and dynamic properties of water on both pristine and strained phosphorene. Our simulations indicate that the diffusion of water molecules on the phosphorene surface is anisotropic, with strain-enhanced diffusion clearly present, which arises from strain-induced smoothing of the energy landscape. The contact angle of water droplet on phosphorene exhibits a non-monotonic variation with the transverse strain. The structure of water on transverse stretched phosphorene is demonstrated to be different from that on longitudinal stretched phosphorene. Moreover, the contact angle of water on strained phosphorene is proportional to the quotient of the longitudinal and transverse diffusion coefficients of the interfacial water. These findings thereby offer helpful insights into the mechanism of the wetting and transport of water at nanoscale, and provide a better foundation for future biomedical applications of phosphorene.

  14. Quantifying information transfer by protein domains: Analysis of the Fyn SH2 domain structure

    Directory of Open Access Journals (Sweden)

    Serrano Luis

    2008-10-01

    Full Text Available Abstract Background Efficient communication between distant sites within a protein is essential for cooperative biological response. Although often associated with large allosteric movements, more subtle changes in protein dynamics can also induce long-range correlations. However, an appropriate formalism that directly relates protein structural dynamics to information exchange between functional sites is still lacking. Results Here we introduce a method to analyze protein dynamics within the framework of information theory and show that signal transduction within proteins can be considered as a particular instance of communication over a noisy channel. In particular, we analyze the conformational correlations between protein residues and apply the concept of mutual information to quantify information exchange. Mapping out changes of mutual information on the protein structure then allows visualizing how distal communication is achieved. We illustrate the approach by analyzing information transfer by the SH2 domain of Fyn tyrosine kinase, obtained from Monte Carlo dynamics simulations. Our analysis reveals that the Fyn SH2 domain forms a noisy communication channel that couples residues located in the phosphopeptide and specificity binding sites and a number of residues at the other side of the domain near the linkers that connect the SH2 domain to the SH3 and kinase domains. We find that for this particular domain, communication is affected by a series of contiguous residues that connect distal sites by crossing the core of the SH2 domain. Conclusion As a result, our method provides a means to directly map the exchange of biological information on the structure of protein domains, making it clear how binding triggers conformational changes in the protein structure. As such it provides a structural road, next to the existing attempts at sequence level, to predict long-range interactions within protein structures.

  15. Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains.

    Science.gov (United States)

    Vishwanath, Sneha; de Brevern, Alexandre G; Srinivasan, Narayanaswamy

    2018-02-01

    The majority of the proteins encoded in the genomes of eukaryotes contain more than one domain. Reasons for high prevalence of multi-domain proteins in various organisms have been attributed to higher stability and functional and folding advantages over single-domain proteins. Despite these advantages, many proteins are composed of only one domain while their homologous domains are part of multi-domain proteins. In the study presented here, differences in the properties of protein domains in single-domain and multi-domain systems and their influence on functions are discussed. We studied 20 pairs of identical protein domains, which were crystallized in two forms (a) tethered to other proteins domains and (b) tethered to fewer protein domains than (a) or not tethered to any protein domain. Results suggest that tethering of domains in multi-domain proteins influences the structural, dynamic and energetic properties of the constituent protein domains. 50% of the protein domain pairs show significant structural deviations while 90% of the protein domain pairs show differences in dynamics and 12% of the residues show differences in the energetics. To gain further insights on the influence of tethering on the function of the domains, 4 pairs of homologous protein domains, where one of them is a full-length single-domain protein and the other protein domain is a part of a multi-domain protein, were studied. Analyses showed that identical and structurally equivalent functional residues show differential dynamics in homologous protein domains; though comparable dynamics between in-silico generated chimera protein and multi-domain proteins were observed. From these observations, the differences observed in the functions of homologous proteins could be attributed to the presence of tethered domain. Overall, we conclude that tethered domains in multi-domain proteins not only provide stability or folding advantages but also influence pathways resulting in differences in

  16. An Algebro-Topological Description of Protein Domain Structure

    Science.gov (United States)

    Penner, Robert Clark; Knudsen, Michael; Wiuf, Carsten; Andersen, Jørgen Ellegaard

    2011-01-01

    The space of possible protein structures appears vast and continuous, and the relationship between primary, secondary and tertiary structure levels is complex. Protein structure comparison and classification is therefore a difficult but important task since structure is a determinant for molecular interaction and function. We introduce a novel mathematical abstraction based on geometric topology to describe protein domain structure. Using the locations of the backbone atoms and the hydrogen bonds, we build a combinatorial object – a so-called fatgraph. The description is discrete yet gives rise to a 2-dimensional mathematical surface. Thus, each protein domain corresponds to a particular mathematical surface with characteristic topological invariants, such as the genus (number of holes) and the number of boundary components. Both invariants are global fatgraph features reflecting the interconnectivity of the domain by hydrogen bonds. We introduce the notion of robust variables, that is variables that are robust towards minor changes in the structure/fatgraph, and show that the genus and the number of boundary components are robust. Further, we invesigate the distribution of different fatgraph variables and show how only four variables are capable of distinguishing different folds. We use local (secondary) and global (tertiary) fatgraph features to describe domain structures and illustrate that they are useful for classification of domains in CATH. In addition, we combine our method with two other methods thereby using primary, secondary, and tertiary structure information, and show that we can identify a large percentage of new and unclassified structures in CATH. PMID:21629687

  17. Nanoscale Structure of Type I Collagen Fibrils: Quantitative Measurement of D-spacing

    Science.gov (United States)

    Erickson, Blake; Fang, Ming; Wallace, Joseph M.; Orr, Bradford G.; Les, Clifford M.; Holl, Mark M. Banaszak

    2012-01-01

    This paper details a quantitative method to measure the D-periodic spacing of Type I collagen fibrils using Atomic Force Microscopy coupled with analysis using a 2D Fast Fourier Transform approach. Instrument calibration, data sampling and data analysis are all discussed and comparisons of the data to the complementary methods of electron microscopy and X-ray scattering are made. Examples of the application of this new approach to the analysis of Type I collagen morphology in disease models of estrogen depletion and Osteogenesis Imperfecta are provided. We demonstrate that it is the D-spacing distribution, not the D-spacing mean, that showed statistically significant differences in estrogen depletion associated with early stage Osteoporosis and Osteogenesis Imperfecta. The ability to quantitatively characterize nanoscale morphological features of Type I collagen fibrils will provide important structural information regarding Type I collagen in many research areas, including tissue aging and disease, tissue engineering, and gene knock out studies. Furthermore, we also envision potential clinical applications including evaluation of tissue collagen integrity under the impact of diseases or drug treatments. PMID:23027700

  18. Nanoscale “Quantum” Islands on Metal Substrates: Microscopy Studies and Electronic Structure Analyses

    Directory of Open Access Journals (Sweden)

    Da-Jiang Liu

    2010-07-01

    Full Text Available Confinement of electrons can occur in metal islands or in continuous films grown heteroepitaxially upon a substrate of a different metal or on a metallic alloy. Associated quantum size effects (QSE can produce a significant height-dependence of the surface free energy for nanoscale thicknesses of up to 10–20 layers. This may suffice to induce height selection during film growth. Scanning STM analysis has revealed remarkable flat-topped or mesa-like island and film morphologies in various systems. We discuss in detail observations of QSE and associated film growth behavior for Pb/Cu(111, Ag/Fe(100, and Cu/fcc-Fe/Cu(100 [A/B or A/B/A], and for Ag/NiAl(110 with brief comments offered for Fe/Cu3Au(001 [A/BC binary alloys]. We also describe these issues for Ag/5-fold i-Al-Pd-Mn and Bi/5-fold i-Al-Cu-Fe [A/BCD ternary icosohedral quasicrystals]. Electronic structure theory analysis, either at the level of simple free electron gas models or more sophisticated Density Functional Theory calculations, can provide insight into the QSE-mediated thermodynamic driving force underlying height selection.

  19. Comparative structural analysis of lipid binding START domains.

    Directory of Open Access Journals (Sweden)

    Ann-Gerd Thorsell

    Full Text Available Steroidogenic acute regulatory (StAR protein related lipid transfer (START domains are small globular modules that form a cavity where lipids and lipid hormones bind. These domains can transport ligands to facilitate lipid exchange between biological membranes, and they have been postulated to modulate the activity of other domains of the protein in response to ligand binding. More than a dozen human genes encode START domains, and several of them are implicated in a disease.We report crystal structures of the human STARD1, STARD5, STARD13 and STARD14 lipid transfer domains. These represent four of the six functional classes of START domains.Sequence alignments based on these and previously reported crystal structures define the structural determinants of human START domains, both those related to structural framework and those involved in ligand specificity.This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

  20. Enhanced functional and structural domain assignments using

    Indian Academy of Sciences (India)

    Unknown

    using remote similarity detection procedures for proteins encoded in the genome of Mycobacterium tuberculosis H37Rv” (J. Biosci. 29 (3) 245–. 259, 2004) by Seema Namboori, Natasha Mhatre, Sentivel Sujatha,. Narayanaswamy Srinivasan and Shashi Bhushan Pandit. The three-dimensional structure and subcellular ...

  1. Laboratory micro- and nanoscale X-ray tomographic investigation of Al–7 at.%Cu solidification structures

    International Nuclear Information System (INIS)

    Patterson, B.M.; Henderson, K.C.; Gibbs, P.J.; Imhoff, S.D.; Clarke, A.J.

    2014-01-01

    X-ray computed tomography across multiple length scales provides an opportunity to non-destructively visualize and quantify the micro- to nano-scale microstructural features of solidification structures in three dimensions. Aluminum–7 at.%copper samples were directionally solidified at three cooling rates (0.44, 0.67, and 1.33 °C/s), resulting in systematic changes in the as-solidified microstructure, which are difficult to quantify using traditional microscopic techniques. The cooling rate of a material affects its ultimate microstructure, and characterizing that microstructure is key to predicting and understanding its bulk properties. Here, two different laboratory X-ray computed tomography instruments were used to characterize as-solidified microstructures, including micro-scale computed tomography with approximately 1 mm field-of-view, ∼ 1.7 μm resolution, and nano-scale X-ray computed tomography ∼ 65 μm FOV, 150 nm resolution. Micro-scale X-ray radiography and computed tomography enabled a quantitative investigation of changes in the primary dendritic solidification structure with increasing cooling rate. Nano-scale absorption contrast X-ray computed tomography resolved the distinct phases of the lamellar eutectic structure and three dimensional measurements of the ∼ 1 μm interlamellar spacing. It is found that the lamella eutectic structure thickness is inversely proportional to the cooling rate. Nano-scale Zernike phase contrast was also used to image voids at eutectic colony boundaries. The application and resolution of these two instruments are discussed with respect to the resolvable features of the solidification structures. - Highlights: • Al–Cu eutectic is a model system for studying solidification microstructure. • X-ray computed tomography provides a 3D picture of these complex structures. • Micro-scale tomography images the primary and secondary dendritic structures. • Nano-scale tomography images the eutectic lamella and

  2. Laboratory micro- and nanoscale X-ray tomographic investigation of Al–7 at.%Cu solidification structures

    Energy Technology Data Exchange (ETDEWEB)

    Patterson, B.M., E-mail: bpatterson@lanl.gov; Henderson, K.C.; Gibbs, P.J.; Imhoff, S.D.; Clarke, A.J.

    2014-09-15

    X-ray computed tomography across multiple length scales provides an opportunity to non-destructively visualize and quantify the micro- to nano-scale microstructural features of solidification structures in three dimensions. Aluminum–7 at.%copper samples were directionally solidified at three cooling rates (0.44, 0.67, and 1.33 °C/s), resulting in systematic changes in the as-solidified microstructure, which are difficult to quantify using traditional microscopic techniques. The cooling rate of a material affects its ultimate microstructure, and characterizing that microstructure is key to predicting and understanding its bulk properties. Here, two different laboratory X-ray computed tomography instruments were used to characterize as-solidified microstructures, including micro-scale computed tomography with approximately 1 mm field-of-view, ∼ 1.7 μm resolution, and nano-scale X-ray computed tomography ∼ 65 μm FOV, 150 nm resolution. Micro-scale X-ray radiography and computed tomography enabled a quantitative investigation of changes in the primary dendritic solidification structure with increasing cooling rate. Nano-scale absorption contrast X-ray computed tomography resolved the distinct phases of the lamellar eutectic structure and three dimensional measurements of the ∼ 1 μm interlamellar spacing. It is found that the lamella eutectic structure thickness is inversely proportional to the cooling rate. Nano-scale Zernike phase contrast was also used to image voids at eutectic colony boundaries. The application and resolution of these two instruments are discussed with respect to the resolvable features of the solidification structures. - Highlights: • Al–Cu eutectic is a model system for studying solidification microstructure. • X-ray computed tomography provides a 3D picture of these complex structures. • Micro-scale tomography images the primary and secondary dendritic structures. • Nano-scale tomography images the eutectic lamella and

  3. Correlative nanoscale 3D imaging of structure and composition in extended objects.

    Directory of Open Access Journals (Sweden)

    Feng Xu

    Full Text Available Structure and composition at the nanoscale determine the behavior of biological systems and engineered materials. The drive to understand and control this behavior has placed strong demands on developing methods for high resolution imaging. In general, the improvement of three-dimensional (3D resolution is accomplished by tightening constraints: reduced manageable specimen sizes, decreasing analyzable volumes, degrading contrasts, and increasing sample preparation efforts. Aiming to overcome these limitations, we present a non-destructive and multiple-contrast imaging technique, using principles of X-ray laminography, thus generalizing tomography towards laterally extended objects. We retain advantages that are usually restricted to 2D microscopic imaging, such as scanning of large areas and subsequent zooming-in towards a region of interest at the highest possible resolution. Our technique permits correlating the 3D structure and the elemental distribution yielding a high sensitivity to variations of the electron density via coherent imaging and to local trace element quantification through X-ray fluorescence. We demonstrate the method by imaging a lithographic nanostructure and an aluminum alloy. Analyzing a biological system, we visualize in lung tissue the subcellular response to toxic stress after exposure to nanotubes. We show that most of the nanotubes are trapped inside alveolar macrophages, while a small portion of the nanotubes has crossed the barrier to the cellular space of the alveolar wall. In general, our method is non-destructive and can be combined with different sample environmental or loading conditions. We therefore anticipate that correlative X-ray nano-laminography will enable a variety of in situ and in operando 3D studies.

  4. Mapping domain structures in silks from insects and spiders related to protein assembly.

    Science.gov (United States)

    Bini, Elisabetta; Knight, David P; Kaplan, David L

    2004-01-02

    The exceptional solubility in vivo (20-30%, w/v) of the silk proteins of insects and spiders is dictated by both the need to produce solid fibres with a high packing fraction and the high mesogen concentration required for lyotropic liquid crystalline spinning. A further design requirement for silk proteins is a strong predominance of hydrophobic amino acid residues to provide for the hydrophobic interactions, water exclusion, and beta-crystallite formation required to produce strong insoluble threads. Thus, the domain structure of silk proteins needs to enable nanoscale phase separation to achieve high solubility of hydrophobic proteins in aqueous solutions. Additionally, silk proteins need to avoid premature precipitation as beta-sheets during storage and processing. Here we use mapping of domain types, sizes and distributions in silks to identify consistent design features that have evolved to meet these requirements. We show that silk proteins consist of conspicuously hydrophilic terminal domains flanking a very long central portion constructed from hydrophobic blocks separated by hydrophilic ones, discussing the domain structure in detail. The general rules of construction for silk proteins based on our observations should give a useful guide to the way in which Nature has solved the problem of processing hydrophobic proteins in water and how this can be copied industrially. Following these rules may also help in obtaining adequate expression, soluble products and controllable conformational switches in the production of genetically engineered or chemically synthesized silk analogues. Thus these insights have implications for structural biology and relevance to fundamental and applied questions in material science and engineering.

  5. Structure of the first PDZ domain of human PSD-93

    DEFF Research Database (Denmark)

    Fiorentini, Monica; Nielsen, Ann Kallehauge; Kristensen, Ole

    2009-01-01

    The crystal structure of the PDZ1 domain of human PSD-93 has been determined to 2.0 A resolution. The PDZ1 domain forms a crystallographic trimer that is also predicted to be stable in solution. The main contributions to the stabilization of the trimer seem to arise from interactions involving...... the PDZ1-PDZ2 linker region at the extreme C-terminus of PDZ1, implying that the oligomerization that is observed is not of biological significance in full-length PSD-93. Comparison of the structures of the binding cleft of PSD-93 PDZ1 with the previously reported structures of PSD-93 PDZ2 and PDZ3...

  6. Domain Structures in Nematic Liquid Crystals on a Polycarbonate Surface

    Directory of Open Access Journals (Sweden)

    Vasily F. Shabanov

    2013-08-01

    Full Text Available Alignment of nematic liquid crystals on polycarbonate films obtained with the use of solvents with different solvations is studied. Domain structures occurring during the growth on the polymer surface against the background of the initial thread-like or schlieren texture are demonstrated. It is established by optical methods that the domains are stable formations visualizing the polymer surface structures. In nematic droplets, the temperature-induced transition from the domain structure with two extinction bands to the structure with four bands is observed. This transition is shown to be caused by reorientation of the nematic director in the liquid crystal volume from the planar alignment to the homeotropic state with the pronounced radial configuration of nematic molecules on the surface. The observed textures are compared with different combinations of the volume LC orientations and the radial distribution of the director field and the disclination lines at the polycarbonate surface.

  7. Oxide films at the nanoscale: new structures, new functions, and new materials.

    Science.gov (United States)

    Giordano, Livia; Pacchioni, Gianfranco

    2011-11-15

    We all make use of oxide ultrathin films, even if we are unaware of doing so. They are essential components of many common devices, such as mobile phones and laptops. The films in these ubiquitous electronics are composed of silicon dioxide, an unsurpassed material in the design of transistors. But oxide films at the nanoscale (typically just 10 nm or less in thickness) are integral to many other applications. In some cases, they form under normal reactive conditions and confer new properties to a material: one example is the corrosion protection of stainless steel, which is the result of a passive film. A new generation of devices for energy production and communications technology, such as ferroelectric ultrathin film capacitors, tunneling magnetoresistance sensors, solar energy materials, solid oxide fuel cells, and many others, are being specifically designed to exploit the unusual properties afforded by reduced oxide thickness. Oxide ultrathin films also have tremendous potential in chemistry, representing a rich new source of catalytic materials. About 20 years ago, researchers began to prepare model systems of truly heterogeneous catalysts based on thin oxide layers grown on single crystals of metal. Only recently, however, was it realized that these systems may behave quite differently from their corresponding bulk oxides. One of the phenomena uncovered is the occurrence of a spontaneous charge transfer from the metal support to an adsorbed species through the thin insulating layer (or vice versa). The importance of this property is clear: conceptually, the activation and bond breaking of adsorbed molecules begin with precisely the same process, electron transfer into an antibonding orbital. But electron transfer can also be harnessed to make a supported metal particle more chemically active, increase its adhesion energy, or change its shape. Most importantly, the basic principles underlying electron transfer and other phenomena (such as structural

  8. Nanoscale Structural and Mechanical Analysis of Bacillus anthracis Spores Inactivated with Rapid Dry Heating

    Science.gov (United States)

    Felker, Daniel L.; Burggraf, Larry W.

    2014-01-01

    Effective killing of Bacillus anthracis spores is of paramount importance to antibioterrorism, food safety, environmental protection, and the medical device industry. Thus, a deeper understanding of the mechanisms of spore resistance and inactivation is highly desired for developing new strategies or improving the known methods for spore destruction. Previous studies have shown that spore inactivation mechanisms differ considerably depending upon the killing agents, such as heat (wet heat, dry heat), UV, ionizing radiation, and chemicals. It is believed that wet heat kills spores by inactivating critical enzymes, while dry heat kills spores by damaging their DNA. Many studies have focused on the biochemical aspects of spore inactivation by dry heat; few have investigated structural damages and changes in spore mechanical properties. In this study, we have inactivated Bacillus anthracis spores with rapid dry heating and performed nanoscale topographical and mechanical analysis of inactivated spores using atomic force microscopy (AFM). Our results revealed significant changes in spore morphology and nanomechanical properties after heat inactivation. In addition, we also found that these changes were different under different heating conditions that produced similar inactivation probabilities (high temperature for short exposure time versus low temperature for long exposure time). We attributed the differences to the differential thermal and mechanical stresses in the spore. The buildup of internal thermal and mechanical stresses may become prominent only in ultrafast, high-temperature heat inactivation when the experimental timescale is too short for heat-generated vapor to efficiently escape from the spore. Our results thus provide direct, visual evidences of the importance of thermal stresses and heat and mass transfer to spore inactivation by very rapid dry heating. PMID:24375142

  9. Solution structure of the isolated Pelle death domain.

    Science.gov (United States)

    Moncrieffe, Martin C; Stott, Katherine M; Gay, Nicholas J

    2005-07-18

    The interaction between the death domains (DDs) of Tube and the protein kinase Pelle is an important component of the Toll pathway. Published crystallographic data suggests that the Pelle-Tube DD interface is plastic and implies that in addition to the two predominant Pelle-Tube interfaces, a third interaction is possible. We present the NMR solution structure of the isolated death domain of Pelle and a study of the interaction between the DDs of Pelle and Tube. Our data suggests the solution structure of the isolated Pelle DD is similar to that of Pelle DD in complex with Tube. Additionally, they suggest that the plasticity observed in the crystal structure may not be relevant in the functioning death domain complex.

  10. Transcript structure and domain display: a customizable transcript visualization tool.

    Science.gov (United States)

    Watanabe, Kenneth A; Ma, Kaiwang; Homayouni, Arielle; Rushton, Paul J; Shen, Qingxi J

    2016-07-01

    Transcript Structure and Domain Display (TSDD) is a publicly available, web-based program that provides publication quality images of transcript structures and domains. TSDD is capable of producing transcript structures from GFF/GFF3 and BED files. Alternatively, the GFF files of several model organisms have been pre-loaded so that users only needs to enter the locus IDs of the transcripts to be displayed. Visualization of transcripts provides many benefits to researchers, ranging from evolutionary analysis of DNA-binding domains to predictive function modeling. TSDD is freely available for non-commercial users at http://shenlab.sols.unlv.edu/shenlab/software/TSD/transcript_display.html : jeffery.shen@unlv.nevada.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  11. Grazing incidence x-ray diffraction at free-standing nanoscale islands: fine structure of diffuse scattering

    International Nuclear Information System (INIS)

    Grigoriev, D; Hanke, M; Schmidbauer, M; Schaefer, P; Konovalov, O; Koehler, R

    2003-01-01

    We have investigated the x-ray intensity distribution around 220 reciprocal lattice point in case of grazing incidence diffraction at SiGe nanoscale free-standing islands grown on Si(001) substrate by LPE. Experiments and computer simulations based on the distorted wave Born approximation utilizing the results of elasticity theory obtained by FEM modelling have been carried out. The data reveal fine structure in the distribution of scattered radiation with well-pronounced maxima and complicated fringe pattern. Explanation of the observed diffraction phenomena in their relation to structure and morphology of the island is given. An optimal island model including its shape, size and Ge spatial distribution was elaborated

  12. Microscale and nanoscale hierarchical structured mesh films with superhydrophobic and superoleophilic properties induced by long-chain fatty acids

    International Nuclear Information System (INIS)

    Wang Shutao; Song Yanlin; Jiang Lei

    2007-01-01

    Inspired by the lotus effect, we fabricate new microscale and nanoscale hierarchical structured copper mesh films by a simple electrochemical deposition. After modification of the long-chain fatty acid monolayer, these films show superhydrophobic and superoleophilic properties, which could be used for the effective separation of oil and water. The length of the fatty acid chain strongly influences the surface wettability of as-prepared films. It is confirmed that the cooperative effect of the hierarchical structure of the copper film and the nature of the long-chain fatty acid contribute to this unique surface wettability

  13. Crystal structure of the Ig1 domain of the neural cell adhesion molecule NCAM2 displays domain swapping

    DEFF Research Database (Denmark)

    Rasmussen, Kim Krighaar; Kulahin, Nikolaj; Kristensen, Ole

    2008-01-01

    The crystal structure of the first immunoglobulin (Ig1) domain of neural cell adhesion molecule 2 (NCAM2/OCAM/RNCAM) is presented at a resolution of 2.7 A. NCAM2 is a member of the immunoglobulin superfamily of cell adhesion molecules (IgCAMs). In the structure, two Ig domains interact by domain...

  14. Phase behavior and nanoscale structure of phospholipid membranes incorporated with acylated C-14-peptides

    DEFF Research Database (Denmark)

    Pedersen, T.B.; Kaasgaard, Thomas; Jensen, M.O.

    2005-01-01

    The thermotropic phase behavior and lateral structure of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers containing an acylated peptide has been characterized by differential scanning calorimetry (DSC) on vesicles and atomic force microscopy (AFM) on mica-supported bilayers. The acylated...... peptide, which is a synthetic decapeptide N-terminally linked to a C-14 acyl chain (C-14-peptide), is incorporated into DPPC bilayers in amounts ranging from 0-20 mol %. The calorimetric scans of the two-component system demonstrate a distinct influence of the C-14-peptide on the lipid bilayer...... gel phase DPPC bilayers, inserts preferentially into preexisting defect regions and has a noticeable influence on the organization of the surrounding lipids. The presence of the C-14-peptide gives rise to a laterally heterogeneous bilayer structure with coexisting lipid domains characterized by a 10...

  15. Structural Basis for Endosomal Targeting by the Bro1 Domain

    Science.gov (United States)

    Kim, Jaewon; Sitaraman, Sujatha; Hierro, Aitor; Beach, Bridgette M.; Odorizzi, Greg; Hurley, James H.

    2010-01-01

    Summary Proteins delivered to the lysosome or the yeast vacuole via late endosomes are sorted by the ESCRT complexes and by associated proteins, including Alix and its yeast homolog Bro1. Alix, Bro1, and several other late endosomal proteins share a conserved 160 residue Bro1 domain whose boundaries, structure, and function have not been characterized. The crystal structure of the Bro1 domain of Bro1 reveals a folded core of 367 residues. The extended Bro1 domain is necessary and sufficient for binding to the ESCRT-III subunit Snf7 and for the recruitment of Bro1 to late endosomes. The structure resembles a boomerang with its concave face filled in and contains a triple tetratricopeptide repeat domain as a substructure. Snf7 binds to a conserved hydrophobic patch on Bro1 that is required for protein complex formation and for the protein-sorting function of Bro1. These results define a conserved mechanism whereby Bro1 domain-containing proteins are targeted to endosomes by Snf7 and its orthologs. PMID:15935782

  16. Modeling investigation of the stability and irradiation-induced evolution of nanoscale precipitates in advanced structural materials

    International Nuclear Information System (INIS)

    Wirth, Brian

    2015-01-01

    Materials used in extremely hostile environment such as nuclear reactors are subject to a high flux of neutron irradiation, and thus vast concentrations of vacancy and interstitial point defects are produced because of collisions of energetic neutrons with host lattice atoms. The fate of these defects depends on various reaction mechanisms which occur immediately following the displacement cascade evolution and during the longer-time kinetically dominated evolution such as annihilation, recombination, clustering or trapping at sinks of vacancies, interstitials and their clusters. The long-range diffusional transport and evolution of point defects and self-defect clusters drive a microstructural and microchemical evolution that are known to produce degradation of mechanical properties including the creep rate, yield strength, ductility, or fracture toughness, and correspondingly affect material serviceability and lifetimes in nuclear applications. Therefore, a detailed understanding of microstructural evolution in materials at different time and length scales is of significant importance. The primary objective of this work is to utilize a hierarchical computational modeling approach i) to evaluate the potential for nanoscale precipitates to enhance point defect recombination rates and thereby the self-healing ability of advanced structural materials, and ii) to evaluate the stability and irradiation-induced evolution of such nanoscale precipitates resulting from enhanced point defect transport to and annihilation at precipitate interfaces. This project will utilize, and as necessary develop, computational materials modeling techniques within a hierarchical computational modeling approach, principally including molecular dynamics, kinetic Monte Carlo and spatially-dependent cluster dynamics modeling, to identify and understand the most important physical processes relevant to promoting the ''selfhealing'' or radiation resistance in advanced

  17. Modeling investigation of the stability and irradiation-induced evolution of nanoscale precipitates in advanced structural materials

    Energy Technology Data Exchange (ETDEWEB)

    Wirth, Brian [Univ. of Tennessee, Knoxville, TN (United States)

    2015-04-08

    Materials used in extremely hostile environment such as nuclear reactors are subject to a high flux of neutron irradiation, and thus vast concentrations of vacancy and interstitial point defects are produced because of collisions of energetic neutrons with host lattice atoms. The fate of these defects depends on various reaction mechanisms which occur immediately following the displacement cascade evolution and during the longer-time kinetically dominated evolution such as annihilation, recombination, clustering or trapping at sinks of vacancies, interstitials and their clusters. The long-range diffusional transport and evolution of point defects and self-defect clusters drive a microstructural and microchemical evolution that are known to produce degradation of mechanical properties including the creep rate, yield strength, ductility, or fracture toughness, and correspondingly affect material serviceability and lifetimes in nuclear applications. Therefore, a detailed understanding of microstructural evolution in materials at different time and length scales is of significant importance. The primary objective of this work is to utilize a hierarchical computational modeling approach i) to evaluate the potential for nanoscale precipitates to enhance point defect recombination rates and thereby the self-healing ability of advanced structural materials, and ii) to evaluate the stability and irradiation-induced evolution of such nanoscale precipitates resulting from enhanced point defect transport to and annihilation at precipitate interfaces. This project will utilize, and as necessary develop, computational materials modeling techniques within a hierarchical computational modeling approach, principally including molecular dynamics, kinetic Monte Carlo and spatially-dependent cluster dynamics modeling, to identify and understand the most important physical processes relevant to promoting the “selfhealing” or radiation resistance in advanced materials containing

  18. Structure and composition of magnetocaloric Ni-Mn-In-Co thin films on the nanoscale - a TEM study

    Energy Technology Data Exchange (ETDEWEB)

    Erkartal, Burak; Schuermann, Ulrich; Kienle, Lorenz [Institute for Materials Science, Synthesis and Real Structure, Christian Albrechts University, Kiel (Germany); Duppel, Viola [Nanochemistry Max Planck Institute for Solid State Research, Stuttgart (Germany); Niemann, Robert; Schultz, Ludwig; Faehler, Sebastian [IFW Dresden (Germany)

    2012-08-15

    A complementary set of electron microscopy techniques is applied for the determination of structural and chemical segregation phenomena within a 300 nm thick metamagnetic Ni-Mn-In-Co thin film. The structure is predominantly composed of distinct modulated martensites of the 5M-, 6M-, 7M-, and 8M-type. Additionally these modulated structures exhibit twinning and stacking disordering. The nature of the disordering and the structural misfit at the twin interface were analyzed via high resolution micrographs. Next to an adhesion layer of Cr interdiffusion on the nanoscale was observed producing a penternary chemically and structurally homogeneous precipitate. The structure can be assigned to a twinned non-modulated pseudocubic model. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  19. Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler.

    Science.gov (United States)

    Bindewald, Eckart; Grunewald, Calvin; Boyle, Brett; O'Connor, Mary; Shapiro, Bruce A

    2008-10-01

    One approach to designing RNA nanoscale structures is to use known RNA structural motifs such as junctions, kissing loops or bulges and to construct a molecular model by connecting these building blocks with helical struts. We previously developed an algorithm for detecting internal loops, junctions and kissing loops in RNA structures. Here we present algorithms for automating or assisting many of the steps that are involved in creating RNA structures from building blocks: (1) assembling building blocks into nanostructures using either a combinatorial search or constraint satisfaction; (2) optimizing RNA 3D ring structures to improve ring closure; (3) sequence optimisation; (4) creating a unique non-degenerate RNA topology descriptor. This effectively creates a computational pipeline for generating molecular models of RNA nanostructures and more specifically RNA ring structures with optimized sequences from RNA building blocks. We show several examples of how the algorithms can be utilized to generate RNA tecto-shapes.

  20. Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler☆

    Science.gov (United States)

    Bindewald, Eckart; Grunewald, Calvin; Boyle, Brett; O’Connor, Mary; Shapiro, Bruce A.

    2013-01-01

    One approach to designing RNA nanoscale structures is to use known RNA structural motifs such as junctions, kissing loops or bulges and to construct a molecular model by connecting these building blocks with helical struts. We previously developed an algorithm for detecting internal loops, junctions and kissing loops in RNA structures. Here we present algorithms for automating or assisting many of the steps that are involved in creating RNA structures from building blocks: (1) assembling building blocks into nanostructures using either a combinatorial search or constraint satisfaction; (2) optimizing RNA 3D ring structures to improve ring closure; (3) sequence optimisation; (4) creating a unique non-degenerate RNA topology descriptor. This effectively creates a computational pipeline for generating molecular models of RNA nanostructures and more specifically RNA ring structures with optimized sequences from RNA building blocks. We show several examples of how the algorithms can be utilized to generate RNA tecto-shapes. PMID:18838281

  1. Crystal Structure of the FERM Domain of Focal Adhesion Kinase

    International Nuclear Information System (INIS)

    Ceccarelli, D.; Song, H.; Poy, F.; Schaller, M.; Eck, M.

    2006-01-01

    Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase that localizes to focal adhesions in adherent cells. Through phosphorylation of proteins assembled at the cytoplasmic tails of integrins, FAK promotes signaling events that modulate cellular growth, survival, and migration. The amino-terminal region of FAK contains a region of sequence homology with band 4.1 and ezrin/radixin/moesin (ERM) proteins termed a FERM domain. FERM domains are found in a variety of signaling and cytoskeletal proteins and are thought to mediate intermolecular interactions with partner proteins and phospholipids at the plasma membrane and intramolecular regulatory interactions. Here we report two crystal structures of an NH2-terminal fragment of avian FAK containing the FERM domain and a portion of the regulatory linker that connects the FERM and kinase domains. The tertiary folds of the three subdomains (F1, F2, and F3) are similar to those of known FERM structures despite low sequence conservation. Differences in the sequence and relative orientation of the F3 subdomain alters the nature of the interdomain interface, and the phosphoinositide binding site found in ERM family FERM domains is not present in FAK. A putative protein interaction site on the F3 lobe is masked by the proximal region of the linker. Additionally, in one structure the adjacent Src SH3 and SH2 binding sites in the linker associate with the surfaces of the F3 and F1 lobes, respectively. These structural features suggest the possibility that protein interactions of the FAK FERM domain can be regulated by binding of Src kinases to the linker segment

  2. Effect of domains configuration on crystal structure in ferroelectric ...

    Indian Academy of Sciences (India)

    2017-09-09

    Sep 9, 2017 ... It is well known that domains and crystal structure control the physical properties of ferroelectrics. ... The as-prepared ceramics were crushed to fine pow- ders. ..... [1] Gao J, Xue D, Wang Y, Wang D, Zhang L, Wu H et al 2011.

  3. Parental Provision of Structure: Implementation and Correlates in Three Domains

    Science.gov (United States)

    Grolnick, Wendy S.; Raftery-Helmer, Jacquelyn N.; Marbell, Kristine N; Flamm, Elizabeth S.; Cardemil, Esteban V.

    2014-01-01

    This study examined parents' provision of "structure," defined as the organization of the environment to facilitate competence, and the degree to which it supports versus controls children's autonomy, in the domains of homework and studying, unsupervised time, and responsibilities in a diverse sample of sixth-grade children and their…

  4. Structural Time Domain Identification (STDI) Toolbox for Use with MATLAB

    DEFF Research Database (Denmark)

    Kirkegaard, Poul Henning; Andersen, P.; Brincker, Rune

    1997-01-01

    The Structural Time Domain Identification (STDI) toolbox for use with MATLABTM is developed at Aalborg University, Denmark, based on the system identification research performed during recent years. By now, a reliable set of functions offers a wide spectrum of services for all the important steps...

  5. Structural Time Domain Identification (STDI) Toolbox for Use with MATLAB

    DEFF Research Database (Denmark)

    Kirkegaard, Poul Henning; Andersen, P.; Brincker, Rune

    The Structural Time Domain Identification (STDI) toolbox for use with MATLABTM is developed at Aalborg University, Denmark, based on the system identification research performed during recent years. By now, a reliable set of functions offers a wide spectrum of services for all the important steps...

  6. Probing and tuning the size, morphology, chemistry and structure of nanoscale cerium oxide

    Science.gov (United States)

    Kuchibhatla, Satyanarayana Vnt

    Cerium oxide (ceria)-based materials in the nanoscale regime are of significant fundamental and technological interest. Nanoceria in pure and doped forms has current and potential use in solid oxide fuel cells, catalysis, UV-screening, chemical mechanical planarization, oxygen sensors, and bio-medical applications. The characteristic feature of Ce to switch between the +3 and +4 oxidation states renders oxygen buffering capability to ceria. The ease of this transformation was expected to be enhanced in the nanoceria. In most the practical scenarios, it is necessary to have a stable suspension of ceria nanoparticles (CNPs) over longer periods of time. However, the existing literature is confined to short term studies pertaining to synthesis and property evaluation. Having understood the need for a comprehensive understanding of the CNP suspensions, this dissertation is primarily aimed at understanding the behavior of CNPs in various chemical and physical environments. We have synthesized CNPs in the absence of any surfactants at room temperature and studied the aging characteristics. After gaining some understanding about the behavior of this functional oxide, the synthesis environment and aging temperature were varied, and their affects were carefully analyzed using various materials analysis techniques such as high resolution transmission electron microscopy (HRTEM), UV-Visible spectroscopy (UV-Vis), and X-ray photoelectron spectroscopy (XPS). When the CNPs were aged at room temperature in as-synthesized condition, they were observed to spontaneously assemble and evolve as fractal superoctahedral structures. The reasons for this unique polycrystalline morphology were attributed to the symmetry driven assembly of the individual truncated octahedral and octahedral seed of the ceria. HRTEM and Fast Fourier Transform (FFT) analyses were used to explain the agglomeration behavior and evolution of the octahedral morphology. Some of the observations were supported by

  7. Analysis of the nano-scale structure of a natural clayey soil using the small angle neutron scattering method

    International Nuclear Information System (INIS)

    Itakura, T.; Bertram, W.K.; Hathaway, P.V.; Knott, R.B.

    2001-01-01

    The small angle neutron scattering method (SANS) was used to analyze the nano-structure of a natural clayey soil used for containment of industrial liquid wastes. A Tertiary clay deposit called the Londonderry clay was used to contain the wastes in a state-run landfill facility in NSW. A number of site assessments have been carried out at the site and continual efforts have been made to characterize interactions between soil materials and contaminants at the site. Hence, it is of research and practical interest to investigate the effects of deformation on the nano-scale structure of the soil. Experiments have been conducted to analyze the structure of reconstituted clayey soil samples that were subjected to uniaxial compression ranging from 200 kPa to 800 kPa. The small angle neutron scattering instrument was used to measure the scattering intensity of these samples at a scattering vector (q) range between 0.01 and 0.1 Angstroms -1 . The sector integration technique was used to analyse elliptical scattering patterns along the major and minor axes. A relation between stress, void ratio and nano-scale structure properties was then briefly discussed for use in assessing the performance of clayey soils as in situ barriers

  8. ASH structure alignment package: Sensitivity and selectivity in domain classification

    Directory of Open Access Journals (Sweden)

    Toh Hiroyuki

    2007-04-01

    Full Text Available Abstract Background Structure alignment methods offer the possibility of measuring distant evolutionary relationships between proteins that are not visible by sequence-based analysis. However, the question of how structural differences and similarities ought to be quantified in this regard remains open. In this study we construct a training set of sequence-unique CATH and SCOP domains, from which we develop a scoring function that can reliably identify domains with the same CATH topology and SCOP fold classification. The score is implemented in the ASH structure alignment package, for which the source code and a web service are freely available from the PDBj website http://www.pdbj.org/ASH/. Results The new ASH score shows increased selectivity and sensitivity compared with values reported for several popular programs using the same test set of 4,298,905 structure pairs, yielding an area of .96 under the receiver operating characteristic (ROC curve. In addition, weak sequence homologies between similar domains are revealed that could not be detected by BLAST sequence alignment. Also, a subset of domain pairs is identified that exhibit high similarity, even though their CATH and SCOP classification differs. Finally, we show that the ranking of alignment programs based solely on geometric measures depends on the choice of the quality measure. Conclusion ASH shows high selectivity and sensitivity with regard to domain classification, an important step in defining distantly related protein sequence families. Moreover, the CPU cost per alignment is competitive with the fastest programs, making ASH a practical option for large-scale structure classification studies.

  9. Mapping small molecule binding data to structural domains.

    Science.gov (United States)

    Kruger, Felix A; Rostom, Raghd; Overington, John P

    2012-01-01

    Large-scale bioactivity/SAR Open Data has recently become available, and this has allowed new analyses and approaches to be developed to help address the productivity and translational gaps of current drug discovery. One of the current limitations of these data is the relative sparsity of reported interactions per protein target, and complexities in establishing clear relationships between bioactivity and targets using bioinformatics tools. We detail in this paper the indexing of targets by the structural domains that bind (or are likely to bind) the ligand within a full-length protein. Specifically, we present a simple heuristic to map small molecule binding to Pfam domains. This profiling can be applied to all proteins within a genome to give some indications of the potential pharmacological modulation and regulation of all proteins. In this implementation of our heuristic, ligand binding to protein targets from the ChEMBL database was mapped to structural domains as defined by profiles contained within the Pfam-A database. Our mapping suggests that the majority of assay targets within the current version of the ChEMBL database bind ligands through a small number of highly prevalent domains, and conversely the majority of Pfam domains sampled by our data play no currently established role in ligand binding. Validation studies, carried out firstly against Uniprot entries with expert binding-site annotation and secondly against entries in the wwPDB repository of crystallographic protein structures, demonstrate that our simple heuristic maps ligand binding to the correct domain in about 90 percent of all assessed cases. Using the mappings obtained with our heuristic, we have assembled ligand sets associated with each Pfam domain. Small molecule binding has been mapped to Pfam-A domains of protein targets in the ChEMBL bioactivity database. The result of this mapping is an enriched annotation of small molecule bioactivity data and a grouping of activity classes

  10. Polar and chemical domain structures of lead scandium tantalate (PST)

    International Nuclear Information System (INIS)

    Peng, J.L.; Bursill, L.A.

    1993-01-01

    The local structure of chemical and polar domains and domain walls is determined directly by atomic resolution high-resolution electron microscopy. Thus the Pb, Ta and Sc atomic positions may be located in the images of very thin crystals. Furthermore the Pb cation displacements away from the ideal perovskite A-site have been measured directly for the first time. Local variations in polarization direction may be mapped directly off the images, provided certain electron optical conditions are met. The results are relevant to recent theories of polar-glass behaviour in relaxor-type complex oxide functional ceramics. 17 refs., 9 figs

  11. Evaporation characteristics of a hydrophilic surface with micro-scale and/or nano-scale structures fabricated by sandblasting and aluminum anodization

    International Nuclear Information System (INIS)

    Kim, Hyungmo; Kim, Joonwon

    2010-01-01

    This paper presents the results of evaporation experiments using water droplets on aluminum sheets that were either smooth or had surface structures at the micro-scale, at the nano-scale or at both micro- and nano-scales (dual-scale). The smooth surface was a polished aluminum sheet; the surface with micro-scale structures was obtained by sandblasting; the surface with nano-scale structures was obtained using conventional aluminum anodization and the surface with dual-scale structures was prepared using sandblasting and anodization sequentially. The wetting properties and evaporation rates were measured for each surface. The evaporation rates were affected by their static and dynamic wetting properties. Evaporation on the surface with dual-scale structures was fastest and the evaporation rate was analyzed quantitatively.

  12. Structural and magnetic domains characterization of magnetite nanoparticles

    International Nuclear Information System (INIS)

    Santoyo-Salazar, J.; Castellanos-Roman, M.A.; Beatriz Gomez, L.

    2007-01-01

    Recently, important advances have been achieved in application, reproducibility and response ability of magnetic materials due to the relationships among processing, structure and nanometric size particle. Features like homogeneity of compounds and nanoparticle-sizing have improved some magnetic properties of materials and their field application. Of particular interest is the study of magnetic materials at the atomic and microstuctural level because the orientation and magnetic domains (large numbers of atoms moments coupled together in a preferential direction) can be observed. In this work, magnetite (Fe 3 O 4 ) powders which were obtained by precipitation route in alkaline medium are analyzed to identify the structure and mechanism formation of domains over the core and border of nanoparticles. Results obtained by XRD, atomic force microscopy (AFM) and magnetic force microscopy (MFM) showed a structural phase corresponding to Fe 3 O 4 and nanoparticles in a range of 20-40 nm. Samples scanned by MFM in nanometric resolution and profile images showed orientation of magnetic domains in the border and cores of the material. Finally, an analysis of repulsion and attraction in magnetic field and direction changes of domains formed by magnetite (Fe 3 O 4 ) powders were done

  13. Structure of the Nucleoprotein Binding Domain of Mokola Virus Phosphoprotein▿

    Science.gov (United States)

    Assenberg, René; Delmas, Olivier; Ren, Jingshan; Vidalain, Pierre-Olivier; Verma, Anil; Larrous, Florence; Graham, Stephen C.; Tangy, Frédéric; Grimes, Jonathan M.; Bourhy, Hervé

    2010-01-01

    Mokola virus (MOKV) is a nonsegmented, negative-sense RNA virus that belongs to the Lyssavirus genus and Rhabdoviridae family. MOKV phosphoprotein P is an essential component of the replication and transcription complex and acts as a cofactor for the viral RNA-dependent RNA polymerase. P recruits the viral polymerase to the nucleoprotein-bound viral RNA (N-RNA) via an interaction between its C-terminal domain and the N-RNA complex. Here we present a structure for this domain of MOKV P, obtained by expression of full-length P in Escherichia coli, which was subsequently truncated during crystallization. The structure has a high degree of homology with P of rabies virus, another member of Lyssavirus genus, and to a lesser degree with P of vesicular stomatitis virus (VSV), a member of the related Vesiculovirus genus. In addition, analysis of the crystal packing of this domain reveals a potential binding site for the nucleoprotein N. Using both site-directed mutagenesis and yeast two-hybrid experiments to measure P-N interaction, we have determined the relative roles of key amino acids involved in this interaction to map the region of P that binds N. This analysis also reveals a structural relationship between the N-RNA binding domain of the P proteins of the Rhabdoviridae and the Paramyxoviridae. PMID:19906936

  14. Sub-nanoscale surface ruggedness provides a water-tight seal for exposed regions in soluble protein structure.

    Directory of Open Access Journals (Sweden)

    Erica Schulz

    2010-09-01

    Full Text Available Soluble proteins must maintain backbone hydrogen bonds (BHBs water-tight to ensure structural integrity. This protection is often achieved by burying the BHBs or wrapping them through intermolecular associations. On the other hand, water has low coordination resilience, with loss of hydrogen-bonding partnerships carrying significant thermodynamic cost. Thus, a core problem in structural biology is whether natural design actually exploits the water coordination stiffness to seal the backbone in regions that are exposed to the solvent. This work explores the molecular design features that make this type of seal operative, focusing on the side-chain arrangements that shield the protein backbone. We show that an efficient sealing is achieved by adapting the sub-nanoscale surface topography to the stringency of water coordination: an exposed BHB may be kept dry if the local concave curvature is small enough to impede formation of the coordination shell of a penetrating water molecule. Examination of an exhaustive database of uncomplexed proteins reveals that exposed BHBs invariably occur within such sub-nanoscale cavities in native folds, while this level of local ruggedness is absent in other regions. By contrast, BHB exposure in misfolded proteins occurs with larger local curvature promoting backbone hydration and consequently, structure disruption. These findings unravel physical constraints fitting a spatially dependent least-action for water coordination, introduce a molecular design concept, and herald the advent of water-tight peptide-based materials with sufficient backbone exposure to remain flexible.

  15. Restoration the domain structure from magnetic force microscopy image

    Science.gov (United States)

    Wu, Dongping; Lou, Yuanfu; Wei, Fulin; Wei, Dan

    2012-04-01

    This contribution gives an approximation method to calculate the stray field of the scanning plane from the magnetic force microscopy (MFM) force gradient image. Before calculation, a Butterworth low-pass filter has been used to remove a part of the noise of the image. The discrete Fourier transform (DFT) method has been used to calculate the magnetic potential of the film surface. It shows that the potential is not correct because the low-frequency noise has been enlarged. The approximation method gives a better result of the potential and proves that the MFM force gradient of the perpendicular component image also gives the perpendicular component of the stray field. Supposing that the distance between the tip and the sample is as small as near zero, the force gradient image also gives the magnetic charge distribution of the film surface. So if the orientation of the film from hysteresis loop is known, then the domain structure of the film can be determined. For perpendicular orientation, the absolution value of the perpendicular component of stray field gives the domain and domain wall position. For in-plane orientation, the absolution value of in-plane component of stray field gives the domain and domain wall position.

  16. Quantifying information transfer by protein domains: Analysis of the Fyn SH2 domain structure

    DEFF Research Database (Denmark)

    Lenaerts, Tom; Ferkinghoff-Borg, Jesper; Stricher, Francois

    2008-01-01

    instance of communication over a noisy channel. In particular, we analyze the conformational correlations between protein residues and apply the concept of mutual information to quantify information exchange. Mapping out changes of mutual information on the protein structure then allows visualizing how...... distal communication is achieved. We illustrate the approach by analyzing information transfer by the SH2 domain of Fyn tyrosine kinase, obtained from Monte Carlo dynamics simulations. Our analysis reveals that the Fyn SH2 domain forms a noisy communication channel that couples residues located......Background: Efficient communication between distant sites within a protein is essential for cooperative biological response. Although often associated with large allosteric movements, more subtle changes in protein dynamics can also induce long-range correlations. However, an appropriate formalism...

  17. Correlation of electron backscatter diffraction and piezoresponse force microscopy for the nanoscale characterization of ferroelectric domains in polycrystalline lead zirconate titanate

    Science.gov (United States)

    Burnett, T. L.; Weaver, P. M.; Blackburn, J. F.; Stewart, M.; Cain, M. G.

    2010-08-01

    The functional properties of ferroelectric ceramic bulk or thin film materials are strongly influenced by their nanostructure, crystallographic orientation, and structural geometry. In this paper, we show how, by combining textural analysis, through electron backscattered diffraction, with piezoresponse force microscopy, quantitative measurements of the piezoelectric properties can be made at a scale of 25 nm, smaller than the domain size. The combined technique is used to obtain data on the domain-resolved effective single crystal piezoelectric response of individual crystallites in Pb(Zr0.4Ti0.6)O3 ceramics. The results offer insight into the science of domain engineering and provide a tool for the future development of new nanostructured ferroelectric materials for memory, nanoactuators, and sensors based on magnetoelectric multiferroics.

  18. Structure and dynamics of the human pleckstrin DEP domain: distinct molecular features of a novel DEP domain subfamily.

    Science.gov (United States)

    Civera, Concepcion; Simon, Bernd; Stier, Gunter; Sattler, Michael; Macias, Maria J

    2005-02-01

    Pleckstrin1 is a major substrate for protein kinase C in platelets and leukocytes, and comprises a central DEP (disheveled, Egl-10, pleckstrin) domain, which is flanked by two PH (pleckstrin homology) domains. DEP domains display a unique alpha/beta fold and have been implicated in membrane binding utilizing different mechanisms. Using multiple sequence alignments and phylogenetic tree reconstructions, we find that 6 subfamilies of the DEP domain exist, of which pleckstrin represents a novel and distinct subfamily. To clarify structural determinants of the DEP fold and to gain further insight into the role of the DEP domain, we determined the three-dimensional structure of the pleckstrin DEP domain using heteronuclear NMR spectroscopy. Pleckstrin DEP shares main structural features with the DEP domains of disheveled and Epac, which belong to different DEP subfamilies. However, the pleckstrin DEP fold is distinct from these structures and contains an additional, short helix alpha4 inserted in the beta4-beta5 loop that exhibits increased backbone mobility as judged by NMR relaxation measurements. Based on sequence conservation, the helix alpha4 may also be present in the DEP domains of regulator of G-protein signaling (RGS) proteins, which are members of the same DEP subfamily. In pleckstrin, the DEP domain is surrounded by two PH domains. Structural analysis and charge complementarity suggest that the DEP domain may interact with the N-terminal PH domain in pleckstrin. Phosphorylation of the PH-DEP linker, which is required for pleckstrin function, could regulate such an intramolecular interaction. This suggests a role of the pleckstrin DEP domain in intramolecular domain interactions, which is distinct from the functions of other DEP domain subfamilies found so far.

  19. The Role of Isolation Methods on a Nanoscale Surface Structure and Its Effect on the Size of Exosomes

    Directory of Open Access Journals (Sweden)

    JungReem Woo

    2016-06-01

    Full Text Available Exosomes are ~100 nanometre diameter vesicles secreted by mammalian cells. These emerging disease biomarkers carry nucleic acids, proteins and lipids specific to the parental cells that secrete them. Exosomes are typically isolated in bulk by ultracentrifugation, filtration or immu‐ noaffinity precipitation for downstream proteomic, genomic, or lipidomic analysis. However, the structural properties and heterogeneity of isolated exosomes at the single vesicle level are not well characterized due to their small size. In this paper, by using high-resolution atomic force microscope imaging, we show the nanoscale mor‐ phology and structural heterogeneity in exosomes derived from U87 cells. Quantitative assessment of single exosomes reveals nanoscale variations in morphology, surface roughness and counts isolated by ultracentrifugation (UC and immunoaffinity (IA purification. Both methods produce intact globular, 30-120 nm sized vesicles when imaged under fluid and in air. However, IA exosomes had higher surface roughness and bimodal size population compared to UC exosomes. The study highlights the differences in size and surface topography of exosomes purified from a single cell type using different isolation methods.

  20. NASA GSFC Strategic Nanotechnology Interests: Symposium on High-Rate Nanoscale Printing for Devices and Structures

    Science.gov (United States)

    Ericsson, Aprille J.

    2014-01-01

    The seminars invitees include representatives from industry, nonprofit research facility and universities. The presentation provides an overview of the NASAGSFC locations, technical capabilities and applied nanotechnology interests. Initially presented are advances by the broader technological communities on current miniaturized multiscale advanced manufacturing and 3D printing products on the micro and macro scale. Briefly assessed is the potential of moving toward the nanoscale for possible space flight applications and challenges. Lastly, highlighted are GSFCs current successes in nano-technology developments and targeted future applications.

  1. Structure and evolution of N-domains in AAA metalloproteases.

    Science.gov (United States)

    Scharfenberg, Franka; Serek-Heuberger, Justyna; Coles, Murray; Hartmann, Marcus D; Habeck, Michael; Martin, Jörg; Lupas, Andrei N; Alva, Vikram

    2015-02-27

    Metalloproteases of the AAA (ATPases associated with various cellular activities) family play a crucial role in protein quality control within the cytoplasmic membrane of bacteria and the inner membrane of eukaryotic organelles. These membrane-anchored hexameric enzymes are composed of an N-terminal domain with one or two transmembrane helices, a central AAA ATPase module, and a C-terminal Zn(2+)-dependent protease. While the latter two domains have been well studied, so far, little is known about the N-terminal regions. Here, in an extensive bioinformatic and structural analysis, we identified three major, non-homologous groups of N-domains in AAA metalloproteases. By far, the largest one is the FtsH-like group of bacteria and eukaryotic organelles. The other two groups are specific to Yme1: one found in plants, fungi, and basal metazoans and the other one found exclusively in animals. Using NMR and crystallography, we determined the subunit structure and hexameric assembly of Escherichia coli FtsH-N, exhibiting an unusual α+β fold, and the conserved part of fungal Yme1-N from Saccharomyces cerevisiae, revealing a tetratricopeptide repeat fold. Our bioinformatic analysis showed that, uniquely among these proteins, the N-domain of Yme1 from the cnidarian Hydra vulgaris contains both the tetratricopeptide repeat region seen in basal metazoans and a region of homology to the N-domains of animals. Thus, it is a modern-day representative of an intermediate in the evolution of animal Yme1 from basal eukaryotic precursors. Copyright © 2015. Published by Elsevier Ltd.

  2. Structurally Stable Attractive Nanoscale Emulsions with Dipole-Dipole Interaction-Driven Interdrop Percolation.

    Science.gov (United States)

    Shin, Kyounghee; Gong, Gyeonghyeon; Cuadrado, Jonas; Jeon, Serim; Seo, Mintae; Choi, Hong Sung; Hwang, Jae Sung; Lee, Youngbok; Fernandez-Nieves, Alberto; Kim, Jin Woong

    2017-03-28

    This study introduces an extremely stable attractive nanoscale emulsion fluid, in which the amphiphilic block copolymer, poly(ethylene oxide)-block-poly(ϵ-caprolactone) (PEO-b-PCL), is tightly packed with lecithin, thereby forming a mechanically robust thin-film at the oil-water interface. The molecular association of PEO-b-PCL with lecithin is critical for formation of a tighter and denser molecular assembly at the interface, which is systematically confirmed by T 2 relaxation and DSC analyses. Moreover, suspension rheology studies also reflect the interdroplet attractions over a wide volume fraction range of the dispersed oil phase; this results in a percolated network of stable drops that exhibit no signs of coalescence or phase separation. This unique rheological behavior is attributed to the dipolar interaction between the phosphorylcholine groups of lecithin and the methoxy end groups of PEO-b-PCL. Finally, the nanoemulsion system significantly enhances transdermal delivery efficiency due to its favorable attraction to the skin, as well as high diffusivity of the nanoscale emulsion drops. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Identification of nanoscale structure and morphology reconstruction in oxidized a-SiC:H thin films

    Energy Technology Data Exchange (ETDEWEB)

    Vasin, A.V.; Rusavsky, A.V.; Nazarov, A.N.; Lysenko, V.S.; Lytvyn, P.M.; Strelchuk, V.V. [Lashkaryov Institute of Semiconductor Physics, 41 Nauki Pr., Kiev 03028 (Ukraine); Kholostov, K.I.; Bondarenko, V.P. [Belarusian State University of Informatics and Radioelectronics, 6P. Brovki Str., Minsk 220013 (Belarus); Starik, S.P. [Bakul Institute of Superhard Materials, 2 Avtzavodskaya Str., Kiev 04074 (Ukraine)

    2012-11-01

    Highlights: Black-Right-Pointing-Pointer Increase of magnetron discharge power results in densification of a-SiC:H thin films. Black-Right-Pointing-Pointer The denser a-SiC:H material the better resistance to oxidation by oxygen. Black-Right-Pointing-Pointer Oxidation of soft a-SiC:H films can result in increase of electric conductivity. Black-Right-Pointing-Pointer Formation of graphitic clusters was found in a-SiC:H after annealing in oxygen. - Abstract: Oxidation behavior of a-SiC:H layers deposited by radio-frequency magnetron sputtering technique was examined by Kelvin probe force microscopy (KPFM) in combination with scanning electron microscopy, Fourier-transform infra-red spectroscopy and submicron selected area Raman scattering spectroscopy. Partially oxidized a-SiC:H samples (oxidation at 600 Degree-Sign C in oxygen) were examined to clarify mechanism of the oxidation process. Nanoscale and microscale morphological defects (pits) with dimension of about 50 nm and several microns respectively have appeared after thermal treatment. KPFM measurements exhibited the surface potential of the material in micro pits is significantly smaller in comparison with surrounding material. Submicron RS measurements indicates formation of graphite-like nano-inclusions in the pit defects. We conclude that initial stage of oxidation process in a-SiC:H films takes place not homogeneously throughout the layer but it is initiated in local nanoscale regions followed by spreading over all layer.

  4. The Effect of the Nanoscale Structure of Nanobioceramics on Their In Vitro Bioactivity and Cell Differentiation Properties

    Directory of Open Access Journals (Sweden)

    Cristian Covarrubias

    2015-01-01

    Full Text Available The effect of the nanoscale structure of bioceramics on their in vitro bioactivity and capacity to osteogenically differentiate stem cell is studied. Nanoparticles of hydroxyapatite (nHA, bioactive glass (nBG, nanoporous bioactive glass (MBG, and nanoporous bioactive glass nanospheres (nMBG are investigated. The nanometric particle size of bioceramics seems to be more determining in controlling the ability to induce bone-like apatite as compared to the nanoporous structure. At short incubation time, nBG also produces a bioactive extracellular medium capable of upregulating key osteogenic markers involved in the development of a mineralizing phenotype in DPSCs. The bioactive properties of nBG are promissory for accelerating the bone regeneration process in tissue engineering applications.

  5. Effects of sub-domain structure on initial magnetization curve and domain size distribution of stacked media

    International Nuclear Information System (INIS)

    Sato, S.; Kumagai, S.; Sugita, R.

    2015-01-01

    In this paper, in order to confirm the sub-domain structure in stacked media demagnetized with in-plane field, initial magnetization curves and magnetic domain size distribution were investigated. Both experimental and simulation results showed that an initial magnetization curve for the medium demagnetized with in-plane field (MDI) initially rose faster than that for the medium demagnetized with perpendicular field (MDP). It is inferred that this is because the MDI has a larger number of domain walls than the MDP due to the existence of the sub-domains, resulting in an increase in the probability of domain wall motion. Dispersion of domain size for the MDI was larger than that for the MDP. This is because sub-domains are formed not only inside the domain but also at the domain boundary region, and they change the position of the domain boundary to affect the domain size. - Highlights: • An initial magnetization curve for MDI initially rose faster than that for MDP. • Dispersion of domain size for the MDI was larger than that for the MDP. • Experimental and simulation results can be explained by existence of sub-domains

  6. Crystal Structure of the Marburg Virus VP35 Oligomerization Domain

    Energy Technology Data Exchange (ETDEWEB)

    Bruhn, Jessica F.; Kirchdoerfer, Robert N.; Urata, Sarah M.; Li, Sheng; Tickle, Ian J.; Bricogne, Gérard; Saphire, Erica Ollmann (Scripps); (Globel Phasing); (UCSD)

    2016-11-09

    ABSTRACT

    Marburg virus (MARV) is a highly pathogenic filovirus that is classified in a genus distinct from that of Ebola virus (EBOV) (generaMarburgvirusandEbolavirus, respectively). Both viruses produce a multifunctional protein termed VP35, which acts as a polymerase cofactor, a viral protein chaperone, and an antagonist of the innate immune response. VP35 contains a central oligomerization domain with a predicted coiled-coil motif. This domain has been shown to be essential for RNA polymerase function. Here we present crystal structures of the MARV VP35 oligomerization domain. These structures and accompanying biophysical characterization suggest that MARV VP35 is a trimer. In contrast, EBOV VP35 is likely a tetramer in solution. Differences in the oligomeric state of this protein may explain mechanistic differences in replication and immune evasion observed for MARV and EBOV.

    IMPORTANCEMarburg virus can cause severe disease, with up to 90% human lethality. Its genome is concise, only producing seven proteins. One of the proteins, VP35, is essential for replication of the viral genome and for evasion of host immune responses. VP35 oligomerizes (self-assembles) in order to function, yet the structure by which it assembles has not been visualized. Here we present two crystal structures of this oligomerization domain. In both structures, three copies of VP35 twist about each other to form a coiled coil. This trimeric assembly is in contrast to tetrameric predictions for VP35 of Ebola virus and to known structures of homologous proteins in the measles, mumps, and Nipah viruses. Distinct oligomeric states of the Marburg and Ebola virus VP35 proteins may explain differences between them in polymerase function and immune evasion. These findings may provide a more accurate understanding of the

  7. Local and Nanoscale Structure and Speciation in the PuO2+x-y(OH)2y ·zH2O System

    International Nuclear Information System (INIS)

    Conradson, Steven D.; Begg, Bruce D.; Clark, David L.; Den Auwer, Christophe J.; Ding, Mei; Dorhout, Peter K.; Espinosa-Faller, Francisco J.; Gordon, Pamela L.; Haire, Richard G.; Hess, Nancy J.; Hess, Ryan F.; Keogh, D. Webster; Morales, Luis A.; Neu, Mary P.; Paviet-Hartmann, Patricia; Runde, Wolfgang; Tait, C DREW; Veirs, D. Kirk; Villella, Phillip M.

    2004-01-01

    Pu L3 X-ray absorption fine structure spectra from 24 samples of PuO 2+x (and two related Pu substituted oxides), prepared by a variety of methods, demonstrate that (1) although the Pu sublattice remains the ordered part of the Pu distribution, the nearest-neighbor O atoms even at x = 0 are found in a multisite distribution with Pu-O distances consistent with the stable incorporation of OH - (and possibly H 2 O and H + ) into the PuO 2 lattice; (2) the excess O from oxidation is found at Pu-O distances 2 + moieties that are aperiodically distributed through the lattice; and (4) the collective interactions between these defect sites most likely cause them to cluster so as give nanoscale heterogeneity in the form of domains that may have unusual reactivity, observed as sequential oxidation by H 2 O at ambient conditions. The most accurate description of PuO 2 is therefore actually PuO 2+x-y (OH) 2y · zH 2 O, with pure, ordered, homogeneous PuO 2 attained only when H 2 O is rigorously excluded and the O activity is relatively low

  8. Broadband photosensor with a tunable frequency range, built on the basis of nanoscale carbon structure with field localization

    Science.gov (United States)

    Yakunin, Alexander N.; Akchurin, Garif G.; Aban'shin, Nikolay P.; Gorfinkel, Boris I.

    2014-03-01

    The work is devoted to the development of a new direction in creating of broadband photo sensors which distinctive feature is the possibility of dynamic adjustment of operating frequency range. The author's results of study of red threshold control of classic photoelectric effect were the basis for the work implementation. This effect was predicted theoretically and observed experimentally during irradiation of nanoscale carbon structure of planar-edge type by stream of low-energy photons. The variation of the accelerating voltage within a small range allows you to change photoelectric threshold for carbon in a wide range - from UV to IR. This is the consequence of the localization of electrostatic field at tip of the blade planar structure and of changes in the conditions of non-equilibrium electrons tunneling from the boundary surface of the cathode into the vacuum. The generation of nonequilibrium electrons in the carbon film thickness of 20 nm has a high speed which provides high performance of photodetector. The features of the use of nanoscale carbon structure photocurrent registration as in the prethreshold regime, and in the mode of field emission existence are discussed. The results of simulation and experimental examination of photosensor samples are given. It is shown that the observed effect is a single-photon tunneling. This in combination with the possibility of highspeed dynamic tuning determines the good perspectives for creation of new devices working in the mode of select multiple operating spectral bands for the signal recording. The architecture of such devices is expected to be significantly simpler than the conventional ones, based on the use of tunable filters.

  9. Quantitative analysis of nanoscale intranuclear structural alterations in hippocampal cells in chronic alcoholism via transmission electron microscopy imaging.

    Science.gov (United States)

    Sahay, Peeyush; Shukla, Pradeep K; Ghimire, Hemendra M; Almabadi, Huda M; Tripathi, Vibha; Mohanty, Samarendra K; Rao, Radhakrishna; Pradhan, Prabhakar

    2017-03-01

    Chronic alcoholism is known to alter the morphology of the hippocampus, an important region of cognitive function in the brain. Therefore, to understand the effect of chronic alcoholism on hippocampal neural cells, we employed a mouse model of chronic alcoholism and quantified intranuclear nanoscale structural alterations in these cells. Transmission electron microscopy (TEM) images of hippocampal neurons were obtained, and the degree of structural alteration in terms of mass density fluctuation was determined using the light-localization properties of optical media generated from TEM imaging. The results, which were obtained at length scales ranging from ~30 to 200 nm, show that 10-12 week-old mice fed a Lieber-DeCarli liquid (alcoholic) diet had a higher degree of structural alteration than control mice fed a normal diet without alcohol. The degree of structural alteration became significantly distinguishable at a sample length of ~100 nm, which is the typical length scale of the building blocks of cells, such as DNA, RNA, proteins and lipids. Interestingly, different degrees of structural alteration at such length scales suggest possible structural rearrangement of chromatin inside the nuclei in chronic alcoholism.

  10. Nanoscale Cu{sub 2}O films: Radio-frequency magnetron sputtering and structural and optical studies

    Energy Technology Data Exchange (ETDEWEB)

    Kudryashov, D. A., E-mail: kudryashovda@apbau.ru; Gudovskikh, A. S. [Russian Academy of Sciences, St. Petersburg National Research Academic University — Nanotechnology Research and Education Center (Russian Federation); Babichev, A. V.; Filimonov, A. V. [Connector Optics LLC (Russian Federation); Mozharov, A. M. [Russian Academy of Sciences, St. Petersburg National Research Academic University — Nanotechnology Research and Education Center (Russian Federation); Agekyan, V. F.; Borisov, E. V.; Serov, A. Yu.; Filosofov, N. G. [St. Petersburg State University (Russian Federation)

    2017-01-15

    Nanoscale copper (I) oxide layers are formed by magnetron-assisted sputtering onto glassy and silicon substrates in an oxygen-free environment at room temperature, and the structural and optical properties of the layers are studied. It is shown that copper oxide formed on a silicon substrate exhibits a lower degree of disorder than that formed on a glassy substrate, which is supported by the observation of a higher intensity and a smaller half-width of reflections in the diffraction pattern. The highest intensity of reflections in the diffraction pattern is observed for Cu{sub 2}O films grown on silicon at a magnetron power of 150 W. The absorption and transmittance spectra of these Cu{sub 2}O films are in agreement with the well-known spectra of bulk crystals. In the Raman spectra of the films, phonons inherent in the crystal lattice of cubic Cu{sub 2}O crystals are identified.

  11. Confinement in F4 Exceptional Gauge Group Using Domain Structures

    Science.gov (United States)

    Rafibakhsh, Shahnoosh; Shahlaei, Amir

    2017-03-01

    We calculate the potential between static quarks in the fundamental representation of the F4 exceptional gauge group using domain structures of the thick center vortex model. As non-trivial center elements are absent, the asymptotic string tension is lost while an intermediate linear potential is observed. SU(2) is a subgroup of F4. Investigating the decomposition of the 26 dimensional representation of F4 to the SU(2) representations, might explain what accounts for the intermediate linear potential, in the exceptional groups with no center element.

  12. Domain structure and magnetotransport in epitaxial colossal magnetoresistance thin films

    OpenAIRE

    Suzuki, Yuri; Wu, Yan; Yu, Jun; Rüdiger, Ulrich; Kent, Andrew D.; Nath, Tapan K.; Eom, Chang-Beom

    2000-01-01

    Our studies of compressively strained La0.7 Sr0.3 MnO7 (LSMO) thin films reveal the importance of domain structure and strain effects in the magnetization reversal and magnetotransport. Normal and grazing incidence x-ray diffraction indicate that the compressive strain on these LSMO thin films on (100) LaAlO3 is not completely relaxed up to thicknesses on the order of 1000 Å. The effect of the compressive strain is evident in the shape of the magnetization loops and the magnetotransport measu...

  13. Shear-stress-induced structural arrangement of water molecules in nanoscale Couette flow with slipping at wall boundary

    International Nuclear Information System (INIS)

    Lin, Jau-Wen

    2014-01-01

    This study investigated the structuring of water molecules in a nanoscale Couette flow with the upper plate subjected to lateral forces with various magnitudes and water slipping against a metal wall. It was found that when the upper plate is subjected to a force, the water body deforms into a parallelepiped. Water molecules in the channel are then gradually arranged into lattice positions, creating a layered structure. The structural arrangement of water molecules is caused by the water molecules accommodating themselves to the increase in energy under the application of a lateral force on the moving plate. The ordering arrangement of water molecules increases the rotational degree of freedom, allowing the molecules to increase their Coulomb potential energy through polar rotation that accounts for the energy input through the upper plate. With a force continuously applied to the upper plate, the water molecules in contact with the upper plate move forward until slip between the water and upper plate occurs. The relation between the structural arrangement of water molecules, slip at the wall, and the shear force is studied. The relation between the slip and the locking/unlocking of water molecules to metal atoms is also studied

  14. Domain shape instabilities and dendrite domain growth in uniaxial ferroelectrics

    Science.gov (United States)

    Shur, Vladimir Ya.; Akhmatkhanov, Andrey R.

    2018-01-01

    The effects of domain wall shape instabilities and the formation of nanodomains in front of moving walls obtained in various uniaxial ferroelectrics are discussed. Special attention is paid to the formation of self-assembled nanoscale and dendrite domain structures under highly non-equilibrium switching conditions. All obtained results are considered in the framework of the unified kinetic approach to domain structure evolution based on the analogy with first-order phase transformation. This article is part of the theme issue `From atomistic interfaces to dendritic patterns'.

  15. Building and Using Object-Oriented Frameworks for Semi-Structures Domains: The Sales Promotion Domain as Example

    NARCIS (Netherlands)

    A. Dalebout; J. van Hillegersberg (Jos); B. Wierenga (Berend)

    1998-01-01

    textabstractObject-oriented (00) frameworks are considered an important step forward in developing software applications efficiently. Success of frameworks has however predominantly been limited to structured domains.This paper describes a method for developing 00 domainframeworks for

  16. Atomic Resolution Imaging of Nanoscale Structural Ordering in a Complex Metal Oxide Catalyst

    KAUST Repository

    Zhu, Yihan; Wang, Qingxiao; Zhao, Lan; Teng, Baiyang; Lu, Weimin; Han, Yu

    2012-01-01

    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

  17. Color centers in KCN: a structural analysis of crystalline domains

    International Nuclear Information System (INIS)

    Carmo, L.C.S. do.

    1976-03-01

    Pure singlecrystals of KCN exposed to X-rays showed several color centers detected by EPR. The F center was identified through the correlation of its optical absorption band which satisfies the Ivey law for the KCN lattice parameter and the EPR spectrum typical of a center in an anionic site. Two other color centers were identified: N - 2 and HCN - . Two centers assigned to hydrogen atoms have their models proposed: U 2 and U 3 centers. Two other centers remain unidentified: an anionic and an extrinsic centers. The orthorhombic character of the N - 2 center EPR parameters allowed an structural analysis of the crystal line domains in the orthorhombic phase. The optical absorption spectrum of the HCN - center in KCl matrix was investigated and showed a set of resolved bands with a constant energy splitting; this splitting was associated to a vibrational mode of the excited state of this molecular ion. (author) [pt

  18. Structural Basis of Actin Filament Nucleation by Tandem W Domains

    Science.gov (United States)

    Chen, Xiaorui; Ni, Fengyun; Tian, Xia; Kondrashkina, Elena; Wang, Qinghua; Ma, Jianpeng

    2013-01-01

    SUMMARY Spontaneous nucleation of actin is very inefficient in cells. To overcome this barrier, cells have evolved a set of actin filament nucleators to promote rapid nucleation and polymerization in response to specific stimuli. However, the molecular mechanism of actin nucleation remains poorly understood. This is hindered largely by the fact that actin nucleus, once formed, rapidly polymerizes into filament, thus making it impossible to capture stable multisubunit actin nucleus. Here, we report an effective double-mutant strategy to stabilize actin nucleus by preventing further polymerization. Employing this strategy, we solved the crystal structure of AMPPNP-actin in complex with the first two tandem W domains of Cordon-bleu (Cobl), a potent actin filament nucleator. Further sequence comparison and functional studies suggest that the nucleation mechanism of Cobl is probably shared by the p53 cofactor JMY, but not Spire. Moreover, the double-mutant strategy opens the way for atomic mechanistic study of actin nucleation and polymerization. PMID:23727244

  19. Analysis and modelling of engineering structures in frequency domain

    International Nuclear Information System (INIS)

    Ishtev, K.; Bonev, Z.; Petrov, P.; Philipov, P.

    1987-01-01

    This paper deals with some possible applications for modelling and analysis of engineering structures, basing on technique, mentioned above. The governing system of equations is written by using frequency domain approach since elemination technique has computational significance in this field. Modelling is made basing on the well known relationship Y(jw) = W(jw) * X(jw). Here X(jw) is a complex Fourier spectra associated with the imput signals being defined as earthquake, wind, hydrodynamic, control or other type of action. W(jw) is a matrix complex transfer function which reveals the correlation between input X und output Y spectra. Y (ja) represents a complex Fourier spectra of output signals. Input and output signals are both associated with master degrees of freedom, thus matrix transfer function is composed of elements in such a manner that solve unknown parameters are implemented implicitly. It is available an integration algorithm of 'condensed' system of equations. (orig./GL)

  20. Bulk magnetic domain structures visualized by neutron dark-field imaging

    International Nuclear Information System (INIS)

    Gruenzweig, C.; David, C.; Bunk, O.; Dierolf, M.; Frei, G.; Kuehne, G.; Schaefer, R.; Pofahl, S.; Roennow, H. M. R.; Pfeiffer, F.

    2008-01-01

    We report on how a neutron grating interferometer can yield projection images of the internal domain structure in bulk ferromagnetic samples. The image contrast relies on the ultrasmall angle scattering of unpolarized neutrons at domain wall structures in the specimen. The results show the basic domains of (110)-oriented sheets in an FeSi test sample. The obtained domain structures could be correlated with surface sensitive magneto-optical Kerr effect micrographs

  1. Bulk magnetic domain structures visualized by neutron dark-field imaging

    Science.gov (United States)

    Grünzweig, C.; David, C.; Bunk, O.; Dierolf, M.; Frei, G.; Kühne, G.; Schäfer, R.; Pofahl, S.; Rønnow, H. M. R.; Pfeiffer, F.

    2008-09-01

    We report on how a neutron grating interferometer can yield projection images of the internal domain structure in bulk ferromagnetic samples. The image contrast relies on the ultrasmall angle scattering of unpolarized neutrons at domain wall structures in the specimen. The results show the basic domains of (110)-oriented sheets in an FeSi test sample. The obtained domain structures could be correlated with surface sensitive magneto-optical Kerr effect micrographs.

  2. Time domain structures in a colliding magnetic flux rope experiment

    Science.gov (United States)

    Tang, Shawn Wenjie; Gekelman, Walter; Dehaas, Timothy; Vincena, Steve; Pribyl, Patrick

    2017-10-01

    Electron phase-space holes, regions of positive potential on the scale of the Debye length, have been observed in auroras as well as in laboratory experiments. These potential structures, also known as Time Domain Structures (TDS), are packets of intense electric field spikes that have significant components parallel to the local magnetic field. In an ongoing investigation at UCLA, TDS were observed on the surface of two magnetized flux ropes produced within the Large Plasma Device (LAPD). A barium oxide (BaO) cathode was used to produce an 18 m long magnetized plasma column and a lanthanum hexaboride (LaB6) source was used to create 11 m long kink unstable flux ropes. Using two probes capable of measuring the local electric and magnetic fields, correlation analysis was performed on tens of thousands of these structures and their propagation velocities, probability distribution function and spatial distribution were determined. The TDS became abundant as the flux ropes collided and appear to emanate from the reconnection region in between them. In addition, a preliminary analysis of the permutation entropy and statistical complexity of the data suggests that the TDS signals may be chaotic in nature. Work done at the Basic Plasma Science Facility (BaPSF) at UCLA which is supported by DOE and NSF.

  3. Structure of the Ebola VP35 interferon inhibitory domain.

    Science.gov (United States)

    Leung, Daisy W; Ginder, Nathaniel D; Fulton, D Bruce; Nix, Jay; Basler, Christopher F; Honzatko, Richard B; Amarasinghe, Gaya K

    2009-01-13

    Ebola viruses (EBOVs) cause rare but highly fatal outbreaks of viral hemorrhagic fever in humans, and approved treatments for these infections are currently lacking. The Ebola VP35 protein is multifunctional, acting as a component of the viral RNA polymerase complex, a viral assembly factor, and an inhibitor of host interferon (IFN) production. Mutation of select basic residues within the C-terminal half of VP35 abrogates its dsRNA-binding activity, impairs VP35-mediated IFN antagonism, and attenuates EBOV growth in vitro and in vivo. Because VP35 contributes to viral escape from host innate immunity and is required for EBOV virulence, understanding the structural basis for VP35 dsRNA binding, which correlates with suppression of IFN activity, is of high importance. Here, we report the structure of the C-terminal VP35 IFN inhibitory domain (IID) solved to a resolution of 1.4 A and show that VP35 IID forms a unique fold. In the structure, we identify 2 basic residue clusters, one of which is important for dsRNA binding. The dsRNA binding cluster is centered on Arg-312, a highly conserved residue required for IFN inhibition. Mutation of residues within this cluster significantly changes the surface electrostatic potential and diminishes dsRNA binding activity. The high-resolution structure and the identification of the conserved dsRNA binding residue cluster provide opportunities for antiviral therapeutic design. Our results suggest a structure-based model for dsRNA-mediated innate immune antagonism by Ebola VP35 and other similarly constructed viral antagonists.

  4. Mapping the structural and dynamical features of kinesin motor domains.

    Directory of Open Access Journals (Sweden)

    Guido Scarabelli

    Full Text Available Kinesin motor proteins drive intracellular transport by coupling ATP hydrolysis to conformational changes that mediate directed movement along microtubules. Characterizing these distinct conformations and their interconversion mechanism is essential to determining an atomic-level model of kinesin action. Here we report a comprehensive principal component analysis of 114 experimental structures along with the results of conventional and accelerated molecular dynamics simulations that together map the structural dynamics of the kinesin motor domain. All experimental structures were found to reside in one of three distinct conformational clusters (ATP-like, ADP-like and Eg5 inhibitor-bound. These groups differ in the orientation of key functional elements, most notably the microtubule binding α4-α5, loop8 subdomain and α2b-β4-β6-β7 motor domain tip. Group membership was found not to correlate with the nature of the bound nucleotide in a given structure. However, groupings were coincident with distinct neck-linker orientations. Accelerated molecular dynamics simulations of ATP, ADP and nucleotide free Eg5 indicate that all three nucleotide states could sample the major crystallographically observed conformations. Differences in the dynamic coupling of distal sites were also evident. In multiple ATP bound simulations, the neck-linker, loop8 and the α4-α5 subdomain display correlated motions that are absent in ADP bound simulations. Further dissection of these couplings provides evidence for a network of dynamic communication between the active site, microtubule-binding interface and neck-linker via loop7 and loop13. Additional simulations indicate that the mutations G325A and G326A in loop13 reduce the flexibility of these regions and disrupt their couplings. Our combined results indicate that the reported ATP and ADP-like conformations of kinesin are intrinsically accessible regardless of nucleotide state and support a model where neck

  5. Crystal structure of the N domain of human somatic angiotensin I-converting enzyme provides a structural basis for domain-specific inhibitor design.

    Science.gov (United States)

    Corradi, Hazel R; Schwager, Sylva L U; Nchinda, Aloysius T; Sturrock, Edward D; Acharya, K Ravi

    2006-03-31

    Human somatic angiotensin I-converting enzyme (sACE) is a key regulator of blood pressure and an important drug target for combating cardiovascular and renal disease. sACE comprises two homologous metallopeptidase domains, N and C, joined by an inter-domain linker. Both domains are capable of cleaving the two hemoregulatory peptides angiotensin I and bradykinin, but differ in their affinities for a range of other substrates and inhibitors. Previously we determined the structure of testis ACE (C domain); here we present the crystal structure of the N domain of sACE (both in the presence and absence of the antihypertensive drug lisinopril) in order to aid the understanding of how these two domains differ in specificity and function. In addition, the structure of most of the inter-domain linker allows us to propose relative domain positions for sACE that may contribute to the domain cooperativity. The structure now provides a platform for the design of "domain-specific" second-generation ACE inhibitors.

  6. Engineering of Nanoscale Antifouling and Hydrophobic Surfaces on Naval Structural Steel HY-80 by Anodizing

    Science.gov (United States)

    2015-06-01

    stainless steel by anodization. The oxide structures produced under these conditions granted the material significant visible light photo catalytic...metallurgically classified as quenched and tempered martensitic steels . They have a martensitic microstructure resulting from the 9 combination of...producing a martensitic structure is carbon. The as-quenched steel manifests high strength and hardness but also is brittle and susceptible to hydrogen

  7. Structural evolution of plasma-sprayed nanoscale 3 mol% and 5 mol% yttria-stabilized zirconia coatings during sintering

    Science.gov (United States)

    Zhao, Yan; Gao, Yang

    2017-12-01

    The microstructure of plasma-sprayed nanostructured yttria-stabilized zirconia (YSZ) coatings may change during high-temperature exposure, which would influence the coating performance and service lifetime. In this study, the phase structure and the microstructural evolution of 3YSZ (zirconia-3 mol% yttria) and 5YSZ (zirconia-5 mol% yttria) nanostructured coatings were investigated by means of sintering at 1400 °C for 50-100 h. The microhardness, elastic moduli, and thermal shock cycles of the 3YSZ and 5YSZ nanostructured coatings were also investigated. The results showed that the redistribution of yttrium ions at 1400 °C caused the continuous increase of monoclinic-phase zirconia, but no obvious inter-splat cracking formed at the cross-sections, even after 100 h. Large voids appeared around the nanoporous zone because of the sintering of nanoscale granules upon high-temperature exposure. The microhardness and elastic moduli of the nanostructured coatings first increased and then decreased with increasing sintering times. The growth rate of the nanograins in the 3YSZ coating was lower than that in 5YSZ, which slowed the changes in 3YSZ coating porosity during sintering. Although the 3YSZ coating was prone to monoclinic phase transition, the experimental results showed that the thermal shock resistance of the 3YSZ coating was better than that of the 5YSZ coating.

  8. Cellular behavior on TiO2 nanonodular structures in a micro-to-nanoscale hierarchy model.

    Science.gov (United States)

    Kubo, Katsutoshi; Tsukimura, Naoki; Iwasa, Fuminori; Ueno, Takeshi; Saruwatari, Lei; Aita, Hideki; Chiou, Wen-An; Ogawa, Takahiro

    2009-10-01

    Biological tissues involve hierarchical organizations of structures and components. We created a micropit-and-nanonodule hybrid topography of TiO(2) by applying a recently reported nanonodular self-assembly technique on acid-etch-created micropit titanium surfaces. The size of the nanonodules was controllable by changing the assembly time. The created micro-nano-hybrid surface rendered a greater surface area and roughness, and extensive geographical undercut on the existing micropit surface and resembled the surface morphology of biomineralized matrices. Rat bone marrow-derived osteoblasts were cultured on titanium disks with either micropits alone, micropits with 100-nm nodules, micropits with 300-nm nodules, or micropits with 500-nm nodules. The addition of nanonodules to micropits selectively promoted osteoblast but not fibroblast function. Unlike the reported advantages of microfeatures that promote osteoblast differentiation but inhibit its proliferation, micro-nano-hybrid topography substantially enhanced both. We also demonstrated that these biological effects were most pronounced when the nanonodules were tailored to a diameter of 300nm within the micropits. An implant biomechanical test in a rat femur model revealed that the strength of bone-titanium integration was more than three times greater for the implants with micropits and 300-nm nanonodules than the implants with micropits alone. These results suggest the establishment of functionalized nano-in-microtitanium surfaces for improved osteoconductivity, and may provide a biomimetic micro-to-nanoscale hierarchical model to study the nanofeatures of biomaterials.

  9. Enhanced osteointegration of medical titanium implant with surface modifications in micro/nanoscale structures

    Directory of Open Access Journals (Sweden)

    Liwen Lin

    2014-01-01

    Full Text Available Biomimetic design and substrate-based surface modification of medical implants will help to improve the integration of tissue to its material interfaces. Surface energy, composition, roughness, and topography all influence the biological responses of the implants, such as protein adsorption and cell adhesion, proliferation and differentiation. In the current study, different surface structures of Ti implants were constructed using facile surface techniques to create various micro-, nano-, and nano/micro composite scale topography. We have fabricated three types of hierarchical structures of TiO2 coating on Ti implants, including nanotube structure, nano sponge-like structure, and nano/micro nest-like structure. The osteointegration and biomechanical performance of the coated Ti screws were evaluated by histology and removal of torque force test in vivo. We found that the nano/micro nest-like and nanotube structured surface possessed better osteointegration ability. It indicated that the alkaline hydrothermally treated Ti substrate was the best for bone-implant integration in terms of all in vitro and in vivo testing parameters. The alkaline hydrothermally treated surface displayed a hydrophilic (contact angle value 5.92 ± 1.2, higher roughness (Ra value 911.3 ± 33.8 nm, higher specific surface area (8.26 ± 1.051 m2/g, and greater apatite inductivity. The electrochemical surface modification may become a powerful approach to enhance metal implant to bone integration in orthopaedic applications.

  10. Investigation of Amyloid Structures at Nanoscale via AFM based Dynamic Nanomechncial Microscopy

    DEFF Research Database (Denmark)

    Zhang, Shuai

    2014-01-01

    Amyloid structures are one important kind of protein aggregations. They are a group of stable misfolded species, other than native states, which have been found to accumulate as plaques on neuron cells. This behavior is considered to associate with tens of human neurodegenerative diseases...... summarized the main methodologies of DNM. I also utilized DNM to explore the path way of amyloid self-assembly, and the substrate effect to the conformation of amyloid structures. Furthermore, 2D peptide based material has also been characterized by DNM....

  11. Facial Image Compression Based on Structured Codebooks in Overcomplete Domain

    Directory of Open Access Journals (Sweden)

    Vila-Forcén JE

    2006-01-01

    Full Text Available We advocate facial image compression technique in the scope of distributed source coding framework. The novelty of the proposed approach is twofold: image compression is considered from the position of source coding with side information and, contrarily to the existing scenarios where the side information is given explicitly; the side information is created based on a deterministic approximation of the local image features. We consider an image in the overcomplete transform domain as a realization of a random source with a structured codebook of symbols where each symbol represents a particular edge shape. Due to the partial availability of the side information at both encoder and decoder, we treat our problem as a modification of the Berger-Flynn-Gray problem and investigate a possible gain over the solutions when side information is either unavailable or available at the decoder. Finally, the paper presents a practical image compression algorithm for facial images based on our concept that demonstrates the superior performance in the very-low-bit-rate regime.

  12. Comparison of structure, function and regulation of plant cold shock domain proteins to bacterial and animal cold shock domain proteins.

    Science.gov (United States)

    Chaikam, Vijay; Karlson, Dale T

    2010-01-01

    The cold shock domain (CSD) is among the most ancient and well conserved nucleic acid binding domains from bacteria to higher animals and plants. The CSD facilitates binding to RNA, ssDNA and dsDNA and most functions attributed to cold shock domain proteins are mediated by this nucleic acid binding activity. In prokaryotes, cold shock domain proteins only contain a single CSD and are termed cold shock proteins (Csps). In animal model systems, various auxiliary domains are present in addition to the CSD and are commonly named Y-box proteins. Similar to animal CSPs, plant CSPs contain auxiliary C-terminal domains in addition to their N-terminal CSD. Cold shock domain proteins have been shown to play important roles in development and stress adaptation in wide variety of organisms. In this review, the structure, function and regulation of plant CSPs are compared and contrasted to the characteristics of bacterial and animal CSPs. [BMB reports 2010; 43(1): 1-8].

  13. The in vivo structure of biological membranes and evidence for lipid domains

    Energy Technology Data Exchange (ETDEWEB)

    Nickels, Jonathan D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States); Chatterjee, Sneha [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Stanley, Christopher B. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Qian, Shuo [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Cheng, Xiaolin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States); Myles, Dean A. A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Standaert, Robert F. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States); Elkins, James G. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States); Katsaras, John [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States); Lopez, Daniel [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)

    2017-05-23

    Examining the fundamental structure and processes of living cells at the nanoscale poses a unique analytical challenge, as cells are dynamic, chemically diverse, and fragile. A case in point is the cell membrane, which is too small to be seen directly with optical microscopy and provides little observational contrast for other methods. As a consequence, nanoscale characterization of the membrane has been performed ex vivo or in the presence of exogenous labels used to enhance contrast and impart specificity. Here, we introduce an isotopic labeling strategy in the gram-positive bacterium Bacillus subtilis to investigate the nanoscale structure and organization of its plasma membrane in vivo. Through genetic and chemical manipulation of the organism, we labeled the cell and its membrane independently with specific amounts of hydrogen (H) and deuterium (D). These isotopes have different neutron scattering properties without altering the chemical composition of the cells. From neutron scattering spectra, we confirmed that the B. subtilis cell membrane is lamellar and determined that its average hydrophobic thickness is 24.3 ± 0.9 Ångstroms (Å). Furthermore, by creating neutron contrast within the plane of the membrane using a mixture of H- and D-fatty acids, we detected lateral features smaller than 40 nm that are consistent with the notion of lipid rafts. These experiments—performed under biologically relevant conditions—answer long-standing questions in membrane biology and illustrate a fundamentally new approach for systematic in vivo investigations of cell membrane structure.

  14. Domain structure in soft ferrites by the longitudinal Kerr effect

    International Nuclear Information System (INIS)

    Kaczmarek, R.; Dautain, M.; Barradi-Ismail, T.

    1992-01-01

    For the first time, the longitudinal Kerr effect has been used in order to observe magnetic domains and their development in power ferrites. Image subtraction and processing leads to a magnetic contrast being a quasi derivative of the domains. A kind of integration procedure applied to them permits a reconstruction of a local hysteresis which parameters closely approach the global hysteresis data. (orig.)

  15. Nanoscale structural heterogeneity in Ni-rich half-Heusler TiNiSn

    International Nuclear Information System (INIS)

    Douglas, Jason E.; Pollock, Tresa M.; Chater, Philip A.; Brown, Craig M.; Seshadri, Ram

    2014-01-01

    The structural implications of excess Ni in the TiNiSn half-Heusler compound are examined through a combination of synchrotron x-ray and neutron scattering studies, in conjunction with first principles density functional theory calculations on supercells. Despite the phase diagram suggesting that TiNiSn is a line compound with no solid solution, for small x in TiNi 1+x Sn there is indeed an appearance—from careful analysis of the scattering—of some solubility, with the excess Ni occupying the interstitial tetrahedral site in the half-Heusler structure. The analysis performed here would point to the excess Ni not being statistically distributed, but rather occurring as coherent nanoclusters. First principles calculations of energetics, carried out using supercells, support a scenario of Ni interstitials clustering, rather than a statistical distribution.

  16. Enhanced osteointegration of medical titanium implant with surface modifications in micro/nanoscale structures

    OpenAIRE

    Lin, Liwen; Wang, Hui; Ni, Ming; Rui, Yunfeng; Cheng, Tian-Yuan; Cheng, Cheng-Kung; Pan, Xiaohua; Li, Gang; Lin, Changjian

    2014-01-01

    Biomimetic design and substrate-based surface modification of medical implants will help to improve the integration of tissue to its material interfaces. Surface energy, composition, roughness, and topography all influence the biological responses of the implants, such as protein adsorption and cell adhesion, proliferation and differentiation. In the current study, different surface structures of Ti implants were constructed using facile surface techniques to create various micro-, nano-, and...

  17. Nanoscale discontinuities at the boundary of flowing liquids: a look into structure

    International Nuclear Information System (INIS)

    Wolff, Max; Gutfreund, Philipp; Zabel, Hartmut; Ruehm, Adrian; Akgun, Bulent

    2011-01-01

    When downsizing technology, confinement and interface effects become enormously important. Shear imposes additional anisotropy on a liquid. This may induce inhomogeneities, which may have their origin close to the solid interface. For advancing the understanding of flow, information on structures on all length scales and in particular close to the solid interface is indispensable. Neutron scattering offers an excellent tool to contribute in this context. In this work, surface sensitive scattering techniques were used to resolve the structure of liquids under flow in the vicinity of a solid interface. Our results are summarized as follows. First, for a Newtonian liquid we report a depletion distance on the order of nanometers which is far too small to explain the amount of surface slip, on the order of micrometers, found by complementary techniques. Second, for a grafted polymer brush we find no entanglement-disentanglement transition under shear but the grafted film gets ripped off the surface. Third, by evaluating the local structure factor of a micellar solution close to the solid interface it turns out that the degree of order and local relaxation depends critically on the surface energy of the solid surface.

  18. Effect of nanoscale flows on the surface structure of nanoporous catalysts.

    Science.gov (United States)

    Montemore, Matthew M; Montessori, Andrea; Succi, Sauro; Barroo, Cédric; Falcucci, Giacomo; Bell, David C; Kaxiras, Efthimios

    2017-06-07

    The surface structure and composition of a multi-component catalyst are critical factors in determining its catalytic performance. The surface composition can depend on the local pressure of the reacting species, leading to the possibility that the flow through a nanoporous catalyst can affect its structure and reactivity. Here, we explore this possibility for oxidation reactions on nanoporous gold, an AgAu bimetallic catalyst. We use microscopy and digital reconstruction to obtain the morphology of a two-dimensional slice of a nanoporous gold sample. Using lattice Boltzmann fluid dynamics simulations along with thermodynamic models based on first-principles total-energy calculations, we show that some sections of this sample have low local O 2 partial pressures when exposed to reaction conditions, which leads to a pure Au surface in these regions, instead of the active bimetallic AgAu phase. We also explore the effect of temperature on the surface structure and find that moderate temperatures (≈300-450 K) should result in the highest intrinsic catalytic performance, in apparent agreement with experimental results.

  19. Strain-controlled magnetic domain wall propagation in hybrid piezoelectric/ferromagnetic structures.

    Science.gov (United States)

    Lei, Na; Devolder, Thibaut; Agnus, Guillaume; Aubert, Pascal; Daniel, Laurent; Kim, Joo-Von; Zhao, Weisheng; Trypiniotis, Theodossis; Cowburn, Russell P; Chappert, Claude; Ravelosona, Dafiné; Lecoeur, Philippe

    2013-01-01

    The control of magnetic order in nanoscale devices underpins many proposals for integrating spintronics concepts into conventional electronics. A key challenge lies in finding an energy-efficient means of control, as power dissipation remains an important factor limiting future miniaturization of integrated circuits. One promising approach involves magnetoelectric coupling in magnetostrictive/piezoelectric systems, where induced strains can bear directly on the magnetic anisotropy. While such processes have been demonstrated in several multiferroic heterostructures, the incorporation of such complex materials into practical geometries has been lacking. Here we demonstrate the possibility of generating sizeable anisotropy changes, through induced strains driven by applied electric fields, in hybrid piezoelectric/spin-valve nanowires. By combining magneto-optical Kerr effect and magnetoresistance measurements, we show that domain wall propagation fields can be doubled under locally applied strains. These results highlight the prospect of constructing low-power domain wall gates for magnetic logic devices.

  20. Structural basis for phosphopantetheinyl carrier domain interactions in the terminal module of nonribosomal peptide synthetases

    Science.gov (United States)

    Liu, Ye; Zheng, Tengfei; Bruner, Steven D.

    2011-01-01

    Summary Phosphopantetheine-modified carrier domains play a central role in the template-directed, biosynthesis of several classes of primary and secondary metabolites. Fatty acids, polyketides and nonribosomal peptides are constructed on multidomain enzyme assemblies using phosphopantetheinyl thioester-linked carrier domains to traffic and activate building blocks. The carrier domain is a dynamic component of the process, shuttling pathway intermediates to sequential enzyme active sites. Here we report an approach to structurally fix carrier domain/enzyme constructs suitable for X-ray crystallographic analysis. The structure of a two-domain construct of E. coli EntF was determined with a conjugated phosphopantetheinyl-based inhibitor. The didomain structure is locked in an active orientation relevant to the chemistry of nonribosomal peptide biosynthesis. This structure provides details into the interaction of phosphopantetheine arm with the carrier domain and the active site of the thioesterase domain. PMID:22118682

  1. Self assembly of amphiphilic C60 fullerene derivatives into nanoscale supramolecular structures

    Directory of Open Access Journals (Sweden)

    Casscells S Ward

    2007-08-01

    Full Text Available Abstract Background The amphiphilic fullerene monomer (AF-1 consists of a "buckyball" cage to which a Newkome-like dendrimer unit and five lipophilic C12 chains positioned octahedrally to the dendrimer unit are attached. In this study, we report a novel fullerene-based liposome termed 'buckysome' that is water soluble and forms stable spherical nanometer sized vesicles. Cryogenic electron microscopy (Cryo-EM, transmission electron microscopy (TEM, and dynamic light scattering (DLS studies were used to characterize the different supra-molecular structures readily formed from the fullerene monomers under varying pH, aqueous solvents, and preparative conditions. Results Electron microscopy results indicate the formation of bilayer membranes with a width of ~6.5 nm, consistent with previously reported molecular dynamics simulations. Cryo-EM indicates the formation of large (400 nm diameter multilamellar, liposome-like vesicles and unilamellar vesicles in the size range of 50–150 nm diameter. In addition, complex networks of cylindrical, tube-like aggregates with varying lengths and packing densities were observed. Under controlled experimental conditions, high concentrations of spherical vesicles could be formed. In vitro results suggest that these supra-molecular structures impose little to no toxicity. Cytotoxicity of 10–200 μM buckysomes were assessed in various cell lines. Ongoing studies are aimed at understanding cellular internalization of these nanoparticle aggregates. Conclusion In this current study, we have designed a core platform based on a novel amphiphilic fullerene nanostructure, which readily assembles into supra-molecular structures. This delivery vector might provide promising features such as ease of preparation, long-term stability and controlled release.

  2. Application of modern tensor calculus to engineered domain structures. 2. Tensor distinction of domain states

    Czech Academy of Sciences Publication Activity Database

    Kopský, Vojtěch

    2006-01-01

    Roč. 62, - (2006), s. 65-76 ISSN 0108-7673 R&D Projects: GA ČR GA202/04/0992 Institutional research plan: CEZ:AV0Z10100520 Keywords : tensorial covariants * domain states * stability spaces Subject RIV: BE - Theoretical Physics Impact factor: 1.676, year: 2006

  3. Structure evolution and magnetic properties of annealed nanoscale Gd/Ti multilayers

    Directory of Open Access Journals (Sweden)

    Larrañaga A.

    2013-01-01

    Full Text Available The structure and magnetic properties were comparatively analyzed for [Gd/Ti]n multilayers with Gd layer thickness of 1.5 to 12 nm. Multilayers were deposited by sputtering technique at room temperature and annealed for the temperatures up to 400 ºC. It was observed that the samples are highly textured in a different way depending on the Gd layer thickness and annealing temperature. It was found that the heat treatment practically does not change the Gd grain size. The lattice parameters obtained from X-ray results change significantly only for [Gd(1.5nm/Ti]50 multilayers, but their values remain higher than for the bulk Gd. The initial slope of the temperature dependence of magnetization near Curie temperature becomes steeper and Curie temperature increases upon annealing. Curie temperature variation can be understood by taking into account both relaxation of the lattice imperfections and change in lattice constants.

  4. Theoretical Methods of Domain Structures in Ultrathin Ferroelectric Films: A Review

    Directory of Open Access Journals (Sweden)

    Jianyi Liu

    2014-09-01

    Full Text Available This review covers methods and recent developments of the theoretical study of domain structures in ultrathin ferroelectric films. The review begins with an introduction to some basic concepts and theories (e.g., polarization and its modern theory, ferroelectric phase transition, domain formation, and finite size effects, etc. that are relevant to the study of domain structures in ultrathin ferroelectric films. Basic techniques and recent progress of a variety of important approaches for domain structure simulation, including first-principles calculation, molecular dynamics, Monte Carlo simulation, effective Hamiltonian approach and phase field modeling, as well as multiscale simulation are then elaborated. For each approach, its important features and relative merits over other approaches for modeling domain structures in ultrathin ferroelectric films are discussed. Finally, we review recent theoretical studies on some important issues of domain structures in ultrathin ferroelectric films, with an emphasis on the effects of interfacial electrostatics, boundary conditions and external loads.

  5. Structure function relations in PDZ-domain-containing proteins ...

    Indian Academy of Sciences (India)

    G P Manjunath

    2017-12-30

    Dec 30, 2017 ... Implications for protein networks in cellular signalling ..... However, surface plasmon resonance .... entiate between conformation changes in the PDZ domain or .... NHERF1, through long-range electrostatic and hydrophobic.

  6. Performance and Structural Evolution of Nano-Scale Infiltrated Solid Oxide Fuel Cell Cathodes

    Science.gov (United States)

    Call, Ann Virginia

    Nano-structured mixed ionic and electronic conducting (MIEC) materials have garnered intense interest in electrode development for solid oxide fuel cells due to their high surface areas which allow for effective catalytic activity and low polarization resistances. In particular, composite solid oxide fuel cell (SOFC) cathodes consisting of ionic conducting scaffolds infiltrated with MIEC nanoparticles have exhibited some of the lowest reported polarization resistances. In order for cells utilizing nanostructured moRPhologies to be viable for commercial implementation, more information on their initial performance and long term stability is necessary. In this study, symmetric cell cathodes were prepared via wet infiltration of Sr0.5Sm 0.5CoO3 (SSC) nano-particles via a nitrate process into porous Ce0.9Gd0.1O1.95 (GDC) scaffolds to be used as a model system to investigate performance and structural evolution. Detailed analysis of the cells and cathodes was carried out using electrochemical impedance spectroscopy (EIS). Initial polarization resistances (RP) as low as 0.11 O cm2 at 600ºC were obtained for these SSC-GDC cathodes, making them an ideal candidate for studying high performance nano-structured electrodes. The present results show that the infiltrated cathode microstructure has a direct impact on the initial performance of the cell. Small initial particle sizes and high infiltration loadings (up to 30 vol% SSC) improved initial RP. A simple microstructure-based electrochemical model successfully explained these trends in RP. Further understanding of electrode performance was gleaned from fitting EIS data gathered under varying temperatures and oxygen partial pressures to equivalent circuit models. Both RQ and Gerischer impedance elements provided good fits to the main response in the EIS data, which was associated with the combination of oxygen surface exchange and oxygen diffusion in the electrode. A gas diffusion response was also observed at relatively

  7. Nanoscale carbon materials from hydrocarbons pyrolysis: Structure, chemical behavior, utilisation for non-aqueous supercapacitors

    International Nuclear Information System (INIS)

    Savilov, Serguei V.; Strokova, Natalia E.; Ivanov, Anton S.; Arkhipova, Ekaterina A.; Desyatov, Andrey V.; Hui, Xia; Aldoshin, Serguei M.; Lunin, Valery V.

    2015-01-01

    Highlights: • N-doped and regular carbon nanomaterials were obtained by pyrolitic technique. • Dynamic vapor sorption of different solvents reveals smaller S BET values. • Steric hindrance and specific chemical interactions are the reasons for this. • Nitrogen doping leads to raise of capacitance and coulombic efficiency with non-aqueous N-containing electrolyte. - Abstract: This work systematically studies adsorption properties of carbon nanomaterials that are synthesized through hydrocarbons that is a powerful technique to fabricate different kinds of carbon materials, e.g., nanotubes, nanoshells, onions, including nitrogen substituted. The adsorption properties of the as-synthesized carbons are achieved by low temperature nitrogen adsorption and organic vapors sorption. Heptane, acetonitrile, water, ethanol, benzene and 1-methylimidazole, which are of great importance for development of supercapacitors, are used as substrates. It is discovered that while nitrogen adsorption reveals a high specific surface area, this parameter for most of organic compounds is rather small depending not only on the size of its molecule but also on chemical interactions for a pair adsorbent–adsorbate. The experimental values of heat of adsorption for carbon and N-substituted structures, when Coulomb cross-coupling of nitrogen atoms in adsorbent and adsorbate takes place, confirms this supposition

  8. Electronic and structural properties of TiB2: Bulk, surface, and nanoscale effects

    International Nuclear Information System (INIS)

    Volonakis, George; Tsetseris, Leonidas; Logothetidis, Stergios

    2011-01-01

    Titanium diboride (TiB 2 ), is a widely used hard material that comprises graphene-like layers of B and intercalated Ti atoms. Here we report the results of extensive first-principles calculations on key properties of bulk TiB 2 , TiB 2 surfaces, and TiB 2 nanocrystals (NCs). The computational approach is first validated based on the agreement between calculated structural and electronic properties of bulk TiB 2 and available experimental and theoretical data. We then obtain the formation energies for several surface cuts and use these values to construct TiB 2 NCs based on the Wulff theorem. Finally, we demonstrate by studying the adsorption of small molecules that hydrogen and oxygen adatoms can be attached through strongly exothermic chemisorption reactions on TiB 2 surfaces. Likewise, water molecules bind on various TiB 2 surfaces and NC facets, with an energetic preference for the latter. The results are relevant to applications that depend on reactivity-related TiB 2 properties, for example resistance to corrosion and interactions with water-based solutions.

  9. Nanoscale carbon materials from hydrocarbons pyrolysis: Structure, chemical behavior, utilisation for non-aqueous supercapacitors

    Energy Technology Data Exchange (ETDEWEB)

    Savilov, Serguei V., E-mail: savilov@chem.msu.ru [Lomonosov Moscow State University, Chemistry Department (Russian Federation); Strokova, Natalia E.; Ivanov, Anton S.; Arkhipova, Ekaterina A. [Lomonosov Moscow State University, Chemistry Department (Russian Federation); Desyatov, Andrey V. [D. Mendeleyev University of Chemical Technology of Russia (Russian Federation); Hui, Xia [Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology (China); Aldoshin, Serguei M. [Lomonosov Moscow State University, Faculty of Fundamental Physical and Chemical Engineering (Russian Federation); Lunin, Valery V. [Lomonosov Moscow State University, Chemistry Department (Russian Federation)

    2015-09-15

    Highlights: • N-doped and regular carbon nanomaterials were obtained by pyrolitic technique. • Dynamic vapor sorption of different solvents reveals smaller S{sub BET} values. • Steric hindrance and specific chemical interactions are the reasons for this. • Nitrogen doping leads to raise of capacitance and coulombic efficiency with non-aqueous N-containing electrolyte. - Abstract: This work systematically studies adsorption properties of carbon nanomaterials that are synthesized through hydrocarbons that is a powerful technique to fabricate different kinds of carbon materials, e.g., nanotubes, nanoshells, onions, including nitrogen substituted. The adsorption properties of the as-synthesized carbons are achieved by low temperature nitrogen adsorption and organic vapors sorption. Heptane, acetonitrile, water, ethanol, benzene and 1-methylimidazole, which are of great importance for development of supercapacitors, are used as substrates. It is discovered that while nitrogen adsorption reveals a high specific surface area, this parameter for most of organic compounds is rather small depending not only on the size of its molecule but also on chemical interactions for a pair adsorbent–adsorbate. The experimental values of heat of adsorption for carbon and N-substituted structures, when Coulomb cross-coupling of nitrogen atoms in adsorbent and adsorbate takes place, confirms this supposition.

  10. Structure of a two-CAP-domain protein from the human hookworm parasite Necator americanus

    Energy Technology Data Exchange (ETDEWEB)

    Asojo, Oluwatoyin A., E-mail: oasojo@unmc.edu [Pathology and Microbiology Department, 986495 Nebraska Medical Center, Omaha, NE 68198-6495 (United States)

    2011-05-01

    The first structure of a two-CAP-domain protein, Na-ASP-1, from the major human hookworm parasite N. americanus refined to a resolution limit of 2.2 Å is presented. Major proteins secreted by the infective larval stage hookworms upon host entry include Ancylostoma secreted proteins (ASPs), which are characterized by one or two CAP (cysteine-rich secretory protein/antigen 5/pathogenesis related-1) domains. The CAP domain has been reported in diverse phylogenetically unrelated proteins, but has no confirmed function. The first structure of a two-CAP-domain protein, Na-ASP-1, from the major human hookworm parasite Necator americanus was refined to a resolution limit of 2.2 Å. The structure was solved by molecular replacement (MR) using Na-ASP-2, a one-CAP-domain ASP, as the search model. The correct MR solution could only be obtained by truncating the polyalanine model of Na-ASP-2 and removing several loops. The structure reveals two CAP domains linked by an extended loop. Overall, the carboxyl-terminal CAP domain is more similar to Na-ASP-2 than to the amino-terminal CAP domain. A large central cavity extends from the amino-terminal CAP domain to the carboxyl-terminal CAP domain, encompassing the putative CAP-binding cavity. The putative CAP-binding cavity is a characteristic cavity in the carboxyl-terminal CAP domain that contains a His and Glu pair. These residues are conserved in all single-CAP-domain proteins, but are absent in the amino-terminal CAP domain. The conserved His residues are oriented such that they appear to be capable of directly coordinating a zinc ion as observed for CAP proteins from reptile venoms. This first structure of a two-CAP-domain ASP can serve as a template for homology modeling of other two-CAP-domain proteins.

  11. Structure of a two-CAP-domain protein from the human hookworm parasite Necator americanus

    International Nuclear Information System (INIS)

    Asojo, Oluwatoyin A.

    2011-01-01

    The first structure of a two-CAP-domain protein, Na-ASP-1, from the major human hookworm parasite N. americanus refined to a resolution limit of 2.2 Å is presented. Major proteins secreted by the infective larval stage hookworms upon host entry include Ancylostoma secreted proteins (ASPs), which are characterized by one or two CAP (cysteine-rich secretory protein/antigen 5/pathogenesis related-1) domains. The CAP domain has been reported in diverse phylogenetically unrelated proteins, but has no confirmed function. The first structure of a two-CAP-domain protein, Na-ASP-1, from the major human hookworm parasite Necator americanus was refined to a resolution limit of 2.2 Å. The structure was solved by molecular replacement (MR) using Na-ASP-2, a one-CAP-domain ASP, as the search model. The correct MR solution could only be obtained by truncating the polyalanine model of Na-ASP-2 and removing several loops. The structure reveals two CAP domains linked by an extended loop. Overall, the carboxyl-terminal CAP domain is more similar to Na-ASP-2 than to the amino-terminal CAP domain. A large central cavity extends from the amino-terminal CAP domain to the carboxyl-terminal CAP domain, encompassing the putative CAP-binding cavity. The putative CAP-binding cavity is a characteristic cavity in the carboxyl-terminal CAP domain that contains a His and Glu pair. These residues are conserved in all single-CAP-domain proteins, but are absent in the amino-terminal CAP domain. The conserved His residues are oriented such that they appear to be capable of directly coordinating a zinc ion as observed for CAP proteins from reptile venoms. This first structure of a two-CAP-domain ASP can serve as a template for homology modeling of other two-CAP-domain proteins

  12. First Principles Modeling of Phonon Heat Conduction in Nanoscale Crystalline Structures

    International Nuclear Information System (INIS)

    Mazumder, Sandip; Li, Ju

    2010-01-01

    of optical phonons, and (2) by developing a suite of numerical algorithms for solution of the BTE for phonons. The suite of numerical algorithms includes Monte Carlo techniques and deterministic techniques based on the Discrete Ordinates Method and the Ballistic-Diffusive approximation of the BTE. These methods were applied to calculation of thermal conductivity of silicon thin films, and to simulate heat conduction in multi-dimensional structures. In addition, thermal transport in silicon nanowires was investigated using two different first principles methods. One was to apply the Green-Kubo formulation to an equilibrium system. The other was to use Non-Equilibrium Molecular Dynamics (NEMD). Results of MD simulations showed that the nanowire cross-sectional shape and size significantly affects the thermal conductivity, as has been found experimentally. In summary, the project clarified the role of various phonon modes - in particular, optical phonon - in non-equilibrium transport in silicon. It laid the foundation for the solution of the BTE in complex three-dimensional structures using deterministic techniques, paving the way for the development of robust numerical tools that could be coupled to existing device simulation tools to enable coupled electro-thermal modeling of practical electronic/optoelectronic devices. Finally, it shed light on why the thermal conductivity of silicon nanowires is so sensitive to its cross-sectional shape.

  13. Structure, microstructure and magnetic properties of electrodeposited Co and Co-Pt in different nanoscale geometries

    Energy Technology Data Exchange (ETDEWEB)

    Khatri, Manvendra Singh

    2010-07-09

    Thin films and nanowires of Co-Pt have been prepared by means of electrodeposition. Composition, structure, microstructure and magnetic properties have been intensively studied using X-ray diffraction, scanning electron microscopy and vibrating sample magnetometry and correlated to the deposition parameters such as electrolyte composition, deposition current and/or potential. Co rich Co-Pt films have been deposited at various current densities. A nearly constant composition of Co{sub 70}Pt{sub 30} was achieved for current densities between 18 and 32 mA/cm{sup 2}. Detailed texture measurements confirmed an increasing fraction of the hexagonal phase with its c-axis aligned perpendicular to the film plane with increasing current density. Accordingly, magnetic properties are strongly affected by the magnetocrystalline anisotropy of the hexagonal phase that competes with the shape anisotropy of the thin film geometry. Co-Pt nanowires have been prepared within alumina templates at different deposition potentials between -0.6 and -0.9 V{sub SCE} changing the composition from nearly pure Pt to Co. The composition Co{sub 80}Pt{sub 20} was observed at a deposition potential of -0.7 V{sub SCE}. Co-Pt nanowires are nanocrystalline in the as-deposited state. Magnetic measurements reveal changing fcc and hcp phase fractions within the wires as the effective anisotropy significantly differs from the expected shape anisotropy for nanowires with high aspect ratio. This change in effective anisotropy is attributed to the preferential alignment of the c-axis of hcp Co-Pt phase perpendicular to the nanowires axis. A promising alternative with much smaller feature sizes is the diblock copolymer template. Electrodeposition of Co and Co-Pt into these templates has been carried out. Inhomogeneities in the template thickness as well as a certain substrate roughness have been identified to be the reasons for inhomogeneous template filling. Thus magnetic properties are dominated by large

  14. The crystal structures of EAP domains from Staphylococcus aureus reveal an unexpected homology to bacterial superantigens.

    Science.gov (United States)

    Geisbrecht, Brian V; Hamaoka, Brent Y; Perman, Benjamin; Zemla, Adam; Leahy, Daniel J

    2005-04-29

    The Eap (extracellular adherence protein) of Staphylococcus aureus functions as a secreted virulence factor by mediating interactions between the bacterial cell surface and several extracellular host proteins. Eap proteins from different Staphylococcal strains consist of four to six tandem repeats of a structurally uncharacterized domain (EAP domain). We have determined the three-dimensional structures of three different EAP domains to 1.8, 2.2, and 1.35 A resolution, respectively. These structures reveal a core fold that is comprised of an alpha-helix lying diagonally across a five-stranded, mixed beta-sheet. Comparison of EAP domains with known structures reveals an unexpected homology with the C-terminal domain of bacterial superantigens. Examination of the structure of the superantigen SEC2 bound to the beta-chain of a T-cell receptor suggests a possible ligand-binding site within the EAP domain (Fields, B. A., Malchiodi, E. L., Li, H., Ysern, X., Stauffacher, C. V., Schlievert, P. M., Karjalainen, K., and Mariuzza, R. (1996) Nature 384, 188-192). These results provide the first structural characterization of EAP domains, relate EAP domains to a large class of bacterial toxins, and will guide the design of future experiments to analyze EAP domain structure/function relationships.

  15. Structure of the thioredoxin-fold domain of human phosducin-like protein 2

    International Nuclear Information System (INIS)

    Lou, Xiaochu; Bao, Rui; Zhou, Cong-Zhao; Chen, Yuxing

    2009-01-01

    The X-ray crystal structure of the Trx-fold domain of hPDCL2 was solved at 2.70 Å resolution and resembled the Trx-fold domain of rat phosducin. Human phosducin-like protein 2 (hPDCL2) has been identified as belonging to subgroup II of the phosducin (Pdc) family. The members of this family share an N-terminal helix domain and a C-terminal thioredoxin-fold (Trx-fold) domain. The X-ray crystal structure of the Trx-fold domain of hPDCL2 was solved at 2.70 Å resolution and resembled the Trx-fold domain of rat phosducin. Comparative structural analysis revealed the structural basis of their putative functional divergence

  16. Structural, electronic, optical and vibrational properties of nanoscale carbons and nanowires: a colloquial review.

    Science.gov (United States)

    Cole, Milton W; Crespi, Vincent H; Dresselhaus, Mildred S; Dresselhaus, Gene; Fischer, John E; Gutierrez, Humberto R; Kojima, K; Mahan, Gerald D; Rao, Apparao M; Sofo, Jorge O; Tachibana, M; Wako, K; Xiong, Qihua

    2010-08-25

    This review addresses the field of nanoscience as viewed through the lens of the scientific career of Peter Eklund, thus with a special focus on nanocarbons and nanowires. Peter brought to his research an intense focus, imagination, tenacity, breadth and ingenuity rarely seen in modern science. His goal was to capture the essential physics of natural phenomena. This attitude also guides our writing: we focus on basic principles, without sacrificing accuracy, while hoping to convey an enthusiasm for the science commensurate with Peter's. The term 'colloquial review' is intended to capture this style of presentation. The diverse phenomena of condensed matter physics involve electrons, phonons and the structures within which excitations reside. The 'nano' regime presents particularly interesting and challenging science. Finite size effects play a key role, exemplified by the discrete electronic and phonon spectra of C(60) and other fullerenes. The beauty of such molecules (as well as nanotubes and graphene) is reflected by the theoretical principles that govern their behavior. As to the challenge, 'nano' requires special care in materials preparation and treatment, since the surface-to-volume ratio is so high; they also often present difficulties of acquiring an experimental signal, since the samples can be quite small. All of the atoms participate in the various phenomena, without any genuinely 'bulk' properties. Peter was a master of overcoming such challenges. The primary activity of Eklund's research was to measure and understand the vibrations of atoms in carbon materials. Raman spectroscopy was very dear to Peter. He published several papers on the theory of phonons (Eklund et al 1995a Carbon 33 959-72, Eklund et al 1995b Thin Solid Films 257 211-32, Eklund et al 1992 J. Phys. Chem. Solids 53 1391-413, Dresselhaus and Eklund 2000 Adv. Phys. 49 705-814) and many more papers on measuring phonons (Pimenta et al 1998b Phys. Rev. B 58 16016-9, Rao et al 1997a Nature

  17. Structural, electronic, optical and vibrational properties of nanoscale carbons and nanowires: a colloquial review

    International Nuclear Information System (INIS)

    Cole, Milton W; Crespi, Vincent H; Dresselhaus, Mildred S; Dresselhaus, Gene; Fischer, John E; Gutierrez, Humberto R; Kojima, K; Wako, K; Mahan, Gerald D; Rao, Apparao M; Sofo, Jorge O; Tachibana, M; Xiong Qihua

    2010-01-01

    This review addresses the field of nanoscience as viewed through the lens of the scientific career of Peter Eklund, thus with a special focus on nanocarbons and nanowires. Peter brought to his research an intense focus, imagination, tenacity, breadth and ingenuity rarely seen in modern science. His goal was to capture the essential physics of natural phenomena. This attitude also guides our writing: we focus on basic principles, without sacrificing accuracy, while hoping to convey an enthusiasm for the science commensurate with Peter's. The term 'colloquial review' is intended to capture this style of presentation. The diverse phenomena of condensed matter physics involve electrons, phonons and the structures within which excitations reside. The 'nano' regime presents particularly interesting and challenging science. Finite size effects play a key role, exemplified by the discrete electronic and phonon spectra of C 60 and other fullerenes. The beauty of such molecules (as well as nanotubes and graphene) is reflected by the theoretical principles that govern their behavior. As to the challenge, 'nano' requires special care in materials preparation and treatment, since the surface-to-volume ratio is so high; they also often present difficulties of acquiring an experimental signal, since the samples can be quite small. All of the atoms participate in the various phenomena, without any genuinely 'bulk' properties. Peter was a master of overcoming such challenges. The primary activity of Eklund's research was to measure and understand the vibrations of atoms in carbon materials. Raman spectroscopy was very dear to Peter. He published several papers on the theory of phonons (Eklund et al 1995a Carbon 33 959-72, Eklund et al 1995b Thin Solid Films 257 211-32, Eklund et al 1992 J. Phys. Chem. Solids 53 1391-413, Dresselhaus and Eklund 2000 Adv. Phys. 49 705-814) and many more papers on measuring phonons (Pimenta et al 1998b Phys. Rev. B 58 16016-9, Rao et al 1997a Nature

  18. Surface potential domains on lamellar P3OT structures

    Energy Technology Data Exchange (ETDEWEB)

    Perez-GarcIa, B [Departamento Fisica, Facultad de Quimica (Campus Espinardo), Universidad de Murcia, E-30100 Murcia (Spain); Abad, J [Departamento Fisica, Facultad de Quimica (Campus Espinardo), Universidad de Murcia, E-30100 Murcia (Spain); Urbina, A [Departamento Electronica, TecnologIa de Computadoras y Proyectos, Universidad Politecnica de Cartagena, E-30202 Cartagena (Spain); Colchero, J [Departamento Fisica, Facultad de Quimica (Campus Espinardo), Universidad de Murcia, E-30100 Murcia (Spain); Palacios-Lidon, E [Departamento Fisica, Facultad de Quimica (Campus Espinardo), Universidad de Murcia, E-30100 Murcia (Spain)

    2008-02-13

    In this work the electrostatic properties of poly(3-octylthiophene) thin films have been studied on a nanometer scale by means of electrostatic force microscopy and Kelvin probe microscopy (KPM). The KPM images reveal that different surface contact potential domains coexist on the polymer surface. This result, together with additional capacitance measurements, indicates that the potential domains are related to the existence of dipoles due to different molecular arrangements. Finally, capacitance measurements as a function of the tip-sample bias voltage show that in all regions large band bending effects take place.

  19. Surface potential domains on lamellar P3OT structures

    International Nuclear Information System (INIS)

    Perez-GarcIa, B; Abad, J; Urbina, A; Colchero, J; Palacios-Lidon, E

    2008-01-01

    In this work the electrostatic properties of poly(3-octylthiophene) thin films have been studied on a nanometer scale by means of electrostatic force microscopy and Kelvin probe microscopy (KPM). The KPM images reveal that different surface contact potential domains coexist on the polymer surface. This result, together with additional capacitance measurements, indicates that the potential domains are related to the existence of dipoles due to different molecular arrangements. Finally, capacitance measurements as a function of the tip-sample bias voltage show that in all regions large band bending effects take place

  20. Individual domain wall resistance in submicron ferromagnetic structures.

    Science.gov (United States)

    Danneau, R; Warin, P; Attané, J P; Petej, I; Beigné, C; Fermon, C; Klein, O; Marty, A; Ott, F; Samson, Y; Viret, M

    2002-04-15

    The resistance generated by individual domain walls is measured in a FePd nanostructure. Combining transport and magnetic imaging measurements, the intrinsic domain wall resistance is quantified. It is found positive and of a magnitude consistent with that predicted by models based on spin scattering effects within the walls. This magnetoresistance at a nanometer scale allows a direct counting of the number of walls inside the nanostructure. The effect is then used to measure changes in the magnetic configuration of submicron stripes under application of a magnetic field.

  1. Nanoscale characterization of local structures and defects in photonic crystals using synchrotron-based transmission soft X-ray microscopy

    Science.gov (United States)

    Nho, Hyun Woo; Kalegowda, Yogesh; Shin, Hyun-Joon; Yoon, Tae Hyun

    2016-01-01

    For the structural characterization of the polystyrene (PS)-based photonic crystals (PCs), fast and direct imaging capabilities of full field transmission X-ray microscopy (TXM) were demonstrated at soft X-ray energy. PS-based PCs were prepared on an O2-plasma treated Si3N4 window and their local structures and defects were investigated using this label-free TXM technique with an image acquisition speed of ~10 sec/frame and marginal radiation damage. Micro-domains of face-centered cubic (FCC (111)) and hexagonal close-packed (HCP (0001)) structures were dominantly found in PS-based PCs, while point and line defects, FCC (100), and 12-fold symmetry structures were also identified as minor components. Additionally, in situ observation capability for hydrated samples and 3D tomographic reconstruction of TXM images were also demonstrated. This soft X-ray full field TXM technique with faster image acquisition speed, in situ observation, and 3D tomography capability can be complementally used with the other X-ray microscopic techniques (i.e., scanning transmission X-ray microscopy, STXM) as well as conventional characterization methods (e.g., electron microscopic and optical/fluorescence microscopic techniques) for clearer structure identification of self-assembled PCs and better understanding of the relationship between their structures and resultant optical properties. PMID:27087141

  2. Structure determination of human Lck unique and SH3 domains by nuclear magnetic resonance spectroscopy

    Directory of Open Access Journals (Sweden)

    Willbold Dieter

    2003-05-01

    Full Text Available Abstract Background Protein tyrosine kinases are involved in signal transduction pathways that regulate cell growth, differentiation, activation and transformation. Human lymphocyte specific kinase (Lck is a 56 kDa protein involved in T-cell- and IL2-receptor signaling. Three-dimensional structures are known for SH3, SH2 and kinase domains of Lck as well as for other tyrosine kinases. No structure is known for the unique domain of any Src-type tyrosine kinase. Results Lck(1–120 comprising unique and SH3 domains was structurally investigated by nuclear magnetic resonance spectroscopy. We found the unique domain, in contrast to the SH3 part, to have basically no defined structural elements. The solution structure of the SH3 part could be determined with very high precision. It does not show significant differences to Lck SH3 in the absence of the unique domain. Minor differences were observed to the X-ray structure of Lck SH3. Conclusion The unique domain of Lck does not contain any defined structure elements in the absence of ligands and membranes. Presence of the unique domain is not relevant to the three-dimensional structure of the Lck SH3 domain.

  3. Dynamic Analysis of Partially Embedded Structures Considering Soil-Structure Interaction in Time Domain

    Directory of Open Access Journals (Sweden)

    Sanaz Mahmoudpour

    2011-01-01

    Full Text Available Analysis and design of structures subjected to arbitrary dynamic loadings especially earthquakes have been studied during past decades. In practice, the effects of soil-structure interaction on the dynamic response of structures are usually neglected. In this study, the effect of soil-structure interaction on the dynamic response of structures has been examined. The substructure method using dynamic stiffness of soil is used to analyze soil-structure system. A coupled model based on finite element method and scaled boundary finite element method is applied. Finite element method is used to analyze the structure, and scaled boundary finite element method is applied in the analysis of unbounded soil region. Due to analytical solution in the radial direction, the radiation condition is satisfied exactly. The material behavior of soil and structure is assumed to be linear. The soil region is considered as a homogeneous half-space. The analysis is performed in time domain. A computer program is prepared to analyze the soil-structure system. Comparing the results with those in literature shows the exactness and competency of the proposed method.

  4. Structural rearrangement of the intracellular domains during AMPA receptor activation

    DEFF Research Database (Denmark)

    Zachariassen, Linda Grønborg; Katchan, Ljudmila; Jensen, Anna Guldvang

    2016-01-01

    -clamp fluorometry of the double- and single-insert constructs showed that both the intracellular C-terminal domain (CTD) and the loop region between the M1 and M2 helices move during activation and the CTD is detached from the membrane. Our time-resolved measurements revealed unexpectedly complex fluorescence...

  5. Inference of domain structure at elevated temperature in fine ...

    African Journals Online (AJOL)

    The thermal variation of the number of domains (nd) for Fe7S8 particles (within the size range 1-30 mm and between 20 and 300°C), has been inferred from the room temperature analytic expression between nd and particle size (L), the temperature dependences of the anisotropy energy constant (K) and the spontaneous ...

  6. Broadening microwave absorption via a multi-domain structure

    Directory of Open Access Journals (Sweden)

    Zhengwang Liu

    2017-04-01

    Full Text Available Materials with a high saturation magnetization have gained increasing attention in the field of microwave absorption; therefore, the magnetization value depends on the magnetic configuration inside them. However, the broad-band absorption in the range of microwave frequency (2-18 GHz is a great challenge. Herein, the three-dimensional (3D Fe/C hollow microspheres are constructed by iron nanocrystals permeating inside carbon matrix with a saturation magnetization of 340 emu/g, which is 1.55 times as that of bulk Fe, unexpectedly. Electron tomography, electron holography, and Lorentz transmission electron microscopy imaging provide the powerful testimony about Fe/C interpenetration and multi-domain state constructed by vortex and stripe domains. Benefiting from the unique chemical and magnetic microstructures, the microwave minimum absorption is as strong as −55 dB and the bandwidth (<−10 dB spans 12.5 GHz ranging from 5.5 to 18 GHz. Morphology and distribution of magnetic nano-domains can be facilely regulated by a controllable reduction sintering under H2/Ar gas and an optimized temperature over 450–850 °C. The findings might shed new light on the synthesis strategies of the materials with the broad-band frequency and understanding the association between multi-domain coupling and microwave absorption performance.

  7. Purification of SOCS (Suppressor of Cytokine Signaling) SH2 Domains for Structural and Functional Studies.

    Science.gov (United States)

    Liau, Nicholas P D; Laktyushin, Artem; Babon, Jeffrey J

    2017-01-01

    Src Homology 2 (SH2) domains are protein domains which have a high binding affinity for specific amino acid sequences containing a phosphorylated tyrosine residue. The Suppressors of Cytokine Signaling (SOCS) proteins use an SH2 domain to bind to components of certain cytokine signaling pathways to downregulate the signaling cascade. The recombinantly produced SH2 domains of various SOCS proteins have been used to undertake structural and functional studies elucidating the method of how such targeting occurs. Here, we describe the protocol for the recombinant production and purification of SOCS SH2 domains, with an emphasis on SOCS3.

  8. The Nanoscale Observation of the Three-Dimensional Structures of Neurosynapses, Membranous Conjunctions Between Cultured Hippocampal Neurons and Their Significance in the Development of Epilepsy.

    Science.gov (United States)

    Sun, Lan; Jiang, Shuang; Tang, Xianhua; Zhang, Yingge; Qin, Luye; Jiang, Xia; Yu, Albert Cheung Hoi

    2016-12-01

    The nanoscale three-dimensional structures of neurosynapses are unknown, and the neuroanatomical basis of epilepsy remains to be elucidated. Here, we studied the nanoscale three-dimensional synapses between hippocampal neurons, and membranous conjunctions between neurons were found with atomic force microscopy (AFM) and confirmed by transmission electron microscope (TEM), and their pathophysiological significance was primarily investigated. The neurons and dendrites were marked by MAP-2, axons by neurofilament 200, and synapses by synapsin I immunological staining. In the synapsin I-positive neurite ends of the neurons positively stained with MAP-2 and neurofilament 200, neurosynapses with various nanoscale morphology and structure could be found by AFM. The neurosynapses had typical three-dimensional structures of synaptic triplet including the presynaptic neurite end, synaptic cleft of 30 ∼ 40 in chemical synapses and 2 ∼ 6 nm in electrical ones, the postsynaptic neurite or dendrite spine, the typical neurite end button, the distinct pre- and postsynaptic membranes, and the obvious thickening of the postsynaptic membranes or neurites. Some membranous connections including membrane-like junctions (MLJ) and fiber-tube links (FTL) without triplet structures and cleft were found between neurons. The development frequencies of the two membranous conjunctions increased while those of the synaptic conjunctions decreased between the neurons from Otx1 knock-out mice in comparison with those between the neurons from normal mice. These results suggested that the neuroanatomical basis of Otx1 knock-out epilepsy is the combination of the decreased synaptic conjunctions and the increased membranous conjunctions.

  9. Adapting Bayes Network Structures to Non-stationary Domains

    DEFF Research Database (Denmark)

    Nielsen, Søren Holbech; Nielsen, Thomas Dyhre

    2008-01-01

    When an incremental structural learning method gradually modifies a Bayesian network (BN) structure to fit a sequential stream of observations, we call the process structural adaptation. Structural adaptation is useful when the learner is set to work in an unknown environment, where a BN is gradu...

  10. Heat transfer across the interface between nanoscale solids and gas.

    Science.gov (United States)

    Cheng, Chun; Fan, Wen; Cao, Jinbo; Ryu, Sang-Gil; Ji, Jie; Grigoropoulos, Costas P; Wu, Junqiao

    2011-12-27

    When solid materials and devices scale down in size, heat transfer from the active region to the gas environment becomes increasingly significant. We show that the heat transfer coefficient across the solid-gas interface behaves very differently when the size of the solid is reduced to the nanoscale, such as that of a single nanowire. Unlike for macroscopic solids, the coefficient is strongly pressure dependent above ∼10 Torr, and at lower pressures it is much higher than predictions of the kinetic gas theory. The heat transfer coefficient was measured between a single, free-standing VO(2) nanowire and surrounding air using laser thermography, where the temperature distribution along the VO(2) nanowire was determined by imaging its domain structure of metal-insulator phase transition. The one-dimensional domain structure along the nanowire results from the balance between heat generation by the focused laser and heat dissipation to the substrate as well as to the surrounding gas, and thus serves as a nanoscale power-meter and thermometer. We quantified the heat loss rate across the nanowire-air interface, and found that it dominates over all other heat dissipation channels for small-diameter nanowires near ambient pressure. As the heat transfer across the solid-gas interface is nearly independent of the chemical identity of the solid, the results reveal a general scaling relationship for gaseous heat dissipation from nanostructures of all solid materials, which is applicable to nanoscale electronic and thermal devices exposed to gaseous environments.

  11. Magnetic domain structure of MnAs thin films as a function of temperature

    International Nuclear Information System (INIS)

    Mizuguchi, Masaki; Manago, Takashi; Akinaga, Hiroyuki; Kuramochi, Hiromi; Okabayashi, Jun

    2003-01-01

    We have investigate magnetic domain structures of MnAs thin films grown on GaAs substrates by a magnetic force microscope. We observed, by an atomic force microscope, rectangular defects along GaAs [110] direction which disperse randomly on the surface of MnAs/GaAs(001). The Curie temperature of MnAs is 45degC, and it is successfully confirmed directly by the variable temperature magnetic force microscope observation. We also investigated magnetic domain structures of MnAs/GaAs(111)B, and no apparent relation was observed between the topographic structure and the magnetic domain structure. (author)

  12. Photoinduced domain structures in monocrystalline films of yttrium-iron garnets

    International Nuclear Information System (INIS)

    Doroshenko, R.A.; Vladimirov, I.V.; Setchenkov, M.S.

    1988-01-01

    Results of investigating the domain structure in Y 3 Fe 5 O 12 epitaxial films under polarized light effect are presented. The domain structure was observed using Faraday effect at 80 K, crystallographic directions were determined by X-ray method. The sample structure is shown to consist of macrodomains, which parallel boundaries are oriented on (011), (110), (101) and are reoriented under the light effect, therewith easiest magnetization axes are brought about perpendicular to vector E of the affecting light. When explaining such changes in domain structure elastic stresses and induced anisotropy of elastic nature must be taken accout of

  13. Ferromagnetic domain structures and spin configurations measured in doped manganite

    DEFF Research Database (Denmark)

    He, J.Q.; Volkov, V.V.; Beleggia, Marco

    2010-01-01

    We report on measurements of the spin configuration across ferromagnetic domains in La0.325Pr0.3Ca0.375MnO3 films obtained by means of low-temperature Lorentz electron microscopy with in situ magnetizing capabilities. Due to the particular crystal symmetry of the material, we observe two sets of ...... and the crystal symmetry might affect the magnetoresistivity under an applied magnetic field in a strongly correlated electron system....

  14. CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures.

    Directory of Open Access Journals (Sweden)

    Oliver C Redfern

    2007-11-01

    Full Text Available We present CATHEDRAL, an iterative protocol for determining the location of previously observed protein folds in novel multidomain protein structures. CATHEDRAL builds on the features of a fast secondary-structure-based method (using graph theory to locate known folds within a multidomain context and a residue-based, double-dynamic programming algorithm, which is used to align members of the target fold groups against the query protein structure to identify the closest relative and assign domain boundaries. To increase the fidelity of the assignments, a support vector machine is used to provide an optimal scoring scheme. Once a domain is verified, it is excised, and the search protocol is repeated in an iterative fashion until all recognisable domains have been identified. We have performed an initial benchmark of CATHEDRAL against other publicly available structure comparison methods using a consensus dataset of domains derived from the CATH and SCOP domain classifications. CATHEDRAL shows superior performance in fold recognition and alignment accuracy when compared with many equivalent methods. If a novel multidomain structure contains a known fold, CATHEDRAL will locate it in 90% of cases, with <1% false positives. For nearly 80% of assigned domains in a manually validated test set, the boundaries were correctly delineated within a tolerance of ten residues. For the remaining cases, previously classified domains were very remotely related to the query chain so that embellishments to the core of the fold caused significant differences in domain sizes and manual refinement of the boundaries was necessary. To put this performance in context, a well-established sequence method based on hidden Markov models was only able to detect 65% of domains, with 33% of the subsequent boundaries assigned within ten residues. Since, on average, 50% of newly determined protein structures contain more than one domain unit, and typically 90% or more of these

  15. Solution structure of the Grb2 SH2 domain complexed with a high-affinity inhibitor

    International Nuclear Information System (INIS)

    Ogura, Kenji; Shiga, Takanori; Yokochi, Masashi; Yuzawa, Satoru; Burke, Terrence R.; Inagaki, Fuyuhiko

    2008-01-01

    The solution structure of the growth factor receptor-bound protein 2 (Grb2) SH2 domain complexed with a high-affinity inhibitor containing a non-phosphorus phosphate mimetic within a macrocyclic platform was determined by nuclear magnetic resonance (NMR) spectroscopy. Unambiguous assignments of the bound inhibitor and intermolecular NOEs between the Grb2 SH2 domain and the inhibitor was accomplished using perdeuterated Grb2 SH2 protein. The well-defined solution structure of the complex was obtained and compared to those by X-ray crystallography. Since the crystal structure of the Grb2 SH2 domain formed a domain-swapped dimer and several inhibitors were bound to a hinge region, there were appreciable differences between the solution and crystal structures. Based on the binding interactions between the inhibitor and the Grb2 SH2 domain in solution, we proposed a design of second-generation inhibitors that could be expected to have higher affinity

  16. Structure and Dynamics of the tRNA-like Structure Domain of Brome Mosaic Virus

    Science.gov (United States)

    Vieweger, Mario; Nesbitt, David

    2014-03-01

    Conformational switching is widely accepted as regulatory mechanism in gene expression in bacterial systems. More recently, similar regulation mechanisms are emerging for viral systems. One of the most abundant and best studied systems is the tRNA-like structure domain that is found in a number of plant viruses across eight genera. In this work, the folding dynamics of the tRNA-like structure domain of Brome Mosaic Virus are investigated using single-molecule Fluorescence Resonance Energy Transfer techniques. In particular, Burst fluorescence is applied to observe metal-ion induced folding in freely diffusing RNA constructs resembling the 3'-terminal 169nt of BMV RNA3. Histograms of EFRET probabilities reveal a complex equilibrium of three distinct populations. A step-wise kinetic model for TLS folding is developed in accord with the evolution of conformational populations and structural information in the literature. In this mechanism, formation of functional TLS domains from unfolded RNAs requires two consecutive steps; 1) hybridization of a long-range stem interaction followed by 2) formation of a 3' pseudoknot. This three-state equilibrium is well described by step-wise dissociation constants K1(328(30) μM) and K2(1092(183) μM) for [Mg2+] and K1(74(6) mM) and K2(243(52) mM) for [Na+]-induced folding. The kinetic model is validated by oligo competition with the STEM interaction. Implications of this conformational folding mechanism are discussed in regards to regulation of virus replication.

  17. A structural analysis of the AAA+ domains in Saccharomyces cerevisiae cytoplasmic dynein.

    Science.gov (United States)

    Gleave, Emma S; Schmidt, Helgo; Carter, Andrew P

    2014-06-01

    Dyneins are large protein complexes that act as microtubule based molecular motors. The dynein heavy chain contains a motor domain which is a member of the AAA+ protein family (ATPases Associated with diverse cellular Activities). Proteins of the AAA+ family show a diverse range of functionalities, but share a related core AAA+ domain, which often assembles into hexameric rings. Dynein is unusual because it has all six AAA+ domains linked together, in one long polypeptide. The dynein motor domain generates movement by coupling ATP driven conformational changes in the AAA+ ring to the swing of a motile element called the linker. Dynein binds to its microtubule track via a long antiparallel coiled-coil stalk that emanates from the AAA+ ring. Recently the first high resolution structures of the dynein motor domain were published. Here we provide a detailed structural analysis of the six AAA+ domains using our Saccharomycescerevisiae crystal structure. We describe how structural similarities in the dynein AAA+ domains suggest they share a common evolutionary origin. We analyse how the different AAA+ domains have diverged from each other. We discuss how this is related to the function of dynein as a motor protein and how the AAA+ domains of dynein compare to those of other AAA+ proteins. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  18. Structure of the C-terminal heme-binding domain of THAP domain containing protein 4 from Homo sapiens

    Energy Technology Data Exchange (ETDEWEB)

    Bianchetti, Christopher M.; Bingman, Craig A.; Phillips, Jr., George N. (UW)

    2012-03-15

    The thanatos (the Greek god of death)-associated protein (THAP) domain is a sequence-specific DNA-binding domain that contains a C2-CH (Cys-Xaa{sub 2-4}-Cys-Xaa{sub 35-50}-Cys-Xaa{sub 2}-His) zinc finger that is similar to the DNA domain of the P element transposase from Drosophila. THAP-containing proteins have been observed in the proteome of humans, pigs, cows, chickens, zebrafish, Drosophila, C. elegans, and Xenopus. To date, there are no known THAP domain proteins in plants, yeast, or bacteria. There are 12 identified human THAP domain-containing proteins (THAP0-11). In all human THAP protein, the THAP domain is located at the N-terminus and is {approx}90 residues in length. Although all of the human THAP-containing proteins have a homologous N-terminus, there is extensive variation in both the predicted structure and length of the remaining protein. Even though the exact function of these THAP proteins is not well defined, there is evidence that they play a role in cell proliferation, apoptosis, cell cycle modulation, chromatin modification, and transcriptional regulation. THAP-containing proteins have also been implicated in a number of human disease states including heart disease, neurological defects, and several types of cancers. Human THAP4 is a 577-residue protein of unknown function that is proposed to bind DNA in a sequence-specific manner similar to THAP1 and has been found to be upregulated in response to heat shock. THAP4 is expressed in a relatively uniform manner in a broad range of tissues and appears to be upregulated in lymphoma cells and highly expressed in heart cells. The C-terminal domain of THAP4 (residues 415-577), designated here as cTHAP4, is evolutionarily conserved and is observed in all known THAP4 orthologs. Several single-domain proteins lacking a THAP domain are found in plants and bacteria and show significant levels of homology to cTHAP4. It appears that cTHAP4 belongs to a large class of proteins that have yet to be fully

  19. Structure of Concatenated HAMP Domains Provides a Mechanism for Signal Transduction

    Energy Technology Data Exchange (ETDEWEB)

    Airola, Michael V.; Watts, Kylie J.; Bilwes, Alexandrine M.; Crane, Brian R. (Cornell); (Lorma Linda U)

    2010-08-23

    HAMP domains are widespread prokaryotic signaling modules found as single domains or poly-HAMP chains in both transmembrane and soluble proteins. The crystal structure of a three-unit poly-HAMP chain from the Pseudomonas aeruginosa soluble receptor Aer2 defines a universal parallel four-helix bundle architecture for diverse HAMP domains. Two contiguous domains integrate to form a concatenated di-HAMP structure. The three HAMP domains display two distinct conformations that differ by changes in helical register, crossing angle, and rotation. These conformations are stabilized by different subsets of conserved residues. Known signals delivered to HAMP would be expected to switch the relative stability of the two conformations and the position of a coiled-coil phase stutter at the junction with downstream helices. We propose that the two conformations represent opposing HAMP signaling states and suggest a signaling mechanism whereby HAMP domains interconvert between the two states, which alternate down a poly-HAMP chain.

  20. C-terminal domains of bacterial proteases: structure, function and the biotechnological applications.

    Science.gov (United States)

    Huang, J; Wu, C; Liu, D; Yang, X; Wu, R; Zhang, J; Ma, C; He, H

    2017-01-01

    C-terminal domains widely exist in the C-terminal region of multidomain proteases. As a β-sandwich domain in multidomain protease, the C-terminal domain plays an important role in proteolysis including regulation of the secretory process, anchoring and swelling the substrate molecule, presenting as an inhibitor for the preprotease and adapting the protein structural flexibility and stability. In this review, the diversity, structural characteristics and biological function of C-terminal protease domains are described. Furthermore, the application prospects of C-terminal domains, including polycystic kidney disease, prepeptidase C-terminal and collagen-binding domain, in the area of medicine and biological artificial materials are also discussed. © 2016 The Society for Applied Microbiology.

  1. Functional Properties at Domain Walls in BiFeO3: Electrical, Magnetic, and Structural investigations

    Science.gov (United States)

    He, Qing; Yang, C.-H.; Yu, P.; Gajek, M.; Seidel, J.; Ramesh, R.; Wang, F.; Chu, Y.-H.; Martin, L. W.; Spaldin, N.; Rother, A.

    2009-03-01

    BiFeO3 (BFO) is a widely studied robust ferroelectric, antiferromagnetic multiferroic. Conducting-atomic force microscopy studies reveal the presence of enhanced conductivity at certain types of domain walls in BFO. We have completed detailed TEM studies of the physical structure at these domain walls as well as in-depth DFT calculations of the evolution of electronic structure at these domain walls. These studies reveal two major contributions to the observed conduction: the formation of an electrostatic potential at the domain walls as well as a structurally-driven change in the electronic structure (i.e., a lower band gap locally) at the domain walls. We will discuss the use of optical characterization techniques as a way of probing this change in electronic structure at domain walls as well as detailed IV characterization both in atmospheric and UHV environments. Finally, the evolution of magnetism at these domain walls has been studied through the use of photoemission measurements. Initial findings point to a significant change in the magnetic order at these domain walls in BFO.

  2. Ferroelectric and ferroelastic domain structures in piezoelectric ceramics

    International Nuclear Information System (INIS)

    Bursill, L.A.; Julin Peng.

    1990-01-01

    A discussion of the results of conventional and high-resolution high-voltage electron microscopic studies of two ferroelectrics, barium sodium niobate and lead zirconium titanate is presented. It is shown that a rich variety of information such as ferroelectric and/or ferroelastic domains discommensurations versus antiphase boundaries, extended versus localized chemical defects and multiphase versus grain boundaries, become accessible in both single crystal and polycrystalline piezoelectrics, when a combination of high-resolution and conventional electron optical techniques is used. 15 refs., 8 figs

  3. Structural-Functional Analysis Reveals a Specific Domain Organization in Family GH20 Hexosaminidases.

    Science.gov (United States)

    Val-Cid, Cristina; Biarnés, Xevi; Faijes, Magda; Planas, Antoni

    2015-01-01

    Hexosaminidases are involved in important biological processes catalyzing the hydrolysis of N-acetyl-hexosaminyl residues in glycosaminoglycans and glycoconjugates. The GH20 enzymes present diverse domain organizations for which we propose two minimal model architectures: Model A containing at least a non-catalytic GH20b domain and the catalytic one (GH20) always accompanied with an extra α-helix (GH20b-GH20-α), and Model B with only the catalytic GH20 domain. The large Bifidobacterium bifidum lacto-N-biosidase was used as a model protein to evaluate the minimal functional unit due to its interest and structural complexity. By expressing different truncated forms of this enzyme, we show that Model A architectures cannot be reduced to Model B. In particular, there are two structural requirements general to GH20 enzymes with Model A architecture. First, the non-catalytic domain GH20b at the N-terminus of the catalytic GH20 domain is required for expression and seems to stabilize it. Second, the substrate-binding cavity at the GH20 domain always involves a remote element provided by a long loop from the catalytic domain itself or, when this loop is short, by an element from another domain of the multidomain structure or from the dimeric partner. Particularly, the lacto-N-biosidase requires GH20b and the lectin-like domain at the N- and C-termini of the catalytic GH20 domain to be fully soluble and functional. The lectin domain provides this remote element to the active site. We demonstrate restoration of activity of the inactive GH20b-GH20-α construct (model A architecture) by a complementation assay with the lectin-like domain. The engineering of minimal functional units of multidomain GH20 enzymes must consider these structural requirements.

  4. Magnetic domain structure and domain-wall energy in UFe8Ni2Si2 and UFe6Ni4Si2 intermetallic compounds

    International Nuclear Information System (INIS)

    Wyslocki, J.J.; Suski, W.; Wochowski, K.

    1994-01-01

    Magnetic domain structures in the UFe 8 Ni 2 Si 2 and UFe 6 Ni 4 Si 2 compounds were studied using the powder pattern method. The domain structure observed is typical for uniaxial materials. The domain-wall energy density γ was determined from the average surface domain width D s observed on surfaces perpendicular to the easy axis as equal to 16 erg/cm 2 for UFe 8 Ni 2 Si 2 and 10 erg/cm 2 for UFe 6 Ni 4 Si 2 . Moreover, the critical diameter for single domain particle D c was calculated for the studied compounds

  5. Structural basis of antifreeze activity of a bacterial multi-domain antifreeze protein.

    Directory of Open Access Journals (Sweden)

    Chen Wang

    Full Text Available Antifreeze proteins (AFPs enhance the survival of organisms inhabiting cold environments by affecting the formation and/or structure of ice. We report the crystal structure of the first multi-domain AFP that has been characterized. The two ice binding domains are structurally similar. Each consists of an irregular β-helix with a triangular cross-section and a long α-helix that runs parallel on one side of the β-helix. Both domains are stabilized by hydrophobic interactions. A flat plane on the same face of each domain's β-helix was identified as the ice binding site. Mutating any of the smaller residues on the ice binding site to bulkier ones decreased the antifreeze activity. The bulky side chain of Leu174 in domain A sterically hinders the binding of water molecules to the protein backbone, partially explaining why antifreeze activity by domain A is inferior to that of domain B. Our data provide a molecular basis for understanding differences in antifreeze activity between the two domains of this protein and general insight on how structural differences in the ice-binding sites affect the activity of AFPs.

  6. A structural role for the PHP domain in E. coli DNA polymerase III.

    Science.gov (United States)

    Barros, Tiago; Guenther, Joel; Kelch, Brian; Anaya, Jordan; Prabhakar, Arjun; O'Donnell, Mike; Kuriyan, John; Lamers, Meindert H

    2013-05-14

    In addition to the core catalytic machinery, bacterial replicative DNA polymerases contain a Polymerase and Histidinol Phosphatase (PHP) domain whose function is not entirely understood. The PHP domains of some bacterial replicases are active metal-dependent nucleases that may play a role in proofreading. In E. coli DNA polymerase III, however, the PHP domain has lost several metal-coordinating residues and is likely to be catalytically inactive. Genomic searches show that the loss of metal-coordinating residues in polymerase PHP domains is likely to have coevolved with the presence of a separate proofreading exonuclease that works with the polymerase. Although the E. coli Pol III PHP domain has lost metal-coordinating residues, the structure of the domain has been conserved to a remarkable degree when compared to that of metal-binding PHP domains. This is demonstrated by our ability to restore metal binding with only three point mutations, as confirmed by the metal-bound crystal structure of this mutant determined at 2.9 Å resolution. We also show that Pol III, a large multi-domain protein, unfolds cooperatively and that mutations in the degenerate metal-binding site of the PHP domain decrease the overall stability of Pol III and reduce its activity. While the presence of a PHP domain in replicative bacterial polymerases is strictly conserved, its ability to coordinate metals and to perform proofreading exonuclease activity is not, suggesting additional non-enzymatic roles for the domain. Our results show that the PHP domain is a major structural element in Pol III and its integrity modulates both the stability and activity of the polymerase.

  7. Terahertz Time Domain Spectroscopy for Structure-II Gas Hydrates

    DEFF Research Database (Denmark)

    Takeya, Kei; Zhang, Caihong; Kawayama, Iwao

    2009-01-01

    For the nondestructive inspection of gas hydrates, terahertz (THz) time-domain spectroscopy (TDS) was applied to tetrahydrofuran (THF) hydrate and propane hydrate. The absorption of propane hydrate monotonically increases with frequency, similar to the case of ice, while THF hydrate has...... a characteristic broad absorption peak at 0.5 THz corresponding to the dipole moment of THF molecules. The refractive indices of THF and propane hydrates are 1.725 and 1.775 at 1 THz, respectively, and show a slight but clear difference from the refractive index of ice (1.79). THz-TDS is a potentially useful...... technique for the ondestructive inspection of gas hydrates. # 2009 The Japan Society of Applied Physics...

  8. Structure discrimination for the C-terminal domain of Escherichia coli trigger factor in solution

    International Nuclear Information System (INIS)

    Yao Yong; Bhabha, Gira; Kroon, Gerard; Landes, Mindy; Dyson, H. Jane

    2008-01-01

    NMR measurements can give important information on solution structure, without the necessity for a full-scale solution structure determination. The C-terminal protein binding domain of the ribosome-associated chaperone protein trigger factor is composed of non-contiguous parts of the polypeptide chain, with an interpolated prolyl isomerase domain. A construct of the C-terminal domain of Escherichia coli trigger factor containing residues 113-149 and 247-432, joined by a Gly-Ser-Gly-Ser linker, is well folded and gives excellent NMR spectra in solution. We have used NMR measurements on this construct, and on a longer construct that includes the prolyl isomerase domain, to distinguish between two possible structures for the C-terminal domain of trigger factor, and to assess the behavior of the trigger factor C-terminal domain in solution. Two X-ray crystal structures, of intact trigger factor from E. coli (Ferbitz et al., Nature 431:590-596, 2004), and of a truncated trigger factor from Vibrio cholerae (Ludlam et al., Proc Natl Acad Sci USA 101:13436-13441, 2004) showed significant differences in the structure of the C-terminal domain, such that the two structures could not be superimposed. We show using NMR chemical shifts and long range nuclear Overhauser effects that the secondary and tertiary structure of the E. coli C-terminal domain in solution is consistent with the crystal structure of the E. coli trigger factor and not with the V. cholerae protein. Given the similarity of the amino acid sequences of the E. coli and V. cholerae proteins, it appears likely that the structure of the V. cholerae protein has been distorted as a result of truncation of a 44-amino acid segment at the C-terminus. Analysis of residual dipolar coupling measurements shows that the overall topology of the solution structure is completely inconsistent with both structures. Dynamics analysis of the C-terminal domain using T 1 , T 2 and heteronuclear NOE parameters show that the protein is

  9. Radiation-damage-assisted ferroelectric domain structuring in magnesium-doped lithium niobate

    Science.gov (United States)

    Jentjens, L.; Peithmann, K.; Maier, K.; Steigerwald, H.; Jungk, T.

    2009-06-01

    Irradiation of 5% magnesium-doped lithium niobate crystals (LiNbO3:Mg) with high-energy, low-mass 3He ions, which are transmitted through the crystal, changes the domain reversal properties of the material. This enables easier domain engineering compared to non-irradiated material and assists the formation of small-sized periodically poled domains in LiNbO3:Mg. Periodic domain structures exhibiting a width of ≈520 nm are obtained in radiation-damaged sections of the crystals. The ferroelectric poling behavior between irradiated and non-treated material is compared.

  10. Structure and function of the TIR domain from the grape NLR protein RPV1

    Directory of Open Access Journals (Sweden)

    Simon John Williams

    2016-12-01

    Full Text Available The N-terminal Toll/interleukin-1 receptor/resistance protein (TIR domain has been shown to be both necessary and sufficient for defence signalling in the model plants flax and Arabidopsis. In examples from these organisms, TIR domain self-association is required for signalling function, albeit through distinct interfaces. Here, we investigate these properties in the TIR domain containing resistance protein RPV1 from the wild grapevine Muscadinia rotundifolia. The RPV1 TIR domain, without additional flanking sequence present, is autoactive when transiently expressed in tobacco, demonstrating that the TIR domain alone is capable of cell-death signalling. We determined the crystal structure of the RPV1 TIR domain at 2.3 Å resolution. In the crystals, the RPV1 TIR domain forms a dimer, mediated predominantly through residues in the αA and αE helices (AE interface. This interface is shared with the interface discovered in the dimeric complex of the TIR domains from the Arabidopsis RPS4/RRS1 resistance protein pair. We show that surface-exposed residues in the AE interface that mediate the dimer interaction in the crystals are highly conserved among plant TIR domain-containing proteins. While we were unable to demonstrate self-association of the RPV1 TIR domain in solution or using yeast 2-hybrid, mutations of surface-exposed residues in the AE interface prevent the cell-death autoactive phenotype. In addition, mutation of residues known to be important in the cell-death signalling function of the flax L6 TIR domain were also shown to be required for RPV1 TIR domain mediated cell-death. Our data demonstrate that multiple TIR domain surfaces control the cell-death function of the RPV1 TIR domain and we suggest that the conserved AE interface may have a general function in TIR-NLR signalling.

  11. Structure of the GH1 domain of guanylate kinase-associated protein from Rattus norvegicus

    International Nuclear Information System (INIS)

    Tong, Junsen; Yang, Huiseon; Eom, Soo Hyun; Chun, ChangJu; Im, Young Jun

    2014-01-01

    Graphical abstract: - Highlights: • The crystal structure of GKAP homology domain 1 (GH1) was determined. • GKAP GH1 is a three-helix bundle connected by short flexible loops. • The predicted helix α4 associates weakly with the helix α3, suggesting dynamic nature of the GH1 domain. - Abstract: Guanylate-kinase-associated protein (GKAP) is a scaffolding protein that links NMDA receptor-PSD-95 to Shank–Homer complexes by protein–protein interactions at the synaptic junction. GKAP family proteins are characterized by the presence of a C-terminal conserved GKAP homology domain 1 (GH1) of unknown structure and function. In this study, crystal structure of the GH1 domain of GKAP from Rattus norvegicus was determined in fusion with an N-terminal maltose-binding protein at 2.0 Å resolution. The structure of GKAP GH1 displays a three-helix bundle connected by short flexible loops. The predicted helix α4 which was not visible in the crystal structure associates weakly with the helix α3 suggesting dynamic nature of the GH1 domain. The strict conservation of GH1 domain across GKAP family members and the lack of a catalytic active site required for enzyme activity imply that the GH1 domain might serve as a protein–protein interaction module for the synaptic protein clustering

  12. Structure of the GH1 domain of guanylate kinase-associated protein from Rattus norvegicus

    Energy Technology Data Exchange (ETDEWEB)

    Tong, Junsen; Yang, Huiseon [College of Pharmacy, Chonnam National University, Gwangju 500-757 (Korea, Republic of); Eom, Soo Hyun [School of Life Sciences, Steitz Center for Structural Biology, and Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 500-712 (Korea, Republic of); Chun, ChangJu, E-mail: cchun1130@jnu.ac.kr [College of Pharmacy, Chonnam National University, Gwangju 500-757 (Korea, Republic of); Im, Young Jun, E-mail: imyoungjun@jnu.ac.kr [College of Pharmacy, Chonnam National University, Gwangju 500-757 (Korea, Republic of)

    2014-09-12

    Graphical abstract: - Highlights: • The crystal structure of GKAP homology domain 1 (GH1) was determined. • GKAP GH1 is a three-helix bundle connected by short flexible loops. • The predicted helix α4 associates weakly with the helix α3, suggesting dynamic nature of the GH1 domain. - Abstract: Guanylate-kinase-associated protein (GKAP) is a scaffolding protein that links NMDA receptor-PSD-95 to Shank–Homer complexes by protein–protein interactions at the synaptic junction. GKAP family proteins are characterized by the presence of a C-terminal conserved GKAP homology domain 1 (GH1) of unknown structure and function. In this study, crystal structure of the GH1 domain of GKAP from Rattus norvegicus was determined in fusion with an N-terminal maltose-binding protein at 2.0 Å resolution. The structure of GKAP GH1 displays a three-helix bundle connected by short flexible loops. The predicted helix α4 which was not visible in the crystal structure associates weakly with the helix α3 suggesting dynamic nature of the GH1 domain. The strict conservation of GH1 domain across GKAP family members and the lack of a catalytic active site required for enzyme activity imply that the GH1 domain might serve as a protein–protein interaction module for the synaptic protein clustering.

  13. Spin-dependent hot electron transport and nano-scale magnetic imaging of metal/Si structures

    International Nuclear Information System (INIS)

    Kaidatzis, A.

    2008-10-01

    In this work, we experimentally study spin-dependent hot electron transport through metallic multilayers (ML), containing single magnetic layers or 'spin-valve' (SV) tri layers. For this purpose, we have set up a ballistic electron emission microscope (BEEM), a three terminal extension of scanning tunnelling microscopy on metal/semiconductor structures. The implementation of the BEEM requirements into the sample fabrication is described in detail. Using BEEM, the hot electron transmission through the ML's was systematically measured in the energy range 1-2 eV above the Fermi level. By varying the magnetic layer thickness, the spin-dependent hot electron attenuation lengths were deduced. For the materials studied (Co and NiFe), they were compared to calculations and other determinations in the literature. For sub-monolayer thickness, a non uniform morphology was observed, with large transmission variations over sub-nano-metric distances. This effect is not yet fully understood. In the imaging mode, the magnetic configurations of SV's were studied under field, focusing on 360 degrees domain walls in Co layers. The effects of the applied field intensity and direction on the DW structure were studied. The results were compared quantitatively to micro-magnetic calculations, with an excellent agreement. From this, it can be shown that the BEEM magnetic resolution is better than 50 nm. (author)

  14. Wake force computation in the time domain for long structures

    International Nuclear Information System (INIS)

    Bane, K.; Weiland, T.

    1983-07-01

    One is often interested in calculating the wake potentials for short bunches in long structures using TBCI. For ultra-relativistic particles it is sufficient to solve for the fields only over a window containing the bunch and moving along with it. This technique reduces both the memory and the running time required by a factor that equals the ratio of the structure length to the window length. For example, for a bunch with sigma/sub z/ of one picosecond traversing a single SLAC cell this improvement factor is 15. It is thus possible to solve for the wakefields in very long structures: for a given problem, increasing the structure length will not change the memory required while only adding linearly to the CPU time needed

  15. An Optimized Table-Top Small-Angle X-ray Scattering Set-up for the Nanoscale Structural Analysis of Soft Matter

    KAUST Repository

    Sibillano, T.; De Caro, L.; Altamura, D.; Siliqi, D.; Ramella, M.; Boccafoschi, F.; Ciasca, G.; Campi, G.; Tirinato, Luca; Di Fabrizio, Enzo M.; Giannini, C.

    2014-01-01

    The paper shows how a table top superbright microfocus laboratory X-ray source and an innovative restoring-data algorithm, used in combination, allow to analyze the super molecular structure of soft matter by means of Small Angle X-ray Scattering ex-situ experiments. The proposed theoretical approach is aimed to restore diffraction features from SAXS profiles collected from low scattering biomaterials or soft tissues, and therefore to deal with extremely noisy diffraction SAXS profiles/maps. As biological test cases we inspected: i) residues of exosomes' drops from healthy epithelial colon cell line and colorectal cancer cells; ii) collagen/human elastin artificial scaffolds developed for vascular tissue engineering applications; iii) apoferritin protein in solution. Our results show how this combination can provide morphological/structural nanoscale information to characterize new artificial biomaterials and/or to get insight into the transition between healthy and pathological tissues during the progression of a disease, or to morphologically characterize nanoscale proteins, based on SAXS data collected in a room-sized laboratory.

  16. An Optimized Table-Top Small-Angle X-ray Scattering Set-up for the Nanoscale Structural Analysis of Soft Matter

    KAUST Repository

    Sibillano, T.

    2014-11-10

    The paper shows how a table top superbright microfocus laboratory X-ray source and an innovative restoring-data algorithm, used in combination, allow to analyze the super molecular structure of soft matter by means of Small Angle X-ray Scattering ex-situ experiments. The proposed theoretical approach is aimed to restore diffraction features from SAXS profiles collected from low scattering biomaterials or soft tissues, and therefore to deal with extremely noisy diffraction SAXS profiles/maps. As biological test cases we inspected: i) residues of exosomes\\' drops from healthy epithelial colon cell line and colorectal cancer cells; ii) collagen/human elastin artificial scaffolds developed for vascular tissue engineering applications; iii) apoferritin protein in solution. Our results show how this combination can provide morphological/structural nanoscale information to characterize new artificial biomaterials and/or to get insight into the transition between healthy and pathological tissues during the progression of a disease, or to morphologically characterize nanoscale proteins, based on SAXS data collected in a room-sized laboratory.

  17. An Optimized Table-Top Small-Angle X-ray Scattering Set-up for the Nanoscale Structural Analysis of Soft Matter

    Science.gov (United States)

    Sibillano, T.; de Caro, L.; Altamura, D.; Siliqi, D.; Ramella, M.; Boccafoschi, F.; Ciasca, G.; Campi, G.; Tirinato, L.; di Fabrizio, E.; Giannini, C.

    2014-11-01

    The paper shows how a table top superbright microfocus laboratory X-ray source and an innovative restoring-data algorithm, used in combination, allow to analyze the super molecular structure of soft matter by means of Small Angle X-ray Scattering ex-situ experiments. The proposed theoretical approach is aimed to restore diffraction features from SAXS profiles collected from low scattering biomaterials or soft tissues, and therefore to deal with extremely noisy diffraction SAXS profiles/maps. As biological test cases we inspected: i) residues of exosomes' drops from healthy epithelial colon cell line and colorectal cancer cells; ii) collagen/human elastin artificial scaffolds developed for vascular tissue engineering applications; iii) apoferritin protein in solution. Our results show how this combination can provide morphological/structural nanoscale information to characterize new artificial biomaterials and/or to get insight into the transition between healthy and pathological tissues during the progression of a disease, or to morphologically characterize nanoscale proteins, based on SAXS data collected in a room-sized laboratory.

  18. The structure of the nucleoprotein binding domain of lyssavirus phosphoprotein reveals a structural relationship between the N-RNA binding domains of Rhabdoviridae and Paramyxoviridae.

    Science.gov (United States)

    Delmas, Olivier; Assenberg, Rene; Grimes, Jonathan M; Bourhy, Hervé

    2010-01-01

    The phosphoprotein P of non-segmented negative-sense RNA viruses is an essential component of the replication and transcription complex and acts as a co-factor for the viral RNA-dependent RNA polymerase. P recruits the viral polymerase to the nucleoprotein-bound viral RNA (N-RNA) via an interaction between its C-terminal domain and the N-RNA complex. We have obtained the structure of the C-terminal domain of P of Mokola virus (MOKV), a lyssavirus that belongs to the Rhabdoviridae family and mapped at the amino acid level the crucial positions involved in interaction with N and in the formation of the viral replication complex. Comparison of the N-RNA binding domains of P solved to date suggests that the N-RNA binding domains are structurally conserved among paramyxoviruses and rhabdoviruses in spite of low sequence conservation. We also review the numerous other functions of this domain and more generally of the phosphoprotein.

  19. Structural Studies of the SET Domain from RIZ1 Tumor Suppressor

    Energy Technology Data Exchange (ETDEWEB)

    Briknarova, Klara; Zhou, Xinliang; Satterthwait, Arnold C.; Hoyt, David W.; Ely, Kathryn R.; Huang, Shi

    2008-02-15

    Histone lysine methyltransferases (HKMTs) are involved in regulation of chromatin structure, and, as such, are important for longterm gene activation and repression that is associated with cell memory and establishment of cell-type specific transcriptional programs. Most HKMTs contain a SET domain, which is responsible for their catalytic activity. RIZ1 is a transcription regulator and tumor suppressor that catalyzes methylation of lysine 9 of histone H3 and contains a rather distinct SET domain. Similar SET domains, sometimes refererred to as PR (PRDI-BF1 and RIZ1 homology) domains, are also found in other proteins including Blimp-1/PRDI-BF1, MDS1-EVI1 and Meisetz. We determined the solution structure of the PR domain from RIZ1 and characterized its interaction with S-adenosyl homocysteine (SAH) and a peptide from histone H3. Despite low sequence identity with canonical SET domains, the PR domain displays a typical SET fold including a pseudo-knot at the C-terminus. The N-flanking sequence of RIZ1 PR domain adopts a novel conformation and interacts closely with the SET fold. The C-flanking sequence contains an α-helix that exhibits higher mobility than the SET fold and points away from the protein face that harbors active site in other SET domains. Residues that interact with the methylation cofactor in SET domains are not conserved in RIZ1 or other PR domains, and the SET fold of RIZ1 does not bind SAH. However, the PR domain of RIZ1 interacts specifically with a synthetic peptide comprising residues 1-20 of histone H3.

  20. Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain

    DEFF Research Database (Denmark)

    Sükösd, Zsuzsanna; Andersen, Ebbe Sloth; Seemann, Ernst Stefan

    2015-01-01

    of the HIV-1 genome is highly variable in most regions, with a limited number of stable and conserved RNA secondary structures. Most interesting, a set of long distance interactions form a core organizing structure (COS) that organize the genome into three major structural domains. Despite overlapping...

  1. Solution structure of the dimeric cytoplasmic domain of syndecan-4

    DEFF Research Database (Denmark)

    Shin, J; Lee, W; Lee, D

    2001-01-01

    The syndecans, transmembrane proteoglycans which are involved in the organization of cytoskeleton and/or actin microfilaments, have important roles as cell surface receptors during cell-cell and/or cell-matrix interactions. Since previous studies indicate that the function of the syndecan-4...... between peptides at physiological pH. Commensurately, the NMR structures demonstrate that syndecan-4L is a compact intertwined dimer with a symmetric clamp shape in the central variable V region with a root-mean-square deviation between backbone atom coordinates of 0.95 A for residues Leu(186)-Ala(195...... in the center of the dimeric twist similar to our previously reported 4V structure. The overall topology of the central variable region within the 4L structure is very similar to that of 4V complexed with the phosphatidylinositol 4,5-bisphosphate; however, the intersubunit interaction mode is affected...

  2. Changing the cubic ferrimagnetic domain structure in temperature region of spin flip transition

    International Nuclear Information System (INIS)

    Djuraev, D.R.; Niyazov, L.N.; Saidov, K.S.; Sokolov, B.Yu.

    2011-01-01

    The transformation of cubic ferrimagnetic Tb 0.2 Y 2.8 Fe 5 O 12 domain structure has been studied by magneto optic method in the temperature region of spontaneous spin flip phase transition (SPT). It has been found that SPT occurs in a finite temperature interval where the coexistence of low- and high- temperature magnetic phase domains has observed. A character of domain structure evolution in temperature region of spin flip essentially depends on the presence of mechanical stresses in crystal. Interpretation of experimental results has been carried out within the framework of SPT theory for a cubic crystal. (authors)

  3. A model for the magnetic domain structure of Gd at 77K

    International Nuclear Information System (INIS)

    Corner, W.D.; Saad, F.M.; Jones, D.W.; Jordan, R.G.

    1978-01-01

    Magnetic domain structures have been observed on planes perpendicular to the c and b axes of Gd crystals at 77K. Various types of domain boundary which might be found in an easy-cone ferromagnet are discussed. A model is presented which is consistent with observations. In this the easy-cone structure is maintained, but it is assumed that owing to the lower basal-plane anisotropy the magnetization component in the basal plane may change in direction within a single domain. (author)

  4. Structure of Pseudoknot PK26 Shows 3D Domain Swapping in an RNA

    Science.gov (United States)

    Lietzke, Susan E; Barnes, Cindy L.

    1998-01-01

    3D domain swapping provides a facile pathway for the evolution of oligomeric proteins and allosteric mechanisms and a means for using monomer-oligomer equilibria to regulate biological activity. The term "3D domain swapping" describes the exchange of identical domains between two protein monomers to create an oligomer. 3D domain swapping has, so far, only been recognized in proteins. In this study, the structure of the pseudoknot PK26 is reported and it is a clear example of 3D domain swapping in RNA. PK26 was chosen for study because RNA pseudoknots are required structures in several biological processes and they arise frequently in in vitro selection experiments directed against protein targets. PK26 specifically inhibits HIV-1 reverse transcriptase with nanomolar affinity. We have now determined the 3.1 A resolution crystal structure of PK26 and find that it forms a 3D domain swapped dimer. PK26 shows extensive base pairing between and within strands. Formation of the dimer requires the linker region between the pseudoknot folds to adopt a unique conformation that allows a base within a helical stem to skip one base in the stacking register. Rearrangement of the linker would permit a monomeric pseudoknot to form. This structure shows how RNA can use 3D domain swapping to build large scale oligomers like the putative hexamer in the packaging RNA of bacteriophage Phi29.

  5. Structural Modification and Self-Assembly of Nanoscale Magnetite Synthesised in the Presence of an Anionic Surfactant

    Directory of Open Access Journals (Sweden)

    Malik S.

    2014-07-01

    Full Text Available The earliest reported medical use of magnetite powder for internal applications was in the 10th century A.D. by the Persian physician and philosopher Avicenna of Bokhara [1,2]. Today magnetic nanoparticles are used for magnetic resonance imaging (MRI and are potential colloidal mediators for cancer magnetic hyperthermia [3]. Twenty years ago magnetite (Fe3O4 was found to be present in the human brain [4] and more recently it has been reported that nanoscale biogenic magnetite (origin and formation uncertain is associated with neurodegenerative diseases such as Parkinson’s, Huntington’s and Alzheimer’s [5]. Here we show that the synthesis of magnetite in the presence of the surfactant sodium dodecyl sulphate (SDS gives rise to a variety of nanoscale morphologies, some of which look remarkably similar to magnetite found in organisms, suggesting that similar processes may be involved. Furthermore, these 1D materials with diameters of quantum confined size are of interest in the areas of biosensors [6] and biomedical imaging [7].

  6. Confirming the Revised C-Terminal Domain of the MscL Crystal Structure

    OpenAIRE

    Maurer, Joshua A.; Elmore, Donald E.; Clayton, Daniel; Xiong, Li; Lester, Henry A.; Dougherty, Dennis A.

    2008-01-01

    The structure of the C-terminal domain of the mechanosensitive channel of large conductance (MscL) has generated significant controversy. As a result, several structures have been proposed for this region: the original crystal structure (1MSL) of the Mycobacterium tuberculosis homolog (Tb), a model of the Escherichia coli homolog, and, most recently, a revised crystal structure of Tb-MscL (2OAR). To understand which of these structures represents a physiological conformation, we measured the ...

  7. A New Method for Determining Structure Ensemble: Application to a RNA Binding Di-Domain Protein.

    Science.gov (United States)

    Liu, Wei; Zhang, Jingfeng; Fan, Jing-Song; Tria, Giancarlo; Grüber, Gerhard; Yang, Daiwen

    2016-05-10

    Structure ensemble determination is the basis of understanding the structure-function relationship of a multidomain protein with weak domain-domain interactions. Paramagnetic relaxation enhancement has been proven a powerful tool in the study of structure ensembles, but there exist a number of challenges such as spin-label flexibility, domain dynamics, and overfitting. Here we propose a new (to our knowledge) method to describe structure ensembles using a minimal number of conformers. In this method, individual domains are considered rigid; the position of each spin-label conformer and the structure of each protein conformer are defined by three and six orthogonal parameters, respectively. First, the spin-label ensemble is determined by optimizing the positions and populations of spin-label conformers against intradomain paramagnetic relaxation enhancements with a genetic algorithm. Subsequently, the protein structure ensemble is optimized using a more efficient genetic algorithm-based approach and an overfitting indicator, both of which were established in this work. The method was validated using a reference ensemble with a set of conformers whose populations and structures are known. This method was also applied to study the structure ensemble of the tandem di-domain of a poly (U) binding protein. The determined ensemble was supported by small-angle x-ray scattering and nuclear magnetic resonance relaxation data. The ensemble obtained suggests an induced fit mechanism for recognition of target RNA by the protein. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  8. Structure of the C-terminal domain of lettuce necrotic yellows virus phosphoprotein.

    Science.gov (United States)

    Martinez, Nicolas; Ribeiro, Euripedes A; Leyrat, Cédric; Tarbouriech, Nicolas; Ruigrok, Rob W H; Jamin, Marc

    2013-09-01

    Lettuce necrotic yellows virus (LNYV) is a prototype of the plant-adapted cytorhabdoviruses. Through a meta-prediction of disorder, we localized a folded C-terminal domain in the amino acid sequence of its phosphoprotein. This domain consists of an autonomous folding unit that is monomeric in solution. Its structure, solved by X-ray crystallography, reveals a lollipop-shaped structure comprising five helices. The structure is different from that of the corresponding domains of other Rhabdoviridae, Filoviridae, and Paramyxovirinae; only the overall topology of the polypeptide chain seems to be conserved, suggesting that this domain evolved under weak selective pressure and varied in size by the acquisition or loss of functional modules.

  9. Structure of the C-Terminal Domain of Lettuce Necrotic Yellows Virus Phosphoprotein

    Science.gov (United States)

    Martinez, Nicolas; Ribeiro, Euripedes A.; Leyrat, Cédric; Tarbouriech, Nicolas; Ruigrok, Rob W. H.

    2013-01-01

    Lettuce necrotic yellows virus (LNYV) is a prototype of the plant-adapted cytorhabdoviruses. Through a meta-prediction of disorder, we localized a folded C-terminal domain in the amino acid sequence of its phosphoprotein. This domain consists of an autonomous folding unit that is monomeric in solution. Its structure, solved by X-ray crystallography, reveals a lollipop-shaped structure comprising five helices. The structure is different from that of the corresponding domains of other Rhabdoviridae, Filoviridae, and Paramyxovirinae; only the overall topology of the polypeptide chain seems to be conserved, suggesting that this domain evolved under weak selective pressure and varied in size by the acquisition or loss of functional modules. PMID:23785215

  10. Structural insights into FRS2α PTB domain recognition by neurotrophin receptor TrkB.

    Science.gov (United States)

    Zeng, Lei; Kuti, Miklos; Mujtaba, Shiraz; Zhou, Ming-Ming

    2014-07-01

    The fibroblast growth factor receptor (FGFR) substrate 2 (FRS2) family proteins function as scaffolding adapters for receptor tyrosine kinases (RTKs). The FRS2α proteins interact with RTKs through the phosphotyrosine-binding (PTB) domain and transfer signals from the activated receptors to downstream effector proteins. Here, we report the nuclear magnetic resonance structure of the FRS2α PTB domain bound to phosphorylated TrkB. The structure reveals that the FRS2α-PTB domain is comprised of two distinct but adjacent pockets for its mutually exclusive interaction with either nonphosphorylated juxtamembrane region of the FGFR, or tyrosine phosphorylated peptides TrkA and TrkB. The new structural insights suggest rational design of selective small molecules through targeting of the two conjunct pockets in the FRS2α PTB domain. © 2014 Wiley Periodicals, Inc.

  11. In situ observations of crack arrest and bridging by nanoscale twins in copper thin films

    International Nuclear Information System (INIS)

    Kim, Seong-Woong; Li Xiaoyan; Gao Huajian; Kumar, Sharvan

    2012-01-01

    In situ tensile experiments in a transmission electron microscope revealed that micro-cracks in ultrafine grained, free-standing, thin copper foils containing nanoscale twins initiated in matrix domains separated by the twins and then arrested at twin boundaries as twin boundary sliding proceeded. The adjacent microcracks eventually coalesced through shear failure of the bridging twins. To investigate the atomic mechanism of this rarely seen nanoscale crack bridging behavior, molecular dynamics simulations were performed to show that during crack propagation twin boundaries are impinged upon by numerous dislocations from the plastically deforming matrix. These dislocations react at the interface and evolve into substantially impenetrable dislocation walls that strongly confine crack nucleation and resist crack propagation, leading to the experimentally observed crack bridging behavior. The present results raise an approach to significantly toughening polycrystalline thin films by incorporating nanoscale twin structures into individual grains that serve as crack bridging ligaments.

  12. Comparison of S. cerevisiae F-BAR domain structures reveals a conserved inositol phosphate binding site

    Science.gov (United States)

    Moravcevic, Katarina; Alvarado, Diego; Schmitz, Karl R.; Kenniston, Jon A.; Mendrola, Jeannine M.; Ferguson, Kathryn M.; Lemmon, Mark A.

    2015-01-01

    SUMMARY F-BAR domains control membrane interactions in endocytosis, cytokinesis, and cell signaling. Although generally thought to bind curved membranes containing negatively charged phospholipids, numerous functional studies argue that differences in lipid-binding selectivities of F-BAR domains are functionally important. Here, we compare membrane-binding properties of the S. cerevisiae F-BAR domains in vitro and in vivo. Whereas some F-BAR domains (such as Bzz1p and Hof1p F-BARs) bind equally well to all phospholipids, the F-BAR domain from the RhoGAP Rgd1p preferentially binds phosphoinositides. We determined X-ray crystal structures of F-BAR domains from Hof1p and Rgd1p, the latter bound to an inositol phosphate. The structures explain phospholipid-binding selectivity differences, and reveal an F-BAR phosphoinositide binding site that is fully conserved in a mammalian RhoGAP called Gmip, and is partly retained in certain other F-BAR domains. Our findings reveal previously unappreciated determinants of F-BAR domain lipid-binding specificity, and provide a basis for its prediction from sequence. PMID:25620000

  13. Investigation of the Structural, Electrical, and Optical Properties of the Nano-Scale GZO Thin Films on Glass and Flexible Polyimide Substrates

    Directory of Open Access Journals (Sweden)

    Fang-Hsing Wang

    2016-05-01

    Full Text Available In this study, Ga2O3-doped ZnO (GZO thin films were deposited on glass and flexible polyimide (PI substrates at room temperature (300 K, 373 K, and 473 K by the radio frequency (RF magnetron sputtering method. After finding the deposition rate, all the GZO thin films with a nano-scale thickness of about 150 ± 10 nm were controlled by the deposition time. X-ray diffraction patterns indicated that the GZO thin films were not amorphous and all exhibited the (002 peak, and field emission scanning electron microscopy showed that only nano-scale particles were observed. The dependences of the structural, electrical, and optical properties of the GZO thin films on different deposition temperatures and substrates were investigated. X-ray photoemission spectroscopy (XPS was used to measure the elemental composition at the chemical and electronic states of the GZO thin films deposited on different substrates, which could be used to clarify the mechanism of difference in electrical properties of the GZO thin films. In this study, the XPS binding energy spectra of Ga2p3/2 and Ga2p1/2 peaks, Zn2p3/2 and Zn2p1/2 peaks, the Ga3d peak, and O1s peaks for GZO thin films on glass and PI substrates were well compared.

  14. The growth of nanoscale ZnO films by pulsed-spray evaporation chemical vapor deposition and their structural, electric and optical properties

    International Nuclear Information System (INIS)

    Jiang Yinzhu; Bahlawane, Naoufal

    2010-01-01

    Great interest in nanoscale thin films (sub-100 nm) has been stimulated by the developing demands of functional devices. In this paper, nanoscale zinc oxide (ZnO) thin films were deposited on glass substrates at 300 o C by pulsed-spray evaporation chemical vapor deposition. Scanning electron micrographs indicate uniform surface morphologies composed of nanometer-sized spherical particles. The growth kinetics and growth mode are studied and the relationship between the film thickness and the electric properties with respect to the growth mode is interpreted. X-ray diffraction shows that all ZnO films grown by this process were crystallized in a hexagonal structure and highly oriented with their c-axes perpendicular to the plane of the substrate. Optical measurements show transparencies above 85% in the visible spectral range for all films. The absorbance in the UV spectral range respects well the Beer-Lambert law, enabling an accurate optical thickness measurement, and the absorption coefficient was measured for a selected wavelength. The measured band gap energies exhibit an almost constant value of 3.41 eV for all films with different thicknesses, which attributed to the thickness-independent crystallite size.

  15. FDTD based model of ISOCT imaging for validation of nanoscale sensitivity (Conference Presentation)

    Science.gov (United States)

    Eid, Aya; Zhang, Di; Yi, Ji; Backman, Vadim

    2017-02-01

    Many of the earliest structural changes associated with neoplasia occur on the micro and nanometer scale, and thus appear histologically normal. Our group has established Inverse Spectroscopic OCT (ISOCT), a spectral based technique to extract nanoscale sensitive metrics derived from the OCT signal. Thus, there is a need to model light transport through relatively large volumes (< 50 um^3) of media with nanoscale level resolution. Finite Difference Time Domain (FDTD) is an iterative approach which directly solves Maxwell's equations to robustly estimate the electric and magnetic fields propagating through a sample. The sample's refractive index for every spatial voxel and wavelength are specified upon a grid with voxel sizes on the order of λ/20, making it an ideal modelling technique for nanoscale structure analysis. Here, we utilize the FDTD technique to validate the nanoscale sensing ability of ISOCT. The use of FDTD for OCT modelling requires three components: calculating the source beam as it propagates through the optical system, computing the sample's scattered field using FDTD, and finally propagating the scattered field back through the optical system. The principles of Fourier optics are employed to focus this interference field through a 4f optical system and onto the detector. Three-dimensional numerical samples are generated from a given refractive index correlation function with known parameters, and subsequent OCT images and mass density correlation function metrics are computed. We show that while the resolvability of the OCT image remains diffraction limited, spectral analysis allows nanoscale sensitive metrics to be extracted.

  16. Crystal structure of an EAL domain in complex with reaction product 5'-pGpG.

    Directory of Open Access Journals (Sweden)

    Julien Robert-Paganin

    Full Text Available FimX is a large multidomain protein containing an EAL domain and involved in twitching motility in Pseudomonas aeruginosa. We present here two crystallographic structures of the EAL domain of FimX (residues 438-686: one of the apo form and the other of a complex with 5'-pGpG, the reaction product of the hydrolysis of c-di-GMP. In both crystal forms, the EAL domains form a dimer delimiting a large cavity encompassing the catalytic pockets. The ligand is trapped in this cavity by its sugar phosphate moiety. We confirmed by NMR that the guanine bases are not involved in the interaction in solution. We solved here the first structure of an EAL domain bound to the reaction product 5'-pGpG. Though isolated FimX EAL domain has a very low catalytic activity, which would not be significant compared to other catalytic EAL domains, the structure with the product of the reaction can provides some hints in the mechanism of hydrolysis of the c-di-GMP by EAL domains.

  17. Crystal structure of an EAL domain in complex with reaction product 5'-pGpG.

    Science.gov (United States)

    Robert-Paganin, Julien; Nonin-Lecomte, Sylvie; Réty, Stéphane

    2012-01-01

    FimX is a large multidomain protein containing an EAL domain and involved in twitching motility in Pseudomonas aeruginosa. We present here two crystallographic structures of the EAL domain of FimX (residues 438-686): one of the apo form and the other of a complex with 5'-pGpG, the reaction product of the hydrolysis of c-di-GMP. In both crystal forms, the EAL domains form a dimer delimiting a large cavity encompassing the catalytic pockets. The ligand is trapped in this cavity by its sugar phosphate moiety. We confirmed by NMR that the guanine bases are not involved in the interaction in solution. We solved here the first structure of an EAL domain bound to the reaction product 5'-pGpG. Though isolated FimX EAL domain has a very low catalytic activity, which would not be significant compared to other catalytic EAL domains, the structure with the product of the reaction can provides some hints in the mechanism of hydrolysis of the c-di-GMP by EAL domains.

  18. Solution structure, dynamics and thermodynamics of the three SH3 domains of CD2AP

    Energy Technology Data Exchange (ETDEWEB)

    Roldan, Jose L. Ortega [Universidad de Granada, Departamento de Quimica Fisica e Instituto de Biotecnologia, Facultad de Ciencias (Spain); Blackledge, Martin [Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, UJF UMR 5075, Protein Dynamics and Flexibility by NMR (France); Nuland, Nico A. J. van, E-mail: nvnuland@vub.ac.be [Vrije Universiteit Brussel, Structural Biology Brussels (Belgium); Azuaga, Ana I. [Universidad de Granada, Departamento de Quimica Fisica e Instituto de Biotecnologia, Facultad de Ciencias (Spain)

    2011-06-15

    CD2 associated protein (CD2AP) is an adaptor protein that plays an important role in cell to cell union needed for the kidney function. It contains three N-terminal SH3 domains that are able to interact among others with CD2, ALIX, c-Cbl and Ubiquitin. To understand the role of the individual SH3 domains of this adaptor protein we have performed a complete structural, thermodynamic and dynamic characterization of the separate domains using NMR and DSC. The energetic contributions to the stability and the backbone dynamics have been related to the structural features of each domain using the structure-based FoldX algorithm. We have found that the N-terminal SH3 domain of both adaptor proteins CD2AP and CIN85 are the most stable SH3 domains that have been studied until now. This high stability is driven by a more extensive network of intra-molecular interactions. We believe that this increased stabilization of N-terminal SH3 domains in adaptor proteins is crucial to maintain the necessary conformation to establish the proper interactions critical for the recruitment of their natural targets.

  19. Sensing at the nanoscale

    Science.gov (United States)

    Demming, Anna; Hierold, Christofer

    2013-11-01

    label-free detection of DNA at concentrations as low as 1-10 fM, a sensitivity comparable to the best signal amplification-assisted electrochemical sensors reported [12]. In another study actin-conjugated gold and silver nanorods are used to detect ATP, a common indicator of cell viability [13]. They show how aggregation induced by ATP-induced polymerization of the G-actin gives rise to a measurable change in the plasmon resonance absorbance of the nanorods. A review of the use of fluorescent silica nanoparticles for biomedical applications is provided by researchers at Dublin City University in Ireland [14]. The first scanning tunnelling microscope in the early 1980s and subsequent scanning probe developments brought the world of nanoscale structures into view in a manner that gorged the imaginations of scientists and the public. New ways of probing structures at this scale revealed a wealth of curious properties that triggered a surge of research activity in nanotechnology, now a multibillion dollar industry. One good turn deserves another and in fact nanostructures provide the perfect tools for the type of sensing and imaging applications that brought such widespread research interest to nanotechnology. This special issue highlights just how broad and innovative the range of sensing nanotechnologies has grown. References [1] Zappa D, Comini E and Sberveglieri G 2013 Thermally-oxidized zinc oxide nanowires chemical sensors Nanotechnology 24 444008 [2] Kemmler J A, Pokhrel S, Mädler L, Weimar U and Barsan N 2013 Flame spray pyrolysis for sensing at the nanoscale Nanotechnology 24 442001 [3] Bache M et al 2013 Nanomechanical recognition of prognostic biomarker suPAR with DVD-ROM optical technology Nanotechnology 24 444011 [4] Hu C-F, Wang J-Y, Liu Y-C, Tsai M-H and Fang W 2013 Development of 3D carbon nanotubes interdigitated finger electrodes on polymer substrate for flexible capacitive sensor application Nanotechnology 24 444006 [5] Neumann C, Volk C, Engels S and

  20. Nanoscale Structural/Chemical Characterization of Manganese Oxide Surface Layers and Nanoparticles, and the Associated Implications for Drinking Water

    Science.gov (United States)

    Michel Eduardo Vargas Vallejo

    Water treatment facilities commonly reduce soluble contaminants, such as soluble manganese (Mn2+), in water by oxidation and subsequent filtration. Previous studies have shown that conventional porous filter system removes Mn2+ from drinking water by developing Mn-oxides (MnO x(s)) bearing coating layers on the surface of filter media. Multiple models have been developed to explain this Mn2+ removal process and the formation mechanism of MnOx(s) coatings. Both, experimental and theoretical studies to date have been largely focused on the micrometer to millimeter scale range; whereas, coating layers are composed of nanoscale particles and films. Hence, understanding the nanoscale particle and film formation mechanisms is essential to comprehend the complexity of soluble contaminant removal processes. The primary objective of this study was to understand the initial MnOx(s) coating formation mechanisms and evaluate the influence of filter media characteristics on these processes. We pursued this objective by characterizing at the micro and nanoscale MnO x(s) coatings developed on different filter media by bench-scale column tests with simulating inorganic aqueous chemistry of a typical coagulation fresh water treatment plant, where free chlorine is present across filter bed. Analytical SEM and TEM, powder and synchrotron-based XRD, XPS, and ICPMS were used for characterization of coatings, filter media and water solution elemental chemistry. A secondary objective was to model how surface coating formation occurred and its correlation with experimentally observed physical characteristics. This modeling exercise indicates that surface roughness and morphology of filtering media are the major contributing factors in surface coating formation process. Contrary to previous models that assumed a uniform distribution and growth of surface coating, the experimental results showed that greater amounts of coating were developed in rougher areas. At the very early stage of

  1. Structural mapping of the coiled-coil domain of a bacterial condensin and comparative analyses across all domains of life suggest conserved features of SMC proteins.

    Science.gov (United States)

    Waldman, Vincent M; Stanage, Tyler H; Mims, Alexandra; Norden, Ian S; Oakley, Martha G

    2015-06-01

    The structural maintenance of chromosomes (SMC) proteins form the cores of multisubunit complexes that are required for the segregation and global organization of chromosomes in all domains of life. These proteins share a common domain structure in which N- and C- terminal regions pack against one another to form a globular ATPase domain. This "head" domain is connected to a central, globular, "hinge" or dimerization domain by a long, antiparallel coiled coil. To date, most efforts for structural characterization of SMC proteins have focused on the globular domains. Recently, however, we developed a method to map interstrand interactions in the 50-nm coiled-coil domain of MukB, the divergent SMC protein found in γ-proteobacteria. Here, we apply that technique to map the structure of the Bacillus subtilis SMC (BsSMC) coiled-coil domain. We find that, in contrast to the relatively complicated coiled-coil domain of MukB, the BsSMC domain is nearly continuous, with only two detectable coiled-coil interruptions. Near the middle of the domain is a break in coiled-coil structure in which there are three more residues on the C-terminal strand than on the N-terminal strand. Close to the head domain, there is a second break with a significantly longer insertion on the same strand. These results provide an experience base that allows an informed interpretation of the output of coiled-coil prediction algorithms for this family of proteins. A comparison of such predictions suggests that these coiled-coil deviations are highly conserved across SMC types in a wide variety of organisms, including humans. © 2015 Wiley Periodicals, Inc.

  2. Magnetic domain structures and stray fields of individual elongated magnetite grains revealed by magnetic force microscopy (MFM)

    DEFF Research Database (Denmark)

    Frandsen, Cathrine; Stipp, S. L. S.; McEnroe, S. A.

    2004-01-01

    ), the internal domain structure was determined for individual grains. In general, the lamellae were pseudo-single-domain grains with open-flux domain magnetisations parallel to their long axes. The domain sizes were, in cross-section, on the order of a micrometer for the longer lamellae and about 300 nm...

  3. Designing A Simple Folder Structure For A Complex Domain

    Directory of Open Access Journals (Sweden)

    Torkil Clemmensen

    2011-01-01

    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.

  4. Atomic resolution structure of the E. coli YajR transporter YAM domain

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Daohua [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China); School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); Zhao, Yan [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China); School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China); Fan, Junping; Liu, Xuehui; Wu, Yan; Feng, Wei [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China); Zhang, Xuejun C., E-mail: zhangc@ibp.ac.cn [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China)

    2014-07-25

    Highlights: • We report the crystal structure of the YAM domain of YajR transporter at 1.07 Å. • The YAM dimerization is related to the halogen-dependent high thermal stability. • A belt of poly-pentagonal water molecules was observed in the dimer interface. - Abstract: YajR is an Escherichia coli transporter that belongs to the major facilitator superfamily. Unlike most MFS transporters, YajR contains a carboxyl terminal, cytosolic domain of 67 amino acid residues termed YAM domain. Although it is speculated that the function of this small soluble domain is to regulate the conformational change of the 12-helix transmembrane domain, its precise regulatory role remains unclear. Here, we report the crystal structure of the YAM domain at 1.07-Å resolution, along with its structure determined using nuclear magnetic resonance. Detailed analysis of the high resolution structure revealed a symmetrical dimer in which a belt of well-ordered poly-pentagonal water molecules is embedded. A mutagenesis experiment and a thermal stability assay were used to analyze the putative role of this dimerization in response to changes in halogen concentration.

  5. Structure of the EMMPRIN N-terminal domain 1: Dimerization via [beta]-strand swapping

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Jinquan; Teplyakov, Alexey; Obmolova, Galina; Malia, Thomas; Wu, Sheng-Jiun; Beil, Eric; Baker, Audrey; Swencki-Underwood, Bethany; Zhao, Yonghong; Sprenkle, Justin; Dixon, Ken; Sweet, Raymond; Gilliland, Gary L.; (Centocor)

    2010-09-27

    Extracellular matrix metalloproteinase inducer (EMMPRIN), also known as Hab18G, CD147, Basigin, M6, and neurothelin, is a membrane glycoprotein expressed on the surface of various cell types and many cancer cells. EMMPRIN stimulates adjacent fibroblasts and tumor cells to produce matrix metalloproteinases and plays an important role in tumor invasion and metastasis, angiogenesis, spermatogensis and fertilization, cell-cell adhesion and communication, and other biological processes (reviewed in Ref. 1 and references therein). It was demonstrated that the EMMPRIN extracellular domain (ECD), which structurally belongs to the IgG superfamily, can form homo-oligomers in a cis dependent manner and the N-terminal domain 1 (residues 22-101) was necessary and sufficient to mediate this interaction. The crystal structure of the ECD of recombinant human EMMPRIN (Hab18G/CD147) expressed in E. coli was reported at 2.8 {angstrom} resolution (Yu et al. 2008). The construct consists of residues 22-205 of the mature protein and has both an N-terminal IgC2 domain (ND1, residues 22-101) and a C-terminal IgC2 domain (ND2, residues 107-205). The two domains are joined by a five amino acid residue linker that constitutes a flexible hinge between the two domains. The crystal form has four copies of the molecule in the asymmetric unit, each of which has a different inter-domain angle that varies from 121{sup o} to 144{sup o}. The two domains each have a conserved disulfide bridge and both are comprised of two {beta}-sheets formed by strands EBA and GFCC, and DEBA and AGFCC for ND1 and ND2, respectively. Based on the crystal packing in this structure, the authors proposed that lateral packing between the two IgG domains of EMMPRIN ECD represents a potential mechanism for cell adhesion. Here we report the 2.0-{angstrom} crystal structure of the N-terminal domain of EMMPRIN ECD (ND1) expressed in mammalian cells. The overall structure of the domain is very similar to that in the full length

  6. Solution structure of telomere binding domain of AtTRB2 derived from Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Yun, Ji-Hye; Lee, Won Kyung; Kim, Heeyoun; Kim, Eunhee; Cheong, Chaejoon; Cho, Myeon Haeng; Lee, Weontae

    2014-01-01

    Highlights: • We have determined solution structure of Myb domain of AtTRB2. • The Myb domain of AtTRB2 is located in the N-terminal region. • The Myb domain of AtTRB2 binds to plant telomeric DNA without fourth helix. • Helix 2 and 3 of the Myb domain of AtTRB2 are involved in DNA recognition. • AtTRB2 is a novel protein distinguished from other known plant TBP. - Abstract: Telomere homeostasis is regulated by telomere-associated proteins, and the Myb domain is well conserved for telomere binding. AtTRB2 is a member of the SMH (Single-Myb-Histone)-like family in Arabidopsis thaliana, having an N-terminal Myb domain, which is responsible for DNA binding. The Myb domain of AtTRB2 contains three α-helices and loops for DNA binding, which is unusual given that other plant telomere-binding proteins have an additional fourth helix that is essential for DNA binding. To understand the structural role for telomeric DNA binding of AtTRB2, we determined the solution structure of the Myb domain of AtTRB2 (AtTRB2 1–64 ) using nuclear magnetic resonance (NMR) spectroscopy. In addition, the inter-molecular interaction between AtTRB2 1–64 and telomeric DNA has been characterized by the electrophoretic mobility shift assay (EMSA) and NMR titration analyses for both plant (TTTAGGG)n and human (TTAGGG)n telomere sequences. Data revealed that Trp28, Arg29, and Val47 residues located in Helix 2 and Helix 3 are crucial for DNA binding, which are well conserved among other plant telomere binding proteins. We concluded that although AtTRB2 is devoid of the additional fourth helix in the Myb-extension domain, it is able to bind to plant telomeric repeat sequences as well as human telomeric repeat sequences

  7. Solution structure of telomere binding domain of AtTRB2 derived from Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    Yun, Ji-Hye [Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Lee, Won Kyung [Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Kim, Heeyoun [Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Kim, Eunhee; Cheong, Chaejoon [Magnetic Resonance Team, Korea Basic Science Institute (KBSI), Ochang, Chungbuk 363-883 (Korea, Republic of); Cho, Myeon Haeng [Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Lee, Weontae, E-mail: wlee@spin.yonsei.ac.kr [Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of)

    2014-09-26

    Highlights: • We have determined solution structure of Myb domain of AtTRB2. • The Myb domain of AtTRB2 is located in the N-terminal region. • The Myb domain of AtTRB2 binds to plant telomeric DNA without fourth helix. • Helix 2 and 3 of the Myb domain of AtTRB2 are involved in DNA recognition. • AtTRB2 is a novel protein distinguished from other known plant TBP. - Abstract: Telomere homeostasis is regulated by telomere-associated proteins, and the Myb domain is well conserved for telomere binding. AtTRB2 is a member of the SMH (Single-Myb-Histone)-like family in Arabidopsis thaliana, having an N-terminal Myb domain, which is responsible for DNA binding. The Myb domain of AtTRB2 contains three α-helices and loops for DNA binding, which is unusual given that other plant telomere-binding proteins have an additional fourth helix that is essential for DNA binding. To understand the structural role for telomeric DNA binding of AtTRB2, we determined the solution structure of the Myb domain of AtTRB2 (AtTRB2{sub 1–64}) using nuclear magnetic resonance (NMR) spectroscopy. In addition, the inter-molecular interaction between AtTRB2{sub 1–64} and telomeric DNA has been characterized by the electrophoretic mobility shift assay (EMSA) and NMR titration analyses for both plant (TTTAGGG)n and human (TTAGGG)n telomere sequences. Data revealed that Trp28, Arg29, and Val47 residues located in Helix 2 and Helix 3 are crucial for DNA binding, which are well conserved among other plant telomere binding proteins. We concluded that although AtTRB2 is devoid of the additional fourth helix in the Myb-extension domain, it is able to bind to plant telomeric repeat sequences as well as human telomeric repeat sequences.

  8. The retinal specific CD147 Ig0 domain: from molecular structure to biological activity

    Science.gov (United States)

    Redzic, Jasmina S.; Armstrong, Geoffrey S.; Isern, Nancy. G.; Jones, David N.M.; Kieft, Jeffrey S.; Eisenmesser, Elan Zohar

    2011-01-01

    CD147 is a type I transmembrane protein that is involved in inflammatory diseases, cancer progression, and multiple human pathogens utilize CD147 for efficient infection. In several cancers, CD147 expression is so high that it is now used as a prognostic marker. The two primary isoforms of CD147 that are related to cancer progression have been identified, differing in their number of immunoglobulin (Ig)-like domains. These include CD147 Ig1-Ig2 that is ubiquitously expressed in most tissues and CD147 Ig0-Ig1-Ig2 that is retinal specific and implicated in retinoblastoma. However, little is known in regard to the retinal specific CD147 Ig0 domain despite its potential role in retinoblastoma. We present the first crystal structure of the human CD147 Ig0 domain and show that the CD147 Ig0 domain is a crystallographic dimer with an I-type domain structure, which is maintained in solution. Furthermore, we have utilized our structural data together with mutagenesis to probe the biological activity of CD147-containing proteins both with and without the CD147 Ig0 domain within several model cell lines. Our findings reveal that the CD147 Ig0 domain is a potent stimulator of interleukin-6 and suggest that the CD147 Ig0 domain has its own receptor distinct from that of the other CD147 Ig-like domains, CD147 Ig1-Ig2. Finally, we show that the CD147 Ig0 dimer is the functional unit required for activity and can be disrupted by a single point mutation. PMID:21620857

  9. Nanoscopic studies of domain structure dynamics in ferroelectric La:HfO2 capacitors

    Science.gov (United States)

    Buragohain, P.; Richter, C.; Schenk, T.; Lu, H.; Mikolajick, T.; Schroeder, U.; Gruverman, A.

    2018-05-01

    Visualization of domain structure evolution under an electrical bias has been carried out in ferroelectric La:HfO2 capacitors by a combination of Piezoresponse Force Microscopy (PFM) and pulse switching techniques to study the nanoscopic mechanism of polarization reversal and the wake-up process. It has been directly shown that the main mechanism behind the transformation of the polarization hysteretic behavior and an increase in the remanent polarization value upon the alternating current cycling is electrically induced domain de-pinning. PFM imaging and local spectroscopy revealed asymmetric switching in the La:HfO2 capacitors due to a significant imprint likely caused by the different boundary conditions at the top and bottom interfaces. Domain switching kinetics can be well-described by the nucleation limited switching model characterized by a broad distribution of the local switching times. It has been found that the domain velocity varies significantly throughout the switching process indicating strong interaction with structural defects.

  10. Domain structures and magnetization reversal in Co/Pd and CoFeB/Pd multilayers

    Energy Technology Data Exchange (ETDEWEB)

    Sbiaa, R., E-mail: rachid@squ.edu.om [Department of Physics, Sultan Qaboos University, P.O. Box 36, PC 123 (Oman); Ranjbar, M. [Physics Department, University of Gothenburg, 412 96 Gothenburg (Sweden); Åkerman, J. [Physics Department, University of Gothenburg, 412 96 Gothenburg (Sweden); Materials Physics, School of ICT, Royal Institute of Technology (KTH), 164 40 Kista (Sweden)

    2015-05-07

    Domain structures and magnetization reversal of (Co/Pd) and (CoFeB/Pd) multilayers with 7 and 14 repeats were investigated. The Co-based multilayers show much larger coercivities, a better squareness, and a sharper magnetization switching than CoFeB-based multilayers. From magnetic force microscopy observations, both structures show strong reduction in domains size as the number of repeats increases but the magnetic domains for Co-based multilayers are more than one order of magnitude larger than for CoFeB-based multilayers. By imaging domains at different times, breaks in the (CoFeB/Pd) multilayer stripes were observed within only few hours, while no change could be seen for (Co/Pd) multilayers. Although CoFeB single layers are suitable for magnetoresistive devices due to their large spin polarization and low damping constants, their lamination with Pd suffers mainly from thermal instability.

  11. Is there a domain-general cognitive structuring system? Evidence from structural priming across music, math, action descriptions, and language.

    Science.gov (United States)

    Van de Cavey, Joris; Hartsuiker, Robert J

    2016-01-01

    Cognitive processing in many domains (e.g., sentence comprehension, music listening, and math solving) requires sequential information to be organized into an integrational structure. There appears to be some overlap in integrational processing across domains, as shown by cross-domain interference effects when for example linguistic and musical stimuli are jointly presented (Koelsch, Gunter, Wittfoth, & Sammler, 2005; Slevc, Rosenberg, & Patel, 2009). These findings support theories of overlapping resources for integrational processing across domains (cfr. SSIRH Patel, 2003; SWM, Kljajevic, 2010). However, there are some limitations to the studies mentioned above, such as the frequent use of unnaturalistic integrational difficulties. In recent years, the idea has risen that evidence for domain-generality in structural processing might also be yielded though priming paradigms (cfr. Scheepers, 2003). The rationale behind this is that integrational processing across domains regularly requires the processing of dependencies across short or long distances in the sequence, involving respectively less or more syntactic working memory resources (cfr. SWM, Kljajevic, 2010), and such processing decisions might persist over time. However, whereas recent studies have shown suggestive priming of integrational structure between language and arithmetics (though often dependent on arithmetic performance, cfr. Scheepers et al., 2011; Scheepers & Sturt, 2014), it remains to be investigated to what extent we can also find evidence for priming in other domains, such as music and action (cfr. SWM, Kljajevic, 2010). Experiment 1a showed structural priming from the processing of musical sequences onto the position in the sentence structure (early or late) to which a relative clause was attached in subsequent sentence completion. Importantly, Experiment 1b showed that a similar structural manipulation based on non-hierarchically ordered color sequences did not yield any priming effect

  12. Expression, purification and insights into structure and folding of the ADAM22 pro domain

    DEFF Research Database (Denmark)

    Sørensen, Hans Peter; Jacobsen, Jonas; Nielbo, Steen

    2008-01-01

    . To understand the functions of human ADAM pro domains and to determine three-dimensional structures, we have screened promising targets for expression and purification properties when using Escherichia coli as the host. The pro domain of ADAM22 (ADAM22-P) expressed in E. coli was folded, as determined by CD...... and NMR spectroscopy. An ADAM22-P fragment encoding residues 26-199 could be expressed in high amounts, remained soluble above 1 mM, and was suitable for structural studies by NMR spectroscopy. CD spectroscopy and predictions suggest that the secondary structure in ADAM22-P consists of beta...

  13. Soil-structure interaction analysis of NPP containments: substructure and frequency domain methods

    International Nuclear Information System (INIS)

    Venancio-Filho, F.; Almeida, M.C.F.; Ferreira, W.G.; De Barros, F.C.P.

    1997-01-01

    Substructure and frequency domain methods for soil-structure interaction are addressed in this paper. After a brief description of mathematical models for the soil and of excitation, the equations for dynamic soil-structure interaction are developed for a rigid surface foundation and for an embedded foundation. The equations for the frequency domain analysis of MDOF systems are provided. An example of soil-structure interaction analysis with frequency-dependent soil properties is given and examples of identification of foundation impedance functions and soil properties are presented. (orig.)

  14. The structure of a conserved Piezo channel domain reveals a novel beta sandwich fold

    Science.gov (United States)

    Kamajaya, Aron; Kaiser, Jens; Lee, Jonas; Reid, Michelle; Rees, Douglas C.

    2014-01-01

    Summary Piezo has recently been identified as a family of eukaryotic mechanosensitive channels composed of subunits containing over 2000 amino acids, without recognizable sequence similarity to other channels. Here, we present the crystal structure of a large, conserved extramembrane domain located just before the last predicted transmembrane helix of C. elegans PIEZO, which adopts a novel beta sandwich fold. The structure was also determined of a point mutation located on a conserved surface at the position equivalent to the human PIEZO1 mutation found in Dehydrated Hereditary Stomatocytosis (DHS) patients (M2225R). While the point mutation does not change the overall domain structure, it does alter the surface electrostatic potential that may perturb interactions with a yet-to-be identified ligand or protein. The lack of structural similarity between this domain and any previously characterized fold, including those of eukaryotic and bacterial channels, highlights the distinctive nature of the Piezo family of eukaryotic mechanosensitive channels. PMID:25242456

  15. Crystal structure of the Rasputin NTF2-like domain from Drosophila melanogaster

    DEFF Research Database (Denmark)

    Vognsen, Tina Reinholdt; Kristensen, Ole

    2012-01-01

    The crystal structure of the NTF2-like domain of the Drosophila homolog of Ras GTPase SH3 Binding Protein (G3BP), Rasputin, was determined at 2.7Å resolution. The overall structure is highly similar to nuclear transport factor 2: It is a homodimer comprised of a ß-sheet and three a-helices forming...

  16. Characterization of high-power RF structures using time-domain field codes

    International Nuclear Information System (INIS)

    Shang, C.C.; DeFord, J.F.; Swatloski, T.L.

    1992-01-01

    We have modeled gyrotron windows and gyrotron amplifier sever structures for TE modes in the 100--150 GHz range and have computed the reflection and transmission characteristics from the field data. Good agreement with frequency domain codes and analytic analysis have been obtained for some simple geometries. We present results for realistic structures with lousy coatings and describe implementation of microwave diagnostics

  17. Fast identification of folded human protein domains expressed in E. coli suitable for structural analysis

    Directory of Open Access Journals (Sweden)

    Schlegel Brigitte

    2004-03-01

    Full Text Available Abstract Background High-throughput protein structure analysis of individual protein domains requires analysis of large numbers of expression clones to identify suitable constructs for structure determination. For this purpose, methods need to be implemented for fast and reliable screening of the expressed proteins as early as possible in the overall process from cloning to structure determination. Results 88 different E. coli expression constructs for 17 human protein domains were analysed using high-throughput cloning, purification and folding analysis to obtain candidates suitable for structural analysis. After 96 deep-well microplate expression and automated protein purification, protein domains were directly analysed using 1D 1H-NMR spectroscopy. In addition, analytical hydrophobic interaction chromatography (HIC was used to detect natively folded protein. With these two analytical methods, six constructs (representing two domains were quickly identified as being well folded and suitable for structural analysis. Conclusion The described approach facilitates high-throughput structural analysis. Clones expressing natively folded proteins suitable for NMR structure determination were quickly identified upon small scale expression screening using 1D 1H-NMR and/or analytical HIC. This procedure is especially effective as a fast and inexpensive screen for the 'low hanging fruits' in structural genomics.

  18. Structures of the Gasdermin D C-Terminal Domains Reveal Mechanisms of Autoinhibition.

    Science.gov (United States)

    Liu, Zhonghua; Wang, Chuanping; Rathkey, Joseph K; Yang, Jie; Dubyak, George R; Abbott, Derek W; Xiao, Tsan Sam

    2018-05-01

    Pyroptosis is an inflammatory form of programmed cell death that plays important roles in immune protection against infections and in inflammatory disorders. Gasdermin D (GSDMD) is an executor of pyroptosis upon cleavage by caspases-1/4/5/11 following canonical and noncanonical inflammasome activation. GSDMD N-terminal domain assembles membrane pores to induce cytolysis, whereas its C-terminal domain inhibits cell death through intramolecular association with the N domain. The molecular mechanisms of autoinhibition for GSDMD are poorly characterized. Here we report the crystal structures of the human and murine GSDMD C-terminal domains, which differ from those of the full-length murine GSDMA3 and the human GSDMB C-terminal domain. Mutations of GSDMD C-domain residues predicted to locate at its interface with the N-domain enhanced pyroptosis. Our results suggest that GSDMDs may employ a distinct mode of intramolecular domain interaction and autoinhibition, which may be relevant to its unique role in pyroptosis downstream of inflammasome activation. Copyright © 2018 Elsevier Ltd. All rights reserved.

  19. Structures of the NLRP14 pyrin domain reveal a conformational switch mechanism regulating its molecular interactions

    International Nuclear Information System (INIS)

    Eibl, Clarissa; Hessenberger, Manuel; Wenger, Julia; Brandstetter, Hans

    2014-01-01

    Pyrin domains (PYDs) recruit downstream effector molecules in NLR signalling. A specific charge-relay system suggests a the formation of a signalling complex involving a PYD dimer. The cytosolic tripartite NLR receptors serve as important signalling platforms in innate immunity. While the C-terminal domains act as sensor and activation modules, the N-terminal death-like domain, e.g. the CARD or pyrin domain, is thought to recruit downstream effector molecules by homotypic interactions. Such homotypic complexes have been determined for all members of the death-domain superfamily except for pyrin domains. Here, crystal structures of human NLRP14 pyrin-domain variants are reported. The wild-type protein as well as the clinical D86V mutant reveal an unexpected rearrangement of the C-terminal helix α6, resulting in an extended α5/6 stem-helix. This reordering mediates a novel symmetric pyrin-domain dimerization mode. The conformational switching is controlled by a charge-relay system with a drastic impact on protein stability. How the identified charge relay allows classification of NLRP receptors with respect to distinct recruitment mechanisms is discussed

  20. Elasticity Imaging of Ferroelectric Domain Structure in PZT by Ultrasonic Atomic Force Microscopy

    International Nuclear Information System (INIS)

    Tsuji, T.; Ogiso, H.; Fukuda, K.; Yamanaka, K.

    2004-01-01

    UAFM was applied to the observation of the domain structure in lead zirconate titanate (PZT). It imaged the change of elasticity due to grain and domain boundary (DB). For the quantitative evaluation of the contact stiffness, the lateral contact stiffness was taken into account. The stiffness of DB was 10% lower than that within the domain and the width of the DB was about 30 nm. The implication of this work is the understanding of the fatigue mechanism in a PZT memory and the high resolution imaging for a high-density memory

  1. Vibration sensing in flexible structures using a distributed-effect modal domain optical fiber sensor

    Science.gov (United States)

    Reichard, Karl M.; Lindner, Douglas K.; Claus, Richard O.

    1991-01-01

    Modal domain optical fiber sensors have recently been employed in the implementation of system identification algorithms and the closed-loop control of vibrations in flexible structures. The mathematical model of the modal domain optical fiber sensor used in these applications, however, only accounted for the effects of strain in the direction of the fiber's longitudinal axis. In this paper, we extend this model to include the effects of arbitrary stress. Using this sensor model, we characterize the sensor's sensitivity and dynamic range.

  2. Crystal structure of a PFU-PUL domain pair of Saccharomyces cerevisiae Doa1/Ufd3.

    Science.gov (United States)

    Nishimasu, Rieko; Komori, Hirofumi; Higuchi, Yoshiki; Nishimasu, Hiroshi; Hiroaki, Hidekazu

    2010-10-21

    Doa1/Ufd3 is involved in ubiquitin (Ub)-dependent cellular processes in Saccharomyces cerevisiae, and consists of WD40, PFU, and PUL domains. Previous studies showed that the PFU and PUL domains interact with Ub and Hse1, and Cdc48, respectively. However, their detailed functional interactions with Doa1 remained elusive. We report the crystal structure of the PFU-PUL domain pair of yeast Doa1 at 1.9 Å resolution. The conserved surface of the PFU domain may be involved in binding to Ub and Hse1. Unexpectedly, the PUL domain consists of an Armadillo (ARM)-like repeat structure. The positively charged concave surface of the PUL domain may bind to the negatively charged C-terminal region of Cdc48. A structural comparison of Doa1 with Ufd2 revealed that they share a similar ARM-like repeat, supporting a model in which Doa1 and Ufd2 compete for Cdc48 binding and may dictate the fate of ubiquitinated proteins in the proteasome pathway.

  3. Structure of a WW domain-containing fragment of dystrophin complexed with {beta}-dystroglycan.

    Energy Technology Data Exchange (ETDEWEB)

    Huang, X.; Poy, F.; Zhang, R.; Joachimiak, A.; Sudol, M.; Eck, M. J.; Biosciences Division; Dana Farber Cancer Inst.; Harvard Medical School; Mount Sinai School of Medicine

    2000-08-01

    Dystrophin and {beta}-dystroglycan are components of the dystrophin--glycoprotein complex (DGC), a multimolecular assembly that spans the cell membrane and links the actin cytoskeleton to the extracellular basal lamina. Defects in the dystrophin gene are the cause of Duchenne and Becker muscular dystrophies. The C-terminal region of dystrophin binds the cytoplasmic tail of {beta}-dystroglycan, in part through the interaction of its WW domain with a proline-rich motif in the tail of {beta}-dystroglycan. Here we report the crystal structure of this portion of dystrophin in complex with the proline-rich binding site in {beta}-dystroglycan. The structure shows that the dystrophin WW domain is embedded in an adjacent helical region that contains two EF-hand-like domains. The {beta}-dystroglycan peptide binds a composite surface formed by the WW domain and one of these EF-hands. Additionally, the structure reveals striking similarities in the mechanisms of proline recognition employed by WW domains and SH3 domains.

  4. Structure determination and analysis of a haemolytic gingipain adhesin domain from Porphyromonas gingivalis

    Energy Technology Data Exchange (ETDEWEB)

    Li, N.; Yun, P.; Nadkarni, M.A.; Ghadikolaee, N.B.; Nguyen, K.A.; Lee, M.; Hunter, N.; Collyer, C.A. (Sydney)

    2010-08-27

    Porphyromonas gingivalis is an obligately anaerobic bacterium recognized as an aetiological agent of adult periodontitis. P. gingivalis produces cysteine proteinases, the gingipains. The crystal structure of a domain within the haemagglutinin region of the lysine gingipain (Kgp) is reported here. The domain was named K2 as it is the second of three homologous structural modules in Kgp. The K2 domain structure is a 'jelly-roll' fold with two anti-parallel {beta}-sheets. This fold topology is shared with adhesive domains from functionally diverse receptors such as MAM domains, ephrin receptor ligand binding domains and a number of carbohydrate binding modules. Possible functions of K2 were investigated. K2 induced haemolysis of erythrocytes in a dose-dependent manner that was augmented by the blocking of anion transport. Further, cysteine-activated arginine gingipain RgpB, which degrades glycophorin A, sensitized erythrocytes to the haemolytic effect of K2. Cleaved K2, similar to that found in extracted Kgp, lacks the haemolytic activity indicating that autolysis of Kgp may be a staged process which is artificially enhanced by extraction of the protein. The data indicate a functional role for K2 in the integrated capacity conferred by Kgp to enable the porphyrin auxotroph P. gingivalis to capture essential haem from erythrocytes.

  5. Structure of the caspase-recruitment domain from a zebrafish guanylate-binding protein

    International Nuclear Information System (INIS)

    Jin, Tengchuan; Huang, Mo; Smith, Patrick; Jiang, Jiansheng; Xiao, T. Sam

    2013-01-01

    The crystal structure of the first zebrafish caspase-recruitment domain at 1.47 Å resolution illustrates a six-helix bundle fold similar to that of the human NLRP1 CARD. The caspase-recruitment domain (CARD) mediates homotypic protein–protein interactions that assemble large oligomeric signaling complexes such as the inflammasomes during innate immune responses. Structural studies of the mammalian CARDs demonstrate that their six-helix bundle folds belong to the death-domain superfamily, whereas such studies have not been reported for other organisms. Here, the zebrafish interferon-induced guanylate-binding protein 1 (zIGBP1) was identified that contains an N-terminal GTPase domain and a helical domain typical of the mammalian guanylate-binding proteins, followed by a FIIND domain and a C-terminal CARD similar to the mammalian inflammasome proteins NLRP1 and CARD8. The structure of the zIGBP1 CARD as a fusion with maltose-binding protein was determined at 1.47 Å resolution. This revealed a six-helix bundle fold similar to the NLRP1 CARD structure with the bent α1 helix typical of all known CARD structures. The zIGBP1 CARD surface contains a positively charged patch near its α1 and α4 helices and a negatively charged patch near its α2, α3 and α5 helices, which may mediate its interaction with partner domains. Further studies using binding assays and other analyses will be required in order to address the physiological function(s) of this zebrafish protein

  6. Structural interactions between lipids, water and S1-S4 voltage-sensing domains.

    Science.gov (United States)

    Krepkiy, Dmitriy; Gawrisch, Klaus; Swartz, Kenton J

    2012-11-02

    Membrane proteins serve crucial signaling and transport functions, yet relatively little is known about their structures in membrane environments or how lipids interact with these proteins. For voltage-activated ion channels, X-ray structures suggest that the mobile voltage-sensing S4 helix would be exposed to the membrane, and functional studies reveal that lipid modification can profoundly alter channel activity. Here, we use solid-state NMR to investigate structural interactions of lipids and water with S1-S4 voltage-sensing domains and to explore whether lipids influence the structure of the protein. Our results demonstrate that S1-S4 domains exhibit extensive interactions with lipids and that these domains are heavily hydrated when embedded in a membrane. We also find evidence for preferential interactions of anionic lipids with S1-S4 domains and that these interactions have lifetimes on the timescale of ≤ 10(-3)s. Arg residues within S1-S4 domains are well hydrated and are positioned in close proximity to lipids, exhibiting local interactions with both lipid headgroups and acyl chains. Comparative studies with a positively charged lipid lacking a phosphodiester group reveal that this lipid modification has only modest effects on the structure and hydration of S1-S4 domains. Taken together, our results demonstrate that Arg residues in S1-S4 voltage-sensing domains reside in close proximity to the hydrophobic interior of the membrane yet are well hydrated, a requirement for carrying charge and driving protein motions in response to changes in membrane voltage. Published by Elsevier Ltd.

  7. Crystal Structure of the HEAT Domain from the Pre-mRNA Processing Factor Symplekin

    Energy Technology Data Exchange (ETDEWEB)

    Kennedy, Sarah A.; Frazier, Monica L.; Steiniger, Mindy; Mast, Ann M.; Marzluff, William F.; Redinbo, Matthew R.; (UNC)

    2010-09-30

    The majority of eukaryotic pre-mRNAs are processed by 3'-end cleavage and polyadenylation, although in metazoa the replication-dependent histone mRNAs are processed by 3'-end cleavage but not polyadenylation. The macromolecular complex responsible for processing both canonical and histone pre-mRNAs contains the {approx} 1160-residue protein Symplekin. Secondary-structural prediction algorithms identified putative HEAT domains in the 300 N-terminal residues of all Symplekins of known sequence. The structure and dynamics of this domain were investigated to begin elucidating the role Symplekin plays in mRNA maturation. The crystal structure of the Drosophila melanogaster Symplekin HEAT domain was determined to 2.4 {angstrom} resolution with single-wavelength anomalous dispersion phasing methods. The structure exhibits five canonical HEAT repeats along with an extended 31-amino-acid loop (loop 8) between the fourth and fifth repeat that is conserved within closely related Symplekin sequences. Molecular dynamics simulations of this domain show that the presence of loop 8 dampens correlated and anticorrelated motion in the HEAT domain, therefore providing a neutral surface for potential protein-protein interactions. HEAT domains are often employed for such macromolecular contacts. The Symplekin HEAT region not only structurally aligns with several established scaffolding proteins, but also has been reported to contact proteins essential for regulating 3'-end processing. Together, these data support the conclusion that the Symplekin HEAT domain serves as a scaffold for protein-protein interactions essential to the mRNA maturation process.

  8. Structures of BIR domains from human NAIP and cIAP2.

    Science.gov (United States)

    Herman, Maria Dolores; Moche, Martin; Flodin, Susanne; Welin, Martin; Trésaugues, Lionel; Johansson, Ida; Nilsson, Martina; Nordlund, Pär; Nyman, Tomas

    2009-11-01

    The inhibitor of apoptosis (IAP) family of proteins contains key modulators of apoptosis and inflammation that interact with caspases through baculovirus IAP-repeat (BIR) domains. Overexpression of IAP proteins frequently occurs in cancer cells, thus counteracting the activated apoptotic program. The IAP proteins have therefore emerged as promising targets for cancer therapy. In this work, X-ray crystallography was used to determine the first structures of BIR domains from human NAIP and cIAP2. Both structures harbour an N-terminal tetrapeptide in the conserved peptide-binding groove. The structures reveal that these two proteins bind the tetrapeptides in a similar mode as do other BIR domains. Detailed interactions are described for the P1'-P4' side chains of the peptide, providing a structural basis for peptide-specific recognition. An arginine side chain in the P3' position reveals favourable interactions with its hydrophobic moiety in the binding pocket, while hydrophobic residues in the P2' and P4' pockets make similar interactions to those seen in other BIR domain-peptide complexes. The structures also reveal how a serine in the P1' position is accommodated in the binding pockets of NAIP and cIAP2. In addition to shedding light on the specificity determinants of these two proteins, the structures should now also provide a framework for future structure-based work targeting these proteins.

  9. Variability and conservation of structural domains in divide-and-conquer approaches

    Energy Technology Data Exchange (ETDEWEB)

    Wiegand, Thomas [ETH Zurich, Physical Chemistry (Switzerland); Gardiennet, Carole [CNRS, Université de Lorraine, CRM2, UMR 7036 (France); Cadalbert, Riccardo [ETH Zurich, Physical Chemistry (Switzerland); Lacabanne, Denis; Kunert, Britta; Terradot, Laurent, E-mail: laurent.terradot@ibcp.fr; Böckmann, Anja, E-mail: a.bockmann@ibcp.fr [Université de Lyon, Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS (France); Meier, Beat H., E-mail: beme@ethz.ch [ETH Zurich, Physical Chemistry (Switzerland)

    2016-06-15

    The use of protein building blocks for the structure determination of multidomain proteins and protein–protein complexes, also known as the “divide and conquer” approach, is an important strategy for obtaining protein structures. Atomic-resolution X-ray or NMR data of the individual domains are combined with lower-resolution electron microscopy maps or X-ray data of the full-length protein or the protein complex. Doing so, it is often assumed that the individual domain structures remain invariant in the context of the superstructure. In this work, we show the potentials and limitations of NMR to validate this approach at the example of the dodecameric DnaB helicase from Helicobacter pylori. We investigate how sequentially assigned spectra, as well as unassigned spectral fingerprints can be used to indicate the conservation of individual domains, and also to highlight conformational differences.

  10. Control systems using modal domain optical fiber sensors for smart structure applications

    Science.gov (United States)

    Lindner, Douglas K.; Reichard, Karl M.

    1991-01-01

    Recently, a new class of sensors has emerged for structural control which respond to environmental changes over a significant gauge length; these sensors are called distributed-effect sensors. These sensors can be fabricated with spatially varying sensitivity to the distributed measurand, and can be configured to measure a variety of structural parameters which can not be measured directly using point sensors. Examples of distributed-effect sensors include piezoelectric film, holographic sensors, and modal domain optical fiber sensors. Optical fiber sensors are particularly attractive for smart structure applications because they are flexible, have low mass, and can easily be embedded directly into materials. In this paper we describe the implementation of weighted modal domain optical fiber sensors. The mathematical model of the modal domain optical fiber sensor model is described and used to derive an expression for the sensor sensitivity. The effects of parameter variations on the sensor sensitivity are demonstrated to illustrate methods of spatially varying the sensor sensitivity.

  11. Mutations in actin used for structural studies partially disrupt β-thymosin/WH2 domains interaction.

    Science.gov (United States)

    Deville, Célia; Girard-Blanc, Christine; Assrir, Nadine; Nhiri, Naïma; Jacquet, Eric; Bontems, François; Renault, Louis; Petres, Stéphane; van Heijenoort, Carine

    2016-10-01

    Understanding the structural basis of actin cytoskeleton remodeling requires stabilization of actin monomers, oligomers, and filaments in complex with partner proteins, using various biochemical strategies. Here, we report a dramatic destabilization of the dynamic interaction with a model β-thymosin/WH2 domain induced by mutations in actin. This result underlines that mutant actins should be used with prudence to characterize interactions with intrinsically disordered partners as destabilization of dynamic interactions, although identifiable by NMR, may be invisible to other structural techniques. It also highlights how both β-thymosin/WH2 domains and actin tune local structure and dynamics in regulatory processes involving intrinsically disordered domains. © 2016 Federation of European Biochemical Societies.

  12. A new scaling approach for the mesoscale simulation of magnetic domain structures using Monte Carlo simulations

    Energy Technology Data Exchange (ETDEWEB)

    Radhakrishnan, B., E-mail: radhakrishnb@ornl.gov; Eisenbach, M.; Burress, T.A.

    2017-06-15

    Highlights: • Developed new scaling technique for dipole–dipole interaction energy. • Developed new scaling technique for exchange interaction energy. • Used scaling laws to extend atomistic simulations to micrometer length scale. • Demonstrated transition from mono-domain to vortex magnetic structure. • Simulated domain wall width and transition length scale agree with experiments. - Abstract: A new scaling approach has been proposed for the spin exchange and the dipole–dipole interaction energy as a function of the system size. The computed scaling laws are used in atomistic Monte Carlo simulations of magnetic moment evolution to predict the transition from single domain to a vortex structure as the system size increases. The width of a 180° – domain wall extracted from the simulated structures is in close agreement with experimentally values for an F–Si alloy. The transition size from a single domain to a vortex structure is also in close agreement with theoretically predicted and experimentally measured values for Fe.

  13. On the equilibrium configuration of the Kittel type domain structure with Bloch walls, l80deg

    International Nuclear Information System (INIS)

    Gavrila, H.

    1975-01-01

    Using a phenomenologic method for appreciating different components of the free energy, the equilibrium configuration of the Kittel-type domain structure with Bloch walls is obtained. By improving the known methods, more accurate magnetostatic energy calculations are reported. In order to determine the equilibrium structure, the total free energy is minimized with respect to two system parameters: the Bloch wall width and the structure half-period. (author)

  14. Structural Mechanism of the Oxygenase JMJD6 Recognition by the Extraterminal (ET) Domain of BRD4.

    Science.gov (United States)

    Konuma, Tsuyoshi; Yu, Di; Zhao, Chengcheng; Ju, Ying; Sharma, Rajal; Ren, Chunyan; Zhang, Qiang; Zhou, Ming-Ming; Zeng, Lei

    2017-11-24

    Jumonji domain-containing protein 6 (JMJD6) is a member of the Jumonji C family of Fe(II) and 2-oxoglutarate (2OG) dependent oxygenases. It possesses unique bi-functional oxygenase activities, acting as both an arginine demethylase and a lysyl-hydroxylase. JMJD6 has been reported to be over-expressed in oral, breast, lung, and colon cancers and plays important roles in regulation of transcription through interactions with transcription regulator BRD4, histones, U2AF65, Luc7L3, and SRSF11. Here, we report a structural mechanism revealed by NMR of JMJD6 recognition by the extraterminal (ET) domain of BRD4 in that a JMJD6 peptide (Lys84-Asn96) adapts an α-helix when bound to the ET domain. This intermolecular recognition is established through JMJD6 interactions with the conserved hydrophobic core of the ET domain, and reinforced by electrostatic interactions of JMJD6 with residues in the inter-helical α1-α2 loop of the ET domain. Notably, this mode of ligand recognition is different from that of ET domain recognition of NSD3, LANA of herpesvirus, and integrase of MLV, which involves formation of an intermolecular amphipathic two- or three- strand antiparallel β sheet. Furthermore, we demonstrate that the association between the BRD4 ET domain and JMJD6 likely requires a protein conformational change induced by single-stranded RNA binding.

  15. Domain size polydispersity effects on the structural and dynamical properties in lipid monolayers with phase coexistence

    Science.gov (United States)

    Rufeil-Fiori, Elena; Banchio, Adolfo J.

    Lipid monolayers with phase coexistence are a frequently used model for lipid membranes. In these systems, domains of the liquid-condensed phase always present size polydispersity. However, very few theoretical works consider size distribution effects on the monolayer properties. Because of the difference in surface densities, domains have excess dipolar density with respect to the surrounding liquid expanded phase, originating a dipolar inter-domain interaction. This interaction depends on the domain area, and hence the presence of a domain size distribution is associated with interaction polydispersity. Inter-domain interactions are fundamental to understanding the structure and dynamics of the monolayer. For this reason, it is expected that polydispersity significantly alters monolayer properties. By means of Brownian dynamics simulations, we study the radial distribution function (RDF), the average mean square displacement and the average time-dependent self-diffusion coefficient, D(t), of lipid monolayers with normal distributed size domains. It was found that polydispersity strongly affects the value of the interaction strength obtained, which is greatly underestimated if polydispersity is not considered. However, within a certain range of parameters, the RDF obtained from a polydisperse model can be well approximated by that of a monodisperse model, suitably fitting the interaction strength, even for 40% polydispersities. For small interaction strengths or small polydispersities, the polydisperse systems obtained from fitting the experimental RDF have an average mean square displacement and D(t) in good agreement with that of the monodisperse system.

  16. Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications

    Science.gov (United States)

    Cvicek, Vaclav; Goddard, William A.; Abrol, Ravinder

    2016-01-01

    The understanding of G-protein coupled receptors (GPCRs) is undergoing a revolution due to increased information about their signaling and the experimental determination of structures for more than 25 receptors. The availability of at least one receptor structure for each of the GPCR classes, well separated in sequence space, enables an integrated superfamily-wide analysis to identify signatures involving the role of conserved residues, conserved contacts, and downstream signaling in the context of receptor structures. In this study, we align the transmembrane (TM) domains of all experimental GPCR structures to maximize the conserved inter-helical contacts. The resulting superfamily-wide GpcR Sequence-Structure (GRoSS) alignment of the TM domains for all human GPCR sequences is sufficient to generate a phylogenetic tree that correctly distinguishes all different GPCR classes, suggesting that the class-level differences in the GPCR superfamily are encoded at least partly in the TM domains. The inter-helical contacts conserved across all GPCR classes describe the evolutionarily conserved GPCR structural fold. The corresponding structural alignment of the inactive and active conformations, available for a few GPCRs, identifies activation hot-spot residues in the TM domains that get rewired upon activation. Many GPCR mutations, known to alter receptor signaling and cause disease, are located at these conserved contact and activation hot-spot residue positions. The GRoSS alignment places the chemosensory receptor subfamilies for bitter taste (TAS2R) and pheromones (Vomeronasal, VN1R) in the rhodopsin family, known to contain the chemosensory olfactory receptor subfamily. The GRoSS alignment also enables the quantification of the structural variability in the TM regions of experimental structures, useful for homology modeling and structure prediction of receptors. Furthermore, this alignment identifies structurally and functionally important residues in all human GPCRs

  17. Structural analysis and dimerization profile of the SCAN domain of the pluripotency factor Zfp206

    KAUST Repository

    Liang, Yu; Huimei Hong, Felicia; Ganesan, Pugalenthi; Jiang, Sizun; Jauch, Ralf; Stanton, Lawrence W.; Kolatkar, Prasanna R.

    2012-01-01

    Zfp206 (also named as Zscan10) belongs to the subfamily of C2H2 zinc finger transcription factors, which is characterized by the N-terminal SCAN domain. The SCAN domain mediates self-association and association between the members of SCAN family transcription factors, but the structural basis and selectivity determinants for complex formation is unknown. Zfp206 is important for maintaining the pluripotency of embryonic stem cells presumably by combinatorial assembly of itself or other SCAN family members on enhancer regions. To gain insights into the folding topology and selectivity determinants for SCAN dimerization, we solved the 1.85 crystal structure of the SCAN domain of Zfp206. In vitro binding studies using a panel of 20 SCAN proteins indicate that the SCAN domain Zfp206 can selectively associate with other members of SCAN family transcription factors. Deletion mutations showed that the N-terminal helix 1 is critical for heterodimerization. Double mutations and multiple mutations based on the Zfp206SCAN-Zfp110SCAN model suggested that domain swapped topology is a possible preference for Zfp206SCAN-Zfp110SCAN heterodimer. Together, we demonstrate that the Zfp206SCAN constitutes a protein module that enables C2H2 transcription factor dimerization in a highly selective manner using a domain-swapped interface architecture and identify novel partners for Zfp206 during embryonal development. 2012 The Author(s).

  18. Structural analysis and dimerization profile of the SCAN domain of the pluripotency factor Zfp206

    KAUST Repository

    Liang, Yu

    2012-06-26

    Zfp206 (also named as Zscan10) belongs to the subfamily of C2H2 zinc finger transcription factors, which is characterized by the N-terminal SCAN domain. The SCAN domain mediates self-association and association between the members of SCAN family transcription factors, but the structural basis and selectivity determinants for complex formation is unknown. Zfp206 is important for maintaining the pluripotency of embryonic stem cells presumably by combinatorial assembly of itself or other SCAN family members on enhancer regions. To gain insights into the folding topology and selectivity determinants for SCAN dimerization, we solved the 1.85 crystal structure of the SCAN domain of Zfp206. In vitro binding studies using a panel of 20 SCAN proteins indicate that the SCAN domain Zfp206 can selectively associate with other members of SCAN family transcription factors. Deletion mutations showed that the N-terminal helix 1 is critical for heterodimerization. Double mutations and multiple mutations based on the Zfp206SCAN-Zfp110SCAN model suggested that domain swapped topology is a possible preference for Zfp206SCAN-Zfp110SCAN heterodimer. Together, we demonstrate that the Zfp206SCAN constitutes a protein module that enables C2H2 transcription factor dimerization in a highly selective manner using a domain-swapped interface architecture and identify novel partners for Zfp206 during embryonal development. 2012 The Author(s).

  19. Structural analysis of poly-SUMO chain recognition by the RNF4-SIMs domain.

    Science.gov (United States)

    Kung, Camy C-H; Naik, Mandar T; Wang, Szu-Huan; Shih, Hsiu-Ming; Chang, Che-Chang; Lin, Li-Ying; Chen, Chia-Lin; Ma, Che; Chang, Chi-Fon; Huang, Tai-Huang

    2014-08-15

    The E3 ubiquitin ligase RNF4 (RING finger protein 4) contains four tandem SIM [SUMO (small ubiquitin-like modifier)-interaction motif] repeats for selective interaction with poly-SUMO-modified proteins, which it targets for degradation. We employed a multi-faceted approach to characterize the structure of the RNF4-SIMs domain and the tetra-SUMO2 chain to elucidate the interaction between them. In solution, the SIM domain was intrinsically disordered and the linkers of the tetra-SUMO2 were highly flexible. Individual SIMs of the RNF4-SIMs domains bind to SUMO2 in the groove between the β2-strand and the α1-helix parallel to the β2-strand. SIM2 and SIM3 bound to SUMO with a high affinity and together constituted the recognition module necessary for SUMO binding. SIM4 alone bound to SUMO with low affinity; however, its contribution to tetra-SUMO2 binding avidity is comparable with that of SIM3 when in the RNF4-SIMs domain. The SAXS data of the tetra-SUMO2-RNF4-SIMs domain complex indicate that it exists as an ordered structure. The HADDOCK model showed that the tandem RNF4-SIMs domain bound antiparallel to the tetra-SUMO2 chain orientation and wrapped around the SUMO protamers in a superhelical turn without imposing steric hindrance on either molecule.

  20. Magnonic band structure, complete bandgap, and collective spin wave excitation in nanoscale two-dimensional magnonic crystals

    International Nuclear Information System (INIS)

    Kumar, D.; Barman, A.; Kłos, J. W.; Krawczyk, M.

    2014-01-01

    We present the observation of a complete bandgap and collective spin wave excitation in two-dimensional magnonic crystals comprised of arrays of nanoscale antidots and nanodots, respectively. Considering that the frequencies dealt with here fall in the microwave band, these findings can be used for the development of suitable magnonic metamaterials and spin wave based signal processing. We also present the application of a numerical procedure, to compute the dispersion relations of spin waves for any high symmetry direction in the first Brillouin zone. The results obtained from this procedure have been reproduced and verified by the well established plane wave method for an antidot lattice, when magnetization dynamics at antidot boundaries are pinned. The micromagnetic simulation based method can also be used to obtain iso–frequency contours of spin waves. Iso–frequency contours are analogous of the Fermi surfaces and hence, they have the potential to radicalize our understanding of spin wave dynamics. The physical origin of bands, partial and full magnonic bandgaps have been explained by plotting the spatial distribution of spin wave energy spectral density. Although, unfettered by rigid assumptions and approximations, which afflict most analytical methods used in the study of spin wave dynamics, micromagnetic simulations tend to be computationally demanding. Thus, the observation of collective spin wave excitation in the case of nanodot arrays, which can obviate the need to perform simulations, may also prove to be valuable

  1. Structures of BIR domains from human NAIP and cIAP2

    International Nuclear Information System (INIS)

    Herman, Maria Dolores; Moche, Martin; Flodin, Susanne; Welin, Martin; Trésaugues, Lionel; Johansson, Ida; Nilsson, Martina; Nordlund, Pär; Nyman, Tomas

    2009-01-01

    The crystal structures of the human NAIP BIR2 and cIAP2 BIR3 domains have been determined. Both BIR domains harbors an amino-terminal tetrapeptide in its peptide-binding groove. The inhibitor of apoptosis (IAP) family of proteins contains key modulators of apoptosis and inflammation that interact with caspases through baculovirus IAP-repeat (BIR) domains. Overexpression of IAP proteins frequently occurs in cancer cells, thus counteracting the activated apoptotic program. The IAP proteins have therefore emerged as promising targets for cancer therapy. In this work, X-ray crystallography was used to determine the first structures of BIR domains from human NAIP and cIAP2. Both structures harbour an N-terminal tetrapeptide in the conserved peptide-binding groove. The structures reveal that these two proteins bind the tetrapeptides in a similar mode as do other BIR domains. Detailed interactions are described for the P1′–P4′ side chains of the peptide, providing a structural basis for peptide-specific recognition. An arginine side chain in the P3′ position reveals favourable interactions with its hydrophobic moiety in the binding pocket, while hydrophobic residues in the P2′ and P4′ pockets make similar interactions to those seen in other BIR domain–peptide complexes. The structures also reveal how a serine in the P1′ position is accommodated in the binding pockets of NAIP and cIAP2. In addition to shedding light on the specificity determinants of these two proteins, the structures should now also provide a framework for future structure-based work targeting these proteins

  2. Shapes of isolated domains and field induced evolution of regular and random 2D domain structures in LiNbO3 and LiTaO3

    International Nuclear Information System (INIS)

    Chernykh, A.; Shur, V.; Nikolaeva, E.; Shishkin, E.; Shur, A.; Terabe, K.; Kurimura, S.; Kitamura, K.; Gallo, K.

    2005-01-01

    The variety of the shapes of isolated domains, revealed in congruent and stoichiometric LiTaO 3 and LiNbO 3 by chemical etching and visualized by optical and scanning probe microscopy, was obtained by computer simulation. The kinetic nature of the domain shape was clearly demonstrated. The kinetics of domain structure with the dominance of the growth of the steps formed at the domain walls as a result of domain merging was investigated experimentally in slightly distorted artificial regular two-dimensional (2D) hexagonal domain structure and random natural one. The artificial structure has been realized in congruent LiNbO 3 by 2D electrode pattern produced by photolithography. The polarization reversal in congruent LiTaO 3 was investigated as an example of natural domain growth limited by merging. The switching process defined by domain merging was studied by computer simulation. The crucial dependence of the switching kinetics on the nuclei concentration has been revealed

  3. High-resolution NMR structures of the domains of Saccharomyces cerevisiae Tho1

    International Nuclear Information System (INIS)

    Jacobsen, Julian O. B.; Allen, Mark D.; Freund, Stefan M. V.; Bycroft, Mark

    2016-01-01

    In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and the C-terminal RNA-binding domain of S. cerevisiae Tho1 have been determined. THO is a multi-protein complex involved in the formation of messenger ribonuclear particles (mRNPs) by coupling transcription with mRNA processing and export. THO is thought to be formed from five subunits, Tho2p, Hpr1p, Tex1p, Mft1p and Thp2p, and recent work has determined a low-resolution structure of the complex [Poulsen et al. (2014 ▸), PLoS One, 9, e103470]. A number of additional proteins are thought to be involved in the formation of mRNP in yeast, including Tho1, which has been shown to bind RNA in vitro and is recruited to actively transcribed chromatin in vivo in a THO-complex and RNA-dependent manner. Tho1 is known to contain a SAP domain at the N-terminus, but the ability to suppress the expression defects of the hpr1Δ mutant of THO was shown to reside in the RNA-binding C-terminal region. In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and C-terminal RNA-binding domain have been determined

  4. High-resolution NMR structures of the domains of Saccharomyces cerevisiae Tho1

    Energy Technology Data Exchange (ETDEWEB)

    Jacobsen, Julian O. B.; Allen, Mark D.; Freund, Stefan M. V.; Bycroft, Mark, E-mail: mxb@mrc-lmb.cam.ac.uk [MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH (United Kingdom)

    2016-05-23

    In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and the C-terminal RNA-binding domain of S. cerevisiae Tho1 have been determined. THO is a multi-protein complex involved in the formation of messenger ribonuclear particles (mRNPs) by coupling transcription with mRNA processing and export. THO is thought to be formed from five subunits, Tho2p, Hpr1p, Tex1p, Mft1p and Thp2p, and recent work has determined a low-resolution structure of the complex [Poulsen et al. (2014 ▸), PLoS One, 9, e103470]. A number of additional proteins are thought to be involved in the formation of mRNP in yeast, including Tho1, which has been shown to bind RNA in vitro and is recruited to actively transcribed chromatin in vivo in a THO-complex and RNA-dependent manner. Tho1 is known to contain a SAP domain at the N-terminus, but the ability to suppress the expression defects of the hpr1Δ mutant of THO was shown to reside in the RNA-binding C-terminal region. In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and C-terminal RNA-binding domain have been determined.

  5. Structure of the human histone chaperone FACT Spt16 N-terminal domain

    Energy Technology Data Exchange (ETDEWEB)

    Marcianò, G.; Huang, D. T., E-mail: d.huang@beatson.gla.ac.uk [Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland (United Kingdom)

    2016-01-22

    The Spt16–SSRP1 heterodimer is a histone chaperone that plays an important role in regulating chromatin assembly. Here, a crystal structure of the N-terminal domain of human Spt16 is presented and it is shown that this domain may contribute to histone binding. The histone chaperone FACT plays an important role in facilitating nucleosome assembly and disassembly during transcription. FACT is a heterodimeric complex consisting of Spt16 and SSRP1. The N-terminal domain of Spt16 resembles an inactive aminopeptidase. How this domain contributes to the histone chaperone activity of FACT remains elusive. Here, the crystal structure of the N-terminal domain (NTD) of human Spt16 is reported at a resolution of 1.84 Å. The structure adopts an aminopeptidase-like fold similar to those of the Saccharomyces cerevisiae and Schizosaccharomyces pombe Spt16 NTDs. Isothermal titration calorimetry analyses show that human Spt16 NTD binds histones H3/H4 with low-micromolar affinity, suggesting that Spt16 NTD may contribute to histone binding in the FACT complex. Surface-residue conservation and electrostatic analysis reveal a conserved acidic patch that may be involved in histone binding.

  6. Effect of the SH3-SH2 domain linker sequence on the structure of Hck kinase.

    Science.gov (United States)

    Meiselbach, Heike; Sticht, Heinrich

    2011-08-01

    The coordination of activity in biological systems requires the existence of different signal transduction pathways that interact with one another and must be precisely regulated. The Src-family tyrosine kinases, which are found in many signaling pathways, differ in their physiological function despite their high overall structural similarity. In this context, the differences in the SH3-SH2 domain linkers might play a role for differential regulation, but the structural consequences of linker sequence remain poorly understood. We have therefore performed comparative molecular dynamics simulations of wildtype Hck and of a mutant Hck in which the SH3-SH2 domain linker is replaced by the corresponding sequence from the homologous kinase Lck. These simulations reveal that linker replacement not only affects the orientation of the SH3 domain itself, but also leads to an alternative conformation of the activation segment in the Hck kinase domain. The sequence of the SH3-SH2 domain linker thus exerts a remote effect on the active site geometry and might therefore play a role in modulating the structure of the inactive kinase or in fine-tuning the activation process itself.

  7. Structure of the human histone chaperone FACT Spt16 N-terminal domain

    International Nuclear Information System (INIS)

    Marcianò, G.; Huang, D. T.

    2016-01-01

    The Spt16–SSRP1 heterodimer is a histone chaperone that plays an important role in regulating chromatin assembly. Here, a crystal structure of the N-terminal domain of human Spt16 is presented and it is shown that this domain may contribute to histone binding. The histone chaperone FACT plays an important role in facilitating nucleosome assembly and disassembly during transcription. FACT is a heterodimeric complex consisting of Spt16 and SSRP1. The N-terminal domain of Spt16 resembles an inactive aminopeptidase. How this domain contributes to the histone chaperone activity of FACT remains elusive. Here, the crystal structure of the N-terminal domain (NTD) of human Spt16 is reported at a resolution of 1.84 Å. The structure adopts an aminopeptidase-like fold similar to those of the Saccharomyces cerevisiae and Schizosaccharomyces pombe Spt16 NTDs. Isothermal titration calorimetry analyses show that human Spt16 NTD binds histones H3/H4 with low-micromolar affinity, suggesting that Spt16 NTD may contribute to histone binding in the FACT complex. Surface-residue conservation and electrostatic analysis reveal a conserved acidic patch that may be involved in histone binding

  8. Nano-scale Biophysical and Structural Investigations on Intact and Neuropathic Nerve Fibers by Simultaneous Combination of Atomic Force and Confocal Microscopy

    Directory of Open Access Journals (Sweden)

    Gonzalo Rosso

    2017-08-01

    Full Text Available The links between neuropathies of the peripheral nervous system (PNS, including Charcot-Marie-Tooth1A and hereditary neuropathy with liability to pressure palsies, and impaired biomechanical and structural integrity of PNS nerves remain poorly understood despite the medical urgency. Here, we present a protocol describing simultaneous structural and biomechanical integrity investigations on isolated nerve fibers, the building blocks of nerves. Nerve fibers are prepared from nerves harvested from wild-type and exemplary PNS neuropathy mouse models. The basic principle of the designed experimental approach is based on the simultaneous combination of atomic force microscopy (AFM and confocal microscopy. AFM is used to visualize the surface structure of nerve fibers at nano-scale resolution. The simultaneous combination of AFM and confocal microscopy is used to perform biomechanical, structural, and functional integrity measurements at nano- to micro-scale. Isolation of sciatic nerves and subsequent teasing of nerve fibers take ~45 min. Teased fibers can be maintained at 37°C in a culture medium and kept viable for up to 6 h allowing considerable time for all measurements which require 3–4 h. The approach is designed to be widely applicable for nerve fibers from mice of any PNS neuropathy. It can be extended to human nerve biopsies.

  9. Eukaryotic ribonucleases P/MRP: the crystal structure of the P3 domain.

    Science.gov (United States)

    Perederina, Anna; Esakova, Olga; Quan, Chao; Khanova, Elena; Krasilnikov, Andrey S

    2010-02-17

    Ribonuclease (RNase) P is a site-specific endoribonuclease found in all kingdoms of life. Typical RNase P consists of a catalytic RNA component and a protein moiety. In the eukaryotes, the RNase P lineage has split into two, giving rise to a closely related enzyme, RNase MRP, which has similar components but has evolved to have different specificities. The eukaryotic RNases P/MRP have acquired an essential helix-loop-helix protein-binding RNA domain P3 that has an important function in eukaryotic enzymes and distinguishes them from bacterial and archaeal RNases P. Here, we present a crystal structure of the P3 RNA domain from Saccharomyces cerevisiae RNase MRP in a complex with RNase P/MRP proteins Pop6 and Pop7 solved to 2.7 A. The structure suggests similar structural organization of the P3 RNA domains in RNases P/MRP and possible functions of the P3 domains and proteins bound to them in the stabilization of the holoenzymes' structures as well as in interactions with substrates. It provides the first insight into the structural organization of the eukaryotic enzymes of the RNase P/MRP family.

  10. The structure and dynamics of tandem WW domains in a negative regulator of notch signaling, Suppressor of deltex.

    Science.gov (United States)

    Fedoroff, Oleg Y; Townson, Sharon A; Golovanov, Alexander P; Baron, Martin; Avis, Johanna M

    2004-08-13

    WW domains mediate protein recognition, usually though binding to proline-rich sequences. In many proteins, WW domains occur in tandem arrays. Whether or how individual domains within such arrays cooperate to recognize biological partners is, as yet, poorly characterized. An important question is whether functional diversity of different WW domain proteins is reflected in the structural organization and ligand interaction mechanisms of their multiple domains. We have determined the solution structure and dynamics of a pair of WW domains (WW3-4) from a Drosophila Nedd4 family protein called Suppressor of deltex (Su(dx)), a regulator of Notch receptor signaling. We find that the binding of a type 1 PPPY ligand to WW3 stabilizes the structure with effects propagating to the WW4 domain, a domain that is not active for ligand binding. Both WW domains adopt the characteristic triple-stranded beta-sheet structure, and significantly, this is the first example of a WW domain structure to include a domain (WW4) lacking the second conserved Trp (replaced by Phe). The domains are connected by a flexible linker, which allows a hinge-like motion of domains that may be important for the recognition of functionally relevant targets. Our results contrast markedly with those of the only previously determined three-dimensional structure of tandem WW domains, that of the rigidly oriented WW domain pair from the RNA-splicing factor Prp40. Our data illustrate that arrays of WW domains can exhibit a variety of higher order structures and ligand interaction mechanisms.

  11. LOADS INTERACTION DOMAINS METHODOLOGY FOR THE DESIGN OF STEEL GREENHOUSE STRUCTURES

    Directory of Open Access Journals (Sweden)

    Sergio Castellano

    2007-03-01

    Full Text Available Aim of this research is to develop a design methodology which correlates main structural design parameters, whose production is characterised by high levels of standardization, such as the height of gutter or the distance between frames, with actions on the greenhouse. The methodology, based on the use of charts and abacus, permits a clear and a direct interpretation of the structural response to design load combinations and allows the design of structural improvements with the aim of the optimization of the ratio benefits (structural strength/costs. The study of structural interaction domains allowed a clear and a direct interpretation of the structural response to design load combinations. The diagrams highlight not only if the structure fulfils the standard requirements but also the safety levels with respect to design load combinations and allow the structural designer how to operate in order to optimize the structural response with standard requirements achieving the best ratio benefits (structural safety/ costs. The methodology was developed basing on criteria assigned by EN13031 on two different kinds of greenhouse structures: an arched greenhouse with a film plastic covering and a duo pitched roof greenhouse cover with rigid plastic membranes. Structural interaction domains for arched greenhouse showed a better capability of the structure to resist to vertical loads then to horizontal one. Moreover, the climatic load distribution on the structure assigned by EN13031 is such that the combination of climatic actions is less dangerous for the structure then their individual application. Whilst, duo pitched roof steel greenhouse interaction domains, showed a better capability of the structure to resist to vertical loads then to horizontal one and that, in any case, the serviceability limit states analysis is more strict then the ULS one. The shape of structural domains highlighted that the combination of actions is more dangerous for the

  12. Nanoscale Membrane Domain Formation Driven by Cholesterol

    Czech Academy of Sciences Publication Activity Database

    Javanainen, M.; Martinez-Seara, Hector; Vattulainen, I.

    2017-01-01

    Roč. 7, Apr 25 (2017), č. článku 1143. ISSN 2045-2322 R&D Projects: GA ČR(CZ) GBP208/12/G016 Institutional support: RVO:61388963 Keywords : molecular dynamics simulations * differential scanning calorimetry * pulmonary surfactant membranes Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 4.259, year: 2016 https://www.nature.com/ articles /s41598-017-01247-9

  13. Rift Valley fever phlebovirus NSs protein core domain structure suggests molecular basis for nuclear filaments.

    Science.gov (United States)

    Barski, Michal; Brennan, Benjamin; Miller, Ona K; Potter, Jane A; Vijayakrishnan, Swetha; Bhella, David; Naismith, James H; Elliott, Richard M; Schwarz-Linek, Ulrich

    2017-09-15

    Rift Valley fever phlebovirus (RVFV) is a clinically and economically important pathogen increasingly likely to cause widespread epidemics. RVFV virulence depends on the interferon antagonist non-structural protein (NSs), which remains poorly characterized. We identified a stable core domain of RVFV NSs (residues 83-248), and solved its crystal structure, a novel all-helical fold organized into highly ordered fibrils. A hallmark of RVFV pathology is NSs filament formation in infected cell nuclei. Recombinant virus encoding the NSs core domain induced intranuclear filaments, suggesting it contains all essential determinants for nuclear translocation and filament formation. Mutations of key crystal fibril interface residues in viruses encoding full-length NSs completely abrogated intranuclear filament formation in infected cells. We propose the fibrillar arrangement of the NSs core domain in crystals reveals the molecular basis of assembly of this key virulence factor in cell nuclei. Our findings have important implications for fundamental understanding of RVFV virulence.

  14. Monte Carlo Simulation of Ferroelectric Domain Structure and Applied Field Response in Two Dimensions

    Energy Technology Data Exchange (ETDEWEB)

    Potter, Jr., B.G.; Tikare, V.; Tuttle, B.A.

    1999-06-30

    A 2-D, lattice-Monte Carlo approach was developed to simulate ferroelectric domain structure. The model currently utilizes a Hamiltonian for the total energy based only upon electrostatic terms involving dipole-dipole interactions, local polarization gradients and the influence of applied electric fields. The impact of boundary conditions on the domain configurations obtained was also examined. In general, the model exhibits domain structure characteristics consistent with those observed in a tetragonally distorted ferroelectric. The model was also extended to enable the simulation of ferroelectric hysteresis behavior. Simulated hysteresis loops were found to be very similar in appearance to those observed experimentally in actual materials. This qualitative agreement between the simulated hysteresis loop characteristics and real ferroelectric behavior was also confirmed in simulations run over a range of simulation temperatures and applied field frequencies.

  15. Controlling the anisotropy and domain structure with oblique deposition and substrate rotation

    Directory of Open Access Journals (Sweden)

    N. Chowdhury

    2014-02-01

    Full Text Available Effect of substrate rotation on anisotropy and domain structure for a thin ferromagnetic film has been investigated in this work. For this purpose Co films with 10 nm thickness have been prepared by sputtering with oblique angle of incidence for various substrate rotations. This method of preparation induces a uniaxial anisotropy due to shadow deposition effect. The magnetization reversal is studied by magneto-optic Kerr effect (MOKE based microscope in the longitudinal geometry. The Co films prepared by rotating the substrate with 10 and 20 rpm weakens the anisotropy but does not completely give isotropic films. But this leads to high dispersion in local grain anisotropy resulting in ripple and labyrinth domains. It is observed that the substrate rotation has moderate effect on uniaxial anisotropy but has significant effect on the magnetization reversal process and the domain structure.

  16. Nanoscale structure, dynamics and power conversion efficiency correlations in small molecule and oligomer-based photovoltaic devices

    Science.gov (United States)

    Szarko, Jodi M.; Guo, Jianchang; Rolczynski, Brian S.; Chen, Lin X.

    2011-01-01

    Photovoltaic functions in organic materials are intimately connected to interfacial morphologies of molecular packing in films on the nanometer scale and molecular levels. This review will focus on current studies on correlations of nanoscale morphologies in organic photovoltaic (OPV) materials with fundamental processes relevant to photovoltaic functions, such as light harvesting, exciton splitting, exciton diffusion, and charge separation (CS) and diffusion. Small molecule photovoltaic materials will be discussed here. The donor and acceptor materials in small molecule OPV devices can be fabricated in vacuum-deposited, multilayer, crystalline thin films, or spin-coated together to form blended bulk heterojunction (BHJ) films. These two methods result in very different morphologies of the solar cell active layers. There is still a formidable debate regarding which morphology is favored for OPV optimization. The morphology of the conducting films has been systematically altered; using variations of the techniques above, the whole spectrum of film qualities can be fabricated. It is possible to form a highly crystalline material, one which is completely amorphous, or an intermediate morphology. In this review, we will summarize the past key findings that have driven organic solar cell research and the current state-of-the-art of small molecule and conducting oligomer materials. We will also discuss the merits and drawbacks of these devices. Finally, we will highlight some works that directly compare the spectra and morphology of systematically elongated oligothiophene derivatives and compare these oligomers to their polymer counterparts. We hope this review will shed some new light on the morphology differences of these two systems. PMID:22110870

  17. Nanoscale zerovalent iron alters soil bacterial community structure and inhibits chloroaromatic biodegradation potential in Aroclor 1242-contaminated soil

    International Nuclear Information System (INIS)

    Tilston, Emma L.; Collins, Chris D.; Mitchell, Geoffrey R.; Princivalle, Jessica; Shaw, Liz J.

    2013-01-01

    Nanoscale zerovalent iron (nZVI) has potential for the remediation of organochlorine-contaminated environments. Environmental safety concerns associated with in situ deployment of nZVI include potential negative impacts on indigenous microbes whose biodegradative functions could contribute to contaminant remediation. With respect to a two-step polychlorinated biphenyl remediation scenario comprising nZVI dechlorination followed by aerobic biodegradation, we examined the effect of polyacrylic acid (PAA)-coated nZVI (mean diameter = 12.5 nm) applied at 10 g nZVI kg −1 to Aroclor-1242 contaminated and uncontaminated soil over 28 days. nZVI had a limited effect on Aroclor congener profiles, but, either directly or indirectly via changes to soil physico-chemical conditions (pH, Eh), nZVI addition caused perturbation to soil bacterial community composition, and reduced the activity of chloroaromatic mineralizing microorganisms. We conclude that nZVI addition has the potential to inhibit microbial functions that could be important for PCB remediation strategies combining nZVI treatment and biodegradation. Highlights: ► Impact of nano-sized zerovalent iron on microbes was investigated in soil microcosms. ► Zerovalent iron had short-lived effects on redox potential and Aroclor dechlorination. ► Microbial populations also showed short-lived perturbations in their size. ► The activity of chloroaromatic degrading microbes did not recover within 28 days. ► Zerovalent iron application inhibits ensuing PCB bioremediative microbial functions. - nZVI inhibits microbial functions of potential importance for remediation strategies combining nZVI treatment and biodegradation.

  18. The dynamics of the asymmetric motion of domain walls of sandwich domain structure in a Fe-based amorphous ribbon

    Energy Technology Data Exchange (ETDEWEB)

    Zhmetko, D.N., E-mail: sergey.zhmetko@gmail.com [Department of Physics, Zaporizhzhya National University, 66 Zhukovsky Street, 69063 Zaporizhzhya (Ukraine); Zhmetko, S.D. [Department of Physics, Zaporizhzhya National University, 66 Zhukovsky Street, 69063 Zaporizhzhya (Ukraine); Troschenkov, Y.N. [Institute for Magnetism, 36-b Vernadsky Boulevard, 03142 Kyiv (Ukraine); Matsura, A.V. [Department of Physics, Zaporizhzhya National University, 66 Zhukovsky Street, 69063 Zaporizhzhya (Ukraine)

    2013-08-15

    The frequency dependence of asymmetry of the domain walls velocity relative to the middle plane of amorphous ribbon is investigated. An additional pressure of the same direction acting on each domain wall caused by dependence of eddy current damping on the coordinate of the domain wall is revealed. The microscopic mechanisms of this additional pressure are considered. - Highlights: ► Additional pressure on the domain wall, caused by inhomogeneity of its damping. ► Asymmetry of the coordinate of the nucleation of domain walls and their damping. ► Connection between the components of additional pressure and its direction. ► Interaction of domain walls with the surface defects of the amorphous ribbon.

  19. The dynamics of the asymmetric motion of domain walls of sandwich domain structure in a Fe-based amorphous ribbon

    International Nuclear Information System (INIS)

    Zhmetko, D.N.; Zhmetko, S.D.; Troschenkov, Y.N.; Matsura, A.V.

    2013-01-01

    The frequency dependence of asymmetry of the domain walls velocity relative to the middle plane of amorphous ribbon is investigated. An additional pressure of the same direction acting on each domain wall caused by dependence of eddy current damping on the coordinate of the domain wall is revealed. The microscopic mechanisms of this additional pressure are considered. - Highlights: ► Additional pressure on the domain wall, caused by inhomogeneity of its damping. ► Asymmetry of the coordinate of the nucleation of domain walls and their damping. ► Connection between the components of additional pressure and its direction. ► Interaction of domain walls with the surface defects of the amorphous ribbon

  20. Structure of DSM-5 and ICD-11 personality domains in Iranian community sample.

    Science.gov (United States)

    Lotfi, Mozhgan; Bach, Bo; Amini, Mahdi; Simonsen, Erik

    2018-02-02

    Personality disorders (PD) have been deemed the most problematic diagnostic grouping in terms of validity and utility, which particularly applies to non-Western societies. The current study evaluated the structural validity of PD trait domains in the Diagnostic and Statistical Manual of Mental Disorders-5 (DSM-5) Section III and the proposed International Classification of Diseases-11 (ICD-11) in the Iranian population. Community-dwelling adults (n = 285; 66% women) were administered the Personality Inventory for DSM-5, whereas the proposed ICD-11 trait domains were delineated using an algorithm for Personality Inventory for DSM-5 trait facets. The five-factor organization and higher-order hierarchical structure of both models were examined using exploratory structural equation modelling analyses. The five-factor exploratory structural equation modelling loadings overall resembled international findings on DSM-5 Section III traits (including Psychoticism), whereas the ICD-11 five-factor structure aligned with the proposed ICD-11 domain features (including Anankastia). Additionally, we identified a hierarchical structure from one to five factors for both models that conceptually aligned with established models of personality and psychopathology. This study provided initial support for the structural validity of DSM-5 and ICD-11 PD trait models in Iranian culture. Future research warrants replication in larger samples and clinical populations. Copyright © 2018 John Wiley & Sons, Ltd. Copyright © 2018 John Wiley & Sons, Ltd.

  1. Extracting structural features of rat sciatic nerve using polarization-sensitive spectral domain optical coherence tomography

    NARCIS (Netherlands)

    Islam, M.S.; Oliveira, M.C.; Wang, Y.; Henry, F.P.; Randolph, M.A.; Park, B. H.; de Boer, J.F.

    2012-01-01

    We present spectral domain polarization-sensitive optical coherence tomography (SD PS-OCT) imaging of peripheral nerves. Structural and polarization-sensitive OCT imaging of uninjured rat sciatic nerves was evaluated both qualitatively and quantitatively. OCT and its functional extension, PS-OCT,

  2. Evolution of the RNase P RNA structural domain in Leptospira spp

    NARCIS (Netherlands)

    Ravishankar, Vigneshwaran; Ahmed, Ahmed; Sivagnanam, Ulaganathan; Muthuraman, Krishnaraja; Karthikaichamy, Anbarasu; Wilson, Herald A.; Devendran, Ajay; Hartskeerl, Rudy A.; Raj, Stephen M. L.

    2014-01-01

    We have employed the RNase P RNA (RPR) gene, which is present as single copy in chromosome I of Leptospira spp. to investigate the phylogeny of structural domains present in the RNA subunit of the tRNA processing enzyme, RNase P. RPR gene sequences of 150 strains derived from NCBI database along

  3. alpha-helical structural elements within the voltage-sensing domains of a K(+) channel.

    Science.gov (United States)

    Li-Smerin, Y; Hackos, D H; Swartz, K J

    2000-01-01

    Voltage-gated K(+) channels are tetramers with each subunit containing six (S1-S6) putative membrane spanning segments. The fifth through sixth transmembrane segments (S5-S6) from each of four subunits assemble to form a central pore domain. A growing body of evidence suggests that the first four segments (S1-S4) comprise a domain-like voltage-sensing structure. While the topology of this region is reasonably well defined, the secondary and tertiary structures of these transmembrane segments are not. To explore the secondary structure of the voltage-sensing domains, we used alanine-scanning mutagenesis through the region encompassing the first four transmembrane segments in the drk1 voltage-gated K(+) channel. We examined the mutation-induced perturbation in gating free energy for periodicity characteristic of alpha-helices. Our results are consistent with at least portions of S1, S2, S3, and S4 adopting alpha-helical secondary structure. In addition, both the S1-S2 and S3-S4 linkers exhibited substantial helical character. The distribution of gating perturbations for S1 and S2 suggest that these two helices interact primarily with two environments. In contrast, the distribution of perturbations for S3 and S4 were more complex, suggesting that the latter two helices make more extensive protein contacts, possibly interfacing directly with the shell of the pore domain.

  4. α-Helical Structural Elements within the Voltage-Sensing Domains of a K+ Channel

    Science.gov (United States)

    Li-Smerin, Yingying; Hackos, David H.; Swartz, Kenton J.

    2000-01-01

    Voltage-gated K+ channels are tetramers with each subunit containing six (S1–S6) putative membrane spanning segments. The fifth through sixth transmembrane segments (S5–S6) from each of four subunits assemble to form a central pore domain. A growing body of evidence suggests that the first four segments (S1–S4) comprise a domain-like voltage-sensing structure. While the topology of this region is reasonably well defined, the secondary and tertiary structures of these transmembrane segments are not. To explore the secondary structure of the voltage-sensing domains, we used alanine-scanning mutagenesis through the region encompassing the first four transmembrane segments in the drk1 voltage-gated K+ channel. We examined the mutation-induced perturbation in gating free energy for periodicity characteristic of α-helices. Our results are consistent with at least portions of S1, S2, S3, and S4 adopting α-helical secondary structure. In addition, both the S1–S2 and S3–S4 linkers exhibited substantial helical character. The distribution of gating perturbations for S1 and S2 suggest that these two helices interact primarily with two environments. In contrast, the distribution of perturbations for S3 and S4 were more complex, suggesting that the latter two helices make more extensive protein contacts, possibly interfacing directly with the shell of the pore domain. PMID:10613917

  5. The influence of boundary conditions on domain structure stability in spin wave approximation

    International Nuclear Information System (INIS)

    Wachinewski, A.

    1974-01-01

    Instead of the usually used Born-Karman cyclic conditions, boundary conditions which take into account the situation of the boundary lattice sites lying on the crystal's surface are assumed. It is shown that the particular choice of the boundary conditions secures the stability of domain structure in ferromagnet (positive spin wave energies), without including the Winter term in Hamiltonian. (author)

  6. Preconditioned finite-difference frequency-domain for modelling periodic dielectric structures - comparisons with FDTD

    NARCIS (Netherlands)

    Chabory, A.; Hon, de B.P.; Schilders, W.H.A.; Tijhuis, A.G.

    2008-01-01

    Finite-difference techniques are very popular and versatile numerical tools in computational electromagnetics. In this paper, we propose a preconditioned finite-difference frequency-domain method (FDFD) to model periodic structures in 2D and 3D. The preconditioner follows from a modal decoupling

  7. Preconditioned finite-difference frequency-domain for modelling periodic dielectric structures : comparisons with FDTD

    NARCIS (Netherlands)

    Chabory, A.; Hon, de B.P.; Schilders, W.H.A.; Tijhuis, A.G.

    2008-01-01

    Finite-difference techniques are very popular and versatile numerical tools in computational electromagnetics. In this paper, we propose a preconditioned finite-difference frequency-domain method (FDFD) to model periodic structures in 2D and 3D. The preconditioner follows from a modal decoupling

  8. Study of stratified dielectric slab medium structures using pseudo-spectral time domain (PSTD) algorithm

    DEFF Research Database (Denmark)

    Tong, M.S.; Lu, Y.; Chen, Y.

    2005-01-01

    -layer structures are analyzed. Results show that this method matches satisfactorily the Nyquist sampling theorem in terms of spatial discretization. By comparing the given results, it is found that the PSTD method outperforms the finite-difference time-domain (FDTD) method in general, especially in terms...

  9. Exact diagonalization study of domain structures in integer filling factor quantum Hall ferromagnets

    Czech Academy of Sciences Publication Activity Database

    Rezayi, E. H.; Jungwirth, Tomáš; MacDonald, A. H.; Haldane, F. D. M.

    2003-01-01

    Roč. 67, č. 20 (2003), s. 201305-1 - 201305-4 ISSN 0163-1829 R&D Projects: GA ČR GA202/01/0754 Institutional research plan: CEZ:AV0Z1010914 Keywords : domain structure * integer filling factor * quantum Hall ferromagnets Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.962, year: 2003

  10. Temperature-induced transitions between domain structures of ultrathin magnetic films

    International Nuclear Information System (INIS)

    Polyakova, T.; Zablotskii, V.

    2005-01-01

    Full text: Understanding of the influence of temperature on behavior of domain patterns of ultrathin magnetic films is of high significance for the fundamental physics of nanomagnetism as well as for technological applications. A thickness-dependent Curie temperature of ultrathin films may cause many interesting phenomena in the thermal evolution of domain structures (DS): i) nontrivial changes of the anisotropy constants as a function of the film thickness; ii) so-called inverse melting of DSs (processes where a more symmetric domain phase is found at lower temperatures than at higher temperatures - the inverse phase sequence) [1]; iii) temperature-induced transitions between domain structures. The possibility of such transitions is determined by lowering of the potential barriers separating different magnetization states as the film temperature approaches the Curie point. In this case with an increase of temperature, due to a significant decrease of the anisotropy constant, the domain wall energy is low enough and allows the system to reach equilibrium by a change of the domain wall number in the sample. This manifests itself in a transition from a metastable DS to a more stable DS which corresponds to new values of the anisotropy constant and magnetizations saturation. Thus, the temperature-induced transitions are driven by temperature changes of the magnetic parameters of the film. The key parameters controlling the DS geometry and period are the characteristic length, l c =σ/4πM S 2 (the ratio between the domain wall and demagnetization energies), and the quality factor Q =K/2πM S 2 (K is the first anisotropy constant). We show that for films with a pronounced nonmonotonic temperature dependence of l c one can expect a counter thermodynamic behavior: the inverse phase sequence and cooling-induced disordering. On changing temperature the existing domain structure should accommodate itself under new magnitudes of l c and Q. There are the two possible

  11. Tip-induced domain structures and polarization switching in ferroelectric amino acid glycine

    Energy Technology Data Exchange (ETDEWEB)

    Seyedhosseini, E., E-mail: Seyedhosseini@ua.pt; Ivanov, M. [CICECO-Aveiro Institute of Materials and Department of Physics, University of Aveiro, 3810-193 Aveiro (Portugal); Bdikin, I. [TEMA and Department of Mechanical Engineering, University of Aveiro, 3810-193 Aveiro (Portugal); Vasileva, D. [Institute of Natural Sciences, Ural Federal University, 620000 Ekaterinburg (Russian Federation); Kudryavtsev, A. [Moscow State Institute of Radioengineering, Electronics and Automation, 119454 Moscow (Russian Federation); Rodriguez, B. J. [Conway Institute of Biomolecular and Biomedical Research and School of Physics, University College Dublin, Dublin (Ireland); Kholkin, A. L. [CICECO-Aveiro Institute of Materials and Department of Physics, University of Aveiro, 3810-193 Aveiro (Portugal); Institute of Natural Sciences, Ural Federal University, 620000 Ekaterinburg (Russian Federation)

    2015-08-21

    Bioorganic ferroelectrics and piezoelectrics are becoming increasingly important in view of their intrinsic compatibility with biological environment and biofunctionality combined with strong piezoelectric effect and a switchable polarization at room temperature. Here, we study tip-induced domain structures and polarization switching in the smallest amino acid β-glycine, representing a broad class of non-centrosymmetric amino acids. We show that β-glycine is indeed a room-temperature ferroelectric and polarization can be switched by applying a bias to non-polar cuts via a conducting tip of atomic force microscope (AFM). Dynamics of these in-plane domains is studied as a function of an applied voltage and pulse duration. The domain shape is dictated by polarization screening at the domain boundaries and mediated by growth defects. Thermodynamic theory is applied to explain the domain propagation induced by the AFM tip. Our findings suggest that the properties of β-glycine are controlled by the charged domain walls which in turn can be manipulated by an external bias.

  12. Phase domain structures in cylindrical magnets under conditions of a first-order magnetic phase transition

    International Nuclear Information System (INIS)

    Dzhezherya, Yu.I.; Klymuk, O.S.

    2011-01-01

    The magnetic and resonance properties of cylindrical magnets at first-order phase transition from paramagnetic to ferromagnetic state were theoretically studied. It has been shown that in the external magnetic field directed perpendicularly to the rotation axis, formation of a specific domain structure of paramagnetic and ferromagnetic layers can be energetically favorable. The parameters of cylindrical phase domains as well as their dependences on temperature, magnetic field and material characteristics have been calculated. Peculiarities of the magnetic resonance spectra appearing as a result of the phase domain formation have been considered. Dependence of the resonance field of the system of ferromagnetic domains on magnetization and temperature has been obtained. - Highlights: → Parameters of the equilibrium system of cylindrical phase domains are calculated. → The range of fields for PM and FM phases coexistence is found. → FMR field of the disk domains is found to be lower than that of the PMR field.→ The resonance field increases with the decrease of temperature lower than T || .

  13. Simulations of super-structure domain walls in two dimensional assemblies of magnetic nanoparticles

    International Nuclear Information System (INIS)

    Jordanovic, J.; Frandsen, C.; Beleggia, M.; Schiøtz, J.

    2015-01-01

    We simulate the formation of domain walls in two-dimensional assemblies of magnetic nanoparticles. Particle parameters are chosen to match recent electron holography and Lorentz microscopy studies of almost monodisperse cobalt nanoparticles assembled into regular, elongated lattices. As the particles are small enough to consist of a single magnetic domain each, their magnetic interactions can be described by a spin model in which each particle is assigned a macroscopic “superspin.” Thus, the magnetic behaviour of these lattices may be compared to magnetic crystals with nanoparticle superspins taking the role of the atomic spins. The coupling is, however, different. The superspins interact only by dipolar interactions as exchange coupling between individual nanoparticles may be neglected due to interparticle spacing. We observe that it is energetically favorable to introduce domain walls oriented along the long dimension of nanoparticle assemblies rather than along the short dimension. This is unlike what is typically observed in continuous magnetic materials, where the exchange interaction introduces an energetic cost proportional to the area of the domain walls. Structural disorder, which will always be present in realistic assemblies, pins longitudinal domain walls when the external field is reversed, and makes a gradual reversal of the magnetization by migration of longitudinal domain walls possible, in agreement with previous experimental results

  14. Crystal structure of the Rasputin NTF2-like domain from Drosophila melanogaster

    International Nuclear Information System (INIS)

    Vognsen, Tina; Kristensen, Ole

    2012-01-01

    Highlights: ► The crystal structure of the NTF2-like domain of Rasputin protein is presented. ► Differences to known ligand binding sites of nuclear transport factor 2 are discussed. ► A new ligand binding site for the Rasputin and G3BP proteins is proposed. -- Abstract: The crystal structure of the NTF2-like domain of the Drosophila homolog of Ras GTPase SH3 Binding Protein (G3BP), Rasputin, was determined at 2.7 Å resolution. The overall structure is highly similar to nuclear transport factor 2: It is a homodimer comprised of a β-sheet and three α-helices forming a cone-like shape. However, known binding sites for RanGDP and FxFG containing peptides show electrostatic and steric differences compared to nuclear transport factor 2. A HEPES molecule bound in the structure suggests a new, and possibly physiologically relevant, ligand binding site.

  15. Label-free colorimetric detection of mercury via Hg2+ ions-accelerated structural transformation of nanoscale metal-oxo clusters

    Science.gov (United States)

    Chen, Kun; She, Shan; Zhang, Jiangwei; Bayaguud, Aruuhan; Wei, Yongge

    2015-11-01

    Mercury and its compounds are known to be extremely toxic but widely distributed in environment. Although many works have been reported to efficiently detect mercury, development of simple and convenient sensors is still longed for quick analyzing mercury in water. In this work, a nanoscale metal-oxo cluster, (n-Bu4N)2[Mo5NaO13(OCH3)4(NO)], (MLPOM), organically-derivatized from monolacunary Lindqvist-type polyoxomolybdate, is found to specifically react with Hg2+ in methanol/water via structural transformation. The MLPOM methanol solution displays a color change from purple to brown within seconds after being mixed with an aqueous solution containing Hg2+. By comparing the structure of polyoxomolybdate before and after reaction, the color change is revealed to be the essentially structural transformation of MLPOM accelerated by Hg2+. Based on this discovery, MLPOM could be utilized as a colorimetric sensor to sense the existence of Hg2+, and a simple and label-free method is developed to selectively detect aqueous Hg2+. Furthermore, the colorimetric sensor has been applied to indicating mercury contamination in industrial sewage.

  16. Nanoscale structural and chemical analysis of F-implanted enhancement-mode InAlN/GaN heterostructure field effect transistors

    Science.gov (United States)

    Tang, Fengzai; Lee, Kean B.; Guiney, Ivor; Frentrup, Martin; Barnard, Jonathan S.; Divitini, Giorgio; Zaidi, Zaffar H.; Martin, Tomas L.; Bagot, Paul A.; Moody, Michael P.; Humphreys, Colin J.; Houston, Peter A.; Oliver, Rachel A.; Wallis, David J.

    2018-01-01

    We investigate the impact of a fluorine plasma treatment used to obtain enhancement-mode operation on the structure and chemistry at the nanometer and atomic scales of an InAlN/GaN field effect transistor. The fluorine plasma treatment is successful in that enhancement mode operation is achieved with a +2.8 V threshold voltage. However, the InAlN barrier layers are observed to have been damaged by the fluorine treatment with their thickness being reduced by up to 50%. The treatment also led to oxygen incorporation within the InAlN barrier layers. Furthermore, even in the as-grown structure, Ga was unintentionally incorporated during the growth of the InAlN barrier. The impact of both the reduced barrier thickness and the incorporated Ga within the barrier on the transistor properties has been evaluated theoretically and compared to the experimentally determined two-dimensional electron gas density and threshold voltage of the transistor. For devices without fluorine treatment, the two-dimensional electron gas density is better predicted if the quaternary nature of the barrier is taken into account. For the fluorine treated device, not only the changes to the barrier layer thickness and composition, but also the fluorine doping needs to be considered to predict device performance. These studies reveal the factors influencing the performance of these specific transistor structures and highlight the strengths of the applied nanoscale characterisation techniques in revealing information relevant to device performance.

  17. Evolution of nanoscale zero-valent iron (nZVI) in water: Microscopic and spectroscopic evidence on the formation of nano- and micro-structured iron oxides

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Airong, E-mail: liuairong@tongji.edu.cn; Liu, Jing; Han, Jinhao; Zhang, Wei-xian, E-mail: zhangwx@tongji.edu.cn

    2017-01-15

    Highlights: • A comprehensive study of corrosion products for nZVI under both oxic and anoxic conditions is performed. • Under anoxic conditions, the oxidation products contain a mixture of wustite (FeO), goethite (α-FeOOH) and akaganeite (β-FeOOH). • Under oxic conditions, the final products are mainly crystalline lepidocrocite (γ-FeOOH) with acicular-shaped structures. • Morphological and structural evolution of nZVI under both oxic and anoxic conditions are substantially different. - Abstract: Knowledge on the transformation of nanoscale zero-valent iron (nZVI) in water is essential to predict its surface chemistry including surface charge, colloidal stability and aggregation, reduction and sorption of organic contaminants, heavy metal ions and other pollutants in the environment. In this work, transmission electronic microscopy (TEM), X-ray diffraction (XRD) and Raman spectroscopy are applied to study the compositional and structural evolution of nZVI under oxic and anoxic conditions. Under anoxic conditions, the core–shell structure of nZVI is well maintained even after 72 h, and the corrosion products usually contain a mixture of wustite (FeO), goethite (α-FeOOH) and akaganeite (β-FeOOH). Under oxic conditions, the core–shell structure quickly collapses to flakes or acicular-shaped structures with crystalline lepidocrocite (γ-FeOOH) as the primary end product. This work provides detailed information and fills an important knowledge gap on the physicochemical characteristics and structural evolution of engineered nanomaterials in the environment.

  18. Structural coupling of SH2-kinase domains links Fes and Abl substrate recognition and kinase activation.

    Science.gov (United States)

    Filippakopoulos, Panagis; Kofler, Michael; Hantschel, Oliver; Gish, Gerald D; Grebien, Florian; Salah, Eidarus; Neudecker, Philipp; Kay, Lewis E; Turk, Benjamin E; Superti-Furga, Giulio; Pawson, Tony; Knapp, Stefan

    2008-09-05

    The SH2 domain of cytoplasmic tyrosine kinases can enhance catalytic activity and substrate recognition, but the molecular mechanisms by which this is achieved are poorly understood. We have solved the structure of the prototypic SH2-kinase unit of the human Fes tyrosine kinase, which appears specialized for positive signaling. In its active conformation, the SH2 domain tightly interacts with the kinase N-terminal lobe and positions the kinase alphaC helix in an active configuration through essential packing and electrostatic interactions. This interaction is stabilized by ligand binding to the SH2 domain. Our data indicate that Fes kinase activation is closely coupled to substrate recognition through cooperative SH2-kinase-substrate interactions. Similarly, we find that the SH2 domain of the active Abl kinase stimulates catalytic activity and substrate phosphorylation through a distinct SH2-kinase interface. Thus, the SH2 and catalytic domains of active Fes and Abl pro-oncogenic kinases form integrated structures essential for effective tyrosine kinase signaling.

  19. Fast and non-destructive pore structure analysis using terahertz time-domain spectroscopy.

    OpenAIRE

    Markl, Daniel; Bawuah, Prince; Ridgway, Cathy; van den Ban, Sander; Goodwin, Daniel J; Ketolainen, Jarkko; Gane, Patrick; Peiponen, Kai-Erik; Zeitler, Jochen Axel

    2018-01-01

    Pharmaceutical tablets are typically manufactured by the uni-axial compaction of powder that is confined radially by a rigid die. The directional nature of the compaction process yields not only anisotropic mechanical properties (e.g. tensile strength) but also directional properties of the pore structure in the porous compact. This study derives a new quantitative parameter, $S_a$, to describe the anisotropy in pore structure of pharmaceutical tablets based on terahertz time-domain spectrosc...

  20. Characterization of high-power RF structures using time-domain field codes

    International Nuclear Information System (INIS)

    Shang, C.C.; DeFord, J.F.; Swatloski, T.L.

    1992-01-01

    We have modeled gyrotron windows and gyrotron amplifier sever structures for TE modes in the 100-150 GHz range and have computed the reflection and transmission characteristics from the field data. Good agreement with frequency domain codes and analytic analysis have been obtained for some simple geometries. We present results for realistic structures with lossy coatings and describe implementation of microwave diagnostics. (Author) 5 figs., 7 refs

  1. Observation of the domain structure in Fe-Au superlattices with perpendicular anisotropy

    Energy Technology Data Exchange (ETDEWEB)

    Zoladz, M. E-mail: zoladz@uci.agh.edu.pl; Slezak, T.; Wilgocka-Slezak, D.; Spiridis, N.; Korecki, J.; Stobiecki, T. E-mail: stobieck@uci.agh.edu.pl; Roell, K

    2004-05-01

    Polar Kerr Microscopy was used to visualize characteristic transitions and external magnetic field driven domain structure evolution in a perpendicularly magnetized Fe-Au AF/FM double multilayer structure. Real time imaging performed in the external magnetic field allowed for identification of all sublayers magnetization reversal in accordance with measured PMOKE magnetization curve, showing strong dependence of transition character on the interlayer coupling type and adjacent sublayers magnetization orientation.

  2. Observation of the domain structure in Fe-Au superlattices with perpendicular anisotropy

    International Nuclear Information System (INIS)

    Zoladz, M.; Slezak, T.; Wilgocka-Slezak, D.; Spiridis, N.; Korecki, J.; Stobiecki, T.; Roell, K.

    2004-01-01

    Polar Kerr Microscopy was used to visualize characteristic transitions and external magnetic field driven domain structure evolution in a perpendicularly magnetized Fe-Au AF/FM double multilayer structure. Real time imaging performed in the external magnetic field allowed for identification of all sublayers magnetization reversal in accordance with measured PMOKE magnetization curve, showing strong dependence of transition character on the interlayer coupling type and adjacent sublayers magnetization orientation

  3. Scattering analysis of periodic structures using finite-difference time-domain

    CERN Document Server

    ElMahgoub, Khaled; Elsherbeni, Atef Z

    2012-01-01

    Periodic structures are of great importance in electromagnetics due to their wide range of applications such as frequency selective surfaces (FSS), electromagnetic band gap (EBG) structures, periodic absorbers, meta-materials, and many others. The aim of this book is to develop efficient computational algorithms to analyze the scattering properties of various electromagnetic periodic structures using the finite-difference time-domain periodic boundary condition (FDTD/PBC) method. A new FDTD/PBC-based algorithm is introduced to analyze general skewed grid periodic structures while another algor

  4. Crystal structure of mouse coronavirus receptor-binding domain complexed with its murine receptor

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Guiqing; Sun, Dawei; Rajashankar, Kanagalaghatta R.; Qian, Zhaohui; Holmes, Kathryn V.; Li, Fang (Cornell); (UMM-MED); (Colorado)

    2011-09-28

    Coronaviruses have evolved diverse mechanisms to recognize different receptors for their cross-species transmission and host-range expansion. Mouse hepatitis coronavirus (MHV) uses the N-terminal domain (NTD) of its spike protein as its receptor-binding domain. Here we present the crystal structure of MHV NTD complexed with its receptor murine carcinoembryonic antigen-related cell adhesion molecule 1a (mCEACAM1a). Unexpectedly, MHV NTD contains a core structure that has the same {beta}-sandwich fold as human galectins (S-lectins) and additional structural motifs that bind to the N-terminal Ig-like domain of mCEACAM1a. Despite its galectin fold, MHV NTD does not bind sugars, but instead binds mCEACAM1a through exclusive protein-protein interactions. Critical contacts at the interface have been confirmed by mutagenesis, providing a structural basis for viral and host specificities of coronavirus/CEACAM1 interactions. Sugar-binding assays reveal that galectin-like NTDs of some coronaviruses such as human coronavirus OC43 and bovine coronavirus bind sugars. Structural analysis and mutagenesis localize the sugar-binding site in coronavirus NTDs to be above the {beta}-sandwich core. We propose that coronavirus NTDs originated from a host galectin and retained sugar-binding functions in some contemporary coronaviruses, but evolved new structural features in MHV for mCEACAM1a binding.

  5. Structure-function analysis of the OB and latch domains of chlorella virus DNA ligase.

    Science.gov (United States)

    Samai, Poulami; Shuman, Stewart

    2011-06-24

    Chlorella virus DNA ligase (ChVLig) is a minimized eukaryal ATP-dependent DNA sealing enzyme with an intrinsic nick-sensing function. ChVLig consists of three structural domains, nucleotidyltransferase (NTase), OB-fold, and latch, that envelop the nicked DNA as a C-shaped protein clamp. The OB domain engages the DNA minor groove on the face of the duplex behind the nick, and it makes contacts to amino acids in the NTase domain surrounding the ligase active site. The latch module occupies the DNA major groove flanking the nick. Residues at the tip of the latch contact the NTase domain to close the ligase clamp. Here we performed a structure-guided mutational analysis of the OB and latch domains. Alanine scanning defined seven individual amino acids as essential in vivo (Lys-274, Arg-285, Phe-286, and Val-288 in the OB domain; Asn-214, Phe-215, and Tyr-217 in the latch), after which structure-activity relations were clarified by conservative substitutions. Biochemical tests of the composite nick sealing reaction and of each of the three chemical steps of the ligation pathway highlighted the importance of Arg-285 and Phe-286 in the catalysis of the DNA adenylylation and phosphodiester synthesis reactions. Phe-286 interacts with the nick 5'-phosphate nucleotide and the 3'-OH base pair and distorts the DNA helical conformation at the nick. Arg-285 is a key component of the OB-NTase interface, where it forms a salt bridge to the essential Asp-29 side chain, which is imputed to coordinate divalent metal catalysts during the nick sealing steps.

  6. Structure-Function Analysis of the OB and Latch Domains of Chlorella Virus DNA Ligase*

    Science.gov (United States)

    Samai, Poulami; Shuman, Stewart

    2011-01-01

    Chlorella virus DNA ligase (ChVLig) is a minimized eukaryal ATP-dependent DNA sealing enzyme with an intrinsic nick-sensing function. ChVLig consists of three structural domains, nucleotidyltransferase (NTase), OB-fold, and latch, that envelop the nicked DNA as a C-shaped protein clamp. The OB domain engages the DNA minor groove on the face of the duplex behind the nick, and it makes contacts to amino acids in the NTase domain surrounding the ligase active site. The latch module occupies the DNA major groove flanking the nick. Residues at the tip of the latch contact the NTase domain to close the ligase clamp. Here we performed a structure-guided mutational analysis of the OB and latch domains. Alanine scanning defined seven individual amino acids as essential in vivo (Lys-274, Arg-285, Phe-286, and Val-288 in the OB domain; Asn-214, Phe-215, and Tyr-217 in the latch), after which structure-activity relations were clarified by conservative substitutions. Biochemical tests of the composite nick sealing reaction and of each of the three chemical steps of the ligation pathway highlighted the importance of Arg-285 and Phe-286 in the catalysis of the DNA adenylylation and phosphodiester synthesis reactions. Phe-286 interacts with the nick 5′-phosphate nucleotide and the 3′-OH base pair and distorts the DNA helical conformation at the nick. Arg-285 is a key component of the OB-NTase interface, where it forms a salt bridge to the essential Asp-29 side chain, which is imputed to coordinate divalent metal catalysts during the nick sealing steps. PMID:21527793

  7. Structure of the C-terminal domain of nsp4 from feline coronavirus

    International Nuclear Information System (INIS)

    Manolaridis, Ioannis; Wojdyla, Justyna A.; Panjikar, Santosh; Snijder, Eric J.; Gorbalenya, Alexander E.; Berglind, Hanna; Nordlund, Pär; Coutard, Bruno; Tucker, Paul A.

    2009-01-01

    The structure of the cytosolic C-terminal domain of nonstructural protein 4 from feline coronavirus has been determined and analyzed. Coronaviruses are a family of positive-stranded RNA viruses that includes important pathogens of humans and other animals. The large coronavirus genome (26–31 kb) encodes 15–16 nonstructural proteins (nsps) that are derived from two replicase polyproteins by autoproteolytic processing. The nsps assemble into the viral replication–transcription complex and nsp3, nsp4 and nsp6 are believed to anchor this enzyme complex to modified intracellular membranes. The largest part of the coronavirus nsp4 subunit is hydrophobic and is predicted to be embedded in the membranes. In this report, a conserved C-terminal domain (∼100 amino-acid residues) has been delineated that is predicted to face the cytoplasm and has been isolated as a soluble domain using library-based construct screening. A prototypical crystal structure at 2.8 Å resolution was obtained using nsp4 from feline coronavirus. Unmodified and SeMet-substituted proteins were crystallized under similar conditions, resulting in tetragonal crystals that belonged to space group P4 3 . The phase problem was initially solved by single isomorphous replacement with anomalous scattering (SIRAS), followed by molecular replacement using a SIRAS-derived composite model. The structure consists of a single domain with a predominantly α-helical content displaying a unique fold that could be engaged in protein–protein interactions

  8. Crystal Structure of the Human, FIC-Domain Containing Protein HYPE and Implications for Its Functions

    Science.gov (United States)

    Bunney, Tom D.; Cole, Ambrose R.; Broncel, Malgorzata; Esposito, Diego; Tate, Edward W.; Katan, Matilda

    2014-01-01

    Summary Protein AMPylation, the transfer of AMP from ATP to protein targets, has been recognized as a new mechanism of host-cell disruption by some bacterial effectors that typically contain a FIC-domain. Eukaryotic genomes also encode one FIC-domain protein, HYPE, which has remained poorly characterized. Here we describe the structure of human HYPE, solved by X-ray crystallography, representing the first structure of a eukaryotic FIC-domain protein. We demonstrate that HYPE forms stable dimers with structurally and functionally integrated FIC-domains and with TPR-motifs exposed for protein-protein interactions. As HYPE also uniquely possesses a transmembrane helix, dimerization is likely to affect its positioning and function in the membrane vicinity. The low rate of autoAMPylation of the wild-type HYPE could be due to autoinhibition, consistent with the mechanism proposed for a number of putative FIC AMPylators. Our findings also provide a basis to further consider possible alternative cofactors of HYPE and distinct modes of target-recognition. PMID:25435325

  9. The impact of domain knowledge on structured data collection and templated note design.

    Science.gov (United States)

    Windle, T; McClay, J C; Windle, J R

    2013-01-01

    The objective of this case report is to evaluate the importance of specialized domain knowledge when designing and using structured templated notes in a clinical environment. To analyze the impact of specialization on structured note generation we compared notes generated for three scenarios: 1) We compared the templated history of present illness (HPI) for patients presenting with a dermatology concern to the dermatologist versus the emergency department. 2) We compared the evaluation of chest pain by ED physicians versus cardiologists. 3) Finally, we compared the data elements asked for in the evaluation of the gastrointestinal system between cardiologists and the liver transplant service (LTS). We used the SNOMED CT representation via BioPortal to evaluate specificity and grouping between data elements and specialized physician groups. We found few similarities in structured data elements designed by and for the specific physician groups. The distinctness represented both differences in granularity as well as fundamental differences in data elements requested. When compared to ED physicians, dermatologists had different and more granular elements while cardiologists requested much more granular data. Comparing cardiologists and LTS, there were differences in the data elements requested. This case study supports the importance of domain knowledge in EHR design and implementation. That different specialities should want and use different information is well supported by cognitive science literature. Despite this, it is rare for domain knowledge to be considered in EHR implementation. Physicians with correct domain knowledge should be involved in the design process of templated notes.

  10. Structure of the C-terminal domain of nsp4 from feline coronavirus

    Energy Technology Data Exchange (ETDEWEB)

    Manolaridis, Ioannis; Wojdyla, Justyna A.; Panjikar, Santosh [EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg (Germany); Snijder, Eric J.; Gorbalenya, Alexander E. [Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden (Netherlands); Berglind, Hanna; Nordlund, Pär [Division of Biophysics, Department of Medical Biochemistry and Biophysics, Scheeles väg 2, Karolinska Institute, SE-171 77 Stockholm (Sweden); Coutard, Bruno [Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 6098, AFMB-CNRS-ESIL, Case 925, 163 Avenue de Luminy, 13288 Marseille (France); Tucker, Paul A., E-mail: tucker@embl-hamburg.de [EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg (Germany)

    2009-08-01

    The structure of the cytosolic C-terminal domain of nonstructural protein 4 from feline coronavirus has been determined and analyzed. Coronaviruses are a family of positive-stranded RNA viruses that includes important pathogens of humans and other animals. The large coronavirus genome (26–31 kb) encodes 15–16 nonstructural proteins (nsps) that are derived from two replicase polyproteins by autoproteolytic processing. The nsps assemble into the viral replication–transcription complex and nsp3, nsp4 and nsp6 are believed to anchor this enzyme complex to modified intracellular membranes. The largest part of the coronavirus nsp4 subunit is hydrophobic and is predicted to be embedded in the membranes. In this report, a conserved C-terminal domain (∼100 amino-acid residues) has been delineated that is predicted to face the cytoplasm and has been isolated as a soluble domain using library-based construct screening. A prototypical crystal structure at 2.8 Å resolution was obtained using nsp4 from feline coronavirus. Unmodified and SeMet-substituted proteins were crystallized under similar conditions, resulting in tetragonal crystals that belonged to space group P4{sub 3}. The phase problem was initially solved by single isomorphous replacement with anomalous scattering (SIRAS), followed by molecular replacement using a SIRAS-derived composite model. The structure consists of a single domain with a predominantly α-helical content displaying a unique fold that could be engaged in protein–protein interactions.

  11. Composition, structure and properties of POPC–triolein mixtures. Evidence of triglyceride domains in phospholipid bilayers

    DEFF Research Database (Denmark)

    Duelund, Lars; Jensen, Grethe Vestergaard; Hannibal-Bach, Hans Kristian

    2013-01-01

    We have in this study investigated the composition, structure and spectroscopical properties of multilamellar vesicles composed of a phospholipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and up to 10mol% of triolein (TO), a triglyceride. We found in agreement with previous results...... as vesicular structures containing entrapped water. Bilayer structure of the membranes was supported by small angle X-ray scattering that showed the membranes to form a lamellar phase. Fluorescence spectroscopy with the polarity sensitive dye Nile red revealed, that the LF samples with more than 5mol......% TO contained pure TO domains. These observations are consistent with an earlier MD simulation study by us and our co-workers suggesting triglycerides to be located in lens shaped, blister-like domains between the two lipid bilayer leaflets (Khandelia et al. (2010) [26])....

  12. Crystal structure of a prolactin receptor antagonist bound to the extracellular domain of the prolactin receptor

    DEFF Research Database (Denmark)

    Svensson, L Anders; Bondensgaard, Kent; Nørskov-Lauritsen, Leif

    2008-01-01

    The crystal structure of the complex between an N-terminally truncated G129R human prolactin (PRL) variant and the extracellular domain of the human prolactin receptor (PRLR) was determined at 2.5A resolution by x-ray crystallography. This structure represents the first experimental structure...... studies, the structural data imply that the definition of PRL binding site 1 should be extended to include residues situated in the N-terminal part of loop 1 and in the C terminus. Comparison of the structure of the receptor-bound PRL variant with the structure reported for the unbound form of a similar...... scale rearrangements and structuring occur in the flexible N-terminal part of loop 1. Hydrogen exchange mass spectrometry data imply that the dynamics of the four-helix bundle in solution generally become stabilized upon receptor interaction at binding site 1....

  13. Crystal structure studies of NADP{sup +} dependent isocitrate dehydrogenase from Thermus thermophilus exhibiting a novel terminal domain

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, S.M. [Department of Studies in Physics, University of Mysore, Mysore 570 006 (India); Pampa, K.J. [Department of Studies in Microbiology, University of Mysore, Mysore 570 006 (India); Manjula, M. [Department of Studies in Physics, University of Mysore, Mysore 570 006 (India); Abdoh, M.M.M. [Department of Physics, Faculty of Science, An-Najah National University, Nablus, West Bank, Palestine (Country Unknown); Kunishima, Naoki [Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148 (Japan); Lokanath, N.K., E-mail: lokanath@physics.uni-mysore.ac.in [Department of Studies in Physics, University of Mysore, Mysore 570 006 (India)

    2014-06-20

    Highlights: • We determined the structure of isocitrate dehydrogenase with citrate and cofactor. • The structure reveals a unique novel terminal domain involved in dimerization. • Clasp domain shows significant difference, and catalytic residues are conserved. • Oligomerization of the enzyme is quantized with subunit-subunit interactions. • Novel domain of this enzyme is classified as subfamily of the type IV. - Abstract: NADP{sup +} dependent isocitrate dehydrogenase (IDH) is an enzyme catalyzing oxidative decarboxylation of isocitrate into oxalosuccinate (intermediate) and finally the product α-ketoglutarate. The crystal structure of Thermus thermophilus isocitrate dehydrogenase (TtIDH) ternary complex with citrate and cofactor NADP{sup +} was determined using X-ray diffraction method to a resolution of 1.80 Å. The overall fold of this protein was resolved into large domain, small domain and a clasp domain. The monomeric structure reveals a novel terminal domain involved in dimerization, very unique and novel domain when compared to other IDH’s. And, small domain and clasp domain showing significant differences when compared to other IDH’s of the same sub-family. The structure of TtIDH reveals the absence of helix at the clasp domain, which is mainly involved in oligomerization in other IDH’s. Also, helices/beta sheets are absent in the small domain, when compared to other IDH’s of the same sub family. The overall TtIDH structure exhibits closed conformation with catalytic triad residues, Tyr144-Asp248-Lys191 are conserved. Oligomerization of the protein is quantized using interface area and subunit–subunit interactions between protomers. Overall, the TtIDH structure with novel terminal domain may be categorized as a first structure of subfamily of type IV.

  14. Characterization of radon penetration of different structural domains of concrete. Final project report

    International Nuclear Information System (INIS)

    Nielson, K.K.; Rogers, V.C.

    1996-05-01

    This report documents the research activities by Rogers and Associates Engineering Corporation on grant DE-FG03-93ER61600 during the funded project period from August 1993 to April 1996. The objective of this research was to characterize the mechanisms and rates of radon gas penetration of the different structural domains of the concrete components of residential floor slabs, walls, and associated joints and penetrations. The research was also to characterize the physical properties of the concretes in these domains to relate their radon resistance to their physical properties. These objectives support the broader goal of characterizing which, if any, concrete domains and associated properties constitute robust barriers to radon and which permit radon entry, either inherently or in ways that could be remediated or avoided

  15. Data describing the solution structure of the WW3* domain from human Nedd4-1

    Directory of Open Access Journals (Sweden)

    Vineet Panwalkar

    2016-09-01

    Full Text Available The third WW domain (WW3* of human Nedd4-1 (Neuronal precursor cell expressed developmentally down-regulated gene 4-1 interacts with the poly-proline (PY motifs of the human epithelial Na+ channel (hENaC subunits at micromolar affinity. This data supplements the article (Panwalkar et al., 2015 [1]. We describe the NMR experiments used to solve the solution structure of the WW3* domain. We also present NOE network data for defining the rotameric state of side chains of peptide binding residues, and complement this data with χ1 dihedral angles derived from 3J couplings and molecular dynamics simulations data. Keywords: Chemical shift, Neuronal precursor cell expressed developmentally down-regulated gene 4-1, NMR, NOE distance restraints, WW domain

  16. Structured Literature Review of disruptive innovation theory within the digital domain

    DEFF Research Database (Denmark)

    Vesti, Helle; Nielsen, Christian; Rosenstand, Claus Andreas Foss

    2017-01-01

    The area of interest is disruption is the digital domain. The research questions are: How has the disruption and digital disruption literature developed over time? What is the research focus into disruption regarding the digital domain and how has this changed over time? Which methods are being...... utilized in research regarding disruption and digital disruption? Where are the key contributors to disruption in general and in digital disruption? Is there a future for digital disruption research? The method is a Structured Literature Review (SLR). The contribution is the results of an analysis of 95...... publications within the field of disruption in the digital domain and disruptive innovation theory in general. Works of twelve practitioners and 83 academics are investigated....

  17. The retinal specific CD147 Ig0 domain: from molecular structure to biological activity

    Energy Technology Data Exchange (ETDEWEB)

    Redzic, Jasmina S.; Armstrong, Geoffrey S.; Isern, Nancy G.; Jones, David N.M.; Kieft, Jeffrey S.; Eisenmesser, Elan Z.

    2011-06-18

    CD147 is a type I transmembrane protein that is involved in inflammatory diseases, cancer progression, and multiple human pathogens utilize CD147 for efficient infection. In several cancers, CD147 expression is so high that it is now used as a prognostic marker. The two primary isoforms of CD147 that are related to cancer progression have been identified, differing in their number of immunoglobulin (Ig)-like domains. These include CD147 Ig1-Ig2 that is ubiquitously expressed in most tissues and CD147 Ig0-Ig1-Ig2 that is retinal specific and implicated in retinoblastoma. However, little is known in regard to the retinal specific CD147 Ig0 domain despite its potential role in retinoblastoma. Thus, here we have extensively characterized the CD147 Ig0 domain by elucidating its three-dimensional structure through crystallography and its solution behavior through several biophysical methods that include nuclear magnetic resonance. Furthermore, we have utilized this data together with mutagenesis to probe the biological activity of CD147-containing proteins both with and without the CD147 Ig0 domain within several model cell lines. Our findings reveal that the CD147 Ig0 domain is a potent stimulator of interleukin-6, which is a well-known contributor to retinoblastoma and suggest that the CD147 Ig0 domain has its own receptor distinct from that of the other CD147 Ig-like domains, CD147 Ig1-Ig2. Furthermore, we show that the CD147 Ig0 dimer is the functional unit required for activity and can be disrupted by a single point mutation.

  18. Structure of the SH3 domain of human osteoclast-stimulating factor at atomic resolution

    International Nuclear Information System (INIS)

    Chen, Liqing; Wang, Yujun; Wells, David; Toh, Diana; Harold, Hunt; Zhou, Jing; DiGiammarino, Enrico; Meehan, Edward J.

    2006-01-01

    The crystal structure of the SH3 domain of human osteoclast-stimulating factor has been determined and refined to the ultrahigh resolution of 1.07 Å. The structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors. Osteoclast-stimulating factor (OSF) is an intracellular signaling protein, produced by osteoclasts themselves, that enhances osteoclast formation and bone resorption. It is thought to act via an Src-related signaling pathway and contains SH3 and ankyrin-repeat domains which are involved in protein–protein interactions. As part of a structure-based anti-bone-loss drug-design program, the atomic resolution X-ray structure of the recombinant human OSF SH3 domain (hOSF-SH3) has been determined. The domain, residues 12–72, yielded crystals that diffracted to the ultrahigh resolution of 1.07 Å. The overall structure shows a characteristic SH3 fold consisting of two perpendicular β-sheets that form a β-barrel. Structure-based sequence alignment reveals that the putative proline-rich peptide-binding site of hOSF-SH3 consists of (i) residues that are highly conserved in the SH3-domain family, including residues Tyr21, Phe23, Trp49, Pro62, Asn64 and Tyr65, and (ii) residues that are less conserved and/or even specific to hOSF, including Thr22, Arg26, Thr27, Glu30, Asp46, Thr47, Asn48 and Leu60, which might be key to designing specific inhibitors for hOSF to fight osteoporosis and related bone-loss diseases. There are a total of 13 well defined water molecules forming hydrogen bonds with the above residues in and around the peptide-binding pocket. Some of those water molecules might be important for drug-design approaches. The hOSF-SH3 structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors

  19. Dynamic Analysis of Partially Embedded Structures Considering Soil-Structure Interaction in Time Domain

    OpenAIRE

    Mahmoudpour, Sanaz; Attarnejad, Reza; Behnia, Cambyse

    2011-01-01

    Analysis and design of structures subjected to arbitrary dynamic loadings especially earthquakes have been studied during past decades. In practice, the effects of soil-structure interaction on the dynamic response of structures are usually neglected. In this study, the effect of soil-structure interaction on the dynamic response of structures has been examined. The substructure method using dynamic stiffness of soil is used to analyze soil-structure system. A coupled model based on finite el...

  20. Time domain calculation of connector loads of a very large floating structure

    Science.gov (United States)

    Gu, Jiayang; Wu, Jie; Qi, Enrong; Guan, Yifeng; Yuan, Yubo

    2015-06-01

    Loads generated after an air crash, ship collision, and other accidents may destroy very large floating structures (VLFSs) and create additional connector loads. In this study, the combined effects of ship collision and wave loads are considered to establish motion differential equations for a multi-body VLFS. A time domain calculation method is proposed to calculate the connector load of the VLFS in waves. The Longuet-Higgins model is employed to simulate the stochastic wave load. Fluid force and hydrodynamic coefficient are obtained with DNV Sesam software. The motion differential equation is calculated by applying the time domain method when the frequency domain hydrodynamic coefficient is converted into the memory function of the motion differential equation of the time domain. As a result of the combined action of wave and impact loads, high-frequency oscillation is observed in the time history curve of the connector load. At wave directions of 0° and 75°, the regularities of the time history curves of the connector loads in different directions are similar and the connector loads of C1 and C2 in the X direction are the largest. The oscillation load is observed in the connector in the Y direction at a wave direction of 75° and not at 0°. This paper presents a time domain calculation method of connector load to provide a certain reference function for the future development of Chinese VLFS

  1. Megabase replication domains along the human genome: relation to chromatin structure and genome organisation.

    Science.gov (United States)

    Audit, Benjamin; Zaghloul, Lamia; Baker, Antoine; Arneodo, Alain; Chen, Chun-Long; d'Aubenton-Carafa, Yves; Thermes, Claude

    2013-01-01

    In higher eukaryotes, the absence of specific sequence motifs, marking the origins of replication has been a serious hindrance to the understanding of (i) the mechanisms that regulate the spatio-temporal replication program, and (ii) the links between origins activation, chromatin structure and transcription. In this chapter, we review the partitioning of the human genome into megabased-size replication domains delineated as N-shaped motifs in the strand compositional asymmetry profiles. They collectively span 28.3% of the genome and are bordered by more than 1,000 putative replication origins. We recapitulate the comparison of this partition of the human genome with high-resolution experimental data that confirms that replication domain borders are likely to be preferential replication initiation zones in the germline. In addition, we highlight the specific distribution of experimental and numerical chromatin marks along replication domains. Domain borders correspond to particular open chromatin regions, possibly encoded in the DNA sequence, and around which replication and transcription are highly coordinated. These regions also present a high evolutionary breakpoint density, suggesting that susceptibility to breakage might be linked to local open chromatin fiber state. Altogether, this chapter presents a compartmentalization of the human genome into replication domains that are landmarks of the human genome organization and are likely to play a key role in genome dynamics during evolution and in pathological situations.

  2. The study of co-citation analysis and knowledge structure on healthcare domain

    Science.gov (United States)

    Chu, Kuo-Chung; Liu, Wen-I.; Tsai, Ming-Yu

    2012-11-01

    With the prevalence of Internet and digital archives, the online e-journal database facilitates scholars to search literature in a research domain, or to cross-search an inter-disciplined field; the key literature can be efficiently traced out. This study intends to build a Web-based citation analysis system, which consists of four modules, they are: 1) literature search module; (2) statistics module; (3) articles analysis module; and (4) co-citation analysis module. The system focuses on PubMed Central dataset that has 170,000 records. In a research domain, a specific keyword searches in terms of authors, journals, and core issues. In addition, we use data mining techniques for co-citation analysis. The results assist researchers with in-depth understanding of the domain knowledge. Having an automated system for co-citation analysis, it helps to understand changes, trends, and knowledge structure of research domain. For the best of our knowledge, the proposed system differentiates from existing online electronic retrieval database analysis function. Perhaps, the proposed system is going to be a value-added database of healthcare domain, and hope to contribute the researchers.

  3. Magnetization switching schemes for nanoscale three-terminal spintronics devices

    Science.gov (United States)

    Fukami, Shunsuke; Ohno, Hideo

    2017-08-01

    Utilizing spintronics-based nonvolatile memories in integrated circuits offers a promising approach to realize ultralow-power and high-performance electronics. While two-terminal devices with spin-transfer torque switching have been extensively developed nowadays, there has been a growing interest in devices with a three-terminal structure. Of primary importance for applications is the efficient manipulation of magnetization, corresponding to information writing, in nanoscale devices. Here we review the studies of current-induced domain wall motion and spin-orbit torque-induced switching, which can be applied to the write operation of nanoscale three-terminal spintronics devices. For domain wall motion, the size dependence of device properties down to less than 20 nm will be shown and the underlying mechanism behind the results will be discussed. For spin-orbit torque-induced switching, factors governing the threshold current density and strategies to reduce it will be discussed. A proof-of-concept demonstration of artificial intelligence using an analog spin-orbit torque device will also be reviewed.

  4. Crystal Structures of the Tetratricopeptide Repeat Domains of Kinesin Light Chains: Insight into Cargo Recognition Mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Haizhong; Lee, Han Youl; Tong, Yufeng; Hong, Bum-Soo; Kim, Kyung-Phil; Shen, Yang; Lim, Kyung Jik; Mackenzie, Farrell; Tempel, Wolfram; Park, Hee-Won (SGC-Toronto); (PPCS); (Toronto)

    2012-10-23

    Kinesin-1 transports various cargos along the axon by interacting with the cargos through its light chain subunit. Kinesin light chains (KLC) utilize its tetratricopeptide repeat (TPR) domain to interact with over 10 different cargos. Despite a high sequence identity between their TPR domains (87%), KLC1 and KLC2 isoforms exhibit differential binding properties towards some cargos. We determined the structures of human KLC1 and KLC2 tetratricopeptide repeat (TPR) domains using X-ray crystallography and investigated the different mechanisms by which KLCs interact with their cargos. Using isothermal titration calorimetry, we attributed the specific interaction between KLC1 and JNK-interacting protein 1 (JIP1) cargo to residue N343 in the fourth TRP repeat. Structurally, the N343 residue is adjacent to other asparagines and lysines, creating a positively charged polar patch within the groove of the TPR domain. Whereas, KLC2 with the corresponding residue S328 did not interact with JIP1. Based on these finding, we propose that N343 of KLC1 can form 'a carboxylate clamp' with its neighboring asparagine to interact with JIP1, similar to that of HSP70/HSP90 organizing protein-1's (HOP1) interaction with heat shock proteins. For the binding of cargos shared by KLC1 and KLC2, we propose a different site located within the groove but not involving N343. We further propose a third binding site on KLC1 which involves a stretch of polar residues along the inter-TPR loops that may form a network of hydrogen bonds to JIP3 and JIP4. Together, these results provide structural insights into possible mechanisms of interaction between KLC TPR domains and various cargo proteins.

  5. Structure of metabotropic glutamate receptor C-terminal domains in contact with interacting proteins

    Directory of Open Access Journals (Sweden)

    Ralf eEnz

    2012-04-01

    Full Text Available Metabotropic glutamate receptors (mGluRs regulate intracellular signal pathways that control several physiological tasks, including neuronal excitability, learning and memory. This is achieved by the formation of synaptic signal complexes, in which mGluRs assemble with functionally related proteins such as enzymes, scaffolds and cytoskeletal anchor proteins. Thus, mGluR associated proteins actively participate in the regulation of glutamatergic neurotransmission. Importantly, dysfunction of mGluRs and interacting proteins may lead to impaired signal transduction and finally result in neurological disorders, e.g. night blindness, addiction, epilepsy, schizophrenia, autism spectrum disorders and Parkinson´s disease. In contrast to solved crystal structures of extracellular N-terminal domains of some mGluR types, only a few studies analyzed the conformation of intracellular receptor domains. Intracellular C-termini of most mGluR types are subject to alternative splicing and can be further modified by phosphorylation and SUMOylation. In this way, diverse interaction sites for intracellular proteins that bind to and regulate the glutamate receptors are generated. Indeed, most of the known mGluR binding partners interact with the receptors´ C-terminal domains. Within the last years, different laboratories analyzed the structure of these domains and described the geometry of the contact surface between mGluR C-termini and interacting proteins. Here, I will review recent progress in the structure characterization of mGluR C-termini and provide an up-to-date summary of the geometry of these domains in contact with binding partners.

  6. Structural matching of ferroelectric domains and associated distortion in potassium titanyl phosphate crystals

    CERN Document Server

    Pernot-Rejmankova, P; Cloetens, P; Lyford, T; Baruchel, J

    2003-01-01

    The surface deformation and atomic-level distortions associated with crystal structural matching at ferroelectric inversion domain walls are investigated in periodically poled potassium titanyl phosphate (KTP) crystals. A deformation, of the order of 10 sup - sup 8 m in scale and having the periodicity of the domains, is observed at the surfaces by optical interferometry. It is discussed in terms of the piezoelectric effect. The matching of the crystal structures at the domain walls is studied by combining the hard x-ray Fresnel phase-imaging technique with Bragg diffraction imaging methods ('Bragg-Fresnel imaging') and using synchrotron radiation. Quantitative analysis of the contrast of the Bragg-Fresnel images recorded as a function of the propagation distance is demonstrated to allow the determination of how the domains are matched at the atomic (unit cell) level, even though the spatial resolution of the images is on the scale of micrometres. The atom P(1) is determined as the linking atom for connecting...

  7. Structural landscape of the proline-rich domain of Sos1 nucleotide exchange factor.

    Science.gov (United States)

    McDonald, Caleb B; Bhat, Vikas; Kurouski, Dmitry; Mikles, David C; Deegan, Brian J; Seldeen, Kenneth L; Lednev, Igor K; Farooq, Amjad

    2013-01-01

    Despite its key role in mediating a plethora of cellular signaling cascades pertinent to health and disease, little is known about the structural landscape of the proline-rich (PR) domain of Sos1 guanine nucleotide exchange factor. Herein, using a battery of biophysical tools, we provide evidence that the PR domain of Sos1 is structurally disordered and adopts an extended random coil-like conformation in solution. Of particular interest is the observation that while chemical denaturation of PR domain results in the formation of a significant amount of polyproline II (PPII) helices, it has little or negligible effect on its overall size as measured by its hydrodynamic radius. Our data also show that the PR domain displays a highly dynamic conformational basin in agreement with the knowledge that the intrinsically unstructured proteins rapidly interconvert between an ensemble of conformations. Collectively, our study provides new insights into the conformational equilibrium of a key signaling molecule with important consequences on its physiological function. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. Bifurcation Observation of Combining Spiral Gear Transmission Based on Parameter Domain Structure Analysis

    Directory of Open Access Journals (Sweden)

    He Lin

    2016-01-01

    Full Text Available This study considers the bifurcation evolutions for a combining spiral gear transmission through parameter domain structure analysis. The system nonlinear vibration equations are created with piecewise backlash and general errors. Gill’s numerical integration algorithm is implemented in calculating the vibration equation sets. Based on cell-mapping method (CMM, two-dimensional dynamic domain planes have been developed and primarily focused on the parameters of backlash, transmission error, mesh frequency and damping ratio, and so forth. Solution demonstrates that Period-doubling bifurcation happens as the mesh frequency increases; moreover nonlinear discontinuous jump breaks the periodic orbit and also turns the periodic state into chaos suddenly. In transmission error planes, three cell groups which are Period-1, Period-4, and Chaos have been observed, and the boundary cells are the sensitive areas to dynamic response. Considering the parameter planes which consist of damping ratio associated with backlash, transmission error, mesh stiffness, and external load, the solution domain structure reveals that the system step into chaos undergoes Period-doubling cascade with Period-2m (m: integer periodic regions. Direct simulations to obtain the bifurcation diagram and largest Lyapunov exponent (LE match satisfactorily with the parameter domain solutions.

  9. Local and Nanoscale Structure and Speciation in the PuO{sub 2+x-y}(OH){sub 2y} {center_dot}zH{sub 2}O System

    Energy Technology Data Exchange (ETDEWEB)

    Conradson, Steven D.; Begg, Bruce D.; Clark, David L.; Den Auwer, Christophe J.; Ding, Mei; Dorhout, Peter K.; Espinosa-Faller, Francisco J.; Gordon, Pamela L.; Haire, Richard G.; Hess, Nancy J.; Hess, Ryan F.; Keogh, D. Webster; Morales, Luis A.; Neu, Mary P.; Paviet-Hartmann, Patricia; Runde, Wolfgang; Tait, C DREW.; Veirs, D. Kirk; Villella, Phillip M.

    2004-09-26

    Pu L3 X-ray absorption fine structure spectra from 24 samples of PuO{sub 2+x} (and two related Pu substituted oxides), prepared by a variety of methods, demonstrate that (1) although the Pu sublattice remains the ordered part of the Pu distribution, the nearest-neighbor O atoms even at x = 0 are found in a multisite distribution with Pu-O distances consistent with the stable incorporation of OH{sup -} (and possibly H{sub 2}O and H{sup +}) into the PuO{sub 2} lattice; (2) the excess O from oxidation is found at Pu-O distances <1.9 {angstrom}, consistent with the multiply bound ''oxo''-type ligands found in molecular complexes of Pu(V) and Pu(VI); (3) the Pu associated with these oxo groups is most likely Pu(V), so that the excess O probably occurs as PuO{sub 2}{sup +} moieties that are aperiodically distributed through the lattice; and (4) the collective interactions between these defect sites most likely cause them to cluster so as give nanoscale heterogeneity in the form of domains that may have unusual reactivity, observed as sequential oxidation by H{sub 2}O at ambient conditions. The most accurate description of PuO{sub 2} is therefore actually PuO{sub 2+x-y}(OH){sub 2y} {center_dot} zH{sub 2}O, with pure, ordered, homogeneous PuO{sub 2} attained only when H{sub 2}O is rigorously excluded and the O activity is relatively low.

  10. Structure of a Spumaretrovirus Gag Central Domain Reveals an Ancient Retroviral Capsid.

    Directory of Open Access Journals (Sweden)

    Neil J Ball

    2016-11-01

    Full Text Available The Spumaretrovirinae, or foamy viruses (FVs are complex retroviruses that infect many species of monkey and ape. Despite little sequence homology, FV and orthoretroviral Gag proteins perform equivalent functions, including genome packaging, virion assembly, trafficking and membrane targeting. However, there is a paucity of structural information for FVs and it is unclear how disparate FV and orthoretroviral Gag molecules share the same function. To probe the functional overlap of FV and orthoretroviral Gag we have determined the structure of a central region of Gag from the Prototype FV (PFV. The structure comprises two all α-helical domains NtDCEN and CtDCEN that although they have no sequence similarity, we show they share the same core fold as the N- (NtDCA and C-terminal domains (CtDCA of archetypal orthoretroviral capsid protein (CA. Moreover, structural comparisons with orthoretroviral CA align PFV NtDCEN and CtDCEN with NtDCA and CtDCA respectively. Further in vitro and functional virological assays reveal that residues making inter-domain NtDCEN-CtDCEN interactions are required for PFV capsid assembly and that intact capsid is required for PFV reverse transcription. These data provide the first information that relates the Gag proteins of Spuma and Orthoretrovirinae and suggests a common ancestor for both lineages containing an ancient CA fold.

  11. Structural Conservation and Functional Diversity of the Poxvirus Immune Evasion (PIE) Domain Superfamily.

    Science.gov (United States)

    Nelson, Christopher A; Epperson, Megan L; Singh, Sukrit; Elliott, Jabari I; Fremont, Daved H

    2015-08-28

    Poxviruses encode a broad array of proteins that serve to undermine host immune defenses. Structural analysis of four of these seemingly unrelated proteins revealed the recurrent use of a conserved beta-sandwich fold that has not been observed in any eukaryotic or prokaryotic protein. Herein we propose to call this unique structural scaffolding the PIE (Poxvirus Immune Evasion) domain. PIE domain containing proteins are abundant in chordopoxvirinae, with our analysis identifying 20 likely PIE subfamilies among 33 representative genomes spanning 7 genera. For example, cowpox strain Brighton Red appears to encode 10 different PIEs: vCCI, A41, C8, M2, T4 (CPVX203), and the SECRET proteins CrmB, CrmD, SCP-1, SCP-2, and SCP-3. Characterized PIE proteins all appear to be nonessential for virus replication, and all contain signal peptides for targeting to the secretory pathway. The PIE subfamilies differ primarily in the number, size, and location of structural embellishments to the beta-sandwich core that confer unique functional specificities. Reported ligands include chemokines, GM-CSF, IL-2, MHC class I, and glycosaminoglycans. We expect that the list of ligands and receptors engaged by the PIE domain will grow as we come to better understand how this versatile structural architecture can be tailored to manipulate host responses to infection.

  12. Structure of a Spumaretrovirus Gag Central Domain Reveals an Ancient Retroviral Capsid

    Science.gov (United States)

    Dutta, Moumita; Pollard, Dominic J.; Goldstone, David C.; Ramos, Andres; Müllers, Erik; Stirnnagel, Kristin; Stanke, Nicole; Lindemann, Dirk; Taylor, William R.; Rosenthal, Peter B.

    2016-01-01

    The Spumaretrovirinae, or foamy viruses (FVs) are complex retroviruses that infect many species of monkey and ape. Despite little sequence homology, FV and orthoretroviral Gag proteins perform equivalent functions, including genome packaging, virion assembly, trafficking and membrane targeting. However, there is a paucity of structural information for FVs and it is unclear how disparate FV and orthoretroviral Gag molecules share the same function. To probe the functional overlap of FV and orthoretroviral Gag we have determined the structure of a central region of Gag from the Prototype FV (PFV). The structure comprises two all α-helical domains NtDCEN and CtDCEN that although they have no sequence similarity, we show they share the same core fold as the N- (NtDCA) and C-terminal domains (CtDCA) of archetypal orthoretroviral capsid protein (CA). Moreover, structural comparisons with orthoretroviral CA align PFV NtDCEN and CtDCEN with NtDCA and CtDCA respectively. Further in vitro and functional virological assays reveal that residues making inter-domain NtDCEN—CtDCEN interactions are required for PFV capsid assembly and that intact capsid is required for PFV reverse transcription. These data provide the first information that relates the Gag proteins of Spuma and Orthoretrovirinae and suggests a common ancestor for both lineages containing an ancient CA fold. PMID:27829070

  13. Complex structure of the fission yeast SREBP-SCAP binding domains reveals an oligomeric organization.

    Science.gov (United States)

    Gong, Xin; Qian, Hongwu; Shao, Wei; Li, Jingxian; Wu, Jianping; Liu, Jun-Jie; Li, Wenqi; Wang, Hong-Wei; Espenshade, Peter; Yan, Nieng

    2016-11-01

    Sterol regulatory element-binding protein (SREBP) transcription factors are master regulators of cellular lipid homeostasis in mammals and oxygen-responsive regulators of hypoxic adaptation in fungi. SREBP C-terminus binds to the WD40 domain of SREBP cleavage-activating protein (SCAP), which confers sterol regulation by controlling the ER-to-Golgi transport of the SREBP-SCAP complex and access to the activating proteases in the Golgi. Here, we biochemically and structurally show that the carboxyl terminal domains (CTD) of Sre1 and Scp1, the fission yeast SREBP and SCAP, form a functional 4:4 oligomer and Sre1-CTD forms a dimer of dimers. The crystal structure of Sre1-CTD at 3.5 Å and cryo-EM structure of the complex at 5.4 Å together with in vitro biochemical evidence elucidate three distinct regions in Sre1-CTD required for Scp1 binding, Sre1-CTD dimerization and tetrameric formation. Finally, these structurally identified domains are validated in a cellular context, demonstrating that the proper 4:4 oligomeric complex formation is required for Sre1 activation.

  14. The structure of a conserved piezo channel domain reveals a topologically distinct β sandwich fold.

    Science.gov (United States)

    Kamajaya, Aron; Kaiser, Jens T; Lee, Jonas; Reid, Michelle; Rees, Douglas C

    2014-10-07

    Piezo has recently been identified as a family of eukaryotic mechanosensitive channels composed of subunits containing over 2,000 amino acids, without recognizable sequence similarity to other channels. Here, we present the crystal structure of a large, conserved extramembrane domain located just before the last predicted transmembrane helix of C. elegans PIEZO, which adopts a topologically distinct β sandwich fold. The structure was also determined of a point mutation located on a conserved surface at the position equivalent to the human PIEZO1 mutation found in dehydrated hereditary stomatocytosis patients (M2225R). While the point mutation does not change the overall domain structure, it does alter the surface electrostatic potential that may perturb interactions with a yet-to-be-identified ligand or protein. The lack of structural similarity between this domain and any previously characterized fold, including those of eukaryotic and bacterial channels, highlights the distinctive nature of the Piezo family of eukaryotic mechanosensitive channels. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Structure of PIN-domain protein PH0500 from Pyrococcus horikoshii

    International Nuclear Information System (INIS)

    Jeyakanthan, Jeyaraman; Inagaki, Eiji; Kuroishi, Chizu; Tahirov, Tahir H.

    2005-01-01

    The structure of P. horikoshii OT3 protein PH0500 was determined by the multiple anomalous dispersion method and refined in two crystal forms. The protein is a dimer and has a PIN-domain fold. The Pyrococcus horikoshii OT3 protein PH0500 is highly conserved within the Pyrococcus genus of hyperthermophilic archaea and shows low amino-acid sequence similarity with a family of PIN-domain proteins. The protein has been expressed, purified and crystallized in two crystal forms: PH0500-I and PH0500-II. The structure was determined at 2.0 Å by the multiple anomalous dispersion method using a selenomethionyl derivative of crystal form PH0500-I (PH0500-I-Se). The structure of PH0500-I has been refined at 1.75 Å resolution to an R factor of 20.9% and the structure of PH0500-II has been refined at 2.0 Å resolution to an R factor of 23.4%. In both crystal forms as well as in solution the molecule appears to be a dimer. Searches of the databases for protein-fold similarities confirmed that the PH0500 protein is a PIN-domain protein with possible exonuclease activity and involvement in DNA or RNA editing

  16. Structure validation of the Josephin domain of ataxin-3: Conclusive evidence for an open conformation

    International Nuclear Information System (INIS)

    Nicastro, Giuseppe; Habeck, Michael; Masino, Laura; Svergun, Dmitri I.; Pastore, Annalisa

    2006-01-01

    The availability of new and fast tools in structure determination has led to a more than exponential growth of the number of structures solved per year. It is therefore increasingly essential to assess the accuracy of the new structures by reliable approaches able to assist validation. Here, we discuss a specific example in which the use of different complementary techniques, which include Bayesian methods and small angle scattering, resulted essential for validating the two currently available structures of the Josephin domain of ataxin-3, a protein involved in the ubiquitin/proteasome pathway and responsible for neurodegenerative spinocerebellar ataxia of type 3. Taken together, our results demonstrate that only one of the two structures is compatible with the experimental information. Based on the high precision of our refined structure, we show that Josephin contains an open cleft which could be directly implicated in the interaction with polyubiquitin chains and other partners

  17. Structural analyses of the Ankyrin Repeat Domain of TRPV6 and related TRPV ion channels†‡

    OpenAIRE

    Phelps, Christopher B.; Huang, Robert J.; Lishko, Polina V.; Wang, Ruiqi R.; Gaudet, Rachelle

    2008-01-01

    Transient Receptor Potential (TRP) proteins are cation channels composed of a transmembrane domain flanked by large N- and C-terminal cytoplasmic domains. All members of the vanilloid family of TRP channels (TRPV) possess an N-terminal ankyrin repeat domain (ARD). The ARD of mammalian TRPV6, an important regulator of calcium uptake and homeostasis, is essential for channel assembly and regulation. The 1.7 Å crystal structure of the TRPV6-ARD reveals conserved structural elements unique to the...

  18. Nonlinear time-domain soil–structure interaction analysis of embedded reactor structures subjected to earthquake loads

    Energy Technology Data Exchange (ETDEWEB)

    Solberg, Jerome M., E-mail: solberg2@llnl.gov [Methods Development Group, Lawrence Livermore Nat’l Lab, P.O. Box 808, Mailstop L-125, Livermore, CA 94550 (United States); Hossain, Quazi, E-mail: hossain1@llnl.gov [Structural and Applied Mechanics Group, Lawrence Livermore Nat’l Lab, P.O. Box 808, Mailstop L-129, Livermore, CA 94550 (United States); Mseis, George, E-mail: george.mseis@gmail.com [Structural and Applied Mechanics Group, Lawrence Livermore Nat’l Lab, P.O. Box 808, Mailstop L-129, Livermore, CA 94550 (United States)

    2016-08-01

    Highlights: • Derived modified version of Bielak’s SSI method for nonlinear time-domain analysis. • Utilized a Ramberg–Osgood material with parameters that can be fit to EPRI data. • Matched vertically propagating shear wave results from CARES. • Applied this technique to a representative SMR, compared well with SASSI. • The technique is extensible to other material models and nonlinear effects. - Abstract: A generalized time-domain method for soil–structure interaction analysis is developed, based upon an extension of the work of the domain reduction method of Bielak et al. The methodology is combined with the use of a simple hysteretic soil model based upon the Ramberg–Osgood formulation and applied to a notional Small Modular Reactor. These benchmark results compare well (with some caveats) with those obtained by using the industry-standard frequency-domain code SASSI. The methodology provides a path forward for investigation of other sources of nonlinearity, including those associated with the use of more physically-realistic material models incorporating pore-pressure effects, gap opening/closing, the effect of nonlinear structural elements, and 3D seismic inputs.

  19. Crystal Structure of a Complex of the Intracellular Domain of Interferon λ Receptor 1 (IFNLR1) and the FERM/SH2 Domains of Human JAK1.

    Science.gov (United States)

    Zhang, Di; Wlodawer, Alexander; Lubkowski, Jacek

    2016-11-20

    The crystal structure of a construct consisting of the FERM and SH2-like domains of the human Janus kinase 1 (JAK1) bound to a fragment of the intracellular domain of the interferon-λ receptor 1 (IFNLR1) has been determined at the nominal resolution of 2.1Å. In this structure, the receptor peptide forms an 85-Å-long extended chain, in which both the previously identified box1 and box2 regions bind simultaneously to the FERM and SH2-like domains of JAK1. Both domains of JAK1 are generally well ordered, with regions not seen in the crystal structure limited to loops located away from the receptor-binding regions. The structure provides a much more complete and accurate picture of the interactions between JAK1 and IFNLR1 than those given in earlier reports, illuminating the molecular basis of the JAK-cytokine receptor association. A glutamate residue adjacent to the box2 region in IFNLR1 mimics the mode of binding of a phosphotyrosine in classical SH2 domains. It was shown here that a deletion of residues within the box1 region of the receptor abolishes stable interactions with JAK1, although it was previously shown that box2 alone is sufficient to stabilize a similar complex of the interferon-α receptor and TYK2. Published by Elsevier Ltd.

  20. Effect of antimony nano-scale surface-structures on a GaSb/AlAsSb distributed Bragg reflector

    International Nuclear Information System (INIS)

    Husaini, S.; Shima, D.; Ahirwar, P.; Rotter, T. J.; Hains, C. P.; Dang, T.; Bedford, R. G.; Balakrishnan, G.

    2013-01-01

    Effects of antimony crystallization on the surface of GaSb during low temperature molecular beam epitaxy growth are investigated. The geometry of these structures is studied via transmission electron and atomic force microscopies, which show the surface metal forms triangular-shaped, elongated nano-wires with a structured orientation composed entirely of crystalline antimony. By depositing antimony on a GaSb/AlAsSb distributed Bragg reflector, the field is localized within the antimony layer. Polarization dependent transmission measurements are carried out on these nano-structures deposited on a GaSb/AlAsSb distributed Bragg reflector. It is shown that the antimony-based structures at the surface favor transmission of light polarized perpendicular to the wires.

  1. Influence of different aspect ratios on the structural and electrical properties of GaN thin films grown on nanoscale-patterned sapphire substrates

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Fang-Wei [Department of Electrophysics, National Chiao-Tung University, Hsinchu 300, Taiwan (China); Ke, Wen-Cheng, E-mail: wcke@mail.ntust.edu.tw [Department of Materials Science and Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan (China); Cheng, Chun-Hong; Liao, Bo-Wei; Chen, Wei-Kuo [Department of Electrophysics, National Chiao-Tung University, Hsinchu 300, Taiwan (China)

    2016-07-01

    Highlights: • Nanoscale patterned sapphire substrate was prepared by anodic-aluminum-oxide etching mask. • Influence of aspect ratio of NPSS on structural and electrical properties of GaN films was studied. • Low dislocation density and high carrier mobility of GaN films were grown on high aspect ratio NPSS. - Abstract: This study presents GaN thin films grown on nanoscale-patterned sapphire substrates (NPSSs) with different aspect ratios (ARs) using a homemade metal-organic chemical vapor deposition system. The anodic aluminum oxide (AAO) technique is used to prepare the dry etching mask. The cross-sectional view of the scanning electron microscope image shows that voids exist between the interface of the GaN thin film and the high-AR (i.e. ∼2) NPSS. In contrast, patterns on the low-AR (∼0.7) NPSS are filled full of GaN. The formation of voids on the high-AR NPSS is believed to be due to the enhancement of the lateral growth in the initial growth stage, and the quick-merging GaN thin film blocks the precursors from continuing to supply the bottom of the pattern. The atomic force microscopy images of GaN on bare sapphire show a layer-by-layer surface morphology, which becomes a step-flow surface morphology for GaN on a high-AR NPSS. The edge-type threading dislocation density can be reduced from 7.1 × 10{sup 8} cm{sup −2} for GaN on bare sapphire to 4.9 × 10{sup 8} cm{sup −2} for GaN on a high-AR NPSS. In addition, the carrier mobility increases from 85 cm{sup 2}/Vs for GaN on bare sapphire to 199 cm{sup 2}/Vs for GaN on a high-AR NPSS. However, the increased screw-type threading dislocation density for GaN on a low-AR NPSS is due to the competition of lateral growth on the flat-top patterns and vertical growth on the bottom of the patterns that causes the material quality of the GaN thin film to degenerate. Thus, the experimental results indicate that the AR of the particular patterning of a NPSS plays a crucial role in achieving GaN thin film with

  2. Specific features of the domain structure of (Gd1-xNdx)2(MoO4)3 crystals

    International Nuclear Information System (INIS)

    Bryzgalov, A.N.; Slepchenko, B.M.; Virachev, B.P.

    1989-01-01

    Formation of the domain structures by sample transfer into thermodynamically metastable state using a simultaneous effect of electric field and temperature change is investigated in Gd 1.7 Nd 0.3 (MoO 4 ) 3 monocrystals (GMO). Some new results obtained under investigations into GMO domain structure using neodymium by means of hydrothermal etching and polarization-optical method are presented

  3. Novel Chiral Magnetic Domain Wall Structure in Fe/Ni/Cu(001) Films

    Science.gov (United States)

    Chen, G.; Zhu, J.; Quesada, A.; Li, J.; N'Diaye, A. T.; Huo, Y.; Ma, T. P.; Chen, Y.; Kwon, H. Y.; Won, C.; Qiu, Z. Q.; Schmid, A. K.; Wu, Y. Z.

    2013-04-01

    Using spin-polarized low energy electron microscopy, we discovered a new type of domain wall structure in perpendicularly magnetized Fe/Ni bilayers grown epitaxially on Cu(100). Specifically, we observed unexpected Néel-type walls with fixed chirality in the magnetic stripe phase. Furthermore, we find that the chirality of the domain walls is determined by the film growth order with the chirality being right handed in Fe/Ni bilayers and left handed in Ni/Fe bilayers, suggesting that the underlying mechanism is the Dzyaloshinskii-Moriya interaction at the film interfaces. Our observations may open a new route to control chiral spin structures using interfacial engineering in transition metal heterostructures.

  4. On using moving windows in finite element time domain simulation for long accelerator structures

    International Nuclear Information System (INIS)

    Lee, L.-Q.; Candel, Arno; Ng, Cho; Ko, Kwok

    2010-01-01

    A finite element moving window technique is developed to simulate the propagation of electromagnetic waves induced by the transit of a charged particle beam inside large and long structures. The window moving along with the beam in the computational domain adopts high-order finite element basis functions through p refinement and/or a high-resolution mesh through h refinement so that a sufficient accuracy is attained with substantially reduced computational costs. Algorithms to transfer discretized fields from one mesh to another, which are the keys to implementing a moving window in a finite element unstructured mesh, are presented. Numerical experiments are carried out using the moving window technique to compute short-range wakefields in long accelerator structures. The results are compared with those obtained from the normal finite element time domain (FETD) method and the advantages of using the moving window technique are discussed.

  5. Enhanced magnetostriction derived from magnetic single domain structures in cluster-assembled SmCo films

    Science.gov (United States)

    Bai, Yulong; Yang, Bo; Guo, Fei; Lu, Qingshan; Zhao, Shifeng

    2017-11-01

    Cluster-assembled SmCo alloy films were prepared by low energy cluster beam deposition. The structure, magnetic domain, magnetization, and magnetostriction of the films were characterized. It is shown that the as-prepared films are assembled in compact and uniformly distributed spherical cluster nanoparticles, most of which, after vacuum in situ annealing at 700 K, aggregated to form cluster islands. These cluster islands result in transformations from superparamagnetic states to magnetic single domain (MSD) states in the films. Such MSD structures contribute to the enhanced magnetostrictive behaviors with a saturation magnetostrictive coefficient of 160 × 10-6 in comparison to 105 × 10-6 for the as-prepared films. This work demonstrates candidate materials that could be applied in nano-electro-mechanical systems, low power information storage, and weak magnetic detecting devices.

  6. Structure of the USP15 N-terminal domains: a β-hairpin mediates close association between the DUSP and UBL domains.

    Science.gov (United States)

    Harper, Stephen; Besong, Tabot M D; Emsley, Jonas; Scott, David J; Dreveny, Ingrid

    2011-09-20

    Ubiquitin specific protease 15 (USP15) functions in COP9 signalosome mediated regulation of protein degradation and cellular signaling through catalyzing the ubiquitin deconjugation reaction of a discrete number of substrates. It influences the stability of adenomatous polyposis coli, IκBα, caspase-3, and the human papillomavirus type 16 E6. USP15 forms a subfamily with USP4 and USP11 related through a shared presence of N-terminal "domain present in ubiquitin specific proteases" (DUSP) and "ubiquitin-like" (UBL) domains (DU subfamily). Here we report the 1.5 Å resolution crystal structure of the human USP15 N-terminal domains revealing a 80 Å elongated arrangement with the DU domains aligned in tandem. This architecture is generated through formation of a defined interface that is dominated by an intervening β-hairpin structure (DU finger) that engages in an intricate hydrogen-bonding network between the domains. The UBL domain is closely related to ubiquitin among β-grasp folds but is characterized by the presence of longer loop regions and different surface characteristics, indicating that this domain is unlikely to act as ubiquitin mimic. Comparison with the related murine USP4 DUSP-UBL crystal structure reveals that the main DU interdomain contacts are conserved. Analytical ultracentrifugation, small-angle X-ray scattering, and gel filtration experiments revealed that USP15 DU is monomeric in solution. Our data provide a framework to advance study of the structure and function of the DU subfamily. © 2011 American Chemical Society

  7. Naphtho[2,1-b:3,4-b']dithiophene-based bulk heterojunction solar cells: how molecular structure influences nanoscale morphology and photovoltaic properties.

    Science.gov (United States)

    Kim, Yu Jin; Cheon, Ye Rim; Back, Jang Yeol; Kim, Yun-Hi; Chung, Dae Sung; Park, Chan Eon

    2014-11-10

    Organic bulk heterojunction photovoltaic devices based on a series of three naphtho[2,1-b:3,4-b']dithiophene (NDT) derivatives blended with phenyl-C71-butyric acid methyl ester were studied. These three derivatives, which have NDT units with various thiophene-chain lengths, were employed as the donor polymers. The influence of their molecular structures on the correlation between their solar-cell performances and their degree of crystallization was assessed. The grazing-incidence angle X-ray diffraction and atomic force microscopy results showed that the three derivatives exhibit three distinct nanoscale morphologies. We correlated these morphologies with the device physics by determining the J-V characteristics and the hole and electron mobilities of the devices. On the basis of our results, we propose new rules for the design of future generations of NDT-based polymers for use in bulk heterojunction solar cells. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Structure of the interleukin-2 tyrosine kinase Src homology 2 domain; comparison between X-ray and NMR-derived structures

    International Nuclear Information System (INIS)

    Joseph, Raji E.; Ginder, Nathaniel D.; Hoy, Julie A.; Nix, Jay C.; Fulton, D. Bruce; Honzatko, Richard B.; Andreotti, Amy H.

    2012-01-01

    The interleukin-2 tyrosine kinase Src homology 2 domain was crystallized and its structure was solved to 2.35 Å resolution. The structure reveals a domain-swapped dimer that is related to other dimeric SH2 domains solved previously. The cis–trans-prolyl isomerization that is evident from solution studies of Itk SH2 cannot be observed in the crystal structure. The crystal structure of the interleukin-2 tyrosine kinase Src homology domain (Itk SH2) is described and it is found that unlike in studies of this domain using NMR spectroscopy, cis–trans-prolyl isomerization is not readily detected in the crystal structure. Based on similarities between the Itk SH2 crystal form and the cis form of the Itk SH2 NMR structure, it is concluded that it is likely that the prolyl imide bond at least in part adopts the cis conformation in the crystal form. However, the lack of high-resolution data and the dynamic nature of the proline-containing loop mean that the precise imide-bond conformation cannot be determined and prolyl cis–trans isomerization in the crystal cannot be ruled out. Given the preponderance of structures that have been solved by X-ray crystallography in the Protein Data Bank, this result supports the notion that prolyl isomerization in folded proteins has been underestimated among known structures. Interestingly, while the precise status of the proline residue is ambiguous, Itk SH2 crystallizes as a domain-swapped dimer. The domain-swapped structure of Itk SH2 is similar to the domain-swapped SH2 domains of Grb2 and Nck, with domain swapping occurring at the β-meander region of all three SH2 domains. Thus, for Itk SH2 structural analysis by NMR spectroscopy and X-ray crystallography revealed very different structural features: proline isomerization versus domain-swapped dimerization, respectively

  9. Nanoscale Ionic Liquids

    Science.gov (United States)

    2006-11-01

    Technical Report 11 December 2005 - 30 November 2006 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Nanoscale Ionic Liquids 5b. GRANT NUMBER FA9550-06-1-0012...Title: Nanoscale Ionic Liquids Principal Investigator: Emmanuel P. Giannelis Address: Materials Science and Engineering, Bard Hall, Cornell University...based fluids exhibit high ionic conductivity. The NFs are typically synthesized by grafting a charged, oligomeric corona onto the nanoparticle cores

  10. Spintronics in nanoscale devices

    CERN Document Server

    Hedin, Eric R

    2013-01-01

    By exploiting the novel properties of quantum dots and nanoscale Aharonov-Bohm rings together with the electronic and magnetic properties of various semiconductor materials and graphene, researchers have conducted numerous theoretical and computational modeling studies and experimental tests that show promising behavior for spintronics applications. Spin polarization and spin-filtering capabilities and the ability to manipulate the electron spin state through external magnetic or electric fields have demonstrated the promise of workable nanoscale devices for computing and memory applications.

  11. Structural studies of the activation of the two component receiver domain NTRC by multidimensional heteronuclear NMR

    Energy Technology Data Exchange (ETDEWEB)

    Nohaile, Michael James [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

    1996-05-01

    Multidimensional heteronuclear NMR spectroscopy was used to investigate the N-terminal domain of the transcriptional enhancer NTRC (NiTrogen Regulatory protein C). This domain belongs to the family of receiver domains of two-component regulatory systems involved in signal transduction. Phosphorylation of NTRC at D54 leads to an activated form of the molecule which stimulates transcription of genes involved in nitrogen regulation. Three and four dimensional NMR techniques were used to determine an intermediate resolution structure of the unphosphorylated, inactive form of the N-terminal domain of NTRC. The structure is comprised of five α-helices and a five-stranded β-sheet in a (β/α)5 topology. Analysis of the backbone dynamics of NTRC indicate that helix 4 and strand 5 are significantly more flexible than the rest of the secondary structure of the protein and that the loops making up the active site are flexible. The short lifetime of phospho-NTRC hampers the study of this form. However, conditions for determining the resonance assignments and, possibly, the three dimensional structure of phosphorylated NTRC have been obtained. Tentative assignments of the phosphorylated form indicate that the majority of the changes that NTRC experiences upon phosphorylation occur in helix 3, strand 4, helix 4, strand 5, and the loop between strand 5 and helix 5 (the 3445 face of NTRC) as well as near the site of phosphorylation. In order to examine a stable, activated form of the protein, constitutively active mutants of NTRC were investigated.

  12. A method for analysis of lipid vesicle domain structure from confocal image data

    DEFF Research Database (Denmark)

    Husen, Peter Rasmussen; Fidorra, Matthias; Hartel, Steffen

    2012-01-01

    Quantitative characterization of the lateral structure of curved membranes based on fluorescence microscopy requires knowledge of the fluorophore distribution on the surface. We present an image analysis approach for extraction of the fluorophore distribution on a spherical lipid vesicle from...... confocal imaging stacks. The technique involves projection of volumetric image data onto a triangulated surface mesh representation of the membrane, correction of photoselection effects and global motion of the vesicle during image acquisition and segmentation of the surface into domains using histograms...

  13. Structure of the Reston ebolavirus VP30 C-terminal domain.

    Science.gov (United States)

    Clifton, Matthew C; Kirchdoerfer, Robert N; Atkins, Kateri; Abendroth, Jan; Raymond, Amy; Grice, Rena; Barnes, Steve; Moen, Spencer; Lorimer, Don; Edwards, Thomas E; Myler, Peter J; Saphire, Erica Ollmann

    2014-04-01

    The ebolaviruses can cause severe hemorrhagic fever. Essential to the ebolavirus life cycle is the protein VP30, which serves as a transcriptional cofactor. Here, the crystal structure of the C-terminal, NP-binding domain of VP30 from Reston ebolavirus is presented. Reston VP30 and Ebola VP30 both form homodimers, but the dimeric interfaces are rotated relative to each other, suggesting subtle inherent differences or flexibility in the dimeric interface.

  14. Structure of Alzheimer’s disease amyloid precursor protein copper-binding domain at atomic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Kong, Geoffrey Kwai-Wai; Adams, Julian J. [Biota Structural Biology Laboratory, St Vincent’s Institute, 9 Princes Street, Fitzroy, Victoria 3065 (Australia); Cappai, Roberto [Department of Pathology and Centre for Neuroscience, The University of Melbourne, Victoria 3010 (Australia); The Mental Health Research Institute of Victoria, Parkville, Victoria 3052 (Australia); Bio21 Institute, The University of Melbourne, Victoria 3010 (Australia); Parker, Michael W., E-mail: mparker@svi.edu.au [Biota Structural Biology Laboratory, St Vincent’s Institute, 9 Princes Street, Fitzroy, Victoria 3065 (Australia); Bio21 Institute, The University of Melbourne, Victoria 3010 (Australia)

    2007-10-01

    An atomic resolution structure of the copper-binding domain of the Alzheimer’s disease amyloid precursor protein is presented. Amyloid precursor protein (APP) plays a central role in the pathogenesis of Alzheimer’s disease, as its cleavage generates the Aβ peptide that is toxic to cells. APP is able to bind Cu{sup 2+} and reduce it to Cu{sup +} through its copper-binding domain (CuBD). The interaction between Cu{sup 2+} and APP leads to a decrease in Aβ production and to alleviation of the symptoms of the disease in mouse models. Structural studies of CuBD have been undertaken in order to better understand the mechanism behind the process. Here, the crystal structure of CuBD in the metal-free form determined to ultrahigh resolution (0.85 Å) is reported. The structure shows that the copper-binding residues of CuBD are rather rigid but that Met170, which is thought to be the electron source for Cu{sup 2+} reduction, adopts two different side-chain conformations. These observations shed light on the copper-binding and redox mechanisms of CuBD. The structure of CuBD at atomic resolution provides an accurate framework for structure-based design of molecules that will deplete Aβ production.

  15. Structure of the Escherichia coli RNA polymerase α subunit C-terminal domain

    International Nuclear Information System (INIS)

    Lara-González, Samuel; Birktoft, Jens J.; Lawson, Catherine L.

    2010-01-01

    The crystal structure of the dimethyllysine derivative of the E. coli RNA polymerase α subunit C-terminal domain is reported at 2.0 Å resolution. The α subunit C-terminal domain (αCTD) of RNA polymerase (RNAP) is a key element in transcription activation in Escherichia coli, possessing determinants responsible for the interaction of RNAP with DNA and with transcription factors. Here, the crystal structure of E. coli αCTD (α subunit residues 245–329) determined to 2.0 Å resolution is reported. Crystals were obtained after reductive methylation of the recombinantly expressed domain. The crystals belonged to space group P2 1 and possessed both pseudo-translational symmetry and pseudo-merohedral twinning. The refined coordinate model (R factor = 0.193, R free = 0.236) has improved geometry compared with prior lower resolution determinations of the αCTD structure [Jeon et al. (1995 ▶), Science, 270, 1495–1497; Benoff et al. (2002 ▶), Science, 297, 1562–1566]. An extensive dimerization interface formed primarily by N- and C-terminal residues is also observed. The new coordinates will facilitate the improved modeling of αCTD-containing multi-component complexes visualized at lower resolution using X-ray crystallography and electron-microscopy reconstruction

  16. Molecular Details of Olfactomedin Domains Provide Pathway to Structure-Function Studies.

    Directory of Open Access Journals (Sweden)

    Shannon E Hill

    Full Text Available Olfactomedin (OLF domains are found within extracellular, multidomain proteins in numerous tissues of multicellular organisms. Even though these proteins have been implicated in human disorders ranging from cancers to attention deficit disorder to glaucoma, little is known about their structure(s and function(s. Here we biophysically, biochemically, and structurally characterize OLF domains from H. sapiens olfactomedin-1 (npoh-OLF, also called noelin, pancortin, OLFM1, and hOlfA, and M. musculus gliomedin (glio-OLF, also called collomin, collmin, and CRG-L2, and compare them with available structures of myocilin (myoc-OLF recently reported by us and R. norvegicus glio-OLF and M. musculus latrophilin-3 (lat3-OLF by others. Although the five-bladed β-propeller architecture remains unchanged, numerous physicochemical characteristics differ among these OLF domains. First, npoh-OLF and glio-OLF exhibit prominent, yet distinct, positive surface charges and copurify with polynucleotides. Second, whereas npoh-OLF and myoc-OLF exhibit thermal stabilities typical of human proteins near 55°C, and most myoc-OLF variants are destabilized and highly prone to aggregation, glio-OLF is nearly 20°C more stable and significantly more resistant to chemical denaturation. Phylogenetically, glio-OLF is most similar to primitive OLFs, and structurally, glio-OLF is missing distinguishing features seen in OLFs such as the disulfide bond formed by N- and C- terminal cysteines, the sequestered Ca2+ ion within the propeller central hydrophilic cavity, and a key loop-stabilizing cation-π interaction on the top face of npoh-OLF and myoc-OLF. While deciphering the explicit biological functions, ligands, and binding partners for OLF domains will likely continue to be a challenging long-term experimental pursuit, we used structural insights gained here to generate a new antibody selective for myoc-OLF over npoh-OLF and glio-OLF as a first step in overcoming the impasse in

  17. Molecular dynamics simulations revealed structural differences among WRKY domain-DNA interaction in barley (Hordeum vulgare).

    Science.gov (United States)

    Pandey, Bharati; Grover, Abhinav; Sharma, Pradeep

    2018-02-12

    The WRKY transcription factors are a class of DNA-binding proteins involved in diverse plant processes play critical roles in response to abiotic and biotic stresses. Genome-wide divergence analysis of WRKY gene family in Hordeum vulgare provided a framework for molecular evolution and functional roles. So far, the crystal structure of WRKY from barley has not been resolved; moreover, knowledge of the three-dimensional structure of WRKY domain is pre-requisites for exploring the protein-DNA recognition mechanisms. Homology modelling based approach was used to generate structures for WRKY DNA binding domain (DBD) and its variants using AtWRKY1 as a template. Finally, the stability and conformational changes of the generated model in unbound and bound form was examined through atomistic molecular dynamics (MD) simulations for 100 ns time period. In this study, we investigated the comparative binding pattern of WRKY domain and its variants with W-box cis-regulatory element using molecular docking and dynamics (MD) simulations assays. The atomic insight into WRKY domain exhibited significant variation in the intermolecular hydrogen bonding pattern, leading to the structural anomalies in the variant type and differences in the DNA-binding specificities. Based on the MD analysis, residual contribution and interaction contour, wild-type WRKY (HvWRKY46) were found to interact with DNA through highly conserved heptapeptide in the pre- and post-MD simulated complexes, whereas heptapeptide interaction with DNA was missing in variants (I and II) in post-MD complexes. Consequently, through principal component analysis, wild-type WRKY was also found to be more stable by obscuring a reduced conformational space than the variant I (HvWRKY34). Lastly, high binding free energy for wild-type and variant II allowed us to conclude that wild-type WRKY-DNA complex was more stable relative to variants I. The results of our study revealed complete dynamic and structural information

  18. Nanoscale effects in interdiffusion

    International Nuclear Information System (INIS)

    Erdelyi, Z.; Langer, G.A.; Beke, D.L.; Csik, A.

    2007-01-01

    Complete text of publication follows. Diffusion on the nano/atomic scales in multilayers, thin films has many challenging features even if the role of structural defects can be neglected and 'only' the effects related to the nano/atomic scale raise. The most basic equations to describe the diffusion are Fick's equations. It is important to emphasize that the diffusion coefficient in Fick's equations is in general composition independent and Fick's classical equations do not include the stress effects, which can have important influence onto the diffusion especially on the nano/atomic scale. We illustrate that the continuum descriptions of the diffusion cannot be applied automatically on such short distances, the classical continuum approximations (Fick's laws) cannot describe correctly the atomic movements. They predict faster kinetics than the atomistic models and the interface shift is always proportional to the square root of the time. However, the kinetics can be even linear on the nano/atomic scale. We have shown from computer simulations that Fick's laws violate on the nanoscale either in completely or restricted miscible systems. This is strongly related to the discrete character of the system on the nanoscale and to the highly neglected fact in the literature that the diffusion coefficients depend on the composition. As will be seen the composition dependence of D is very important and has very significant influence on the diffusion kinetics on the nano/atomic scales. It originates from the fact that usually the diffusion coefficients are different in an A and in a B matrix. Consequently in case of a real interface, which is not atomically sharp, i.e. there is a more or less intermixed region between the pure A and B matrixes, the diffusion coefficient changes continuously while e.g. an A atom diffuses from the pure A matrix into the pure B. This feature can be also called diffusion asymmetry. We have also illustrated that in this case not only the

  19. Structure of the nucleotide-binding domain of a dipeptide ABC transporter reveals a novel iron-sulfur cluster-binding domain.

    Science.gov (United States)

    Li, Xiaolu; Zhuo, Wei; Yu, Jie; Ge, Jingpeng; Gu, Jinke; Feng, Yue; Yang, Maojun; Wang, Linfang; Wang, Na

    2013-02-01

    Dipeptide permease (Dpp), which belongs to an ABC transport system, imports peptides consisting of two or three L-amino acids from the matrix to the cytoplasm in microbes. Previous studies have indicated that haem competes with dipeptides to bind DppA in vitro and in vivo and that the Dpp system can also translocate haem. Here, the crystal structure of DppD, the nucleotide-binding domain (NBD) of the ABC-type dipeptide/oligopeptide/nickel-transport system from Thermoanaerobacter tengcongensis, bound with ATP, Mg(2+) and a [4Fe-4S] iron-sulfur cluster is reported. The N-terminal domain of DppD shares a similar structural fold with the NBDs of other ABC transporters. Interestingly, the C-terminal domain of DppD contains a [4Fe-4S] cluster. The UV-visible absorbance spectrum of DppD was consistent with the presence of a [4Fe-4S] cluster. A search with DALI revealed that the [4Fe-4S] cluster-binding domain is a novel structural fold. Structural analysis and comparisons with other ABC transporters revealed that this iron-sulfur cluster may act as a mediator in substrate (dipeptide or haem) binding by electron transfer and may regulate the transport process in Dpp ABC transport systems. The crystal structure provides a basis for understanding the properties of ABC transporters and will be helpful in investigating the functions of NBDs in the regulation of ABC transporter activity.

  20. Effect of preparation conditions on fractal structure and phase transformations in the synthesis of nanoscale M-type barium hexaferrite

    Energy Technology Data Exchange (ETDEWEB)

    Pashkova, E.V. [V.I. Vernadskii Institute of General and Inorganic Chemistry, 32/34 Prospect Palladina, Kyiv-142, 03680 (Ukraine); Solovyova, E.D., E-mail: solovyovak@mail.ru [V.I. Vernadskii Institute of General and Inorganic Chemistry, 32/34 Prospect Palladina, Kyiv-142, 03680 (Ukraine); Kotenko, I.E., E-mail: Hab2420@yahoo.com [National Technical University of Ukraine ' KPI' , Pr. Pobedy, 37, Kyiv-57 (Ukraine); Kolodiazhnyi, T.V., E-mail: kolodiazhnyi.taras@nims.go.jp [National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044 (Japan); Belous, A.G., E-mail: belous@ionc.kar.net [V.I. Vernadskii Institute of General and Inorganic Chemistry, 32/34 Prospect Palladina, Kyiv-142, 03680 (Ukraine)

    2011-10-15

    The conditions of the synthesis of carbonate-hydroxide precursors (pH of FeOOH precipitation and heat treatment regimes) were studied in terms of their effect on the fractal structure and physical-chemical properties of precursors. Phase transformations which occur during the synthesis of nanosize M-type barium hexaferrite (BHF) were studied as well. The first structural level of precursors' aggregation for mass fractals, the correlation between fractal dimension and precursors' activity during the synthesis of BHF were determined. Synthesis parameters for the precursors with the optimal fractal structure were determined. These data permit an enhancement of the filtration coefficient of the precipitates by a factor of 4-5, obtaining substantial decrease in the temperature required for synthesis of a single-phase BHF, and monodispersed plate-like nanoparticles (60 nm diameter) with the shape anisotropy and good magnetic characteristics (saturation magnetization (M{sub s})=68,7 emu/g and coercitivity (H{sub c})=5440 Oe). - Highlights: > The nanosize M-type BHF obtained by precipitation of hydroxicarbonates technique. > Optimal fractal structure of a precursor for nanosize M-type BHF has been determined. > The precursor precipitated at pH 4.3 allows getting monodisperse particles of BHF.

  1. Structural plasticity of the N-terminal capping helix of the TPR domain of kinesin light chain.

    Directory of Open Access Journals (Sweden)

    The Quyen Nguyen

    Full Text Available Kinesin1 plays a major role in neuronal transport by recruiting many different cargos through its kinesin light chain (KLC. Various structurally unrelated cargos interact with the conserved tetratricopeptide repeat (TPR domain of KLC. The N-terminal capping helix of the TPR domain exhibits an atypical sequence and structural features that may contribute to the versatility of the TPR domain to bind different cargos. We determined crystal structures of the TPR domain of both KLC1 and KLC2 encompassing the N-terminal capping helix and show that this helix exhibits two distinct and defined orientations relative to the rest of the TPR domain. Such a difference in orientation gives rise, at the N-terminal part of the groove, to the formation of one hydrophobic pocket, as well as to electrostatic variations at the groove surface. We present a comprehensive structural analysis of available KLC1/2-TPR domain structures that highlights that ligand binding into the groove can be specific of one or the other N-terminal capping helix orientations. Further, structural analysis reveals that the N-terminal capping helix is always involved in crystal packing contacts, especially in a TPR1:TPR1' contact which highlights its propensity to be a protein-protein interaction site. Together, these results underline that the structural plasticity of the N-terminal capping helix might represent a structural determinant for TPR domain structural versatility in cargo binding.

  2. Solution structure and dynamics of C-terminal regulatory domain of Vibrio vulnificus extracellular metalloprotease

    Energy Technology Data Exchange (ETDEWEB)

    Yun, Ji-Hye; Kim, Heeyoun [Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Park, Jung Eun [Department of Biotechnology, College of Natural Sciences, Chosun University, Gwangju 501-759 (Korea, Republic of); Lee, Jung Sup, E-mail: jsplee@mail.chosun.ac.kr [Department of Biotechnology, College of Natural Sciences, Chosun University, Gwangju 501-759 (Korea, Republic of); Lee, Weontae, E-mail: wlee@spin.yonsei.ac.kr [Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of)

    2013-01-11

    Highlights: Black-Right-Pointing-Pointer We have determined solution structures of vEP C-terminal regulatory domain. Black-Right-Pointing-Pointer vEP C-ter100 has a compact {beta}-barrel structure with eight anti-parallel {beta}-strands. Black-Right-Pointing-Pointer Solution structure of vEP C-ter100 shares its molecular topology with that of the collagen-binding domain of collagenase. Black-Right-Pointing-Pointer Residues in the {beta}3 region of vEP C-ter100 might be important in putative ligand/receptor binding. Black-Right-Pointing-Pointer vEP C-ter100 interacts strongly with iron ion. -- Abstract: An extracellular metalloprotease (vEP) secreted by Vibrio vulnificus ATCC29307 is a 45-kDa proteolytic enzyme that has prothrombin activation and fibrinolytic activities during bacterial infection. The action of vEP could result in clotting that could serve to protect the bacteria from the host defense machinery. Very recently, we showed that the C-terminal propeptide (C-ter100), which is unique to vEP, is involved in regulation of vEP activity. To understand the structural basis of this function of vEP C-ter100, we have determined the solution structure and backbone dynamics using multidimensional nuclear magnetic resonance spectroscopy. The solution structure shows that vEP C-ter100 is composed of eight anti-parallel {beta}-strands with a unique fold that has a compact {beta}-barrel formation which stabilized by hydrophobic and hydrogen bonding networks. Protein dynamics shows that the overall structure, including loops, is very rigid and stabilized. By structural database analysis, we found that vEP C-ter100 shares its topology with that of the collagen-binding domain of collagenase, despite low sequence homology between the two domains. Fluorescence assay reveals that vEP C-ter100 interacts strongly with iron (Fe{sup 3+}). These findings suggest that vEP protease might recruit substrate molecules, such as collagen, by binding at C-ter100 and that vEP participates

  3. Simulations of super-structure domain walls in two dimensional assemblies of magnetic nanoparticles

    DEFF Research Database (Denmark)

    Jordanovic, Jelena; Beleggia, Marco; Schiøtz, Jakob

    2015-01-01

    We simulate the formation of domain walls in two-dimensional assemblies of magnetic nanoparticles. Particle parameters are chosen to match recent electron holography and Lorentz microscopy studies of almost monodisperse cobalt nanoparticles assembled into regular, elongated lattices. As the parti......We simulate the formation of domain walls in two-dimensional assemblies of magnetic nanoparticles. Particle parameters are chosen to match recent electron holography and Lorentz microscopy studies of almost monodisperse cobalt nanoparticles assembled into regular, elongated lattices...... taking the role of the atomic spins. The coupling is, however, different. The superspins interact only by dipolar interactions as exchange coupling between individual nanoparticles may be neglected due to interparticle spacing. We observe that it is energetically favorable to introduce domain walls...... oriented along the long dimension of nanoparticle assemblies rather than along the short dimension. This is unlike what is typically observed in continuous magnetic materials, where the exchange interaction introduces an energetic cost proportional to the area of the domain walls. Structural disorder...

  4. The mechanism of domain-wall structure formation in Ar-Kr submonolayer films on graphite

    Directory of Open Access Journals (Sweden)

    A. Patrykiejew

    2014-12-01

    Full Text Available Using Monte Carlo simulation method in the canonical ensemble, we have studied the commensurate-incommensurate transition in two-dimensional finite mixed clusters of Ar and Kr adsorbed on graphite basal plane at low temperatures. It has been demonstrated that the transition occurs when the argon concentration exceeds the value needed to cover the peripheries of the cluster. The incommensurate phase exhibits a similar domain-wall structure as observed in pure krypton films at the densities exceeding the density of a perfect (√3x√3R30º commensurate phase, but the size of commensurate domains does not change much with the cluster size. When the argon concentration increases, the composition of domain walls changes while the commensurate domains are made of pure krypton. We have constructed a simple one-dimensional Frenkel-Kontorova-like model that yields the results being in a good qualitative agreement with the Monte Carlo results obtained for two-dimensional systems.

  5. Crystal Structure of the Extracellular Cholinesterase-Like Domain from Neuroligin-2

    Energy Technology Data Exchange (ETDEWEB)

    Koehnke,J.; Jin, X.; Budreck, E.; Posy, S.; Scheiffele, P.; Hnoig, B.; Shapiro, L.

    2008-01-01

    Neuroligins (NLs) are catalytically inactive members of a family of cholinesterase-like transmembrane proteins that mediate cell adhesion at neuronal synapses. Postsynaptic neuroligins engage in Ca2+-dependent transsynaptic interactions via their extracellular cholinesterase domain with presynaptic neurexins (NRXs). These interactions may be regulated by two short splice insertions (termed A and B) in the NL cholinesterase domain. Here, we present the 3.3- Angstroms crystal structure of the ectodomain from NL2 containing splice insertion A (NL2A). The overall structure of NL2A resembles that of cholinesterases, but several structural features are unique to the NL proteins. First, structural elements surrounding the esterase active-site region differ significantly between active esterases and NL2A. On the opposite surface of the NL2A molecule, the positions of the A and B splice insertions identify a candidate NRX interaction site of the NL protein. Finally, sequence comparisons of NL isoforms allow for mapping the location of residues of previously identified mutations in NL3 and NL4 found in patients with autism spectrum disorders. Overall, the NL2 structure promises to provide a valuable model for dissecting NL isoform- and synapse-specific functions.

  6. Structure and hydration of membranes embedded with voltage-sensing domains.

    Science.gov (United States)

    Krepkiy, Dmitriy; Mihailescu, Mihaela; Freites, J Alfredo; Schow, Eric V; Worcester, David L; Gawrisch, Klaus; Tobias, Douglas J; White, Stephen H; Swartz, Kenton J

    2009-11-26

    Despite the growing number of atomic-resolution membrane protein structures, direct structural information about proteins in their native membrane environment is scarce. This problem is particularly relevant in the case of the highly charged S1-S4 voltage-sensing domains responsible for nerve impulses, where interactions with the lipid bilayer are critical for the function of voltage-activated ion channels. Here we use neutron diffraction, solid-state nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics simulations to investigate the structure and hydration of bilayer membranes containing S1-S4 voltage-sensing domains. Our results show that voltage sensors adopt transmembrane orientations and cause a modest reshaping of the surrounding lipid bilayer, and that water molecules intimately interact with the protein within the membrane. These structural findings indicate that voltage sensors have evolved to interact with the lipid membrane while keeping energetic and structural perturbations to a minimum, and that water penetrates the membrane, to hydrate charged residues and shape the transmembrane electric field.

  7. Hard-magnetic surface layer effect on the erbium orthoferrite plate domain structure in the region of gradual spin reorientation

    International Nuclear Information System (INIS)

    Belyaeva, A.I.; Vojtsenya, S.V.; Yur'ev, V.P.

    1988-01-01

    Rearrangement of domain structures in the erbium orthoferrite plates with hard-magnetic surface layer is investigated during gradual spin reorientation. This phenomenon is explained by means of the proposed physical models. It is shown that in these plates an approach to the temperature interval of spin reorientation causes a decrease in the density of energy of domain walls separating the internal and surface domains. This decrease results in transition to the domain structure which are close to equilibrium ones inside the crystal. 30 refs.; 4 figs

  8. Uncovering nanoscale electromechanical heterogeneity in the subfibrillar structure of collagen fibrils responsible for the piezoelectricity of bone.

    Science.gov (United States)

    Minary-Jolandan, Majid; Yu, Min-Feng

    2009-07-28

    Understanding piezoelectricity, the linear electromechanical transduction, in bone and tendon and its potential role in mechanoelectric transduction leading to their growth and remodeling remains a challenging subject. With high-resolution piezoresponse force microscopy, we probed piezoelectric behavior in relevant biological samples at different scale levels: from the subfibrillar structures of single isolated collagen fibrils to bone. We revealed that, beyond the general understanding of collagen fibril being a piezoelectric material, there existed an intrinsic piezoelectric heterogeneity within a collagen fibril coinciding with the periodic variation of its gap and overlap regions. This piezoelectric heterogeneity persisted even for the collagen fibrils embedded in bone, bringing about new implications for its possible roles in structural formation and remodeling of bone.

  9. Electronic structure of nanoscale Cu/Pt alloys: A combined X-ray diffraction and X-ray absorption investigations

    International Nuclear Information System (INIS)

    Chen Xing; Chu Wangsheng; Cai Quan; Xia Dingguo; Wu Zhonghua; Wu Ziyu

    2006-01-01

    PVP-protected Cu/Pt clusters were prepared by glycol/water reduction method and characterized with transmission electron microscopy (TEM), X-ray diffraction (XRD) and absorption spectra. TEM and XRD analysis show that the Cu/Pt clusters with different molar ratio have fcc structure with particle size of about 4 nm, while the lattice parameters in these clusters reduce with increasing Cu concentration. From the X-ray absorption near edge structure (XANES) at Cu-K edge and Pt-L 2,3 edge, we demonstrate that the d-electronic states of Cu and Pt are affected by the local environment as a function of Cu/Pt molar ratio. With increasing Cu concentration, Pt loses a fraction of 5d electrons and the hybridization between p- and d-states at Cu sites is enhanced

  10. Electronic structure of nanoscale Cu/Pt alloys: A combined X-ray diffraction and X-ray absorption investigations

    Energy Technology Data Exchange (ETDEWEB)

    Chen Xing [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, Beijing (China); Graduate School of the Chinese Academy of Sciences, 100864 Beijing (China); Chu Wangsheng [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, Beijing (China); University of Science and Technology of China, Hefei, 230036 (China); Cai Quan [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, Beijing (China); Graduate School of the Chinese Academy of Sciences, 100864 Beijing (China); Xia Dingguo [College of Environmental and Energy Engineering, Beijing University of Technology, 100022 Beijing (China); Wu Zhonghua [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, Beijing (China); Wu Ziyu [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, Beijing (China) and National Center for Nanoscience and Technology (China)]. E-mail: wuzy@ihep.ac.cn

    2006-11-15

    PVP-protected Cu/Pt clusters were prepared by glycol/water reduction method and characterized with transmission electron microscopy (TEM), X-ray diffraction (XRD) and absorption spectra. TEM and XRD analysis show that the Cu/Pt clusters with different molar ratio have fcc structure with particle size of about 4 nm, while the lattice parameters in these clusters reduce with increasing Cu concentration. From the X-ray absorption near edge structure (XANES) at Cu-K edge and Pt-L{sub 2,3} edge, we demonstrate that the d-electronic states of Cu and Pt are affected by the local environment as a function of Cu/Pt molar ratio. With increasing Cu concentration, Pt loses a fraction of 5d electrons and the hybridization between p- and d-states at Cu sites is enhanced.

  11. Design of a Nanoscale, CMOS-Integrable, Thermal-Guiding Structure for Boolean-Logic and Neuromorphic Computation.

    Science.gov (United States)

    Loke, Desmond; Skelton, Jonathan M; Chong, Tow-Chong; Elliott, Stephen R

    2016-12-21

    One of the requirements for achieving faster CMOS electronics is to mitigate the unacceptably large chip areas required to steer heat away from or, more recently, toward the critical nodes of state-of-the-art devices. Thermal-guiding (TG) structures can efficiently direct heat by "meta-materials" engineering; however, some key aspects of the behavior of these systems are not fully understood. Here, we demonstrate control of the thermal-diffusion properties of TG structures by using nanometer-scale, CMOS-integrable, graphene-on-silica stacked materials through finite-element-methods simulations. It has been shown that it is possible to implement novel, controllable, thermally based Boolean-logic and spike-timing-dependent plasticity operations for advanced (neuromorphic) computing applications using such thermal-guide architectures.

  12. Wire-in-tube structure fabricated by single capillary electrospinning via nanoscale Kirkendall effect: the case of nickel-zinc ferrite.

    Science.gov (United States)

    Fu, Jiecai; Zhang, Junli; Peng, Yong; Zhao, Changhui; He, Yongmin; Zhang, Zhenxing; Pan, Xiaojun; Mellors, Nigel J; Xie, Erqing

    2013-12-21

    Wire-in-tube structures have previously been prepared using an electrospinning method by means of tuning hydrolysis/alcoholysis of a precursor solution. Nickel-zinc ferrite (Ni0.5Zn0.5Fe2O4) nanowire-in-nanotubes have been prepared as a demonstration. The detailed nanoscale characterization, formation process and magnetic properties of Ni0.5Zn0.5Fe2O4 nanowire-in-nanotubes has been studied comprehensively. The average diameters of the outer tubes and inner wires of Ni0.5Zn0.5Fe2O4 nanowire-in-nanotubes are around 120 nm and 42 nm, respectively. Each fully calcined individual nanowire-in-nanotube, either the outer-tube or the inner-wire, is composed of Ni0.5Zn0.5Fe2O4 monocrystallites stacked along the longitudinal direction with random orientation. The process of calcining electrospun polymer composite nanofibres can be viewed as a morphologically template nucleation and precursor diffusion process. This allows the nitrates precursor to diffuse toward the surface of the nanofibres while the oxides (decomposed from hydroxides and nitrates) products diffuse to the core region of the nanofibres; the amorphous nanofibres transforming thereby into crystalline nanowire-in-nanotubes. In addition, the magnetic properties of the Ni0.5Zn0.5Fe2O4 nanowire-in-nanotubes were also examined. It is believed that this nanowire-in-nanotube (sometimes called core-shell) structure, with its uniform size and well-controlled orientation of the long nanowire-in-nanotubes, is particularly attractive for use in the field of nano-fluidic devices and nano-energy harvesting devices.

  13. Role of structural inheritance on present-day deformation in intraplate domains

    Science.gov (United States)

    Tarayoun, A.; Mazzotti, S.; Gueydan, F.

    2017-12-01

    Understanding the role of structural inheritance on present day surface deformation is a key element for better characterizing the dynamism of intraplate earthquakes. Current deformation and seismicity are poorly understood phenomenon in intra-continental domains. A commonly used hypothesis, based on observations, suggests that intraplate deformation is related to the reactivation of large tectonic paleo-structures, which can act as locally weakened domains. The objective of our study is to quantify the impact of these weakened areas on present-day strain localizations and rates. We combine GPS observations and numerical modeling to analyze the role of structural inheritance on strain rates, with specific observations along the St. Lawrence Valley of eastern Canada. We processed 143 GPS stations from five different networks, in particular one dense campaign network situated along a recognized major normal faults system of the Iapetus paleo-rift, in order to accurately determine the GPS velocities and strain rates. Results of strain rates show magnitude varying from 1.5x10-10 to 6.8x10-9 yr-1 in the St Lawrence valley. Weakened area strain rates are up to one order of magnitude higher than surrounding areas. We compare strain rates inferred from GPS and the new postglacial rebound model. We found that GPS signal is one order of magnitude higher in the weakened zone, which is likely due to structural inheritance. The numerical modeling investigates the steady-state deformation of the continental lithosphere with presence of a weak area. Our new approach integrates ductile structural inheritance using a weakening coefficient that decreases the lithosphere strength at different depths. This allows studying crustal strain rates mainly as a function of rheological contrast and geometry of the weakened domains. Comparison between model predictions and observed GPS strain rates will allow us to investigate the respective role of crustal and mantle tectonic inheritance.

  14. Crystal Structure of the N-terminal Domain of the Group B Streptococcus Alpha C Protein

    Energy Technology Data Exchange (ETDEWEB)

    Auperin,T.; Bolduc, G.; Baron, M.; Heroux, A.; Filman, D.; Madoff, L.; Hogle, J.

    2005-01-01

    Group B Streptococcus (GBS) is the leading cause of bacterial pneumonia, sepsis, and meningitis among neonates and an important cause of morbidity among pregnant women and immunocompromised adults. Invasive diseases due to GBS are attributed to the ability of the pathogen to translocate across human epithelial surfaces. The alpha C protein (ACP) has been identified as an invasin that plays a role in internalization and translocation of GBS across epithelial cells. The soluble N-terminal domain of ACP (NtACP) blocks the internalization of GBS. We determined the 1.86-{angstrom} resolution crystal structure of NtACP comprising residues Ser{sup 52} through Leu{sup 225} of the full-length ACP. NtACP has two domains, an N-terminal {beta}-sandwich and a C-terminal three-helix bundle. Structural and topological alignments reveal that the {beta}-sandwich shares structural elements with the type III fibronectin fold (FnIII), but includes structural elaborations that make it unique. We have identified a potential integrin-binding motif consisting of Lys-Thr-Asp{sup 146}, Arg{sup 110}, and Asp{sup 118}. A similar arrangement of charged residues has been described in other invasins. ACP shows a heparin binding activity that requires NtACP. We propose a possible heparin-binding site, including one surface of the three-helix bundle, and nearby portions of the sandwich and repeat domains. We have validated this prediction using assays of the heparin binding and cell-adhesion properties of engineered fragments of ACP. This is the first crystal structure of a member of the highly conserved Gram-positive surface alpha-like protein family, and it will enable the internalization mechanism of GBS to be dissected at the atomic level.

  15. A financial market model with two discontinuities: Bifurcation structures in the chaotic domain

    Science.gov (United States)

    Panchuk, Anastasiia; Sushko, Iryna; Westerhoff, Frank

    2018-05-01

    We continue the investigation of a one-dimensional piecewise linear map with two discontinuity points. Such a map may arise from a simple asset-pricing model with heterogeneous speculators, which can help us to explain the intricate bull and bear behavior of financial markets. Our focus is on bifurcation structures observed in the chaotic domain of the map's parameter space, which is associated with robust multiband chaotic attractors. Such structures, related to the map with two discontinuities, have been not studied before. We show that besides the standard bandcount adding and bandcount incrementing bifurcation structures, associated with two partitions, there exist peculiar bandcount adding and bandcount incrementing structures involving all three partitions. Moreover, the map's three partitions may generate intriguing bistability phenomena.

  16. Structural Basis for Substrate Recognition by the Ankyrin Repeat Domain of Human DHHC17 Palmitoyltransferase

    Energy Technology Data Exchange (ETDEWEB)

    Verardi, Raffaello; Kim, Jin-Sik; Ghirlando, Rodolfo; Banerjee, Anirban

    2017-09-01

    DHHC enzymes catalyze palmitoylation, a major post-translational modification that regulates a number of key cellular processes. There are up to 24 DHHCs in mammals and hundreds of substrate proteins that get palmitoylated. However, how DHHC enzymes engage with their substrates is still poorly understood. There is currently no structural information about the interaction between any DHHC enzyme and protein substrates. In this study we have investigated the structural and thermodynamic bases of interaction between the ankyrin repeat domain of human DHHC17 (ANK17) and Snap25b. We solved a high-resolution crystal structure of the complex between ANK17 and a peptide fragment of Snap25b. Through structure-guided mutagenesis, we discovered key residues in DHHC17 that are critically important for interaction with Snap25b. We further extended our finding by showing that the same residues are also crucial for the interaction of DHHC17 with Huntingtin, one of its most physiologically relevant substrates.

  17. Structures of a Nonribosomal Peptide Synthetase Module Bound to MbtH-like Proteins Support a Highly Dynamic Domain Architecture

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Bradley R.; Drake, Eric J.; Shi, Ce; Aldrich, Courtney C.; Gulick, Andrew M. (UMM); (HWMRI)

    2016-09-05

    Nonribosomal peptide synthetases (NRPSs) produce a wide variety of peptide natural products. During synthesis, the multidomain NRPSs act as an assembly line, passing the growing product from one module to the next. Each module generally consists of an integrated peptidyl carrier protein, an amino acid-loading adenylation domain, and a condensation domain that catalyzes peptide bond formation. Some adenylation domains interact with small partner proteins called MbtH-like proteins (MLPs) that enhance solubility or activity. A structure of an MLP bound to an adenylation domain has been previously reported using a truncated adenylation domain, precluding any insight that might be derived from understanding the influence of the MLP on the intact adenylation domain or on the dynamics of the entire NRPS module. Here, we present the structures of the full-length NRPS EntF bound to the MLPs from Escherichia coli and Pseudomonas aeruginosa. These new structures, along with biochemical and bioinformatics support, further elaborate the residues that define the MLP-adenylation domain interface. Additionally, the structures highlight the dynamic behavior of NRPS modules, including the module core formed by the adenylation and condensation domains as well as the orientation of the mobile thioesterase domain.

  18. Structural modeling of the N-terminal signal–receiving domain of IκBα

    Directory of Open Access Journals (Sweden)

    Samira eYazdi

    2015-06-01

    Full Text Available The transcription factor nuclear factor-κB (NF-κB exerts essential roles in many biological processes including cell growth, apoptosis and innate and adaptive immunity. The NF-kB inhibitor (IκBα retains NF-κB in the cytoplasm and thus inhibits nuclear localization of NF-κB and its association with DNA. Recent protein crystal structures of the C-terminal part of IκBα in complex with NF-κB provided insights into the protein-protein interactions but could not reveal structural details about the N-terminal signal receiving domain (SRD. The SRD of IκBα contains a degron, formed following phosphorylation by IκB kinases (IKK. In current protein X-ray structures, however, the SRD is not resolved and assumed to be disordered. Here, we combined secondary structure annotation and domain threading followed by long molecular dynamics (MD simulations and showed that the SRD possesses well-defined secondary structure elements. We show that the SRD contains 3 additional stable α-helices supplementing the six ARDs present in crystallized IκBα. The IκBα/NF-κB protein-protein complex remained intact and stable during the entire simulations. Also in solution, free IκBα retains its structural integrity. Differences in structural topology and dynamics were observed by comparing the structures of NF-κB free and NF-κB bound IκBα-complex. This study paves the way for investigating the signaling properties of the SRD in the IκBα degron. A detailed atomic scale understanding of molecular mechanism of NF-κB activation, regulation and the protein-protein interactions may assist to design and develop novel chronic inflammation modulators.

  19. Electromagnetic Modelling of Raman Enhancement from Nanoscale Structures as a Means to Predict the Efficacy of SERS Substrates

    Directory of Open Access Journals (Sweden)

    Richard J. C. Brown

    2007-01-01

    Full Text Available The requirement to optimise the balance between signal enhancement and reproducibility in surface enhanced Raman spectroscopy (SERS is stimulating the development of novel substrates for enhancing Raman signals. This paper describes the application of finite element electromagnetic modelling to predict the Raman enhancement produced from a variety of SERS substrates with differently sized, spaced and shaped morphologies with nanometre dimensions. For the first time, a theoretical comparison between four major generic types of SERS substrate (including metal nanoparticles, structured surfaces, and sharp tips has been performed and the results are presented and discussed. The results of the modelling are consistent with published experimental data from similar substrates.

  20. Label-free nanoscale characterization of red blood cell structure and dynamics using single-shot transport of intensity equation

    Science.gov (United States)

    Poola, Praveen Kumar; John, Renu

    2017-10-01

    We report the results of characterization of red blood cell (RBC) structure and its dynamics with nanometric sensitivity using transport of intensity equation microscopy (TIEM). Conventional transport of intensity technique requires three intensity images and hence is not suitable for studying real-time dynamics of live biological samples. However, assuming the sample to be homogeneous, phase retrieval using transport of intensity equation has been demonstrated with single defocused measurement with x-rays. We adopt this technique for quantitative phase light microscopy of homogenous cells like RBCs. The main merits of this technique are its simplicity, cost-effectiveness, and ease of implementation on a conventional microscope. The phase information can be easily merged with regular bright-field and fluorescence images to provide multidimensional (three-dimensional spatial and temporal) information without any extra complexity in the setup. The phase measurement from the TIEM has been characterized using polymeric microbeads and the noise stability of the system has been analyzed. We explore the structure and real-time dynamics of RBCs and the subdomain membrane fluctuations using this technique.

  1. Ulysses transposable element of Drosophila shows high structural similarities to functional domains of retroviruses.

    Science.gov (United States)

    Evgen'ev, M B; Corces, V G; Lankenau, D H

    1992-06-05

    We have determined the DNA structure of the Ulysses transposable element of Drosophila virilis and found that this transposon is 10,653 bp and is flanked by two unusually large direct repeats 2136 bp long. Ulysses shows the characteristic organization of LTR-containing retrotransposons, with matrix and capsid protein domains encoded in the first open reading frame. In addition, Ulysses contains protease, reverse transcriptase, RNase H and integrase domains encoded in the second open reading frame. Ulysses lacks a third open reading frame present in some retrotransposons that could encode an env-like protein. A dendrogram analysis based on multiple alignments of the protease, reverse transcriptase, RNase H, integrase and tRNA primer binding site of all known Drosophila LTR-containing retrotransposon sequences establishes a phylogenetic relationship of Ulysses to other retrotransposons and suggests that Ulysses belongs to a new family of this type of elements.

  2. Bicontinuous structured liquids with sub-micrometre domains using nanoparticle surfactants

    Science.gov (United States)

    Huang, Caili; Forth, Joe; Wang, Weiyu; Hong, Kunlun; Smith, Gregory S.; Helms, Brett A.; Russell, Thomas P.

    2017-11-01

    Bicontinuous jammed emulsions (or bijels) are tortuous, interconnected structures of two immiscible liquids, kinetically trapped by colloidal particles that are irreversibly bound to the oil-water interface. A wealth of applications has been proposed for bijels in catalysis, energy storage and molecular encapsulation, but large domain sizes (on the order of 5 µm or larger) and difficulty in fabrication pose major barriers to their use. Here, we show that bijels with sub-micrometre domains can be formed via homogenization, rather than spinodal decomposition. We achieve this by using nanoparticle surfactants: polymers and nanoparticles of complementary functionality (for example, ion-pairing) that bind to one another at the oil-water interface. This allows the stabilization of the bijel far from the demixing point of the liquids, with interfacial tensions on the order of 20 mN m-1. Furthermore, our strategy is extremely versatile, as solvent, nanoparticle and ligand can all be varied.

  3. Crystal structure of the C-terminal domain of the RAP74 subunit of human transcription factor IIF

    Energy Technology Data Exchange (ETDEWEB)

    Kamada, Katsuhiko; De Angelis, Jacqueline; Roeder, Robert G.; Burley, Stephen K. (Rockefeller)

    2012-12-13

    The x-ray structure of a C-terminal fragment of the RAP74 subunit of human transcription factor (TF) IIF has been determined at 1.02-{angstrom} resolution. The {alpha}/{beta} structure is strikingly similar to the globular domain of linker histone H5 and the DNA-binding domain of hepatocyte nuclear factor 3{gamma} (HNF-3{gamma}), making it a winged-helix protein. The surface electrostatic properties of this compact domain differ significantly from those of bona fide winged-helix transcription factors (HNF-3{gamma} and RFX1) and from the winged-helix domains found within the RAP30 subunit of TFIIF and the {beta} subunit of TFIIE. RAP74 has been shown to interact with the TFIIF-associated C-terminal domain phosphatase FCP1, and a putative phosphatase binding site has been identified within the RAP74 winged-helix domain.

  4. Nanoscale biophysics of the cell

    CERN Document Server

    Ashrafuzzaman, Mohammad

    2018-01-01

    Macroscopic cellular structures and functions are generally investigated using biological and biochemical approaches. But these methods are no longer adequate when one needs to penetrate deep into the small-scale structures and understand their functions. The cell is found to hold various physical structures, molecular machines, and processes that require physical and mathematical approaches to understand and indeed manipulate them. Disorders in general cellular compartments, perturbations in single molecular structures, drug distribution therein, and target specific drug-binding, etc. are mostly physical phenomena. This book will show how biophysics has revolutionized our way of addressing the science and technology of nanoscale structures of cells, and also describes the potential for manipulating the events that occur in them.

  5. Crystal structure of the Rasputin NTF2-like domain from Drosophila melanogaster

    Energy Technology Data Exchange (ETDEWEB)

    Vognsen, Tina, E-mail: tv@farma.ku.dk [Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen (Denmark); Kristensen, Ole, E-mail: ok@farma.ku.dk [Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen (Denmark)

    2012-03-30

    Highlights: Black-Right-Pointing-Pointer The crystal structure of the NTF2-like domain of Rasputin protein is presented. Black-Right-Pointing-Pointer Differences to known ligand binding sites of nuclear transport factor 2 are discussed. Black-Right-Pointing-Pointer A new ligand binding site for the Rasputin and G3BP proteins is proposed. -- Abstract: The crystal structure of the NTF2-like domain of the Drosophila homolog of Ras GTPase SH3 Binding Protein (G3BP), Rasputin, was determined at 2.7 A resolution. The overall structure is highly similar to nuclear transport factor 2: It is a homodimer comprised of a {beta}-sheet and three {alpha}-helices forming a cone-like shape. However, known binding sites for RanGDP and FxFG containing peptides show electrostatic and steric differences compared to nuclear transport factor 2. A HEPES molecule bound in the structure suggests a new, and possibly physiologically relevant, ligand binding site.

  6. Conservation and divergence of C-terminal domain structure in the retinoblastoma protein family

    Energy Technology Data Exchange (ETDEWEB)

    Liban, Tyler J.; Medina, Edgar M.; Tripathi, Sarvind; Sengupta, Satyaki; Henry, R. William; Buchler, Nicolas E.; Rubin, Seth M. (UCSC); (Duke); (MSU)

    2017-04-24

    The retinoblastoma protein (Rb) and the homologous pocket proteins p107 and p130 negatively regulate cell proliferation by binding and inhibiting members of the E2F transcription factor family. The structural features that distinguish Rb from other pocket proteins have been unclear but are critical for understanding their functional diversity and determining why Rb has unique tumor suppressor activities. We describe here important differences in how the Rb and p107 C-terminal domains (CTDs) associate with the coiled-coil and marked-box domains (CMs) of E2Fs. We find that although CTD–CM binding is conserved across protein families, Rb and p107 CTDs show clear preferences for different E2Fs. A crystal structure of the p107 CTD bound to E2F5 and its dimer partner DP1 reveals the molecular basis for pocket protein–E2F binding specificity and how cyclin-dependent kinases differentially regulate pocket proteins through CTD phosphorylation. Our structural and biochemical data together with phylogenetic analyses of Rb and E2F proteins support the conclusion that Rb evolved specific structural motifs that confer its unique capacity to bind with high affinity those E2Fs that are the most potent activators of the cell cycle.

  7. Structure of FGFR3 transmembrane domain dimer: implications for signaling and human pathologies.

    Science.gov (United States)

    Bocharov, Eduard V; Lesovoy, Dmitry M; Goncharuk, Sergey A; Goncharuk, Marina V; Hristova, Kalina; Arseniev, Alexander S

    2013-11-05

    Fibroblast growth factor receptor 3 (FGFR3) transduces biochemical signals via lateral dimerization in the plasma membrane, and plays an important role in human development and disease. Eight different pathogenic mutations, implicated in cancers and growth disorders, have been identified in the FGFR3 transmembrane segment. Here, we describe the dimerization of the FGFR3 transmembrane domain in membrane-mimicking DPC/SDS (9/1) micelles. In the solved NMR structure, the two transmembrane helices pack into a symmetric left-handed dimer, with intermolecular stacking interactions occurring in the dimer central region. Some pathogenic mutations fall within the helix-helix interface, whereas others are located within a putative alternative interface. This implies that although the observed dimer structure is important for FGFR3 signaling, the mechanism of FGFR3-mediated transduction across the membrane is complex. We propose an FGFR3 signaling mechanism that is based on the solved structure, available structures of isolated soluble FGFR domains, and published biochemical and biophysical data. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Alternative splicing originates different domain structure organization of Lutzomyia longipalpis chitinases.

    Science.gov (United States)

    Ortigão-Farias, João Ramalho; Di-Blasi, Tatiana; Telleria, Erich Loza; Andorinho, Ana Carolina; Lemos-Silva, Thais; Ramalho-Ortigão, Marcelo; Tempone, Antônio Jorge; Traub-Csekö, Yara Maria

    2018-02-01

    BACKGROUND The insect chitinase gene family is composed by more than 10 paralogs, which can codify proteins with different domain structures. In Lutzomyia longipalpis, the main vector of visceral leishmaniasis in Brazil, a chitinase cDNA from adult female insects was previously characterized. The predicted protein contains one catalytic domain and one chitin-binding domain (CBD). The expression of this gene coincided with the end of blood digestion indicating a putative role in peritrophic matrix degradation. OBJECTIVES To determine the occurrence of alternative splicing in chitinases of L. longipalpis. METHODS We sequenced the LlChit1 gene from a genomic clone and the three spliced forms obtained by reverse transcription polymerase chain reaction (RT-PCR) using larvae cDNA. FINDINGS We showed that LlChit1 from L. longipalpis immature forms undergoes alternative splicing. The spliced form corresponding to the adult cDNA was named LlChit1A and the two larvae specific transcripts were named LlChit1B and LlChit1C. The B and C forms possess stop codons interrupting the translation of the CBD. The A form is present in adult females post blood meal, L4 larvae and pre-pupae, while the other two forms are present only in L4 larvae and disappear just before pupation. Two bands of the expected size were identified by Western blot only in L4 larvae. MAIN CONCLUSIONS We show for the first time alternative splicing generating chitinases with different domain structures increasing our understanding on the finely regulated digestion physiology and shedding light on a potential target for controlling L. longipalpis larval development.

  9. Time-domain soil-structure interaction analysis of nuclear facilities

    International Nuclear Information System (INIS)

    Coleman, Justin L.; Bolisetti, Chandrakanth; Whittaker, Andrew S.

    2016-01-01

    The Nuclear Regulatory Commission (NRC) regulation 10 CFR Part 50 Appendix S requires consideration of soil-structure interaction (SSI) in nuclear power plant (NPP) analysis and design. Soil-structure interaction analysis for NPPs is routinely carried out using guidance provided in the ASCE Standard 4-98 titled “Seismic Analysis of Safety-Related Nuclear Structures and Commentary”. This Standard, which is currently under revision, provides guidance on linear seismic soil-structure-interaction (SSI) analysis of nuclear facilities using deterministic and probabilistic methods. A new appendix has been added to the forthcoming edition of ASCE Standard 4 to provide guidance for time-domain, nonlinear SSI (NLSSI) analysis. Nonlinear SSI analysis will be needed to simulate material nonlinearity in soil and/or structure, static and dynamic soil pressure effects on deeply embedded structures, local soil failure at the foundation-soil interface, nonlinear coupling of soil and pore fluid, uplift or sliding of the foundation, nonlinear effects of gaps between the surrounding soil and the embedded structure and seismic isolation systems, none of which can be addressed explicitly at present. Appendix B of ASCE Standard 4 provides general guidance for NLSSI analysis but will not provide a methodology for performing the analysis. This paper provides a description of an NLSSI methodology developed for application to nuclear facilities, including NPPs. This methodology is described as series of sequential steps to produce reasonable results using any time-domain numerical code. These steps require some numerical capabilities, such as nonlinear soil constitutive models, which are also described in the paper.

  10. The structure of XIAP BIR2: understanding the selectivity of the BIR domains

    Energy Technology Data Exchange (ETDEWEB)

    Lukacs, Christine, E-mail: cmlukacs230@gmail.com; Belunis, Charles; Crowther, Robert; Danho, Waleed; Gao, Lin; Goggin, Barry; Janson, Cheryl A.; Li, Shirley; Remiszewski, Stacy; Schutt, Andrew [Hoffmann-La Roche, 340 Kingsland Street, Nutley, NJ 07110 (United States); Thakur, Manish K.; Singh, Saroj K.; Swaminathan, Srinivasan; Pandey, Rajat; Tyagi, Rajiv; Gosu, Ramachandraiah; Kamath, Ajith V. [Jubilant Biosys Ltd, Bangalore (India); Kuglstatter, Andreas, E-mail: cmlukacs230@gmail.com [Hoffmann-La Roche, 340 Kingsland Street, Nutley, NJ 07110 (United States)

    2013-09-01

    The high-resolution crystal structures of apo and peptide-bound XIAP BIR2 are presented and compared with BIR3 structures to understand their selectivity. This crystal system can be used to determine the structures of BIR2–inhibitor complexes. XIAP, a member of the inhibitor of apoptosis family of proteins, is a critical regulator of apoptosis. Inhibition of the BIR domain–caspase interaction is a promising approach towards treating cancer. Previous work has been directed towards inhibiting the BIR3–caspase-9 interaction, which blocks the intrinsic apoptotic pathway; selectively inhibiting the BIR2–caspase-3 interaction would also block the extrinsic pathway. The BIR2 domain of XIAP has successfully been crystallized; peptides and small-molecule inhibitors can be soaked into these crystals, which diffract to high resolution. Here, the BIR2 apo crystal structure and the structures of five BIR2–tetrapeptide complexes are described. The structural flexibility observed on comparing these structures, along with a comparison with XIAP BIR3, affords an understanding of the structural elements that drive selectivity between BIR2 and BIR3 and which can be used to design BIR2-selective inhibitors.

  11. Conduction at domain walls in oxide multiferroics

    Science.gov (United States)

    Seidel, J.; Martin, L. W.; He, Q.; Zhan, Q.; Chu, Y.-H.; Rother, A.; Hawkridge, M. E.; Maksymovych, P.; Yu, P.; Gajek, M.; Balke, N.; Kalinin, S. V.; Gemming, S.; Wang, F.; Catalan, G.; Scott, J. F.; Spaldin, N. A.; Orenstein, J.; Ramesh, R.

    2009-03-01

    Domain walls may play an important role in future electronic devices, given their small size as well as the fact that their location can be controlled. Here, we report the observation of room-temperature electronic conductivity at ferroelectric domain walls in the insulating multiferroic BiFeO3. The origin and nature of the observed conductivity are probed using a combination of conductive atomic force microscopy, high-resolution transmission electron microscopy and first-principles density functional computations. Our analyses indicate that the conductivity correlates with structurally driven changes in both the electrostatic potential and the local electronic structure, which shows a decrease in the bandgap at the domain wall. Additionally, we demonstrate the potential for device applications of such conducting nanoscale features.

  12. Structural and functional characterization of the recombinant death domain from death-associated protein kinase.

    Science.gov (United States)

    Dioletis, Evangelos; Dingley, Andrew J; Driscoll, Paul C

    2013-01-01

    Death-associated protein kinase (DAPk) is a calcium/calmodulin-regulated Ser/Thr-protein kinase that functions at an important point of integration for cell death signaling pathways. DAPk has a structurally unique multi-domain architecture, including a C-terminally positioned death domain (DD) that is a positive regulator of DAPk activity. In this study, recombinant DAPk-DD was observed to aggregate readily and could not be prepared in sufficient yield for structural analysis. However, DAPk-DD could be obtained as a soluble protein in the form of a translational fusion protein with the B1 domain of streptococcal protein G. In contrast to other DDs that adopt the canonical six amphipathic α-helices arranged in a compact fold, the DAPk-DD was found to possess surprisingly low regular secondary structure content and an absence of a stable globular fold, as determined by circular dichroism (CD), NMR spectroscopy and a temperature-dependent fluorescence assay. Furthermore, we measured the in vitro interaction between extracellular-regulated kinase-2 (ERK2) and various recombinant DAPk-DD constructs. Despite the low level of structural order, the recombinant DAPk-DD retained the ability to interact with ERK2 in a 1∶1 ratio with a K d in the low micromolar range. Only the full-length DAPk-DD could bind ERK2, indicating that the apparent 'D-motif' located in the putative sixth helix of DAPk-DD is not sufficient for ERK2 recognition. CD analysis revealed that binding of DAPk-DD to ERK2 is not accompanied by a significant change in secondary structure. Taken together our data argue that the DAPk-DD, when expressed in isolation, does not adopt a classical DD fold, yet in this state retains the capacity to interact with at least one of its binding partners. The lack of a stable globular structure for the DAPk-DD may reflect either that its folding would be supported by interactions absent in our experimental set-up, or a limitation in the structural bioinformatics

  13. WE-DE-202-01: Connecting Nanoscale Physics to Initial DNA Damage Through Track Structure Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Schuemann, J. [Massachusetts General Hospital (United States)

    2016-06-15

    Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are the most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological

  14. WE-DE-202-01: Connecting Nanoscale Physics to Initial DNA Damage Through Track Structure Simulations

    International Nuclear Information System (INIS)

    Schuemann, J.

    2016-01-01

    Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are the most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological

  15. Structural basis for different phosphoinositide specificities of the PX domains of sorting nexins regulating G-protein signaling.

    Science.gov (United States)

    Mas, Caroline; Norwood, Suzanne J; Bugarcic, Andrea; Kinna, Genevieve; Leneva, Natalya; Kovtun, Oleksiy; Ghai, Rajesh; Ona Yanez, Lorena E; Davis, Jasmine L; Teasdale, Rohan D; Collins, Brett M

    2014-10-10

    Sorting nexins (SNXs) or phox homology (PX) domain containing proteins are central regulators of cell trafficking and signaling. A subfamily of PX domain proteins possesses two unique PX-associated domains, as well as a regulator of G protein-coupled receptor signaling (RGS) domain that attenuates Gαs-coupled G protein-coupled receptor signaling. Here we delineate the structural organization of these RGS-PX proteins, revealing a protein family with a modular architecture that is conserved in all eukaryotes. The one exception to this is mammalian SNX19, which lacks the typical RGS structure but preserves all other domains. The PX domain is a sensor of membrane phosphoinositide lipids and we find that specific sequence alterations in the PX domains of the mammalian RGS-PX proteins, SNX13, SNX14, SNX19, and SNX25, confer differential phosphoinositide binding preferences. Although SNX13 and SNX19 PX domains bind the early endosomal lipid phosphatidylinositol 3-phosphate, SNX14 shows no membrane binding at all. Crystal structures of the SNX19 and SNX14 PX domains reveal key differences, with alterations in SNX14 leading to closure of the binding pocket to prevent phosphoinositide association. Our findings suggest a role for alternative membrane interactions in spatial control of RGS-PX proteins in cell signaling and trafficking. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. The influence of punching process on residual stress and magnetic domain structure of non-oriented silicon steel

    International Nuclear Information System (INIS)

    Cao, Hongzhi; Hao, Linpo; Yi, Jingwen; Zhang, Xianglin; Luo, Zhonghan; Chen, Shenglin; Li, Rongfeng

    2016-01-01

    The main purpose of this paper is to investigate the influence of punching process on residual stress and magnetic domain structure. The residual stress in non-oriented silicon steel after punching process was measured by nanoindentation. The maximum depth was kept constant as 300 nm during nanoindentation. The material around indentation region exhibited no significant pile-up deformation. The calculation of residual stress was based on the Suresh theoretical model. Our experimental results show that residual compressive stress was generated around the sheared edge after punching. The width of residual stress affected zone by punching was around 0.4–0.5 mm. After annealing treatment, the residual stress was significantly decreased. Magnetic domain structure was observed according to the Bitter method. The un-annealed sample exhibited complicated domain patterns, and the widths of the magnetic domains varied between 3 µm and 8 µm. Most of the domain patterns of the annealed sample were 180°-domains and 90°-domains, and the widths of the domains decreased to 1–3 µm. - Highlights: • The residual stress distribution on sheared edge was measured. • The residual compressive stress was generated around the sheared edge. • The width of residual stress affected zone was about 0.4–0.5 mm. • The shape and width of the domain structure would be changed by annealing.

  17. On The Role of Wetting, Structure Width, and Flow Characteristics in Polymer Replication on Micro- and Nanoscale

    DEFF Research Database (Denmark)

    Rytka, Christian; Opara, Nadia; Andersen, Nis Korsgaard

    2016-01-01

    The replication of functional polymeric micro- and nanostructures requires a deep understanding of material and process interrelations. In this investigation the dewetting potential of a polymer is proposed as a simple rationale for estimation of the replicability of functional micro- and nanostr......The replication of functional polymeric micro- and nanostructures requires a deep understanding of material and process interrelations. In this investigation the dewetting potential of a polymer is proposed as a simple rationale for estimation of the replicability of functional micro......- and nanostructures by injection molding. The dewetting potential of a polymer is determined by integrating the spreading coefficient over the range from melt temperature to no-flow temperature. From all polymers tested, the lowest dewetting potential is calculated for PP and the highest for polymethylmethacrylate....... The dewetting potential correlates well with the replicated height of four different structures covering both the micro- and the nanorange on two different surfaces (brass and fluorocarbon modified nickel) and polymers with different spreading coefficients. It is clearly shown that a lower dewetting potential...

  18. Spatially resolved investigation of competing nanocluster emission in quantum-disks-in-nanowires structure characterized by nanoscale cathodoluminescence

    KAUST Repository

    Prabaswara, Aditya; Stowe, David J.; Janjua, Bilal; Ng, Tien Khee; Anjum, Dalaver H.; Longo, Paolo; Zhao, Chao; Elafandy, Rami T.; Li, Xiaohang; Alyamani, Ahmed Y.; El-Desouki, Munir M.; Ooi, Boon S.

    2017-01-01

    We report on the study and characterization of nanoclusters-related recombination centers within quantum-disks-in-nanowires heterostructure by utilizing microphotoluminescence (mu-PL) and cathodoluminescence scanning transmission electron microscopy (CL-STEM). mu-PL measurement shows that the nanoclusters-related recombination center exhibits different temperature-dependent characteristics compared with the surrounding InGaN quantum-disksrelated recombination center. CL-STEM measurements reveal that these recombination centers mainly arise from irregularities within the quantum disks, with a strong, spatially localized emission when measured at low temperature. The spectra obtained from both CL-STEM and mu-PL correlate well with each other. Our work sheds light on the optical and structural properties of simultaneously coexisting recombination centers within nanowires heterostructures. (C) The Authors. Published by SPIE under a Creative Commons Attribution 3.0 Unported License. Distribution or reproduction of this work in whole or in part requires full attribution of the original publication, including its DOI.

  19. Spatially resolved investigation of competing nanocluster emission in quantum-disks-in-nanowires structure characterized by nanoscale cathodoluminescence

    KAUST Repository

    Prabaswara, Aditya

    2017-06-30

    We report on the study and characterization of nanoclusters-related recombination centers within quantum-disks-in-nanowires heterostructure by utilizing microphotoluminescence (mu-PL) and cathodoluminescence scanning transmission electron microscopy (CL-STEM). mu-PL measurement shows that the nanoclusters-related recombination center exhibits different temperature-dependent characteristics compared with the surrounding InGaN quantum-disksrelated recombination center. CL-STEM measurements reveal that these recombination centers mainly arise from irregularities within the quantum disks, with a strong, spatially localized emission when measured at low temperature. The spectra obtained from both CL-STEM and mu-PL correlate well with each other. Our work sheds light on the optical and structural properties of simultaneously coexisting recombination centers within nanowires heterostructures. (C) The Authors. Published by SPIE under a Creative Commons Attribution 3.0 Unported License. Distribution or reproduction of this work in whole or in part requires full attribution of the original publication, including its DOI.

  20. Magnetic field effect on Gd2(MoO4)3 domain structure formation in the phase transformation range

    International Nuclear Information System (INIS)

    Flerova, S.A.; Tsinman, I.L.

    1987-01-01

    The behaviour of ferroelastic-ferroelectric domain structure of gadolinium molybdate crystal (GMO)during its formation in the magnetic field in the vicinity of phase transformation is studied.It is shown that the formation of domain structure in the presence of a temperature gradient occurs in the field of mechanical stresses whose mainly stretching effect is concentrated near phase boundaries.The magnetic field intensifies summary mechanical stresses where a domain structure in a ferroelectric phase is formed due to interaction with the elements of inhomogeneous and differently oriented currents near phase boundaries

  1. Crystal structure of the Rasputin NTF2-like domain from Drosophila melanogaster.

    Science.gov (United States)

    Vognsen, Tina; Kristensen, Ole

    2012-03-30

    The crystal structure of the NTF2-like domain of the Drosophila homolog of Ras GTPase SH3 Binding Protein (G3BP), Rasputin, was determined at 2.7Å resolution. The overall structure is highly similar to nuclear transport factor 2: It is a homodimer comprised of a β-sheet and three α-helices forming a cone-like shape. However, known binding sites for RanGDP and FxFG containing peptides show electrostatic and steric differences compared to nuclear transport factor 2. A HEPES molecule bound in the structure suggests a new, and possibly physiologically relevant, ligand binding site. Copyright © 2012 Elsevier Inc. All rights reserved.

  2. Combining in situ transmission electron microscopy irradiation experiments with cluster dynamics modeling to study nanoscale defect agglomeration in structural metals

    International Nuclear Information System (INIS)

    Xu Donghua; Wirth, Brian D.; Li Meimei; Kirk, Marquis A.

    2012-01-01

    We present a combinatorial approach that integrates state-of-the-art transmission electron microscopy (TEM) in situ irradiation experiments and high-performance computing techniques to study irradiation defect dynamics in metals. Here, we have studied the evolution of visible defect clusters in nanometer-thick molybdenum foils under 1 MeV krypton ion irradiation at 80 °C through both cluster dynamics modeling and in situ TEM experiments. The experimental details are reported elsewhere; we focus here on the details of model construction and comparing the model with the experiments. The model incorporates continuous production of point defects and/or small clusters, and the accompanying interactions, which include clustering, recombination and loss to the surfaces that result from the diffusion of the mobile defects. To account for the strong surface effect in thin TEM foils, the model includes one-dimensional spatial dependence along the foil depth, and explicitly treats the surfaces as black sinks. The rich amount of data (cluster number density and size distribution at a variety of foil thickness, irradiation dose and dose rate) offered by the advanced in situ experiments has allowed close comparisons with computer modeling and permitted significant validation and optimization of the model in terms of both physical model construct (damage production mode, identities of mobile defects) and parameterization (diffusivities of mobile defects). The optimized model exhibits good qualitative and quantitative agreement with the in situ TEM experiments. The combinatorial approach is expected to bring a unique opportunity for the study of radiation damage in structural materials.

  3. A Bioinspired Alginate-Gum Arabic Hydrogel with Micro-/Nanoscale Structures for Controlled Drug Release in Chronic Wound Healing.

    Science.gov (United States)

    Li, Mi; Li, Haichang; Li, Xiangguang; Zhu, Hua; Xu, Zihui; Liu, Lianqing; Ma, Jianjie; Zhang, Mingjun

    2017-07-12

    Biopolymeric hydrogels have drawn increasing research interest in biomaterials due to their tunable physical and chemical properties for both creating bioactive cellular microenvironment and serving as sustainable therapeutic reagents. Inspired by a naturally occurring hydrogel secreted from the carnivorous Sundew plant for trapping insects, here we have developed a bioinspired hydrogel to deliver mitsugumin 53 (MG53), an important protein in cell membrane repair, for chronic wound healing. Both chemical compositions and micro-/nanomorphological properties inherent from the natural Sundew hydrogel were mimicked using sodium alginate and gum arabic with calcium ion-mediated cross-linking. On the basis of atomic force microscopy (AFM) force measurements, an optimal sticky hydrogel scaffold was obtained through orthogonal experimental design. Imaging and mechanical analysis showed the distinct correlation between structural morphology, adhesion characteristics, and mechanical properties of the Sundew-inspired hydrogel. Combined characterization and biochemistry techniques were utilized to uncover the underlying molecular composition involved in the interactions between hydrogel and protein. In vitro drug release experiments confirmed that the Sundew-inspired hydrogel had a biphasic-kinetics release, which can facilitate both fast delivery of MG53 for improving the reepithelization process of the wounds and sustained release of the protein for treating chronic wounds. In vivo experiments showed that the Sundew-inspired hydrogel encapsulating with rhMG53 could facilitate dermal wound healing in mouse model. Together, these studies confirmed that the Sundew-inspired hydrogel has both tunable micro-/nanostructures and physicochemical properties, which enable it as a delivery vehicle for chronic wounding healing. The research may provide a new way to develop biocompatible and tunable biomaterials for sustainable drug release to meet the needs of biological activities.

  4. Cognitive flexibility and undergraduate physiology students: increasing advanced knowledge acquisition within an ill-structured domain.

    Science.gov (United States)

    Rhodes, Ashley E; Rozell, Timothy G

    2017-09-01

    Cognitive flexibility is defined as the ability to assimilate previously learned information and concepts to generate novel solutions to new problems. This skill is crucial for success within ill-structured domains such as biology, physiology, and medicine, where many concepts are simultaneously required for understanding a complex problem, yet the problem consists of patterns or combinations of concepts that are not consistently used or needed across all examples. To succeed within ill-structured domains, a student must possess a certain level of cognitive flexibility: rigid thought processes and prepackaged informational retrieval schemes relying on rote memorization will not suffice. In this study, we assessed the cognitive flexibility of undergraduate physiology students using a validated instrument entitled Student's Approaches to Learning (SAL). The SAL evaluates how deeply and in what way information is processed, as well as the investment of time and mental energy that a student is willing to expend by measuring constructs such as elaboration and memorization. Our results indicate that students who rely primarily on memorization when learning new information have a smaller knowledge base about physiological concepts, as measured by a prior knowledge assessment and unit exams. However, students who rely primarily on elaboration when learning new information have a more well-developed knowledge base about physiological concepts, which is displayed by higher scores on a prior knowledge assessment and increased performance on unit exams. Thus students with increased elaboration skills possibly possess a higher level of cognitive flexibility and are more likely to succeed within ill-structured domains. Copyright © 2017 the American Physiological Society.

  5. Predicting binding within disordered protein regions to structurally characterised peptide-binding domains.

    Directory of Open Access Journals (Sweden)

    Waqasuddin Khan

    Full Text Available Disordered regions of proteins often bind to structured domains, mediating interactions within and between proteins. However, it is difficult to identify a priori the short disordered regions involved in binding. We set out to determine if docking such peptide regions to peptide binding domains would assist in these predictions.We assembled a redundancy reduced dataset of SLiM (Short Linear Motif containing proteins from the ELM database. We selected 84 sequences which had an associated PDB structures showing the SLiM bound to a protein receptor, where the SLiM was found within a 50 residue region of the protein sequence which was predicted to be disordered. First, we investigated the Vina docking scores of overlapping tripeptides from the 50 residue SLiM containing disordered regions of the protein sequence to the corresponding PDB domain. We found only weak discrimination of docking scores between peptides involved in binding and adjacent non-binding peptides in this context (AUC 0.58.Next, we trained a bidirectional recurrent neural network (BRNN using as input the protein sequence, predicted secondary structure, Vina docking score and predicted disorder score. The results were very promising (AUC 0.72 showing that multiple sources of information can be combined to produce results which are clearly superior to any single source.We conclude that the Vina docking score alone has only modest power to define the location of a peptide within a larger protein region known to contain it. However, combining this information with other knowledge (using machine learning methods clearly improves the identification of peptide binding regions within a protein sequence. This approach combining docking with machine learning is primarily a predictor of binding to peptide-binding sites, and is not intended as a predictor of specificity of binding to particular receptors.

  6. Evolution of the RNase P RNA structural domain in Leptospira spp.

    Science.gov (United States)

    Ravishankar, Vigneshwaran; Ahmed, Ahmed; Sivagnanam, Ulaganathan; Muthuraman, Krishnaraja; Karthikaichamy, Anbarasu; Wilson, Herald A; Devendran, Ajay; Hartskeerl, Rudy A; Raj, Stephen M L

    2014-12-01

    We have employed the RNase P RNA (RPR) gene, which is present as single copy in chromosome I of Leptospira spp. to investigate the phylogeny of structural domains present in the RNA subunit of the tRNA processing enzyme, RNase P. RPR gene sequences of 150 strains derived from NCBI database along with sequences determined from 8 reference strains were examined to fathom strain specific structural differences present in leptospiral RPR. Sequence variations in the RPR gene impacted on the configuration of loops, stems and bulges found in the RPR highlighting species and strain specific structural motifs. In vitro transcribed leptospiral RPR ribozymes are demonstrated to process pre-tRNA into mature tRNA in consonance with the positioning of Leptospira in the taxonomic domain of bacteria. RPR sequence datasets used to construct a phylogenetic tree exemplified the segregation of strains into their respective lineages with a (re)speciation of strain SH 9 to Leptospira borgpetersenii, strains Fiocruz LV 3954 and Fiocruz LV 4135 to Leptospira santarosai, strain CBC 613 to Leptospira kirschneri and strain HAI 1536 to Leptospira noguchii. Furthermore, it allowed characterization of an isolate P2653, presumptively characterized as either serovar Hebdomadis, Kremastos or Longnan to Leptospira weilii, serovar Longnan. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  7. Optimization of Support Structures for Offshore Wind Turbines Using Genetic Algorithm with Domain-Trimming

    Directory of Open Access Journals (Sweden)

    Mohammad AlHamaydeh

    2017-01-01

    Full Text Available The powerful genetic algorithm optimization technique is augmented with an innovative “domain-trimming” modification. The resulting adaptive, high-performance technique is called Genetic Algorithm with Domain-Trimming (GADT. As a proof of concept, the GADT is applied to a widely used benchmark problem. The 10-dimensional truss optimization benchmark problem has well documented global and local minima. The GADT is shown to outperform several published solutions. Subsequently, the GADT is deployed onto three-dimensional structural design optimization for offshore wind turbine supporting structures. The design problem involves complex least-weight topology as well as member size optimizations. The GADT is applied to two popular design alternatives: tripod and quadropod jackets. The two versions of the optimization problem are nonlinearly constrained where the objective function is the material weight of the supporting truss. The considered design variables are the truss members end node coordinates, as well as the cross-sectional areas of the truss members, whereas the constraints are the maximum stresses in members and the maximum displacements of the nodes. These constraints are managed via dynamically modified, nonstationary penalty functions. The structures are subject to gravity, wind, wave, and earthquake loading conditions. The results show that the GADT method is superior in finding best discovered optimal solutions.

  8. Structure and degeneracy of vortex lattice domains in pure superconducting niobium: A small-angle neutron scattering study

    DEFF Research Database (Denmark)

    Laver, M.; Bowell, C.J.; Forgan, E.M.

    2009-01-01

    High-purity niobium exhibits a surprisingly rich assortment of vortex lattice (VL) structures for fields applied parallel to a fourfold symmetry axis, with all observed VL phases made up of degenerate domains that spontaneously break some crystal symmetry. Yet a single regular hexagonal VL domain...

  9. Structural stability of human protein tyrosine phosphatase ρ catalytic domain: effect of point mutations.

    Directory of Open Access Journals (Sweden)

    Alessandra Pasquo

    Full Text Available Protein tyrosine phosphatase ρ (PTPρ belongs to the classical receptor type IIB family of protein tyrosine phosphatase, the most frequently mutated tyrosine phosphatase in human cancer. There are evidences to suggest that PTPρ may act as a tumor suppressor gene and dysregulation of Tyr phosphorylation can be observed in diverse diseases, such as diabetes, immune deficiencies and cancer. PTPρ variants in the catalytic domain have been identified in cancer tissues. These natural variants are nonsynonymous single nucleotide polymorphisms, variations of a single nucleotide occurring in the coding region and leading to amino acid substitutions. In this study we investigated the effect of amino acid substitution on the structural stability and on the activity of the membrane-proximal catalytic domain of PTPρ. We expressed and purified as soluble recombinant proteins some of the mutants of the membrane-proximal catalytic domain of PTPρ identified in colorectal cancer and in the single nucleotide polymorphisms database. The mutants show a decreased thermal and thermodynamic stability and decreased activation energy relative to phosphatase activity, when compared to wild- type. All the variants show three-state equilibrium unfolding transitions similar to that of the wild- type, with the accumulation of a folding intermediate populated at ~4.0 M urea.

  10. Dynamic magnetization models for soft ferromagnetic materials with coarse and fine domain structures

    Energy Technology Data Exchange (ETDEWEB)

    Zirka, S.E., E-mail: zirka@email.dp.ua [Department of Physics and Technology, Dnepropetrovsk National University, Gagarin 72, 49050 Dnepropetrovsk (Ukraine); Moroz, Y.I. [Department of Physics and Technology, Dnepropetrovsk National University, Gagarin 72, 49050 Dnepropetrovsk (Ukraine); Steentjes, S.; Hameyer, K. [Institute of Electrical Machines, RWTH Aachen University, Schinkelstr. 4, 52056 Aachen (Germany); Chwastek, K. [Faculty of Electrical Engineering, Czestochowa University of Technology, al. AK 17, 42-201 Czestochowa (Poland); Zurek, S. [Megger Instruments Ltd., Archcliffe Road, Dover, Kent, CT17 9EN (United Kingdom); Harrison, R.G. [Department of Electronics, Carleton University, Ottawa, Canada K1S 5B6 (Canada)

    2015-11-15

    We consider dynamic models, both numerical and analytical, that reproduce the magnetization field H(B) and the energy loss in ferromagnetic sheet materials with different domain structures. Conventional non-oriented (NO) and grain-oriented (GO) electrical steels are chosen as typical representatives of fine-domain and coarse-domain materials. The commonly-accepted loss separation procedures in these materials are critically analyzed. The use of a well-known simplified (“classical”) expression for the eddy-current loss is identified as the primary source of mistaken evaluations of excess loss in NO steel, in which the loss components can only be evaluated using the Maxwell (penetration) equation. The situation is quite different in GO steel, in which the loss separation is uncertain, but the total dynamic loss is several times higher than that explained by any version (numerical or analytical) of the classical approach. To illustrate the uncertainty of the loss separation in GO steel, we show that the magnetization field, and thus the total loss, in this material can be represented with equal accuracy using either the existing three-component approach or our proposed two-component technique, which makes no distinction between classical eddy-current and excess fields and losses. - Highlights: • Critical analysis of a ferromagnetic-material loss-separation principle. • This is to warn materials-science engineers about the inaccuracies resulting from this principle. • A transient model having a single dynamic component is proposed.

  11. Nucleon structure in the chiral regime with domain wall fermions on an improved staggered sea

    International Nuclear Information System (INIS)

    R.G. Edwards; G. Fleming; Ph. Hagler; J.W. Negele; K. Orginos; A.V. Pochinsky; D.B. Renner; D.G. Richards; W. Schroers

    2006-01-01

    Moments of unpolarized, helicity, and transversity distributions, electromagnetic form factors, and generalized form factors of the nucleon are presented from a preliminary analysis of lattice results using pion masses down to 359 MeV. The twist two matrix elements are calculated using a mixed action of domain wall valence quarks and asqtad staggered sea quarks and are renormalized perturbatively. Several observables are extrapolated to the physical limit using chiral perturbation theory. Results are compared with experimental moments of quark distributions and electromagnetic form factors and phenomenologically determined generalized form factors, and the implications on the transverse structure and spin content of the nucleon are discussed

  12. Crystal structure of the extracellular domain of human myelin protein zero

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Zhigang; Wang, Yong; Yedidi, Ravikiran S.; Brunzelle, Joseph S.; Kovari, Iulia A.; Sohi, Jasloveleen; Kamholz, John; Kovari, Ladislau C. (WSU-MED); (NWU)

    2012-03-27

    Charcot-Marie-Tooth disease (CMT), a hereditary motor and sensory neuropathy, is the most common genetic neuropathy with an incidence of 1 in 2600. Several forms of CMT have been identified arising from different genomic abnormalities such as CMT1 including CMT1A, CMT1B, and CMTX. CMT1 with associated peripheral nervous system (PNS) demyelination, the most frequent diagnosis, demonstrates slowed nerve conduction velocities and segmental demyelination upon nerve biopsy. One of its subtypes, CMT1A, presents a 1.5-Mb duplication in the p11-p12 region of the human chromosome 17 which encodes peripheral myelin protein 22 (PMP22). CMT1B, a less common form, arises from the mutations in the myelin protein zero (MPZ) gene on chromosome 1, region q22-q23, which encodes the major structural component of the peripheral myelin. A rare type of CMT1 has been found recently and is caused by point mutations in early growth response gene 2 (EGR2), encoding a zinc finger transcription factor in Schwann cells. In addition, CMTX, an X-linked form of CMT, arises from a mutation in the connexin-32 gene. Myelin protein zero, associated with CMT1B, is a transmembrane protein of 219 amino acid residues. Human MPZ consists of three domains: 125 residues constitute the glycosylated immunoglobulin-like extracellular domain; 27 residues span the membrane; and 67 residues comprise the highly basic intracellular domain. MPZ makes up approximately 50% of the protein content of myelin, and is expressed predominantly in Schwann cells, the myelinating cell of the PNS. Myelin protein zero, a homophilic adhesion molecule, is a member of the immunoglobulin super-family and is essential for normal myelin structure and function. In addition, MPZ knockout mice displayed abnormal myelin that severely affects the myelination pathway, and overexpression of MPZ causes congenital hypomyelination of peripheral nerves. Myelin protein zero mutations account for {approx}5% of patients with CMT. To date, over 125

  13. Structural transitions in conserved, ordered Beclin 1 domains essential to regulating autophagy

    Energy Technology Data Exchange (ETDEWEB)

    Glover, Karen; Li, Yue; Mukhopadhyay, Shreya; Leuthner, Zoe; Chakravarthy, Srinivas; Colbert, Christopher L.; Sinha, Sangita C. (NDSU); (IIT)

    2017-08-10

    Beclin 1 (BECN1) is a key regulator of autophagy, a critical catabolic homeostasis pathway that involves sequestration of selected cytoplasmic components by multilayered vesicles called autophagosomes, followed by lysosomal fusion and degradation. BECN1 is a core component of class III phosphatidylinositol-3-kinase complexes responsible for autophagosome nucleation. Without heterologous binding partners, BECN1 forms an antiparallel homodimer via its coiled-coil domain (CCD). However, the last 16 CCD residues, composing an “overlap helix” (OH), have been crystallized in two mutually exclusive states: either as part of the CCD or packed against the C-terminal β-α repeated, autophagy-specific domain (BARAD). Here, using CD spectroscopy, isothermal titration calorimetry, and small-angle X-ray scattering, we show that in the homodimeric state, the OH transitions between these two different packing states, with the predominant state comprising the OH packed against the BARAD, contrary to expectations based on known BECN1 interactions with heterologous partners. We confirmed this observation by comparing the impact of mutating four residues that mediate packing of the OH against both the CCD and BARAD on structure and stability of the CCD, the OH+BARAD, and the two-domain CCD–BARAD. Last, we used cellular assays to demonstrate that mutation of these OH-interface residues abrogates starvation-induced up-regulation of autophagy but does not affect basal autophagy. In summary, we have identified a BECN1 helical region that transitions between packing as part of either one of two conserved domains (i.e. the CCD or the BARAD). Our findings have important implications for the relative stability of autophagy-inactive and autophagy-active BECN1 complexes.

  14. Nonlinear Time Domain Seismic Soil-Structure Interaction (SSI) Deep Soil Site Methodology Development

    International Nuclear Information System (INIS)

    Spears, Robert Edward; Coleman, Justin Leigh

    2015-01-01

    Currently the Department of Energy (DOE) and the nuclear industry perform seismic soil-structure interaction (SSI) analysis using equivalent linear numerical analysis tools. For lower levels of ground motion, these tools should produce reasonable in-structure response values for evaluation of existing and new facilities. For larger levels of ground motion these tools likely overestimate the in-structure response (and therefore structural demand) since they do not consider geometric nonlinearities (such as gaping and sliding between the soil and structure) and are limited in the ability to model nonlinear soil behavior. The current equivalent linear SSI (SASSI) analysis approach either joins the soil and structure together in both tension and compression or releases the soil from the structure for both tension and compression. It also makes linear approximations for material nonlinearities and generalizes energy absorption with viscous damping. This produces the potential for inaccurately establishing where the structural concerns exist and/or inaccurately establishing the amplitude of the in-structure responses. Seismic hazard curves at nuclear facilities have continued to increase over the years as more information has been developed on seismic sources (i.e. faults), additional information gathered on seismic events, and additional research performed to determine local site effects. Seismic hazard curves are used to develop design basis earthquakes (DBE) that are used to evaluate nuclear facility response. As the seismic hazard curves increase, the input ground motions (DBE's) used to numerically evaluation nuclear facility response increase causing larger in-structure response. As ground motions increase so does the importance of including nonlinear effects in numerical SSI models. To include material nonlinearity in the soil and geometric nonlinearity using contact (gaping and sliding) it is necessary to develop a nonlinear time domain methodology. This

  15. Structure and catalytic regulatory function of ubiquitin specific protease 11 N-terminal and ubiquitin-like domains.

    Science.gov (United States)

    Harper, Stephen; Gratton, Hayley E; Cornaciu, Irina; Oberer, Monika; Scott, David J; Emsley, Jonas; Dreveny, Ingrid

    2014-05-13

    The ubiquitin specific protease 11 (USP11) is implicated in DNA repair, viral RNA replication, and TGFβ signaling. We report the first characterization of the USP11 domain architecture and its role in regulating the enzymatic activity. USP11 consists of an N-terminal "domain present in USPs" (DUSP) and "ubiquitin-like" (UBL) domain, together referred to as DU domains, and the catalytic domain harboring a second UBL domain. Crystal structures of the DU domains show a tandem arrangement with a shortened β-hairpin at the two-domain interface and altered surface characteristics compared to the homologues USP4 and USP15. A conserved VEVY motif is a signature feature at the two-domain interface that shapes a potential protein interaction site. Small angle X-ray scattering and gel filtration experiments are consistent with the USP11DU domains and full-length USP11 being monomeric. Unexpectedly, we reveal, through kinetic assays of a series of deletion mutants, that the catalytic activity of USP11 is not regulated through intramolecular autoinhibition or activation by the N-terminal DU or UBL domains. Moreover, ubiquitin chain cleavage assays with all eight linkages reveal a preference for Lys(63)-, Lys(6)-, Lys(33)-, and Lys(11)-linked chains over Lys(27)-, Lys(29)-, and Lys(48)-linked and linear chains consistent with USP11's function in DNA repair pathways that is mediated by the protease domain. Our data support a model whereby USP11 domains outside the catalytic core domain serve as protein interaction or trafficking modules rather than a direct regulatory function of the proteolytic activity. This highlights the diversity of USPs in substrate recognition and regulation of ubiquitin deconjugation.

  16. The structure of the actin-smooth muscle myosin motor domain complex in the rigor state.

    Science.gov (United States)

    Banerjee, Chaity; Hu, Zhongjun; Huang, Zhong; Warrington, J Anthony; Taylor, Dianne W; Trybus, Kathleen M; Lowey, Susan; Taylor, Kenneth A

    2017-12-01

    Myosin-based motility utilizes catalysis of ATP to drive the relative sliding of F-actin and myosin. The earliest detailed model based on cryo-electron microscopy (cryoEM) and X-ray crystallography postulated that higher actin affinity and lever arm movement were coupled to closure of a feature of the myosin head dubbed the actin-binding cleft. Several studies since then using crystallography of myosin-V and cryoEM structures of F-actin bound myosin-I, -II and -V have provided details of this model. The smooth muscle myosin II interaction with F-actin may differ from those for striated and non-muscle myosin II due in part to different lengths of important surface loops. Here we report a ∼6 Å resolution reconstruction of F-actin decorated with the nucleotide-free recombinant smooth muscle myosin-II motor domain (MD) from images recorded using a direct electron detector. Resolution is highest for F-actin and the actin-myosin interface (3.5-4 Å) and lowest (∼6-7 Å) for those parts of the MD at the highest radius. Atomic models built into the F-actin density are quite comparable to those previously reported for rabbit muscle actin and show density from the bound ADP. The atomic model of the MD, is quite similar to a recently published structure of vertebrate non-muscle myosin II bound to F-actin and a crystal structure of nucleotide free myosin-V. Larger differences are observed when compared to the cryoEM structure of F-actin decorated with rabbit skeletal muscle myosin subfragment 1. The differences suggest less closure of the 50 kDa domain in the actin bound skeletal muscle myosin structure. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Halbach Effect at the Nanoscale from Chiral Spin Textures.

    Science.gov (United States)

    Marioni, Miguel A; Penedo, Marcos; Baćani, Mirko; Schwenk, Johannes; Hug, Hans J

    2018-04-11

    Mallinson's idea that some spin textures in planar magnetic structures could produce an enhancement of the magnetic flux on one side of the plane at the expense of the other gave rise to permanent magnet configurations known as Halbach magnet arrays. Applications range from wiggler magnets in particle accelerators and free electron lasers to motors and magnetic levitation trains, but exploiting Halbach arrays in micro- or nanoscale spintronics devices requires solving the problem of fabrication and field metrology below a 100 μm size. In this work, we show that a Halbach configuration of moments can be obtained over areas as small as 1 μm × 1 μm in sputtered thin films with Néel-type domain walls of unique domain wall chirality, and we measure their stray field at a controlled probe-sample distance of 12.0 ± 0.5 nm. Because here chirality is determined by the interfacial Dyzaloshinkii-Moriya interaction, the field attenuation and amplification is an intrinsic property of this film, allowing for flexibility of design based on an appropriate definition of magnetic domains. Skyrmions (magnetic fields and mapping of the spin structure shows they funnel the field toward one specific side of the film given by the sign of the Dyzaloshinkii-Moriya interaction parameter D.

  18. Quantitative Structure-Use Relationship Model thresholds for Model Validation, Domain of Applicability, and Candidate Alternative Selection

    Data.gov (United States)

    U.S. Environmental Protection Agency — This file contains value of the model training set confusion matrix, domain of applicability evaluation based on training set to predicted chemicals structural...

  19. Solution structure of GSP13 from Bacillus subtilis exhibits an S1 domain related to cold shock proteins

    International Nuclear Information System (INIS)

    Yu Wenyu; Hu Jicheng; Yu Bingke; Xia Wei; Jin Changwen; Xia Bin

    2009-01-01

    GSP13 encoded by gene yugI is a σ B -dependent general stress protein in Bacillus subtilis, which can be induced by heat shock, salt stress, ethanol stress, glucose starvation, oxidative stress and cold shock. Here we report the solution structure of GSP13 and it is the first structure of S1 domain containing protein in Bacillus subtilis. The structure of GSP13 mainly consists of a typical S1 domain along with a C-terminal 50-residue flexible tail, different from the other known S1 domain containing proteins. Comparison with other S1 domain structures reveals that GSP13 has a conserved RNA binding surface, and it may function similarly to cold shock proteins in response to cold stress

  20. Influence of domain structure induced coupling on magnetization reversal of Co/Pt/Co film with perpendicular anisotropy

    Energy Technology Data Exchange (ETDEWEB)

    Matczak, Michał [Institute of Molecular Physics, Polish Academy of Sciences, M. Smoluchowskiego 17, 60-179 Poznań (Poland); NanoBioMedical Centre, Adam Mickiewicz University, Umultowska 85, 61-614 Poznań (Poland); Schäfer, Rudolf [Leibniz Institute for Solid State and Materials Research (IFW) Dresden, Institute for Metallic Materials, PO 270116, D-01171 Dresden (Germany); Dresden University of Technology, Institute for Materials Science, D-01062 Dresden (Germany); Urbaniak, Maciej; Kuświk, Piotr; Szymański, Bogdan; Schmidt, Marek; Aleksiejew, Jacek [Institute of Molecular Physics, Polish Academy of Sciences, M. Smoluchowskiego 17, 60-179 Poznań (Poland); Stobiecki, Feliks, E-mail: Feliks.Stobiecki@ifmpan.poznan.pl [Institute of Molecular Physics, Polish Academy of Sciences, M. Smoluchowskiego 17, 60-179 Poznań (Poland); NanoBioMedical Centre, Adam Mickiewicz University, Umultowska 85, 61-614 Poznań (Poland)

    2017-01-15

    A magnetic multilayer of substrate/Pt-15 nm/Co-0.8 nm/Pt-wedge 0–7 nm/Co-0.6 nm/Pt-2 nm structure is characterized by a perpendicular anisotropy of the Co layers and by graded interlayer coupling between them. Using magnetooptical Kerr microscopy we observed a distinct influence of magnetic domains in one Co layer on the nucleation field and positions of nucleation sites of reversed domains in the second Co layer. For sufficiently strong interlayer coupling a replication of magnetic domains from the magnetically harder layer to the magnetically softer layer is observed. - Highlights: • Co/Pt-wedge/Co layered film is characterized by a gradient of interlayer coupling. • Magnetic field controls propagation of straight domain wall. • Replication of magnetic domains in multilayers with strong ferromagnetic coupling. • Coupling induced by domains influences magnetization reversal of spin valves.

  1. Nanoscale phase-change materials and devices

    International Nuclear Information System (INIS)

    Zheng, Qinghui; Wang, Yuxi; Zhu, Jia

    2017-01-01

    Phase-change materials (PCMs) that can reversibly transit between crystalline and amorphous phases have been widely used for data-storage and other functional devices. As PCMs scale down to nanoscale, the properties and transition procedures can vary, bringing both challenges and opportunities in scalability. This article describes the physical structures, properties and applications of nanoscale phase-change materials and devices. The limitations and performance of scaling properties in phase-change materials and the recent progress and challenges in phase-change devices are presented. At the end, some emerging applications related to phase-change materials are also introduced. (topical review)

  2. Nanoscale phase-change materials and devices

    Science.gov (United States)

    Zheng, Qinghui; Wang, Yuxi; Zhu, Jia

    2017-06-01

    Phase-change materials (PCMs) that can reversibly transit between crystalline and amorphous phases have been widely used for data-storage and other functional devices. As PCMs scale down to nanoscale, the properties and transition procedures can vary, bringing both challenges and opportunities in scalability. This article describes the physical structures, properties and applications of nanoscale phase-change materials and devices. The limitations and performance of scaling properties in phase-change materials and the recent progress and challenges in phase-change devices are presented. At the end, some emerging applications related to phase-change materials are also introduced.

  3. Magnetic domain structure investigation of Bi: YIG-thin films by combination of AFM and cantilever-based aperture SNOM

    International Nuclear Information System (INIS)

    Vysokikh, Yu E; Shevyakov, V I; Krasnoborodko, S Yu; Shelaev, A V; Prokopov, A R

    2016-01-01

    We present the results of magnetic domain structure investigation by combination of atomic force microscopy (AFM) and scanning near-field optical microscopy (SNOM). Special hollow-pyramid AFM cantilevers with aperture was used. This combination allows us use same probe for both topography and domain structure visualization of Bi -substituted ferrite garnet films of micro- and nano-meter thickness. Samples were excited through aperture by tightly focused linearly polarized laser beam. Magneto-optical effect rotates polarization of transmitted light depend on domain orientation. Visualization of magnetic domains was performed by detecting cross polarized component of transmitted light. SNOM allows to obtain high resolution magnetic domain image and prevent sample from any disturbance by magnetic probe. Same area SNOM and MFM images are presented. (paper)

  4. Correlating structure and function during the evolution of fibrinogen-related domains

    Science.gov (United States)

    Doolittle, Russell F; McNamara, Kyle; Lin, Kevin

    2012-01-01

    Fibrinogen-related domains (FReDs) are found in a variety of animal proteins with widely different functions, ranging from non-self recognition to clot formation. All appear to have a common surface where binding of one sort or other occurs. An examination of 19 completed animal genomes—including a sponge and sea anemone, six protostomes, and 11 deuterostomes—has allowed phylogenies to be constructed that show where various types of FReP (proteins containing FReDs) first made their appearance. Comparisons of sequences and structures also reveal particular features that correlate with function, including the influence of neighbor-domains. A particular set of insertions in the carboxyl-terminal subdomain was involved in the transition from structures known to bind sugars to those known to bind amino-terminal peptides. Perhaps not unexpectedly, FReDs with different functions have changed at different rates, with ficolins by far the fastest changing group. Significantly, the greatest amount of change in ficolin FReDs occurs in the third subdomain (“P domain”), the very opposite of the situation in most other vertebrate FReDs. The unbalanced style of change was also observed in FReDs from non-chordates, many of which have been implicated in innate immunity. PMID:23076991

  5. NMR structure of the N-terminal domain of the replication initiator protein DnaA

    Energy Technology Data Exchange (ETDEWEB)

    Wemmer, David E.; Lowery, Thomas J.; Pelton, Jeffrey G.; Chandonia, John-Marc; Kim, Rosalind; Yokota, Hisao; Wemmer, David E.

    2007-08-07

    DnaA is an essential component in the initiation of bacterial chromosomal replication. DnaA binds to a series of 9 base pair repeats leading to oligomerization, recruitment of the DnaBC helicase, and the assembly of the replication fork machinery. The structure of the N-terminal domain (residues 1-100) of DnaA from Mycoplasma genitalium was determined by NMR spectroscopy. The backbone r.m.s.d. for the first 86 residues was 0.6 +/- 0.2 Angstrom based on 742 NOE, 50 hydrogen bond, 46 backbone angle, and 88 residual dipolar coupling restraints. Ultracentrifugation studies revealed that the domain is monomeric in solution. Features on the protein surface include a hydrophobic cleft flanked by several negative residues on one side, and positive residues on the other. A negatively charged ridge is present on the opposite face of the protein. These surfaces may be important sites of interaction with other proteins involved in the replication process. Together, the structure and NMR assignments should facilitate the design of new experiments to probe the protein-protein interactions essential for the initiation of DNA replication.

  6. Use of Time- and Frequency-Domain Approaches for Damage Detection in Civil Engineering Structures

    Directory of Open Access Journals (Sweden)

    V. H. Nguyen

    2014-01-01

    Full Text Available The aim of this paper is to apply both time- and frequency-domain-based approaches on real-life civil engineering structures and to assess their capability for damage detection. The methodology is based on Principal Component Analysis of the Hankel matrix built from output-only measurements and of Frequency Response Functions. Damage detection is performed using the concept of subspace angles between a current (possibly damaged state and a reference (undamaged state. The first structure is the Champangshiehl Bridge located in Luxembourg. Several damage levels were intentionally created by cutting a growing number of prestressed tendons and vibration data were acquired by the University of Luxembourg for each damaged state. The second example consists in reinforced and prestressed concrete panels. Successive damages were introduced in the panels by loading heavy weights and by cutting steel wires. The illustrations show different consequences in damage identification by the considered techniques.

  7. Structural sensitivity of x-ray Bragg projection ptychography to domain patterns in epitaxial thin films

    International Nuclear Information System (INIS)

    Hruszkewycz, S. O.; Zhang, Q.; Holt, M. V.; Highland, M. J.

    2016-01-01

    Bragg projection ptychography (BPP) is a coherent diffraction imaging technique capable of mapping the spatial distribution of the Bragg structure factor in nanostructured thin films. Here, we show that, because these images are projections, the structural sensitivity of the resulting images depends on the film thickness and the aspect ratio and orientation of the features of interest and that image interpretation depends on these factors. Lastly, we model changes in contrast in the BPP reconstructions of simulated PbTiO_3 ferroelectric thin films with meandering 180° stripe domains as a function of film thickness, discuss their origin, and comment on the implication of these factors on the design of BPP experiments of general nanostructured films.

  8. Improvement of training set structure in fusion data cleaning using Time-Domain Global Similarity method

    International Nuclear Information System (INIS)

    Liu, J.; Lan, T.; Qin, H.

    2017-01-01

    Traditional data cleaning identifies dirty data by classifying original data sequences, which is a class-imbalanced problem since the proportion of incorrect data is much less than the proportion of correct ones for most diagnostic systems in Magnetic Confinement Fusion (MCF) devices. When using machine learning algorithms to classify diagnostic data based on class-imbalanced training set, most classifiers are biased towards the major class and show very poor classification rates on the minor class. By transforming the direct classification problem about original data sequences into a classification problem about the physical similarity between data sequences, the class-balanced effect of Time-Domain Global Similarity (TDGS) method on training set structure is investigated in this paper. Meanwhile, the impact of improved training set structure on data cleaning performance of TDGS method is demonstrated with an application example in EAST POlarimetry-INTerferometry (POINT) system.

  9. Time-domain representation of frequency dependent inertial forces on offshore structures

    DEFF Research Database (Denmark)

    Krenk, Steen

    2013-01-01

    dependence is then approximated by a rational function, corresponding to a set of ordinary differential equations in the time domain. The MacCamy-Fuchs solution leads to a representation of the inertial force coefficient as a complex function with argument mainly corresponding to a 'phase lead', in contrast...... history of the inertial force is determined by processing the stable part of the transformation by a forward time integration, followed by an integration in the negative time-direction to obtain the final inertial force time history. The differential equations of the local inertial force at a cross......The inertial wave force on a vertical cylinder decreases with decreasing wave length, when the wave length is less than about six times the diameter of the diameter of the cylinder. In structures with a largediameter component like mono-towers the resonance frequency of the structure is typically...

  10. Solution structure of a DNA mimicking motif of an RNA aptamer against transcription factor AML1 Runt domain.

    Science.gov (United States)

    Nomura, Yusuke; Tanaka, Yoichiro; Fukunaga, Jun-ichi; Fujiwara, Kazuya; Chiba, Manabu; Iibuchi, Hiroaki; Tanaka, Taku; Nakamura, Yoshikazu; Kawai, Gota; Kozu, Tomoko; Sakamoto, Taiichi

    2013-12-01

    AML1/RUNX1 is an essential transcription factor involved in the differentiation of hematopoietic cells. AML1 binds to the Runt-binding double-stranded DNA element (RDE) of target genes through its N-terminal Runt domain. In a previous study, we obtained RNA aptamers against the AML1 Runt domain by systematic evolution of ligands by exponential enrichment and revealed that RNA aptamers exhibit higher affinity for the Runt domain than that for RDE and possess the 5'-GCGMGNN-3' and 5'-N'N'CCAC-3' conserved motif (M: A or C; N and N' form Watson-Crick base pairs) that is important for Runt domain binding. In this study, to understand the structural basis of recognition of the Runt domain by the aptamer motif, the solution structure of a 22-mer RNA was determined using nuclear magnetic resonance. The motif contains the AH(+)-C mismatch and base triple and adopts an unusual backbone structure. Structural analysis of the aptamer motif indicated that the aptamer binds to the Runt domain by mimicking the RDE sequence and structure. Our data should enhance the understanding of the structural basis of DNA mimicry by RNA molecules.

  11. Atomic structure of the murine norovirus protruding domain and sCD300lf receptor complex.

    Science.gov (United States)

    Kilic, Turgay; Koromyslova, Anna; Malak, Virginie; Hansman, Grant S

    2018-03-21

    Human noroviruses are the leading cause of acute gastroenteritis in human. Noroviruses also infect animals such as cow, mice, cat, and dog. How noroviruses bind and enter host cells is still incompletely understood. Recently, the type I transmembrane protein CD300lf was recently identified as the murine norovirus receptor, yet it is unclear how the virus capsid and receptor interact at the molecular level. In this study, we determined the X-ray crystal structure of the soluble CD300lf (sCD300lf) and murine norovirus capsid-protruding domain complex at 2.05 Å resolution. We found that the sCD300lf binding site is located on the topside of the protruding domain and involves a network of hydrophilic and hydrophobic interactions. The sCD300lf locked nicely into a complementary cavity on the protruding domain that is additionally coordinated with a positive surface charge on the sCD300lf and a negative surface charge on the protruding domain. Five of six protruding domain residues interacting with sCD300lf were maintained between different murine norovirus strains, suggesting that the sCD300lf was capable of binding to a highly conserved pocket. Moreover, a sequence alignment with other CD300 paralogs showed that the sCD300lf interacting residues were partially conserved in CD300ld, but variable in other CD300 family members, consistent with previously reported infection selectivity. Overall, these data provide insights into how a norovirus engages a protein receptor and will be important for a better understanding of selective recognition and norovirus attachment and entry mechanisms. IMPORTANCE Noroviruses exhibit exquisite host-range specificity due to species-specific interactions between the norovirus capsid protein and host molecules. Given this strict host-range restriction it has been unclear how the viruses are maintained within a species between relatively sporadic epidemics. While much data demonstrates that noroviruses can interact with carbohydrates

  12. A domain-independent descriptive design model and its application to structured reflection on design processes

    NARCIS (Netherlands)

    Reymen, Isabelle; Hammer, D.K.; Kroes, P.A.; van Aken, Joan Ernst; van Aken, J.E.; Dorst, C.H.; Bax, M.F.T.; Basten, T

    2006-01-01

    Domain-independent models of the design process are an important means for facilitating interdisciplinary communication and for supporting multidisciplinary design. Many so-called domain-independent models are, however, not really domain independent. We state that to be domain independent, the

  13. Solution structure of the C-terminal X domain of the measles virus phosphoprotein and interaction with the intrinsically disordered C-terminal domain of the nucleoprotein.

    Science.gov (United States)

    Gely, Stéphane; Lowry, David F; Bernard, Cédric; Jensen, Malene R; Blackledge, Martin; Costanzo, Stéphanie; Bourhis, Jean-Marie; Darbon, Hervé; Daughdrill, Gary; Longhi, Sonia

    2010-01-01

    In this report, the solution structure of the nucleocapsid-binding domain of the measles virus phosphoprotein (XD, aa 459-507) is described. A dynamic description of the interaction between XD and the disordered C-terminal domain of the nucleocapsid protein, (N(TAIL), aa 401-525), is also presented. XD is an all alpha protein consisting of a three-helix bundle with an up-down-up arrangement of the helices. The solution structure of XD is very similar to the crystal structures of both the free and bound form of XD. One exception is the presence of a highly dynamic loop encompassing XD residues 489-491, which is involved in the embedding of the alpha-helical XD-binding region of N(TAIL). Secondary chemical shift values for full-length N(TAIL) were used to define the precise boundaries of a transient helical segment that coincides with the XD-binding domain, thus shedding light on the pre-recognition state of N(TAIL). Titration experiments with unlabeled XD showed that the transient alpha-helical conformation of N(TAIL) is stabilized upon binding. Lineshape analysis of NMR resonances revealed that residues 483-506 of N(TAIL) are in intermediate exchange with XD, while the 475-482 and 507-525 regions are in fast exchange. The N(TAIL) resonance behavior in the titration experiments is consistent with a complex binding model with more than two states.

  14. Crystal structure of the second fibronectin type III (FN3) domain from human collagen α1 type XX.

    Science.gov (United States)

    Zhao, Jingfeng; Ren, Jixia; Wang, Nan; Cheng, Zhong; Yang, Runmei; Lin, Gen; Guo, Yi; Cai, Dayong; Xie, Yong; Zhao, Xiaohong

    2017-12-01

    Collagen α1 type XX, which contains fibronectin type III (FN3) repeats involving six FN3 domains (referred to as the FN#1-FN#6 domains), is an unusual member of the fibril-associated collagens with interrupted triple helices (FACIT) subfamily of collagens. The results of standard protein BLAST suggest that the FN3 repeats might contribute to collagen α1 type XX acting as a cytokine receptor. To date, solution NMR structures of the FN#3, FN#4 and FN#6 domains have been determined. To obtain further structural evidence to understand the relationship between the structure and function of the FN3 repeats from collagen α1 type XX, the crystal structure of the FN#2 domain from human collagen α1 type XX (residues Pro386-Pro466; referred to as FN2-HCXX) was solved at 2.5 Å resolution. The crystal structure of FN2-HCXX shows an immunoglobulin-like fold containing a β-sandwich structure, which is formed by a three-stranded β-sheet (β1, β2 and β5) packed onto a four-stranded β-sheet (β3, β4, β6 and β7). Two consensus domains, tencon and fibcon, are structural analogues of FN2-HCXX. Fn8, an FN3 domain from human oncofoetal fibronectin, is the closest structural analogue of FN2-HCXX derived from a naturally occurring sequence. Based solely on the structural similarity of FN2-HCXX to other FN3 domains, the detailed functions of FN2-HCXX and the FN3 repeats in collagen α1 type XX cannot be identified.

  15. Solution structure of tensin2 SH2 domain and its phosphotyrosine-independent interaction with DLC-1.

    Directory of Open Access Journals (Sweden)

    Kun Dai

    Full Text Available Src homology 2 (SH2 domain is a conserved module involved in various biological processes. Tensin family member was reported to be involved in tumor suppression by interacting with DLC-1 (deleted-in-liver-cancer-1 via its SH2 domain. We explore here the important questions that what the structure of tensin2 SH2 domain is, and how it binds to DLC-1, which might reveal a novel binding mode.Tensin2 SH2 domain adopts a conserved SH2 fold that mainly consists of five β-strands flanked by two α-helices. Most SH2 domains recognize phosphorylated ligands specifically. However, tensin2 SH2 domain was identified to interact with nonphosphorylated ligand (DLC-1 as well as phosphorylated ligand.We determined the solution structure of tensin2 SH2 domain using NMR spectroscopy, and revealed the interactions between tensin2 SH2 domain and its ligands in a phosphotyrosine-independent manner.

  16. Analysis of the Sequences, Structures, and Functions of Product-Releasing Enzyme Domains in Fungal Polyketide Synthases

    Directory of Open Access Journals (Sweden)

    Lu Liu

    2017-09-01

    Full Text Available Product-releasing enzyme (PRE domains in fungal non-reducing polyketide synthases (NR-PKSs play a crucial role in catalysis and editing during polyketide biosynthesis, especially accelerating final biosynthetic reactions accompanied with product offloading. However, up to date, the systematic knowledge about PRE domains is deficient. In the present study, the relationships between sequences, structures, and functions of PRE domains were analyzed with 574 NR-PKSs of eight groups (I–VIII. It was found that the PRE domains in NR-PKSs could be mainly classified into three types, thioesterase (TE, reductase (R, and metallo-β-lactamase-type TE (MβL-TE. The widely distributed TE or TE-like domains were involved in NR-PKSs of groups I–IV, VI, and VIII. The R domains appeared in NR-PKSs of groups IV and VII, while the physically discrete MβL-TE domains were employed by most NR-PKSs of group V. The changes of catalytic sites and structural characteristics resulted in PRE functional differentiations. The phylogeny revealed that the evolution of TE domains was accompanied by complex functional divergence. The diverse sequence lengths of TE lid-loops affected substrate specificity with different chain lengths. The volume diversification of TE catalytic pockets contributed to catalytic mechanisms with functional differentiations. The above findings may help to understand the crucial catalysis of fungal aromatic polyketide biosyntheses and govern recombination of NR-PKSs to obtain unnatural target products.

  17. Convergence of Domain Architecture, Structure, and Ligand Affinity in Animal and Plant RNA-Binding Proteins.

    Science.gov (United States)

    Dias, Raquel; Manny, Austin; Kolaczkowski, Oralia; Kolaczkowski, Bryan

    2017-06-01

    Reconstruction of ancestral protein sequences using phylogenetic methods is a powerful technique for directly examining the evolution of molecular function. Although ancestral sequence reconstruction (ASR) is itself very efficient, downstream functional, and structural studies necessary to characterize when and how changes in molecular function occurred are often costly and time-consuming, currently limiting ASR studies to examining a relatively small number of discrete functional shifts. As a result, we have very little direct information about how molecular function evolves across large protein families. Here we develop an approach combining ASR with structure and function prediction to efficiently examine the evolution of ligand affinity across a large family of double-stranded RNA binding proteins (DRBs) spanning animals and plants. We find that the characteristic domain architecture of DRBs-consisting of 2-3 tandem double-stranded RNA binding motifs (dsrms)-arose independently in early animal and plant lineages. The affinity with which individual dsrms bind double-stranded RNA appears to have increased and decreased often across both animal and plant phylogenies, primarily through convergent structural mechanisms involving RNA-contact residues within the β1-β2 loop and a small region of α2. These studies provide some of the first direct information about how protein function evolves across large gene families and suggest that changes in molecular function may occur often and unassociated with major phylogenetic events, such as gene or domain duplications. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  18. Crystal structure of the ligand-bound glucagon-like peptide-1 receptor extracellular domain.

    Science.gov (United States)

    Runge, Steffen; Thøgersen, Henning; Madsen, Kjeld; Lau, Jesper; Rudolph, Rainer

    2008-04-25

    The glucagon-like peptide-1 receptor (GLP-1R) belongs to Family B1 of the seven-transmembrane G protein-coupled receptors, and its natural agonist ligand is the peptide hormone glucagon-like peptide-1 (GLP-1). GLP-1 is involved in glucose homeostasis, and activation of GLP-1R in the plasma membrane of pancreatic beta-cells potentiates glucose-dependent insulin secretion. The N-terminal extracellular domain (nGLP-1R) is an important ligand binding domain that binds GLP-1 and the homologous peptide Exendin-4 with differential affinity. Exendin-4 has a C-terminal extension of nine amino acid residues known as the "Trp cage", which is absent in GLP-1. The Trp cage was believed to interact with nGLP-1R and thereby explain the superior affinity of Exendin-4. However, the molecular details that govern ligand binding and specificity of nGLP-1R remain undefined. Here we report the crystal structure of human nGLP-1R in complex with the antagonist Exendin-4(9-39) solved by the multiwavelength anomalous dispersion method to 2.2A resolution. The structure reveals that Exendin-4(9-39) is an amphipathic alpha-helix forming both hydrophobic and hydrophilic interactions with nGLP-1R. The Trp cage of Exendin-4 is not involved in binding to nGLP-1R. The hydrophobic binding site of nGLP-1R is defined by discontinuous segments including primarily a well defined alpha-helix in the N terminus of nGLP-1R and a loop between two antiparallel beta-strands. The structure provides for the first time detailed molecular insight into ligand binding of the human GLP-1 receptor, an established target for treatment of type 2 diabetes.

  19. Structure-function relationships using spectral-domain optical coherence tomography: comparison with scanning laser polarimetry.

    Science.gov (United States)

    Aptel, Florent; Sayous, Romain; Fortoul, Vincent; Beccat, Sylvain; Denis, Philippe

    2010-12-01

    To evaluate and compare the regional relationships between visual field sensitivity and retinal nerve fiber layer (RNFL) thickness as measured by spectral-domain optical coherence tomography (OCT) and scanning laser polarimetry. Prospective cross-sectional study. One hundred and twenty eyes of 120 patients (40 with healthy eyes, 40 with suspected glaucoma, and 40 with glaucoma) were tested on Cirrus-OCT, GDx VCC, and standard automated perimetry. Raw data on RNFL thickness were extracted for 256 peripapillary sectors of 1.40625 degrees each for the OCT measurement ellipse and 64 peripapillary sectors of 5.625 degrees each for the GDx VCC measurement ellipse. Correlations between peripapillary RNFL thickness in 6 sectors and visual field sensitivity in the 6 corresponding areas were evaluated using linear and logarithmic regression analysis. Receiver operating curve areas were calculated for each instrument. With spectral-domain OCT, the correlations (r(2)) between RNFL thickness and visual field sensitivity ranged from 0.082 (nasal RNFL and corresponding visual field area, linear regression) to 0.726 (supratemporal RNFL and corresponding visual field area, logarithmic regression). By comparison, with GDx-VCC, the correlations ranged from 0.062 (temporal RNFL and corresponding visual field area, linear regression) to 0.362 (supratemporal RNFL and corresponding visual field area, logarithmic regression). In pairwise comparisons, these structure-function correlations were generally stronger with spectral-domain OCT than with GDx VCC and with logarithmic regression than with linear regression. The largest areas under the receiver operating curve were seen for OCT superior thickness (0.963 ± 0.022; P polarimetry, and was better expressed logarithmically than linearly. Measurements with these 2 instruments should not be considered to be interchangeable. Copyright © 2010 Elsevier Inc. All rights reserved.

  20. Comparative structure-function characterization of the saposin-like domains from potato, barley, cardoon and Arabidopsis aspartic proteases.

    Science.gov (United States)

    Bryksa, Brian C; Grahame, Douglas A; Yada, Rickey Y

    2017-05-01

    The present study characterized the aspartic protease saposin-like domains of four plant species, Solanum tuberosum (potato), Hordeum vulgare L. (barley), Cynara cardunculus L. (cardoon; artichoke thistle) and Arabidopsis thaliana, in terms of bilayer disruption and fusion, and structure pH-dependence. Comparison of the recombinant saposin-like domains revealed that each induced leakage of bilayer vesicles composed of a simple phospholipid mixture with relative rates Arabidopsis>barley>cardoon>potato. When compared for leakage of bilayer composed of a vacuole-like phospholipid mixture, leakage was approximately five times higher for potato saposin-like domain compared to the others. In terms of fusogenic activity, distinctions between particle size profiles were noted among the four proteins, particularly for potato saposin-like domain. Bilayer fusion assays in reducing conditions resulted in altered fusion profiles except in the case of cardoon saposin-like domain which was virtually unchanged. Secondary structure profiles were similar across all four proteins under different pH conditions, although cardoon saposin-like domain appeared to have higher overall helix structure. Furthermore, increases in Trp emission upon protein-bilayer interactions suggested that protein structure rearrangements equilibrated with half-times ranging from 52 to 120s, with cardoon saposin-like domain significantly slower than the other three species. Overall, the present findings serve as a foundation for future studies seeking to delineate protein structural features and motifs in protein-bilayer interactions based upon variability in plant aspartic protease saposin-like domain structures. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. A refined Frequency Domain Decomposition tool for structural modal monitoring in earthquake engineering

    Science.gov (United States)

    Pioldi, Fabio; Rizzi, Egidio

    2017-07-01

    Output-only structural identification is developed by a refined Frequency Domain Decomposition ( rFDD) approach, towards assessing current modal properties of heavy-damped buildings (in terms of identification challenge), under strong ground motions. Structural responses from earthquake excitations are taken as input signals for the identification algorithm. A new dedicated computational procedure, based on coupled Chebyshev Type II bandpass filters, is outlined for the effective estimation of natural frequencies, mode shapes and modal damping ratios. The identification technique is also coupled with a Gabor Wavelet Transform, resulting in an effective and self-contained time-frequency analysis framework. Simulated response signals generated by shear-type frames (with variable structural features) are used as a necessary validation condition. In this context use is made of a complete set of seismic records taken from the FEMA P695 database, i.e. all 44 "Far-Field" (22 NS, 22 WE) earthquake signals. The modal estimates are statistically compared to their target values, proving the accuracy of the developed algorithm in providing prompt and accurate estimates of all current strong ground motion modal parameters. At this stage, such analysis tool may be employed for convenient application in the realm of Earthquake Engineering, towards potential Structural Health Monitoring and damage detection purposes.

  2. Structural domains and conformational changes in nuclear chromatin: a quantitative thermodynamic approach by differential scanning calorimetry.

    Science.gov (United States)

    Balbi, C; Abelmoschi, M L; Gogioso, L; Parodi, S; Barboro, P; Cavazza, B; Patrone, E

    1989-04-18

    A good deal of information on the thermodynamic properties of chromatin was derived in the last few years from optical melting experiments. The structural domains of the polynucleosomal chain, the linker, and the core particle denature as independent units. The differential scanning calorimetry profile of isolated chromatin is made up of three endotherms, at approximately 74, 90, and 107 degrees C, having an almost Gaussian shape. Previous work on this matter, however, was mainly concerned with the dependence of the transition enthalpy on external parameters, such as the ionic strength, or with the melting of nuclei from different sources. In this paper we report the structural assignment of the transitions of rat liver nuclei, observed at 58, 66, 75, 92, and 107 degrees C. They are representative of the quiescent state of the cell. The strategy adopted in this work builds on the method developed for the investigation of complex biological macromolecules. The heat absorption profile of the nucleus was related to the denaturation of isolated nuclear components; electron microscopy and electrophoretic techniques were used for their morphological and molecular characterization. The digestion of chromatin by endogenous nuclease mimics perfectly the decondensation of the higher order structure and represented the source of several misinterpretations. This point was carefully examined in order to define unambiguously the thermal profile of native nuclei. The low-temperature transitions, centered around 58 and 66 degrees C, arise from the melting of scaffolding structures and of the proteins associated with heterogeneous nuclear RNA.(ABSTRACT TRUNCATED AT 250 WORDS)

  3. The Structure of a Conserved Domain of TamB Reveals a Hydrophobic β Taco Fold.

    Science.gov (United States)

    Josts, Inokentijs; Stubenrauch, Christopher James; Vadlamani, Grishma; Mosbahi, Khedidja; Walker, Daniel; Lithgow, Trevor; Grinter, Rhys

    2017-12-05

    The translocation and assembly module (TAM) plays a role in the transport and insertion of proteins into the bacterial outer membrane. TamB, a component of this system spans the periplasmic space to engage with its partner protein TamA. Despite efforts to characterize